Re: [Bioc-devel] xps build problem on veracruz2

[Dan Tenenbaum]

Disabling SIP should not be done anywhere. Every page I've read on this topic 
strongly discourages doing this.


- Original Message -
> From: "Hervé Pagès" <hpa...@fredhutch.org>
> To: "cstrato" <cstr...@aon.at>, "Dan Tenenbaum" <dtene...@fredhutch.org>
> Cc: "bioc-devel" <bioc-devel@r-project.org>
> Sent: Thursday, April 20, 2017 3:17:23 PM
> Subject: Re: [Bioc-devel] xps build problem on veracruz2

> On 04/20/2017 03:01 PM, cstrato wrote:
>> Dear Herve,
>>
>> Doing 'csrutil disable' does indeed solve the problem, since:
>>
>> 1, in this way I was able to build xps on Mac OS Sierra
>>
>> 2, in this way I could already help one user of xps, see:
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_90056_-2390247=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg=GfzgU1Ibm_scFWO58Mv_ZfxKtn-FSJgkxMW1ZBYK1Vs=
>>
>> This means, that users of xps seem to be willing to disable csrutil.
> 
> I'm not a statistician but I wouldn't draw conclusions from a sample
> of size 1. Mac users who cannot install xps on their machine will
> use something else, or, if they desperately need xps, they will
> grab a Linux box.
> 
> Sorry but disabling SIP on our Mac builders is not an option.
> 
>>
>>
>>
>> However, I just realized that there may be an even greater problem,
>> namely, which version of ROOT should a user install?
>>
>> People can download ROOT binaries built with XCode 7.x from:
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_content_release-2D53436=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg=LByiYPyOfsHnRc9oOqXOs9xMcfltktXgkTQ3sh5hKFc=
>> for OS X 10.10 and 10.11.
>>
>> Thus for El Capitan they can download the following binaries:
>> - root_v5.34.36.macosx64-10.11-clang70.dmg
>> - root_v5.34.36.macosx64-10.11-clang70.tar.gz
>>
>> Did you install one of those binaries or did you compile ROOT from source?
> 
> As I said earlier, I compiled ROOT 5 from source on veracruz2.
> 
>>
>> With the help of my README file people could compile ROOT from source
>> for XCode 8.x.
>>
>>
>> However, you have mentioned that the CRAN people are using clang 4.0.0
>> for producing the Mac binaries of R and CRAN packages and thus you are
>> using the same on veracruz2.
> 
> Yes.
> 
>>
>> Did you compile ROOT with XCode 7 or 8 or did you use clang 4.0.0, which
>> is not officially supported by Apple?
> 
> With clang 4.0.0.
> 
>>
>> The question is whether xps built with this version of ROOT will work
>> with the ROOT binaries which people can download from ROOT?
> 
> I guess someone will need to figure this out.
> 
> Note that if people need to compile their own ROOT anyway in order to
> be able to use the xps binary we distribute, then they should also be
> able to install xps from source. So that defeats the purpose of
> providing a binary in the first place.
> 
> Cheers,
> H.
> 
>>
>> Best regards,
>> Christian
>>
>>
>>
>> On 04/20/17 20:00, Hervé Pagès wrote:
>>> On 04/20/2017 10:59 AM, Hervé Pagès wrote:
>>>> Hi Christian,
>>>>
>>>> Disabling 'csrutil disable' might help xps on veracruz2 but that
>>>   ^^
>>> oops, no double negative intended here. I meant, doing 'csrutil disable'
>>> might help... etc
>>>
>>> H.
>>>
>>>> won't help your end users.
>>>>
>>>> I'm no expert in developing a package on Mac but other people on
>>>> this list are. Also R-SIG-Mac might be a good place to seek help
>>>> for this.
>>>>
>>>> Cheers,
>>>> H.
>>>>
>>>>
>>>> On 04/20/2017 10:53 AM, cstrato wrote:
>>>>> Dear Herve,
>>>>>
>>>>> Thank you for your efforts to try to install xps. I am glad to hear
>>>>> that
>>>>> you could build ROOT 5 from source.
>>>>>
>>>>> It's a pity that Apple does no longer allow the use of
>>>>> DYLD_LIBRARY_PATH. This seems to break the code of a lot of people
>>>>> (when
>>>>> googling around).
>>>>>
>>>>> I will try to change the build process and will see if I succeed.
>>>>> However, at the moment I have a couple of questions:
&

Re: [Bioc-devel] Problem to install bioconductor for R devel (3.5)

[Dan Tenenbaum]

Don't install R-3.5; install R-3.4 from 
https://cran.rstudio.com/bin/windows/base/rtest.html

Dan


- Original Message -
> From: "bioc-devel" 
> To: "bioc-devel" 
> Sent: Tuesday, March 28, 2017 7:59:57 PM
> Subject: [Bioc-devel] Problem to install bioconductor for R devel (3.5)

> Hi,
>
> I have install development version of r from
>
> https://cran.r-project.org/bin/windows/base/rdevel.html
>
> But when i have tried to install  Bioconductor, i got following error.
> Can any one please explain why ?
>
> It said "Bioconductor does not yet support R version 3.5.0"  but why ??
>
> ##
>> ## try http:// if https:// URLs are not supported
>> source("https://bioconductor.org/biocLite.R
>> ")
> Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
> Bioconductor does not yet support R version 3.5.0
>> biocLite()
> BioC_mirror:
> https://bioconductor.org
> Using Bioconductor 3.5 (BiocInstaller 1.25.3), R Under development (unstable)
> (2017-03-27 r72423).
> Installing package(s) ‘Biobase’, ‘IRanges’, ‘AnnotationDbi’
> also installing the dependency ‘S4Vectors’
>
> Warning: unable to access index for repository
> https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.5:
> cannot open URL
> 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.5/PACKAGES
> '
> Warning: unable to access index for repository
> https://bioconductor.org/packages/3.5/data/annotation/bin/windows/contrib/3.5:
> cannot open URL
> 'https://bioconductor.org/packages/3.5/data/annotation/bin/windows/contrib/3.5/PACKAGES
> '
> Warning: unable to access index for repository
> https://bioconductor.org/packages/3.5/data/experiment/bin/windows/contrib/3.5:
> cannot open URL
> 'https://bioconductor.org/packages/3.5/data/experiment/bin/windows/contrib/3.5/PACKAGES
> '
> Warning: unable to access index for repository
> https://bioconductor.org/packages/3.5/extra/bin/windows/contrib/3.5:
> cannot open URL
> 'https://bioconductor.org/packages/3.5/extra/bin/windows/contrib/3.5/PACKAGES
> '
> Error in readRDS(dest) : unknown input format
>>
>
>
>
> Tanvir Ahamed
>
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Re: [Bioc-devel] Something about time out errors

[Dan Tenenbaum]

- Original Message -
> From: "Martin Morgan" 
> To: "Rainer Johannes" 
> Cc: "Aimin Yan" , "bioc-devel" 
> 
> Sent: Monday, March 27, 2017 12:29:49 PM
> Subject: Re: [Bioc-devel] Something about time out errors

> On 03/27/2017 12:57 PM, Rainer Johannes wrote:
>> Do you have code fetching data from web resources? I also sometimes get 
>> timeout
>> errors on ensembldb and I guess it's because in some unit tests I'm fetching
>> data from the ensembl ftp server.
>>
>
> Testing web resources is a pretty interesting topic. It doesn't really
> make sense to spend a lot of time downloading a large amount of data,
> but rather to focus the test on the existence of the endpoint, and the
> returned data type. It seems like these tests can be fast and
> light-weight. One approach (for static resources) might ask the web
> server for a last-modified or entity tag (ETag) value, and compare that
> to a manually maintained last-known-good exemplar.
>
> Unit tests for parsing the data into R and processing the data once in R
> are really separate from the web resource, and should probably be
> isolated from tests of the web resource itself.
>
> The approach on this page
>
>   http://bioconductor.org/developers/how-to/web-query/
>
> especially use of timeout(), might be a reasonable way to implement
> this; also BiocFileCache is now available and provides appropriate
> functionality (although looking I see that it doesn't currently support
> time-outs -- but it's better to fix this in the one location rather than
> in many different locations).
>

Another approach is to write a function that simply returns the web resource, 
and then 'mock' that function in your unit tests, to have it return an expected 
result. This keeps the scope of your unit tests appropriate (i.e. you are only 
testing your own code, you're not testing if some resource is available on a 
remote server or if the internet is working that day). 

Look at ?with_mock in the `testthat` package for more information. 

Dan



> Martin
>
>> jo
>>
>>> On 27 Mar 2017, at 18:37, Martin Morgan  
>>> wrote:
>>>
>>> On 03/27/2017 12:22 PM, Aimin Yan wrote:
 I am submitting a R package to bioconductor. but I got time out errors when
 I performed R CMD check.


 Is there a possible way that I can set up time to allow more time for R CMD
 check? Or I have to use examples that they do not cost large time.
>>>
>>> Submitted packages need to conform to package guidelines for space and time
>>>
>>>  http://bioconductor.org/developers/package-guidelines/#correctness
>>>
>>> so you'll need to develop realistic examples requiring modest resources.
>>>
>>> Often long-running examples result from inefficient code, so it is 
>>> worth-while
>>> to profile your code to discover where the most time is spent, and seek
>>> efficient implementations for that section of code either through better 
>>> use of
>>> vectorization or more sophisticated algorithms.
>>>
>>> Martin
>>>


 Thank you for your help

 Aimin

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>
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Re: [Bioc-devel] Unit tests

[Dan Tenenbaum]

Here's what BiocCheck says:

Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/

So, unit tests are encouraged but not required.
Dan


- Original Message -
> From: "张腾" <2573552...@qq.com>
> To: "bioc-devel" 
> Sent: Thursday, March 23, 2017 7:33:22 PM
> Subject: [Bioc-devel] Unit tests

> Hello all,
> 
> I am not sure whether the Unit tests are necessary to release a package for
> Bioconductor. In my package, only one main function to export and other
> functions are hidden into the main function. In my package, the input data are
> some files in BAM format and the output is a report in HTML format. So I want
> to know if the unit tests are very important and necessary for releasing a
> package. If it is necessary, how can I add these tests to my package in this
> special input and output situation?
> 
> Can anyone help me solve this problem? Thank you very much
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] xps build problem on veracruz2

[Dan Tenenbaum]

- Original Message -
> From: "Hervé Pagès" 
> To: "cstrato" , "bioc-devel" 
> Sent: Thursday, March 23, 2017 12:14:38 PM
> Subject: Re: [Bioc-devel] xps build problem on veracruz2

> On 03/23/2017 11:09 AM, cstrato wrote:
>> Dear Herve,
>>
>> Thank you for your explanation.
>>
>> The reason that xps does not work with ROOT 6 is that I have tried it
>> but there seem to be so many changes, that I did not succeed.
>> Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5
>> was still supported, I have decided to stay with ROOT 5.
> 
> OK
> 
>>
>> BTW, I have also one question:
>> Why did you decide to set up a new Mac with El Capitan instead of using
>> the newest OS Sierra? (I have the impression that most Mac users are
>> either happy to stay with their old OS or they upgrade to the newest one.)
> 
> Same reason as for the choice of compilers: that's what the R folks
> decided to use for producing the Mac binaries of R and CRAN packages.
> We're just following their lead on that.
> 

Also, it's always good not to require users to upgrade if they don't have to. 
Building on El Capitan means users will not have to upgrade to macOS Sierra if 
they don't want to. Building on Sierra would mean R and packages would not be 
backwards-compatible with El Capitan.

But it's a tradeoff that also involves the difficulty of maintaining build 
machines with old OSes, and wanting to take advantage of newer compiler 
technology. Otherwise R/Bioc would still be building on Mavericks, or Snow 
Leopard...

Dan


> Cheers,
> H.
> 
>>
>> Best regards,
>> Christian
>>
>>
>> On 03/23/17 17:47, Hervé Pagès wrote:
>>> Hi Christian,
>>>
>>> The CRAN folks are currently experimenting with clang 4.0.0 for
>>> producing the Mac binaries of R and CRAN packages so we are using
>>> the same on veracruz2. This is a version of clang that is ahead of
>>> what's in XCode 8.x or XCode 7.x. So I guess that means we'll have
>>> to compile ROOT from source on veracruz2.
>>>
>>> BTW any reason not to make xps work with ROOT 6?
>>>
>>> Cheers,
>>> H.
>>>
>>> On 03/23/2017 07:28 AM, cstrato wrote:
 Dear Valerie,

 I have seen that you have set up a new Mac server, veracruz2, running El
 Capitan.

 Although the development version of xps does even run on Mac OS Sierra,
 one issue still remains the same:

 You need to install the latest ROOT version 5, since xps does not run
 with ROOT 6!

 So you need to install on veracruz2 the same root version that you have
 installed on toluca2 running Maverics, i.e.
 root_v5.34.36.macosx64-10.11-clang70.dmg

 However, if you have installed on El Capitan XCode 8.x instead of XCode
 7.x, then you need to compile ROOT from source, i.e.:
 https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw=



 The README file of xps does explain how to compile ROOT for Sierra. This
 should also be valid for El Capitan running XCode 8.x.

 Thank you in advance.
 Best regards,
 Christian
 _._._._._._._._._._._._._._._._._._
 C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
 V.i.e.n.n.a   A.u.s.t.r.i.a
 e.m.a.i.l:cstrato at aon.at
 _._._._._._._._._._._._._._._._._._

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>>>
> 
> --
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
> 
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Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

[Dan Tenenbaum]

- Original Message -
> From: "Hervé Pagès" 
> To: "Martin Morgan" , "lcollado" 
> , "bioc-devel"
> 
> Cc: "Jeff Leek" , "Andrew Jaffe" 
> Sent: Wednesday, March 22, 2017 10:21:43 AM
> Subject: Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that 
> sometimes popped up, sometimes it didn't.
> Related to IRanges/S4Vectors '$<-'

> On 03/21/2017 05:28 PM, Martin Morgan wrote:
>> On 03/21/2017 08:21 PM, Hervé Pagès wrote:
>>> Hi Leonardo,
>>>
>>> Thanks for hunting down and isolating that bug! I tried to simplify
>>> your code even more and was able to get a segfault with just:
>>>
>>>   setClass("A", representation(stuff="numeric"))
>>>   x <- logical(10)
>>>   x[TRUE] <- new("A")
>>>
>>> I get the segfault about 50% of the time on a fresh R session on Mac.
>>> I tried this with R 3.3.3 on Mavericks, and with R devel (r72372)
>>> on El Capitan. I get the segfault on both.
>>>
>>> So it looks like a bug in the `[<-` primitive to me (subassignment).
>>
>> Any insight from
>>
>>   R -d valgrind -f herve.R
>>
>> where herve.R contains the code above?
> 
> That's a little bit complicated for me at the moment. I was
> actually running this code on build machines toluca2 and (upcoming)
> veracruz2 and we don't have valgrind there for now. I don't have
> access to other Macs so hopefully someone else will be able to help
> with this.
> 

Just running valgrind on linux should reveal something
Dan


> H.
> 
>>
>> Martin
>>
>>>
>>> Cheers,
>>> H.
>>>
>>> On 03/21/2017 03:06 PM, Leonardo Collado Torres wrote:
 Hi bioc-devel,

 This is a story about a bug that took me a long time to trace. The
 behaviour was really weird, so I'm sharing the story in case this
 helps others in the future. I was originally writing it to request
 help, but then I was able to find the issue ^^. The story ends right
 now with code that will reproduce the problem with '$<-' from
 IRanges/S4Vectors.




 During this Bioc cycle, frequently my package derfinder has failed to
 pass R CMD check in OSX. The error is always the same when it appears
 and sometimes it shows up in release, but not devel and viceversa.
 Right now (3/21/2017) it's visible in both
 https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_derfinder_morelia-2Dchecksrc.html=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Bw-1Kqy-M_t4kmpYWTpYkt5bvj_eTpxriUM3UvtOIzQ=RS-lsygPtDdgWKAhjA2BcSLkVy9RxxshXWAJaBZa_Yc=


 and
 https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_derfinder_toluca2-2Dchecksrc.html=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Bw-1Kqy-M_t4kmpYWTpYkt5bvj_eTpxriUM3UvtOIzQ=a_K-yK7w2LEV72lpHrpp0UoKRru_7Aad74T5Uk0R-Fo=

 .
 The end of "test-all.Rout.fail" looks like this:

 Loading required package: foreach
 Loading required package: iterators
 Loading required package: locfit
 locfit 1.5-9.1 2013-03-22
 getSegments: segmenting
 getSegments: splitting
 2017-03-20 02:36:52 findRegions: smoothing
 2017-03-20 02:36:52 findRegions: identifying potential segments
 2017-03-20 02:36:52 findRegions: segmenting information
 2017-03-20 02:36:52 .getSegmentsRle: segmenting with cutoff(s)
 16.3681899295041
 2017-03-20 02:36:52 findRegions: identifying candidate regions
 2017-03-20 02:36:52 findRegions: identifying region clusters
 2017-03-20 02:36:52 findRegions: smoothing
 2017-03-20 02:36:52 findRegions: identifying potential segments
 2017-03-20 02:36:52 findRegions: segmenting information
 2017-03-20 02:36:52 .getSegmentsRle: segmenting with cutoff(s)
 19.7936614060235
 2017-03-20 02:36:52 findRegions: identifying candidate regions
 2017-03-20 02:36:52 findRegions: identifying region clusters
 2017-03-20 02:36:52 findRegions: smoothing

  *** caught segfault ***
 address 0x7f87d2f917e0, cause 'memory not mapped'

 Traceback:
  1: (function (y, x, cluster, weights, smoothFun, ...) {
 hostPackage <- environmentName(environment(smoothFun))
 requireNamespace(hostPackage)smoothed <- .runFunFormal(smoothFun,
 y = y, x = x, cluster = cluster, weights = weights, ...)if
 (any(!smoothed$smoothed)) {smoothed$fitted[!smoothed$smoothed]
 <- y[!smoothed$smoothed]}res <- Rle(smoothed$fitted)
 return(res)})(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]],
 dots[[4L]][[1L]], smoothFun = function (y, x = NULL, cluster,
 weights = NULL, minNum = 7, bpSpan = 1000, minInSpan = 0,
 verbose = TRUE) {if (is.null(dim(y))) y <-
 matrix(y, ncol = 1)if 

Re: [Bioc-devel] Package not being built on Windows or Mac

[Dan Tenenbaum]

As I recall, there were issues building RCytoscape (and packages that depend on 
it) on Mac and Windows. Mostly because this requires a running instance of 
Cytoscape for each platform (and double that for release + devel). That used 
too much infrastructure so we disabled building on those platforms. However, 
since RCytoscape contains no native (C/C++/Fortran) code, it will still be 
available on all platforms and should install just fine.

As long as the same is true of categoryCompare then Mac/Windows users should be 
able to use it.

Dan


- Original Message -
> From: "James W. MacDonald" 
> To: "Robert M. Flight" 
> Cc: "bioc-devel" 
> Sent: Monday, March 20, 2017 2:22:36 PM
> Subject: Re: [Bioc-devel] Package not being built on Windows or Mac

> It's probably because you depend on RCytoscape, which isn't supported on
> Windows or MacOS. And maybe this has something to do with XMLRPC?
> 
> Jim
> 
> 
> 
> On Mon, Mar 20, 2017 at 4:59 PM, Robert M. Flight 
> wrote:
> 
>> As per the exhortation to check the build status on Devel prior to next
>> version of Bioconductor release, I just noticed that my package
>> categoryCompare has a "not supported" on Windows and Mac.
>>
>> Looking at release history, this seems to  I have changed at Bioc v 3.4,
>> and I'm curious why that would be the case.
>>
>> Regards,
>>
>> Robert
>>
>> Robert M Flight, PhD
>> Bioinformatics Research Associate
>> Puller of Rabbits from Hats
>> Resource Center for Stable Isotope Resolved Metabolomics
>> Manager, Systems Biology and Omics Integration Journal Club
>> Markey Cancer Center
>> CC434 Roach Building
>> University of Kentucky
>> Lexington, KY
>>
>> Twitter: @rmflight
>> Web: rmflight.github.io
>> ORCID:
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__orcid.org_-2D0001-2D8141-2D7788=DwICAg=eRAMFD45gAfqt84VtBcfhQ=TF6f93hjWmgMzjqP9F3thRifibmFvfjc5Ae-bzNwDGo=KPLsJPHGh_SklfKfn_epC0AQwKR8K6yNDv7cVLAJ1FQ=n-q_ynuSgrWSRqpLP4_jtAcjUUkBkQS47cGcISvMTH8=
>> EM rfligh...@gmail.com
>> PH 502-509-1827
>>
>> To call in the statistician after the experiment is done may be no more
>> than asking him to perform a post-mortem examination: he may be able to say
>> what the experiment died of. - Ronald Fisher
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=TF6f93hjWmgMzjqP9F3thRifibmFvfjc5Ae-bzNwDGo=KPLsJPHGh_SklfKfn_epC0AQwKR8K6yNDv7cVLAJ1FQ=s4b92CENsDvGb5LJKA-xyg2pTKm6kJHUNfyOrk_ySY4=
>>
> 
> 
> 
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Bioconductor package license: dependency on work under non-commercial license

[Dan Tenenbaum]

I can't speak to the license question (I'd guess the answer is no) but I am 
pretty sure that any dependencies of a Bioconductor package have to be 
available on CRAN or in Bioconductor itself. So you can't depend on packages 
that are only in GitHub.

Dan


- Original Message -
> From: "David J. H. Shih" 
> To: "bioc-devel" 
> Sent: Wednesday, January 25, 2017 12:48:31 PM
> Subject: [Bioc-devel] Bioconductor package license: dependency on work under  
> non-commercial license

> Hello,
> 
> 
> I'd like to ask whether Bioconductor will allow a dependency package
> under a non-commercial license:
> 
> https://github.com/djhshih/mlat/blob/master/LICENSE_blat.txt
> 
> I read the package guidelines:
> http://bioconductor.org/developers/package-guidelines/#license but it
> does not address this question.
> 
> 
> I am putting together a package for somatic variant filtering. One of
> the filters involve re-aligning the supporting reads using a heavily
> refactored version of BLAT: MLAT (https://github.com/djhshih/mlat). BLAT
> remains under a license that restricts commercial users. Although the
> original license mentions no restriction on derivative work, I contacted
> the author, and he maintains that the non-commercial license applies to
> derivative works. Eventually, I'll probably replace BLAT (with another
> aligner like SHRiMP2, which appears to have superior sensitivity and has
> a permissive license), but I was wondering how I might be able to
> assemble my package in the short term.
> 
> Here is my plan:
> 
> 1. Create a BLAT/MLAT package under BLAT's non-commercial license.
> 2. Create the main package under GPLv3 that optionally depends on BLAT.
> 
> Will Bioconductor permit a optional dependency package under a
> non-commercial license?
> 
> 
> Best regards,
> 
> Postdoctoral Research Fellow
> Department of Biostatistics and Computational Biology, Dana-Farber
> Cancer Institute
> Department of Biostatistics, Harvard T.H. Chan School of Public Health
> Cancer Program, Broad Institute
> 3 Blackfan Circle, CLS-11082
> Boston, MA 02115
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Rd] require(..., quietly=TRUE) does not suppress warning

[Dan Tenenbaum]

Well, I'm getting a warning (not an error) when the package doesn't exist.
I interpreted "most often" to mean that suppressing warnings/errors is why 
you'd most often use this argument, as most packages don't emit startup 
messages. 

And technically there isn't a problem with attaching the package, since we 
don't even try to attach packages that don't exist.

So yes, very careful parsing of the docs suggests that the behavior is correct, 
but it does seem to violate the 'spirit' of what a user might expect. I am 
pretty sure I have used the 'if (!require("pkg")) install.packages("pkg")' 
pattern before without seeing this warning, so I wondered if the behavior had 
changed, and that's what prompted me to write.

I know I can squelch the warning by wrapping the require() in 
suppressWarnings(). 

Dan


- Original Message -
> From: "John P. Nolan" <jpno...@american.edu>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "R-devel" 
> <r-devel@r-project.org>
> Sent: Thursday, December 8, 2016 12:37:02 PM
> Subject: RE: require(..., quietly=TRUE) does not suppress warning

> Well, it says "most often" no errors/warnings are given, so it is not
> contradicting the docs!   It looks like the person/team that coded  require( )
> decided you should get an error when the package doesn't exist.
> 
> If you want a silent loading, consider
> aaa <- try( library(foo,verbose=FALSE,quietly=TRUE),silent=TRUE)
> and then check to see if aaa is of class "try-error" and check for failure
> 
> John
> ……..
> 
> John P. Nolan
> Math/Stat Dept., American University
> Gray Hall, 4400 Massachusetts Ave, NW
> Washington, DC 20016-8050
> Phone: 202-885-3140
> E-mail:  jpno...@american.edu
> Web:   http://fs2.american.edu/jpnolan/www/
> 
> 
> 
> -Original Message
> From: R-devel [mailto:r-devel-boun...@r-project.org] On Behalf Of Dan 
> Tenenbaum
> Sent: Thursday, December 8, 2016 2:43 PM
> To: R-devel <r-devel@r-project.org>
> Subject: [Rd] require(..., quietly=TRUE) does not suppress warning
> 
> Hi,
> 
> The `quietly` argument of `require` is documented as follows:
> 
> quietly: a logical.  If ‘TRUE’, no message confirming package
>  attaching is printed, and most often, no errors/warnings are
>  printed if package attaching fails.
> 
> However:
> 
>> require(foo, quietly=TRUE)
> Warning message:
> In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return =
> TRUE,  :
>  there is no package called ‘foo’
> 
> Am I misreading the docs or is R misbehaving?
> 
>> sessionInfo()
> R version 3.3.2 (2016-10-31)
> Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: macOS Sierra 
> 10.12.1
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
> 
> Dan
> 
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

__
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[Rd] require(..., quietly=TRUE) does not suppress warning

[Dan Tenenbaum]

Hi,

The `quietly` argument of `require` is documented as follows:

 quietly: a logical.  If ‘TRUE’, no message confirming package
  attaching is printed, and most often, no errors/warnings are
  printed if package attaching fails.

However:

> require(foo, quietly=TRUE)
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = 
TRUE,  :
  there is no package called ‘foo’

Am I misreading the docs or is R misbehaving?

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.1

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

Dan

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Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

[Dan Tenenbaum]

in\x64>R CMD check
>> > "C:\Users\jvrat\Documents\MSPC"
>> > Warning in dir.create(pkgoutdir, mode = "0755") :
>> >   cannot create dir 'C:\Program Files\R\R-devel\bin\x64\MSPC.Rcheck',
>> > reason 'Permission denied'
>> > ERROR: cannot create check dir 'C:/Program
>> > Files/R/R-devel/bin/x64/MSPC.Rcheck'
>> >
>> > C:\Program Files\R\R-devel\bin\x64>R CMD build
>> > "C:\Users\jvrat\Documents\MSPC"
>> > * checking for file 'C:\Users\jvrat\Documents\MSPC/DESCRIPTION' ... OK
>> > * preparing 'MSPC':
>> > * checking DESCRIPTION meta-information ... OK
>> > * installing the package to build vignettes
>> > * creating vignettes ...Warning: running command
>> > '"C:/PROGRA~1/R/R-devel/bin/x64/Rscript" --vanilla --default-packages=
>> -e
>> > "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
>> >  ERROR
>> > Warning in engine$weave(file, quiet = quiet, encoding = enc) :
>> >   Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back
>> to
>> > R Markdown v1.
>> > Quitting from lines 60-64 (vignette.Rmd)
>> > Error: processing vignette 'vignette.Rmd' failed with diagnostics:
>> > subscript out of bounds
>> > Execution halted
>> >
>> > C:\Program Files\R\R-devel\bin\x64>
>> >
>> >
>> > How I fix R CMD check error above ? system.file() still can't detect
>> > external data. Any idea please ? Thanks a lot
>> >
>> > Best regards :
>> >
>> > Jurat
>> >
>> >
>> > On Fri, Dec 2, 2016 at 5:43 PM, Dan Tenenbaum <dtene...@fredhutch.org>
>> > wrote:
>> >
>> >> See below.
>> >>
>> >> - Original Message -
>> >> > From: "Jurat Shayidin" <juratb...@gmail.com>
>> >> > To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" <
>> >> bioc-devel@r-project.org>
>> >> > Sent: Friday, December 2, 2016 8:32:35 AM
>> >> > Subject: Re: [Bioc-devel] package vignette error : external data can't
>> >> be captured when compiling package vignette
>> >>
>> >> > Dear Dan :
>> >> >
>> >> > Really appreciated for your quick respond. Instead, I am using R CMD
>> >> check
>> >> > on my packages, I have an error. Here is whole session detail :
>> >> >
>> >> > Microsoft Windows [Version 6.3.9600]
>> >> > (c) 2013 Microsoft Corporation. All rights reserved.
>> >> >
>> >> > C:\Users\jvrat>cd C:\Program Files\R\R-devel\bin\x64
>> >> >
>> >> > C:\Program Files\R\R-devel\bin\x64>R CMD INSTALL
>> >> > "C:\Users\jvrat\Documents\MSPC"
>> >> > * installing to library 'C:/Users/jvrat/Documents/R/win-library/3.4'
>> >> > * installing *source* package 'MSPC' ...
>> >> > ** R
>> >> > ** inst
>> >> > ** preparing package for lazy loading
>> >> > ** help
>> >> > *** installing help indices
>> >> > ** building package indices
>> >> > ** installing vignettes
>> >> > ** testing if installed package can be loaded
>> >> > * DONE (MSPC)
>> >> >
>> >> > C:\Program Files\R\R-devel\bin\x64>R CMD check
>> >> > "C:\Users\jvrat\Documents\MSPC"
>> >> > Warning in dir.create(pkgoutdir, mode = "0755") :
>> >> >  cannot create dir 'C:\Program Files\R\R-devel\bin\x64\MSPC.Rcheck',
>> >> reason
>> >> > 'Permission denied'
>> >> > ERROR: cannot create check dir 'C:/Program
>> >> > Files/R/R-devel/bin/x64/MSPC.Rcheck'
>> >>
>> >> You need to run R CMD check in a directory where you have write
>> >> permissions.
>> >>
>> >>
>> >> >
>> >> > C:\Program Files\R\R-devel\bin\x64>R CMD build
>> >> > "C:\Users\jvrat\Documents\MSPC"
>> >> > * checking for file 'C:\Users\jvrat\Documents\MSPC/DESCRIPTION' ...
>> OK
>> >> > * preparing 'MSPC':
>> >> > * checking DESCRIPTION meta-information ... OK
>> >> > * installing the package to build vignettes
>> >> > * creating vignettes ...Warning: running command
>> >> > '"C:/PROGRA~1/R/R-de

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

[Dan Tenenbaum]

I don't really understand your question. But, create an inst/extdata directory:

md inst
md inst\extdata
... add your files to inst\extdata ...
git add inst\extdata
git commit
git push

Dan



- Original Message -
> From: "Jurat Shayidin" <juratb...@gmail.com>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" 
> <bioc-devel@r-project.org>
> Sent: Sunday, December 4, 2016 5:12:50 AM
> Subject: Re: [Bioc-devel] package vignette error : external data can't be 
> captured when compiling package vignette

> Dear Dan :
> 
> Thanks again for your kind help. I did clean up my package git working
> tree, make every commit readable, tractable. I've read about R writing
> extension manual and that helped a lot. Many thanks to Herve' insightful
> answer to overcome file permission issue, R CMD check working perfectly
> now. Through the long list of R CMD check report, CMD check alarmed me
> several possible issues on my packages, and I am working on it.  Plus, R
> CMD check complained about some hidden file such as .gitignore,
> .Rproj.user, .git . Therefore I did strip away these files following this
> way :
> 
> 
> C:\Windows\system32>cd C:\Program Files\R\R-devel\bin\x64
> 
> C:\Program Files\R\R-devel\bin\x64>R CMD build
> "C:\Users\jvrat\Documents\MSPC"
> * checking for file 'C:\Users\jvrat\Documents\MSPC/DESCRIPTION' ... OK
> * preparing 'MSPC':
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... OK
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories
> Removed empty directory 'MSPC/tests/testthat'
> * building 'MSPC_0.99.0.tar.gz'
> 
> 
> C:\Program Files\R\R-devel\bin\x64>R CMD check "MSPC_0.99.0.tar.gz"
> * using log directory 'C:/Program Files/R/R-devel/bin/x64/MSPC.Rcheck'
> * using R Under development (unstable) (2016-11-09 r71642)
> * using platform: x86_64-w64-mingw32 (64-bit)
> * using session charset: ISO8859-1
> * checking for file 'MSPC/DESCRIPTION' ... OK
> * checking extension type ... Package
> * this is package 'MSPC' version '0.99.0'
> * checking package namespace information ... OK
> 
> Now inst/ directory is created in MSPC_0.99.0.tar.gz, I could add my
> external data in extdata (I think I need manually create extdata folder)
> and make available these data for vignette code. But How can I commit these
> changes to git automatically ? Because MSPC_0.99.0.tar.gz was not in my
> package directory, I cannot push these changes to git. Could you give me
> possible idea please ? Many thanks to Bioconductor Project team.
> 
> Best regards :
> Jurat
> 
> On Fri, Dec 2, 2016 at 7:05 PM, Dan Tenenbaum <dtene...@fredhutch.org>
> wrote:
> 
>> I tried building your package, there are a number of issues with it.
>>
>> I recommend that you 1) always be aware of what is and is not in github,
>> by using the 'git status' command. Bear in mind that if files are not
>> committed to git then we will not be able to see them and not be able to
>> help you. Specifically, the inst folder and everything under it does not
>> exist in the github repository. Therefore I get an error in the chunk at
>> lines 45-50, I don't get as far as you (error in lines 60-64).
>>
>> As Herve suggests, please run R CMD check from a directory that you have
>> write permission in, such as your home directory.
>>
>> R CMD check will alert you about various problems, including referring to
>> packages in NAMESPACE but not DESCRIPTION, relying on BiocStyle but not
>> mentioning it in DESCRIPTION, etc.
>>
>> Dan
>>
>>
>>
>> - Original Message -
>> > From: "Jurat Shayidin" <juratb...@gmail.com>
>> > To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" <
>> bioc-devel@r-project.org>
>> > Sent: Friday, December 2, 2016 9:11:29 AM
>> > Subject: Re: [Bioc-devel] package vignette error : external data can't
>> be captured when compiling package vignette
>>
>> > Dear Dan :
>> >
>> > I forgot to commit vignette file,  now I pushed new changes, so now error
>> > could be something else. People in stackoverflow suggest me to put all my
>> > external data (a.k.a, bed files) into vignette folder, try to run R CMD
>> > check and see what happen, I did this solution, but it doesn't work.
>> Plus,
>> > I checked file permission of my package parent directory, seems fine to
>> me.
>> > How I check file permission of my package ?
>> >

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

[Dan Tenenbaum]

I tried building your package, there are a number of issues with it.

I recommend that you 1) always be aware of what is and is not in github, by 
using the 'git status' command. Bear in mind that if files are not committed to 
git then we will not be able to see them and not be able to help you. 
Specifically, the inst folder and everything under it does not exist in the 
github repository. Therefore I get an error in the chunk at lines 45-50, I 
don't get as far as you (error in lines 60-64).

As Herve suggests, please run R CMD check from a directory that you have write 
permission in, such as your home directory.

R CMD check will alert you about various problems, including referring to 
packages in NAMESPACE but not DESCRIPTION, relying on BiocStyle but not 
mentioning it in DESCRIPTION, etc.

Dan



- Original Message -
> From: "Jurat Shayidin" <juratb...@gmail.com>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" 
> <bioc-devel@r-project.org>
> Sent: Friday, December 2, 2016 9:11:29 AM
> Subject: Re: [Bioc-devel] package vignette error : external data can't be 
> captured when compiling package vignette

> Dear Dan :
> 
> I forgot to commit vignette file,  now I pushed new changes, so now error
> could be something else. People in stackoverflow suggest me to put all my
> external data (a.k.a, bed files) into vignette folder, try to run R CMD
> check and see what happen, I did this solution, but it doesn't work. Plus,
> I checked file permission of my package parent directory, seems fine to me.
> How I check file permission of my package ?
> How can I fix this write permission on my machine ? This is not intuitive
> to me, Any hint please ?
> 
> Herve suggest me don't create inst/extdata directory manually, but I still
> can't let external data available for vignette code. FYI, my objective in
> vignette file : let external data available for package use, compile
> trivial version of vignette with no error, then continue to make it
> perfect.  Here is updated session of R CMD check :
> 
> 
> Microsoft Windows [Version 6.3.9600]
> (c) 2013 Microsoft Corporation. All rights reserved.
> 
> C:\Users\jvrat>cd C:\Program Files\R\R-devel\bin\x64
> 
> C:\Program Files\R\R-devel\bin\x64>R CMD INSTALL
> "C:\Users\jvrat\Documents\MSPC"
> * installing to library 'C:/Users/jvrat/Documents/R/win-library/3.4'
> * installing *source* package 'MSPC' ...
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> * DONE (MSPC)
> 
> C:\Program Files\R\R-devel\bin\x64>R CMD check
> "C:\Users\jvrat\Documents\MSPC"
> Warning in dir.create(pkgoutdir, mode = "0755") :
>  cannot create dir 'C:\Program Files\R\R-devel\bin\x64\MSPC.Rcheck',
> reason 'Permission denied'
> ERROR: cannot create check dir 'C:/Program
> Files/R/R-devel/bin/x64/MSPC.Rcheck'
> 
> C:\Program Files\R\R-devel\bin\x64>R CMD build
> "C:\Users\jvrat\Documents\MSPC"
> * checking for file 'C:\Users\jvrat\Documents\MSPC/DESCRIPTION' ... OK
> * preparing 'MSPC':
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ...Warning: running command
> '"C:/PROGRA~1/R/R-devel/bin/x64/Rscript" --vanilla --default-packages= -e
> "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
> ERROR
> Warning in engine$weave(file, quiet = quiet, encoding = enc) :
>  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to
> R Markdown v1.
> Quitting from lines 60-64 (vignette.Rmd)
> Error: processing vignette 'vignette.Rmd' failed with diagnostics:
> subscript out of bounds
> Execution halted
> 
> C:\Program Files\R\R-devel\bin\x64>
> 
> 
> How I fix R CMD check error above ? system.file() still can't detect
> external data. Any idea please ? Thanks a lot
> 
> Best regards :
> 
> Jurat
> 
> 
> On Fri, Dec 2, 2016 at 5:43 PM, Dan Tenenbaum <dtene...@fredhutch.org>
> wrote:
> 
>> See below.
>>
>> - Original Message -
>> > From: "Jurat Shayidin" <juratb...@gmail.com>
>> > To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" <
>> bioc-devel@r-project.org>
>> > Sent: Friday, December 2, 2016 8:32:35 AM
>> > Subject: Re: [Bioc-devel] package vignette error : external data can't
>> be captured when compiling package vignette
>>
>> > Dear Dan :
>> >
>> > Really appreciated for your quick respond. Instead,

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

[Dan Tenenbaum]

See below.

- Original Message -
> From: "Jurat Shayidin" <juratb...@gmail.com>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" 
> <bioc-devel@r-project.org>
> Sent: Friday, December 2, 2016 8:32:35 AM
> Subject: Re: [Bioc-devel] package vignette error : external data can't be 
> captured when compiling package vignette

> Dear Dan :
> 
> Really appreciated for your quick respond. Instead, I am using R CMD check
> on my packages, I have an error. Here is whole session detail :
> 
> Microsoft Windows [Version 6.3.9600]
> (c) 2013 Microsoft Corporation. All rights reserved.
> 
> C:\Users\jvrat>cd C:\Program Files\R\R-devel\bin\x64
> 
> C:\Program Files\R\R-devel\bin\x64>R CMD INSTALL
> "C:\Users\jvrat\Documents\MSPC"
> * installing to library 'C:/Users/jvrat/Documents/R/win-library/3.4'
> * installing *source* package 'MSPC' ...
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> * DONE (MSPC)
> 
> C:\Program Files\R\R-devel\bin\x64>R CMD check
> "C:\Users\jvrat\Documents\MSPC"
> Warning in dir.create(pkgoutdir, mode = "0755") :
>  cannot create dir 'C:\Program Files\R\R-devel\bin\x64\MSPC.Rcheck', reason
> 'Permission denied'
> ERROR: cannot create check dir 'C:/Program
> Files/R/R-devel/bin/x64/MSPC.Rcheck'

You need to run R CMD check in a directory where you have write permissions. 


> 
> C:\Program Files\R\R-devel\bin\x64>R CMD build
> "C:\Users\jvrat\Documents\MSPC"
> * checking for file 'C:\Users\jvrat\Documents\MSPC/DESCRIPTION' ... OK
> * preparing 'MSPC':
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ...Warning: running command
> '"C:/PROGRA~1/R/R-devel/bin/x64/Rscript" --vanilla --default-packages= -e
> "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
> ERROR
> Warning in engine$weave(file, quiet = quiet, encoding = enc) :
>  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to
> R Markdown v1.
> Quitting from lines 62-66 (vignette.Rmd)
> Error: processing vignette 'vignette.Rmd' failed with diagnostics:
> object 'inputData' not found
> Execution halted
> 

Line 61 of the vignette (as it is in Github; it's apparently different on yur 
machine based on the error message) is:

total.ERs <- denoise_ERs(peakGRs = inputData, tau.w = 1.0E-04, .fileName = 
"noiseER", outDir = "", verbose = FALSE)

As you can see, the peakGRs argument is set to inputData, but inputData is not 
defined anywhere.

Dan



> C:\Program Files\R\R-devel\bin\x64>
> 
> 
> How can I fix this R CMD check error ? Instead people in stackoverflow
> remind me that using devtools packages is not stable some times, so I go
> for old fashion : use CMD. Plus, still my external data can't available for
> vignette data, and vignette compilation is failed again. I used
> system.file() to do this, but not working. Any idea please ? How can I
> overcome this problem? Thanks a lot to Bioconductor project team.
> 
> Best regards :
> 
> Jurat
> 
> 
> On Fri, Dec 2, 2016 at 5:20 PM, Dan Tenenbaum <dtene...@fredhutch.org>
> wrote:
> 
>> If your package is in github at https://github.com/julaiti/MSPC , it
>> looks like there is no inst or extdata folder in that repository.
>>
>> Maybe it has not yet been added/committed/pushed to git?
>>
>> Note that everything _under_ inst gets installed when you install the
>> package, but the inst directory itself goes away.
>>
>> If in your package source you have the following structure:
>>
>> inst/extdata/
>> inst/foo.txt
>>
>> In the installed package you end up with:
>>
>> extdata/
>> foo.txt
>>
>> HTH
>> Dan
>>
>>
>> - Original Message -
>> > From: "Jurat Shayidin" <juratb...@gmail.com>
>> > To: "Hervé Pagès" <hpa...@fredhutch.org>, "bioc-devel" <
>> bioc-devel@r-project.org>
>> > Sent: Friday, December 2, 2016 5:36:28 AM
>> > Subject: Re: [Bioc-devel] package vignette error : external data can't
>> be captured when compiling package vignette
>>
>> > Dear Hervé :
>> >
>> > Thanks again for your response on my issue. I've read your message very
>> > carefully and did all you suggested to me, still can't fix the vignette
>> > compilation error. I have developed 

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

[Dan Tenenbaum]

If your package is in github at https://github.com/julaiti/MSPC , it looks like 
there is no inst or extdata folder in that repository.

Maybe it has not yet been added/committed/pushed to git?

Note that everything _under_ inst gets installed when you install the package, 
but the inst directory itself goes away.

If in your package source you have the following structure:

inst/extdata/
inst/foo.txt

In the installed package you end up with:

extdata/
foo.txt

HTH
Dan


- Original Message -
> From: "Jurat Shayidin" 
> To: "Hervé Pagès" , "bioc-devel" 
> 
> Sent: Friday, December 2, 2016 5:36:28 AM
> Subject: Re: [Bioc-devel] package vignette error : external data can't be 
> captured when compiling package vignette

> Dear Hervé :
> 
> Thanks again for your response on my issue. I've read your message very
> carefully and did all you suggested to me, still can't fix the vignette
> compilation error. I have developed my package on windows machine under
> devel version of R and Bioc, all unit test works fine to me. I don't
> understand why inst/ directory was not created when I build and install my
> packages, external data can't be read during vignette compilation.
> However, my objective is, to build my package vignette with no error in the
> first place, then continue to edit the context until getting final version
> of vignette file. When I install packages using devtools::install(), I got
> this :
> 
>> devtools::install()
> Installing MSPC
> "C:/PROGRA~1/R/R-devel/bin/x64/R" \
> --no-site-file --no-environ --no-save \
> --no-restore --quiet CMD INSTALL \
> "C:/Users/jvrat/Documents/MSPC" \
> --library="C:/Users/jvrat/Documents/R/win-library/3.4" \
> --install-tests
> * installing *source* package 'MSPC' ...
> ** R
> ** tests
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> * DONE (MSPC)
> Reloading installed MSPC
> 
> 
> I believe doing this is right in vignette file after I follow your advise :
> 
> ```{r}
> library(MSPC)
> inputBed <- list.files(system.file("extdata", package = "MSPC"), full.names
> = TRUE)
> inputData <- readPeakFile(peakFolder = inputBed)
> 
> inputData
> ```
> 
> 
> However, I should not add inst/extdata manually , without this I can't
> allow to load external data for package use, and vignette compilation keep
> failed. To be honest, this is my very first time building R packages, I
> don't know how to fix this error. Just out of curiosity, during package
> installation, everything is under the inst/ , but I don't have this folder.
> Why is that ? Is that possible to get further help from Bioconductor
> project team to review the package source in github ?
> 
> I am stuck with this problem, I searched all possible answer from all over
> the place, cannot fix my issues. I am very sorry if my question is naive to
> ask here. Could you point me out how to possibly solve this problem? Thanks
> again for your great favor.
> 
> Best regards :
> 
> Jurat
> 
> 
> 
> On Fri, Dec 2, 2016 at 2:04 AM, Hervé Pagès  wrote:
> 
>> Hi,
>>
>> Make sure you understand the difference between the *package source
>> tree*, which you control and where you must create the inst/ folder,
>> and the *package installation folder*, which gets created and
>> populated by 'R CMD INSTALL'. The exact location of the *package
>> installation folder* doesn't really matter but if you are curious
>> you can use the .libPaths() command to see it. The *package installation
>> folder* is the subfolder of .libPaths() that has the name of the
>> package. You can also see it with find.package("mypackage").
>>
>> During installation, everything that is under the inst/ folder will
>> get installed *directly* under the *package installation folder*.
>> So if you created the extdata/ folder under inst/ (as it should be),
>> extdata/ will end up being installed at .libPaths()/mypackage/extdata/
>> The code in your examples can get the path to the *installed* extdata/
>> folder with
>>
>>   system.file(package="mypackage", "extdata")
>>
>> or get the path to any file under extdata/ with e.g.
>>
>>   system.file(package="mypackage", "extdata", "data1.bed")
>>
>> Don't do
>>
>>   system.file(package="mypackage", "extdata/data1.bed")
>>
>> even if it works for you because it's not portable (the use of / as
>> a separator is a platform-dependent thing).
>>
>> Finally note that you should never try to modify anything that is under
>> .libPaths() by hand. Furthermore, and that's a mistake we see sometimes
>> with contributed packages, the code in your package should always
>> treat the *package installation folder* as a read-only folder.
>>
>> Hope this helps,
>>
>> H.
>>
>>
>> On 12/01/2016 04:34 PM, Jurat Shayidin wrote:
>>
>>> Hi BiocDevel :
>>>
>>> I am getting vignette error when I building my 

Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

[Dan Tenenbaum]

- Original Message -
> From: "Sean Davis" 
> To: "Martin Morgan" 
> Cc: "bioc-devel" 
> Sent: Wednesday, November 30, 2016 1:20:58 PM
> Subject: Re: [Bioc-devel] problems installing cran dependencies with BioC 
> devel in mac

>> On Nov 30, 2016, at 4:13 PM, Martin Morgan 
>> wrote:
>> 
>> On 11/30/2016 08:51 AM, Kasper Daniel Hansen wrote:
>>> Full transcript please; you're compiling from source.
>> 
>> Excuse my ignorance about the Mac world but shouldn't these be available for
>> binary installation via the URL Andrea provided,
>> 
>>  https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4/
>>  
> 
> I am not sure if it is supposed to be, but this directory is empty.
> 

Building binaries of packages for R-devel is not always CRAN's highest 
priority, but it could be worth asking about. Simon Urbanek is the Mac person 
at CRAN.

Dan


> Sean
> 
> 
>> 
>> ?
>> 
>> Martin
>> 
>>> 
>>> On Wed, Nov 30, 2016 at 8:24 AM, Rodriguez Martinez, Andrea <
>>> andrea.rodriguez-martine...@imperial.ac.uk> wrote:
>>> 
 Hi,
 
 
 Thanks for your reply.  Maybe I am doing something wrong, but I do get
 errors, after I select the option install from source. See below:
 
 
> source("https://bioconductor.org/biocLite.R;)
> biocLite("MWASTools")
 
 
 The downloaded source packages are in
 ‘/private/var/folders/z8/8jwlrtqx3270h05ncg1xwzs8gn
 /T/Rtmp79qF9E/downloaded_packages’
 Warning messages:
 1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘SparseM’ had non-zero exit status
 2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘irlba’ had non-zero exit status
 3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘minqa’ had non-zero exit status
 4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RcppEigen’ had non-zero exit status
 5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘quantreg’ had non-zero exit status
 6: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘lme4’ had non-zero exit status
 7: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘pbkrtest’ had non-zero exit status
 8: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘car’ had non-zero exit status
 9: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘igraph’ had non-zero exit status
 10: In install.packages(update[instlib == l, "Package"], l, repos =
 repos,  :
  installation of package ‘mgcv’ had non-zero exit status
 
 
> sessionInfo()
 R Under development (unstable) (2016-10-26 r71594)
 Platform: x86_64-apple-darwin13.4.0 (64-bit)
 Running under: OS X El Capitan 10.11.6
 
 locale:
 [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
 
 attached base packages:
 [1] stats graphics  grDevices utils datasets  methods   base
 
 other attached packages:
 [1] BiocInstaller_1.25.2
 
 loaded via a namespace (and not attached):
 [1] tools_3.4.0
 
 
 
 Thanks very much in advance,
 
 
 Best wishes,
 
 
 Andrea
 
 
 From: Vincent Carey 
 Sent: 30 November 2016 12:39:12
 To: Rodriguez Martinez, Andrea
 Cc: bioc-devel@r-project.org
 Subject: Re: [Bioc-devel] problems installing cran dependencies with BioC
 devel in mac
 
 In fact there was a problem installing igraph from source, but that is
 another issue.  That can
 be resolved using the precompiled binary at http://igraph.org/r/#downloads
 
 
> sessionInfo()
 
 R Under development (unstable) (2016-10-26 r71594)
 
 Platform: x86_64-apple-darwin13.4.0 (64-bit)
 
 Running under: OS X El Capitan 10.11.6
 
 
 locale:
 
 [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
 
 
 attached base packages:
 
 [1] stats graphics  grDevices utils datasets  methods   base
 
 
 other attached packages:
 
 [1] BiocInstaller_1.25.2 MWASTools_0.99.10rmarkdown_1.1
 
 
 loaded via a namespace (and not attached):
 
 [1] Rcpp_0.12.8XVector_0.15.0
 
 [3] GenomeInfoDb_1.11.6nloptr_1.0.4
 
 [5] ppcor_1.1  plyr_1.8.4
 
 [7] zlibbioc_1.21.0tools_3.4.0
 
 [9] boot_1.3-18digest_0.6.10
 
 [11] lme4_1.1-12evaluate_0.10
 
 [13] tibble_1.2   

Re: [Bioc-devel] svn permissions

[Dan Tenenbaum]

You have full permissions on minfiDataEPIC, but not for minfiData; I added 
those. Make sure you are committing as user khansen.

Dan


- Original Message -
> From: "Kasper Daniel Hansen" 
> To: "bioc-devel" 
> Sent: Sunday, November 20, 2016 6:11:09 PM
> Subject: [Bioc-devel] svn permissions

> I am trying to update the Experiment data packages
>  minfiData
>  minfiDataEPIC
> 
> but I get
> svn: E175013: Commit failed (details follow):
> svn: E175013: Access to '/bioc-data/!svn/me' forbidden
> 
> I am 100% sure I have updated minfiData myself before.
> 
> Best,
> Kasper
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

___
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Re: [Bioc-devel] GSL on Windows

[Dan Tenenbaum]

You need to make sure both i386 and x64 versions of GSL are installed under 
c:\GnuWin32, for a directory structure like this:

c:\GnuWin32\i386
c:\GnuWin32\x64

(Also I would recommend using a more descriptive name than c:\GnuWin32, perhaps 
call it c:\GSL?)

And then notice how the DirichletMultinomial Makevars.win references R_ARCH, 
will will have the value of 'i386' when building the 32-bit DLL of your 
package, and 'x64' when building the 64-bit DLL.

Dan


- Original Message -
> From: "Dong Li" 
> To: "bioc-devel" 
> Sent: Friday, November 18, 2016 10:08:56 AM
> Subject: [Bioc-devel] GSL on Windows

> Hi
> 
> Sorry about previous post on support.bioconductor.org.
> 
> I am trying to use GSL on Windows to build my package. And I use
> src/Makevars.win as Martin's package
> https://github.com/Bioconductor-mirror/DirichletMultinomial.
> 
> PKG_LIBS += -L$(LIB_GSL)/lib -lgsl -lgslcblas
> PKG_CPPFLAGS += -I$(RHOME)/src/include -I$(LIB_GSL)/include
> 
> I set an environment variable `LIB_GSL` as `C:\GnuWin32` since I
> download http://gnuwin32.sourceforge.net/packages/gsl.htm and installed
> it to that default location. Compilation seems fine but got the
> following error:
> 
> Error in inDL(x, as.logical(local), as.logical(now), ...) :
>   unable to load shared object
> 'D:/Soft/Rlibrary/AMOUNTAIN/libs/x64/AMOUNTAIN.dll':
>   LoadLibrary failure:  %1 is not a valid Win32 application
> 
> Any suggestions? Thanks.
> 
> 
> --
> Best regards,
> 
> Dong
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] stuck in setting up Bioconductor GitHub

[Dan Tenenbaum]

Did you fork the repository first?

- Original Message -
> From: "Leif Väremo" 
> To: "bioc-devel" 
> Sent: Tuesday, November 15, 2016 1:50:37 AM
> Subject: [Bioc-devel] stuck in setting up Bioconductor GitHub

> Hi,
> 
> I am trying to setup up my pre-existing Bioconductor package piano in GitHub. 
> I
> am following the steps listed on the Bioconductor website:
> 
> 
>  1.  git clone https://github.com/USER/REPO to clone the repository to your
>  machine.
>  2.  cd REPO to switch to the REPO directory.
>  3.  bash /path/to/update_remotes.sh to setup the git remotes.
>  4.  Commit to git and push to GitHub as you normally would.
>  5.  Each time you want to push git commits to svn:
> *   git checkout devel to switch to the devel branch. (use release-X.X for
> release branches)
> *   git svn rebase to get the latest SVN changes.
> *   git merge master --log to merge your changes from the master branch 
> or skip
> this step and work directly on the current branch.
> *   git svn dcommit --add-author-from to sync and commit your changes to 
> svn.
> You may be prompted here for your SVN username and password.
> 
> After step 3, I have a local devel branch that does not yet exist in my remote
> (which would be my own fork of the Bioconductor-mirror).
> My interpretation of step 4 is that I can work on any local branch, say devel 
> or
> release-3.4, and then commit+push those changes to GitHub. However, when I try
> to push (either from the devel branch or a release branch) I get this:
> 
> remote: Permission to Bioconductor-mirror/piano.git denied to varemo.
> fatal: unable to access 'https://github.com/Bioconductor-mirror/piano.git/': 
> The
> requested URL returned error: 403
> 
> So it seems like it is trying to push to Bioconductor-mirror/piano.git 
> whereas I
> would like to push to varemo/piano.git, right?
> 
> I assumed it was intended like this at least. So when I would be happy with my
> changes, e.g. updates to the local devel branch and in sync with the devel
> branch on varemo/piano.git, then I would move on and go through step 5 to push
> my edits to svn. But maybe I am missing something here?
> 
> As a side note: I am able to edit the local master branch and push that to
> GitHub, i.e. the master on varemo/piano.git. Is the idea that one should only
> work on master, and just use the other branches when doing step 5?
> 
> Would be grateful if anyone could clarify the system for me.
> 
> Thanks
> 
> /Leif Väremo
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4

[Dan Tenenbaum]

You need to figure out where R is installed, probably in

c:\program files\R-3.4\bin

If you go to that directory (you can do it with this command in a command 
window):

cd c:\progra~1\R-3.4\bin

Then start R like this:

.\R.exe --vanilla

Dan


- Original Message -
> From: "Jurat Shayidin" <juratb...@gmail.com>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" 
> <bioc-devel@r-project.org>
> Sent: Friday, November 11, 2016 1:59:32 PM
> Subject: Re: [Bioc-devel] Fwd: can't install CRAN Packages after installed 
> devel version of R and Bioc 3.4

> Dear Dan :
> I tried same command in terminal, but I got an error : 'R' is not
> recognized as internal or external command, operable program or batch
> file. should
> I change the directory under the current package working directory ? How
> can I fix this error ? Any quick solution ? Thanks a lot
> 
> Best regards :
> Jurat
> 
> On Fri, Nov 11, 2016 at 10:35 PM, Dan Tenenbaum <dtene...@fredhutch.org>
> wrote:
> 
>> Don't do this in RStudio, do it at the command line/terminal. Type in R
>> --vanilla. You won't get the same interface as RStudio but you can see if
>> the problem persists.
>>
>> Dan
>>
>>
>> - Original Message -
>> > From: "Jurat Shayidin" <juratb...@gmail.com>
>> > To: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com>, "bioc-devel"
>> <bioc-devel@r-project.org>
>> > Sent: Friday, November 11, 2016 12:38:57 PM
>> > Subject: Re: [Bioc-devel] Fwd: can't install CRAN Packages after
>> installed devel version of R and Bioc 3.4
>>
>> > Dear Kasper :
>> > Thanks for your explanation. However, I opened the shell from Rstudio and
>> > type the command R --vanilla, seems it works fine, but still not sure
>> about
>> > efficiency of using R -vanilla. I am not confident about using R
>> commands,
>> > so is there any quick example that I can practice and understand this in
>> > depth ? Thanks a lot
>> >
>> > Best regards:
>> > Jurat
>> >
>> > On Fri, Nov 11, 2016 at 7:22 PM, Kasper Daniel Hansen <
>> > kasperdanielhan...@gmail.com> wrote:
>> >
>> >> You're bing asked to use
>> >>   R --vanilla
>> >> because you have a non-standard problem, exemplified by the fact that
>> what
>> >> you have problems with (installing CRAN packages) works for thousands of
>> >> users of Bioconductor (certainly for me).  This suggests that there is
>> >> something wrong with something on your computer.  Starting R with R
>> >> --vanilla disables loading of some user-specific component. If it works
>> >> with R --vanilla the conclusion is that whatever made it fail was
>> something
>> >> loaded by R but not R --vanilla.  If it doesn't work with R --vanilla
>> the
>> >> conclusion is that your problem is elsewhere.
>> >>
>> >> Best,
>> >> Kasper
>> >>
>> >> On Fri, Nov 11, 2016 at 12:09 PM, Jurat Shayidin <juratb...@gmail.com>
>> >> wrote:
>> >>
>> >>> sorry for this simple question. why use R vanilla ? not familiar enough
>> >>> with this term.
>> >>>
>> >>> On Fri, Nov 11, 2016 at 5:51 PM, Martin Morgan <
>> >>> martin.mor...@roswellpark.org> wrote:
>> >>>
>> >>> > On 11/11/2016 11:42 AM, Jurat Shayidin wrote:
>> >>> >
>> >>> >> I'll keep this in mind. Thanks for reminding. Could you please
>> >>> elaborate
>> >>> >> your answer on my doubt ? Thanks
>> >>> >>
>> >>> >> On Fri, Nov 11, 2016 at 5:27 PM, Martin Morgan <
>> >>> >> martin.mor...@roswellpark.org> wrote:
>> >>> >>
>> >>> >> Please respond on the mailing list, so that others in similar
>> >>> situations
>> >>> >>> can benefit / contribute.
>> >>> >>>
>> >>> >>> On 11/11/2016 10:39 AM, Jurat Shayidin wrote:
>> >>> >>>
>> >>> >>> Dear Martin :
>> >>> >>>>
>> >>> >>>> Thanks for your prompt hit . I used to have R release version, so
>> >>> after
>> >>> >>>> I installed devel version of R, I removed R released version,
>> while
>> >

Re: [Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4

[Dan Tenenbaum]

Don't do this in RStudio, do it at the command line/terminal. Type in R 
--vanilla. You won't get the same interface as RStudio but you can see if the 
problem persists.

Dan


- Original Message -
> From: "Jurat Shayidin" 
> To: "Kasper Daniel Hansen" , "bioc-devel" 
> 
> Sent: Friday, November 11, 2016 12:38:57 PM
> Subject: Re: [Bioc-devel] Fwd: can't install CRAN Packages after installed 
> devel version of R and Bioc 3.4

> Dear Kasper :
> Thanks for your explanation. However, I opened the shell from Rstudio and
> type the command R --vanilla, seems it works fine, but still not sure about
> efficiency of using R -vanilla. I am not confident about using R commands,
> so is there any quick example that I can practice and understand this in
> depth ? Thanks a lot
> 
> Best regards:
> Jurat
> 
> On Fri, Nov 11, 2016 at 7:22 PM, Kasper Daniel Hansen <
> kasperdanielhan...@gmail.com> wrote:
> 
>> You're bing asked to use
>>   R --vanilla
>> because you have a non-standard problem, exemplified by the fact that what
>> you have problems with (installing CRAN packages) works for thousands of
>> users of Bioconductor (certainly for me).  This suggests that there is
>> something wrong with something on your computer.  Starting R with R
>> --vanilla disables loading of some user-specific component. If it works
>> with R --vanilla the conclusion is that whatever made it fail was something
>> loaded by R but not R --vanilla.  If it doesn't work with R --vanilla the
>> conclusion is that your problem is elsewhere.
>>
>> Best,
>> Kasper
>>
>> On Fri, Nov 11, 2016 at 12:09 PM, Jurat Shayidin 
>> wrote:
>>
>>> sorry for this simple question. why use R vanilla ? not familiar enough
>>> with this term.
>>>
>>> On Fri, Nov 11, 2016 at 5:51 PM, Martin Morgan <
>>> martin.mor...@roswellpark.org> wrote:
>>>
>>> > On 11/11/2016 11:42 AM, Jurat Shayidin wrote:
>>> >
>>> >> I'll keep this in mind. Thanks for reminding. Could you please
>>> elaborate
>>> >> your answer on my doubt ? Thanks
>>> >>
>>> >> On Fri, Nov 11, 2016 at 5:27 PM, Martin Morgan <
>>> >> martin.mor...@roswellpark.org> wrote:
>>> >>
>>> >> Please respond on the mailing list, so that others in similar
>>> situations
>>> >>> can benefit / contribute.
>>> >>>
>>> >>> On 11/11/2016 10:39 AM, Jurat Shayidin wrote:
>>> >>>
>>> >>> Dear Martin :
>>> 
>>>  Thanks for your prompt hit . I used to have R release version, so
>>> after
>>>  I installed devel version of R, I removed R released version, while
>>> only
>>>  keep devel version instead. Is this correct ? I didn't clean R
>>> session,
>>> 
>>> >>>
>>> > this is not related to your original question. I personally need both a
>>> > release and devel version of R and have both installed.
>>> >
>>> > how can I make it happen on windows?  Plus, How to make R session
>>>  vanilla ? What's right configuration both R devel and Bioc devel
>>> before
>>> 
>>> >>>
>>> > open a Windows shell ('cmd') and type
>>> >
>>> >   R --vanilla
>>> >
>>> > or perhaps
>>> >
>>> >   Rgui --vanilla
>>> >
>>> > building my packages ? Could you elaborate your answer please? Thank you
>>> 
>>> >>>
>>> > again, this isn't related to your original question. See the section
>>> > 'Which version of R?' in
>>> >
>>> >   http://bioconductor.org/developers/how-to/useDevel/
>>> >
>>> > Martin
>>> >
>>> >
>>> > very much
>>> 
>>>  Best regards :
>>> 
>>>  On Fri, Nov 11, 2016 at 4:04 PM, Martin Morgan
>>>  >> >>
>>> 
>>>  wrote:
>>> 
>>>  On 11/11/2016 09:44 AM, Jurat Shayidin wrote:
>>> 
>>>  Dear BiocDevel:
>>> 
>>>  I ran into the issue after installed devel version of R and
>>> Bioc
>>>  3.4.
>>>  Because my packages depends on some packages from CRAN
>>>  repository, now I
>>>  failed to installed paclages from CRAN. I don't have problem
>>>  when I used
>>>  released version of R. Because new packages must coordinate
>>> with
>>>  devel
>>>  version of Bioc and R, so I did it. But can't installl
>>> packages
>>>  from CRAN
>>>  like dplyr. How can I overcome this issue ? Any quick
>>> solution
>>>  ?  I got
>>>  error as follow:
>>> 
>>> 
>>>  BiocInstaller::useDevel()
>>> 
>>>  Error: 'devel' version already in use
>>> 
>>>  install.packages("dplyr")
>>> 
>>>  Error in install.packages : missing value where TRUE/FALSE
>>>  needed
>>> 
>>> 
>>>  this does not happen for me; you'll need to debug on your end,
>>>  minimally, reporting the output of traceback() after the error
>>>  occurs.
>>> 
>>>  are you in 

Re: [Bioc-devel] No release svn repository for proFIA/plasFIA maintainer

[Dan Tenenbaum]

The same credentials work for release.

- Original Message -
> From: "DELABRIÈRE Alexis" 
> To: "bioc-devel" 
> Sent: Tuesday, October 25, 2016 4:43:17 AM
> Subject: [Bioc-devel] No release svn repository for proFIA/plasFIA maintainer

> Hello,
> 
> 
> My packages (proFIA, plasFIA) have been added in the last release of
> Bioconductor and I received an email which gave me svn credential. Howerver
> this email only sent me credential to devel version, and I found some minor
> issues that needs to be fixed on the release version, how may I obtain
> credential to make my bug fixes on release ?
> 
> I though that it was sent automatically, but at the moment I did not receive
> anything.
> 
> Thanks,
> 
> Alexis Delabriere
> PhD Student,
> Laboratoire d'Analyse de Donn�es et d'Intelligence des Syst�mes,
> CEA Saclay,
> DRT/LIST/DM2I/LADIS
> 
> 
>   [[alternative HTML version deleted]]
> 
> 
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] Question about InteractionSet package

[Dan Tenenbaum]

Oops, sorry, my bad.

I read the warning and thought it was trying to install the package from CRAN, 
but I was just reading it wrong, that warning is irrelevant to your situation.

Sounds like your situation is resolved based on your off-list email to me.

Dan


- Original Message -
> From: "Dan Tenenbaum" <dtene...@fredhutch.org>
> To: "Ioannis Vardaxis" <ioannis.varda...@math.ntnu.no>
> Cc: "bioc-devel" <bioc-devel@r-project.org>
> Sent: Friday, October 21, 2016 10:44:26 AM
> Subject: Re: [Bioc-devel] Question about InteractionSet package

> You need to tell us the command that produced that error.
> 
> InteractionSet is a Bioconductor package, not a CRAN package. Maybe you tried 
> to
> install it with install.packages() instead of biocLite()?
> 
> See the "Installlation" section of
> 
> https://bioconductor.org/packages/release/bioc/html/InteractionSet.html
> 
> Dan
> 
> 
> - Original Message -
>> From: "Ioannis Vardaxis" <ioannis.varda...@math.ntnu.no>
>> To: "bioc-devel" <bioc-devel@r-project.org>
>> Sent: Friday, October 21, 2016 7:07:30 AM
>> Subject: [Bioc-devel] Question about InteractionSet package
> 
>> Hi,
>> 
>> I am currently developing a package which I want to submit to Bioconductor. 
>> I am
>> using the R-devel version. I am trying  to install the InteractionSet package
>> with no success. I get the following warnings:
>> 
>> Warning: unable to access index for repository
>> https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4:
>> Package which is only available in source form, and may need compilation of
>> C/C++/Fortran:
>>  'InteractionSet'
>> Do you want to attempt to install these from sources?
>> y/n:
>> 
>> Even if I answer y, the package is not installed. Is there any possible 
>> solution
>> to the problem?
>> 
>> 
>> Best,
>> Ioannis
>> --
>> Ioannis Vardaxis
>> Stipendiat IMF
>> NTNU
>> 
>>  [[alternative HTML version deleted]]
>> 
>> ___
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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] Question about InteractionSet package

[Dan Tenenbaum]

You need to tell us the command that produced that error.

InteractionSet is a Bioconductor package, not a CRAN package. Maybe you tried 
to install it with install.packages() instead of biocLite()?

See the "Installlation" section of

https://bioconductor.org/packages/release/bioc/html/InteractionSet.html

Dan


- Original Message -
> From: "Ioannis Vardaxis" 
> To: "bioc-devel" 
> Sent: Friday, October 21, 2016 7:07:30 AM
> Subject: [Bioc-devel] Question about InteractionSet package

> Hi,
> 
> I am currently developing a package which I want to submit to Bioconductor. I 
> am
> using the R-devel version. I am trying  to install the InteractionSet package
> with no success. I get the following warnings:
> 
> Warning: unable to access index for repository
> https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4:
> Package which is only available in source form, and may need compilation of
> C/C++/Fortran:
>  'InteractionSet'
> Do you want to attempt to install these from sources?
> y/n:
> 
> Even if I answer y, the package is not installed. Is there any possible 
> solution
> to the problem?
> 
> 
> Best,
> Ioannis
> --
> Ioannis Vardaxis
> Stipendiat IMF
> NTNU
> 
>   [[alternative HTML version deleted]]
> 
> ___
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Re: [Bioc-devel] Package "not supported" on some platforms, and dependent packages

[Dan Tenenbaum]

- Original Message -
> From: "Kevin RUE" 
> To: "bioc-devel" 
> Sent: Tuesday, October 18, 2016 3:28:23 PM
> Subject: [Bioc-devel] Package "not supported" on some platforms,  and 
> dependent packages

> Hi all,
> 
> Heartless logic works as follows:
> 
>   - ensemblVEP is "not supported" on Windows (build report
>   ).
>   Completely understandable.
>   - My package depends on ensemblVEP.
>   - The build system reports an error on Windows for my package
> because "dependency
>   'ensemblVEP' is not available for package 'TVTB'" (build report
>   
> 
>   )
>   - As a result, the landing page for my package reports "build error" (
>   page )
> 
> I was hoping to benefit of the same treatment as the ensemblVEP package,
> that is, skipping the nightly build on the Windows machine, to get the nice
> green light "build OK" on the landing page.
> 
> I suppose this is something to control in the build system, right? Or do I
> have to put any kind of keyword in one of my package files?
> Thanks!
> 

The build system is heartless. ;)
ensemblVEP is marked as unsupported on Windows by virtue of a .BBSoptions file 
in the top level (at the same level as DESCRIPTION) containing one line:

UnsupportedPlatforms: win

If you add that to your package it will stop building (and failing) on windows.

If ensemblVEP is ever again supported on windows (I don't know if this is 
planned) you'll need to remove that file.

Dan


> All the best,
> Kevin
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] staging.bioconductor.org not responsive

[Dan Tenenbaum]

Try ssh'ing as the biocadmin user, not ubuntu.

I am able to do both but that just might mean my public keys are in both places.

There is a crash.log in /home/biocadmin/bioc-test-web/bioconductor.org which 
may have some hints as to what happened.



Dan


- Original Message -
> From: "Martin Morgan" <martin.mor...@roswellpark.org>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" 
> <bioc-devel@r-project.org>
> Sent: Tuesday, October 18, 2016 3:25:16 PM
> Subject: staging.bioconductor.org not responsive

> Hi Dan, et al.,
> 
> When I try to ssh I get
> 
> $ ssh ubu...@staging.bioconductor.org
> ssh_exchange_identification: read: Connection reset by peer
> 
> and it seems like the sync with master didn't happen at 3pm / 3:20pm.
> 
> Hints?
> 
> If there was a commit problem, it's most likely config.yaml at
> 
> 
> r122774 | mtmor...@fhcrc.org | 2016-10-18 17:24:05 -0400 (Tue, 18 Oct
> 2016) | 2 lines
> Changed paths:
>M /trunk/bioconductor.org/assets/robots.txt
>M /trunk/bioconductor.org/config.yaml
>M /trunk/bioconductor.org/content/about/release-announcements.md
>M /trunk/bioconductor.org/content/developers/how-to/useDevel.md
>M /trunk/bioconductor.org/content/index.html
>M /trunk/bioconductor.org/layouts/_bioc_older_packages.html
>M /trunk/bioconductor.org/layouts/_release_announcements.html
> 
> release changes
> 
> 
> 
> This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited.  If you have 
> received
> this message in error, please notify the sender immediately by e-mail and
> delete this email message from your computer. Thank you.

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Re: [Bioc-devel] biocLite and useDevel

[Dan Tenenbaum]

Probably related to:

https://stat.ethz.ch/pipermail/bioc-devel/2016-October/009897.html

Dan


- Original Message -
> From: "Kasper Daniel Hansen" 
> To: "bioc-devel" 
> Sent: Friday, October 14, 2016 9:07:34 AM
> Subject: [Bioc-devel] biocLite and useDevel

> This is unexpected, to me at least (below).  I source biocLite and set
> useDevel(TRUE) and it does not switch to current devel branch.  Perhaps
> this has to do with branches and stuff.  Breaks current Travis setup.
> Perhaps this is just a hiccup which will go away.
> 
> # R-3.3
> 
> R version 3.3.1 RC (2016-06-14 r70789) -- "Bug in Your Hair"
> Copyright (C) 2016 The R Foundation for Statistical Computing
> Platform: x86_64-apple-darwin15.5.0 (64-bit)
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> 
>  Natural language support but running in an English locale
> 
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
> 
>> source("http://www.bioconductor.org/biocLite.R;)
> Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
>> useDevel(TRUE)
> Installing package into ‘/usr/local/R/R-3.3/lib/R/site-library’
> (as ‘lib’ is unspecified)
> Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
> 'BiocInstaller' changed to version 1.22.3
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] flowCore fails with GCC 4.4.7 on RHEL 6.0

[Dan Tenenbaum]

- Original Message -
> From: "Kasper Daniel Hansen" 
> To: "Mike" 
> Cc: "bioc-devel" 
> Sent: Tuesday, October 11, 2016 5:57:02 PM
> Subject: Re: [Bioc-devel] flowCore fails with GCC 4.4.7 on RHEL 6.0

> Two things.
> 
> 1. You might be surprised how many HPC facilities uses older versions of
> GCC for stability. We do, and many others I know of.
> 2. In my opinion, you should have a configure script check for newer
> versions of GCC or document it elsewhere.  I don't see that.
> 

flowCore does mention SystemRequirements: C++11 as it is supposed do.
Dan


> Best,
> Kasper
> 
> On Tue, Oct 11, 2016 at 3:07 PM, Mike  wrote:
> 
>> It does use some c++11 code and I think it is reasonable to expect
>> relative newer gcc (>=4.8.4) to be installed.
>>
>>
>>
>> On 10/10/2016 05:42 PM, Kasper Daniel Hansen wrote:
>>
>>> Latest version (1.39.11).
>>>
>>> My guess is that this is a case of the author using C++ stuff which is
>>> not support on 4.4.7.
>>>
>>> ** libs
>>> /usr/bin/g++ -std=c++0x -I/jhpce/shared/community/comp
>>> iler/gcc/4.4.7/R/3.3.x/lib64/R/include -DNDEBUG -I../inst/include/
>>> -I/usr/local/include -I"/jhpce/shared/community/com
>>> piler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/Rcpp/include"
>>> -I"/jhpce/shared/community/compiler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/BH/include"
>>>  -fpic  -g -O2 -march=amdfam10 -c FastLogicle.cpp -o FastLogicle.o
>>> /usr/bin/g++ -std=c++0x -I/jhpce/shared/community/comp
>>> iler/gcc/4.4.7/R/3.3.x/lib64/R/include -DNDEBUG -I../inst/include/
>>> -I/usr/local/include -I"/jhpce/shared/community/com
>>> piler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/Rcpp/include"
>>> -I"/jhpce/shared/community/compiler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/BH/include"
>>>  -fpic  -g -O2 -march=amdfam10 -c Hyperlog.cpp -o Hyperlog.o
>>> /usr/bin/g++ -std=c++0x -I/jhpce/shared/community/comp
>>> iler/gcc/4.4.7/R/3.3.x/lib64/R/include -DNDEBUG -I../inst/include/
>>> -I/usr/local/include -I"/jhpce/shared/community/com
>>> piler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/Rcpp/include"
>>> -I"/jhpce/shared/community/compiler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/BH/include"
>>>  -fpic  -g -O2 -march=amdfam10 -c Logicle.cpp -o Logicle.o
>>> /usr/bin/g++ -std=c++0x -I/jhpce/shared/community/comp
>>> iler/gcc/4.4.7/R/3.3.x/lib64/R/include -DNDEBUG -I../inst/include/
>>> -I/usr/local/include -I"/jhpce/shared/community/com
>>> piler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/Rcpp/include"
>>> -I"/jhpce/shared/community/compiler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/BH/include"
>>>  -fpic  -g -O2 -march=amdfam10 -c RcppExports.cpp -o RcppExports.o
>>> /usr/bin/g++ -std=c++0x -I/jhpce/shared/community/comp
>>> iler/gcc/4.4.7/R/3.3.x/lib64/R/include -DNDEBUG -I../inst/include/
>>> -I/usr/local/include -I"/jhpce/shared/community/com
>>> piler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/Rcpp/include"
>>> -I"/jhpce/shared/community/compiler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/BH/include"
>>>  -fpic  -g -O2 -march=amdfam10 -c biexponential.cpp -o biexponential.o
>>> /usr/bin/g++ -std=c++0x -I/jhpce/shared/community/comp
>>> iler/gcc/4.4.7/R/3.3.x/lib64/R/include -DNDEBUG -I../inst/include/
>>> -I/usr/local/include -I"/jhpce/shared/community/com
>>> piler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/Rcpp/include"
>>> -I"/jhpce/shared/community/compiler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/BH/include"
>>>  -fpic  -g -O2 -march=amdfam10 -c convertRawBytes.cpp -o convertRawBytes.o
>>> convertRawBytes.cpp: In function ‘std::vector>> std::allocator > convertRawBytes(BYTES, bool, std::vector>> unsigned int, std::allocator >, short unsigned int,
>>> bool)’:
>>> convertRawBytes.cpp:48: error: expected initializer before ‘:’ token
>>> convertRawBytes.cpp:53: error: expected primary-expression before ‘auto’
>>> convertRawBytes.cpp:53: error: expected ‘)’ before ‘auto’
>>> convertRawBytes.cpp:56: error: ‘nElement’ was not declared in this scope
>>> convertRawBytes.cpp:61: error: ‘nrow’ was not declared in this scope
>>> convertRawBytes.cpp:97: error: call of overloaded ‘to_string(short
>>> unsigned int&)’ is ambiguous
>>> /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/
>>> c++/4.4.7/bits/basic_string.h:2604: note: candidates are: std::string
>>> std::to_string(long long int)
>>> /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/
>>> c++/4.4.7/bits/basic_string.h:2610: note: std::string
>>> std::to_string(long long unsigned int)
>>> /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/
>>> c++/4.4.7/bits/basic_string.h:2616: note: std::string
>>> std::to_string(long double)
>>> convertRawBytes.cpp:112: error: call of overloaded ‘to_string(short
>>> unsigned int&)’ is ambiguous
>>> /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/
>>> c++/4.4.7/bits/basic_string.h:2604: note: candidates are: std::string
>>> std::to_string(long long int)
>>> 

Re: [Bioc-devel] Automatic build failure notifications

[Dan Tenenbaum]

- Original Message -
> From: "Hervé Pagès" <hpa...@fredhutch.org>
> To: "Emma Schymanski" <emma.schyman...@eawag.ch>, "bioc-devel" 
> <bioc-devel@r-project.org>
> Cc: "Dan Tenenbaum" <dtene...@fredhutch.org>
> Sent: Tuesday, October 11, 2016 10:55:20 AM
> Subject: Re: Automatic build failure notifications

> OK, will do. Thanks Emma for your feedback.
> 

I like the idea of opting in for this. Sometimes there are false positives (for 
example, a package might fail because its dependency failed for some reason, or 
there is an issue with the build system) that the package author can do nothing 
about. I imagine that there might be a lot of traffic on this list asking what 
should be done about such emails, or complaining about receiving such emails. 
The way the notifications are currently set up is that they are sent once a 
week and that could get frustrating for people if the emails are false 
positives.

These sort of false positives were less common in release which was probably 
why these notifications were only enabled in release before.

On the other hand, failing to opt in would mean some maintainers would not see 
true positives. 


My $0.02.
Dan


> H.
> 
> On 10/10/2016 11:22 PM, Schymanski, Emma wrote:
>> Hi Herve, Markus, all,
>>
>>
>>
>> It would really be great if these automatic notifications would be on
>> again –
>>
>> and if this would happen for devel and release. After my last email Dan T.
>>
>> suggested I sign up for the RSS feed – I followed the instructions but even
>>
>> there I seem only to get an old feed of the release build report – which
>> for us is
>>
>> a different error [one that is relates to Java … and has been going on
>> for ages]
>>
>>
>>
>> Manually checking the builds every days is a pain when we know we are
>>
>> waiting for a fix – if there would be a way to automate devel build reports
>>
>> (maybe an opt in so those that don’t want the traffic don’t go crazy), that
>>
>> would be great. I’m sure there’d be quite a few of us that would really
>>
>> appreciate that! We’d have found our error much quicker that way...
>>
>>
>>
>> I would vote for daily in the run up to the release, if doable. A number of
>>
>> us seem to still have some need for this ;)
>>
>>
>>
>> Thanks,
>>
>> Emma
>>
>>
>>
>>>> We would also
>>
>>>> appreciate it to have the e-mail system for failed builds / checks back
>>
>>>> online :-)
>>
>>
>>
>>>Just to clarify, in the past we've only activated the automatic build
>>
>>>failure notifications for the release version of Bioconductor (except
>>
>>>for the current release i.e. BioC 3.3, for which we forgot).
>>
>>>
>>
>>>Our plan was to activate them for BioC 3.4 after it's released.
>>
>>>But we could do it now if nobody objects. We usually run the script
>>
>>>once a week as a cron job but we could change this to run it 2 or
>>
>>>3 times/week until the release (which is in 8 days from now), and
>>
>>>then go back to once a week after the release.
>>
>>>
>>
>>>Cheers,
>>
>>>H.
>>
>>
>>
>>
>>
> 
> --
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319

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Re: [Bioc-devel] unable to install/download IRanges, Biobase, GenomeInfoDb

[Dan Tenenbaum]

Have you tried to install those packages? Note that errors (or warnings) in the 
build report does NOT mean that you cannot install the packages.

Installing them works for me in the devel version of bioconductor.

If you have tried to install the packages, please share the command you used to 
do so, the output R produced in response, and the output of the sessionInfo() 
command.

Dan


- Original Message -
> From: "Rodriguez Martinez, Andrea" 
> 
> To: "bioc-devel" 
> Sent: Thursday, October 6, 2016 3:45:52 PM
> Subject: [Bioc-devel] unable to install/download IRanges, Biobase,
> GenomeInfoDb

> Hi,
> 
> 
> I am a bit worried to see that I'm unable to install 3 central packages of
> Bioconductor: c. IRanges has warnings in the
> build/check report, but the other two seem fine.
> 
> 
> Some dependencies of my package (MetaboSignal) depend on these 3 packages, 
> which
> means that if I try to install my package without prior installation of these 
> 3
> packages, I get an error. The reason why I'm a so worried is because my 
> package
> is now under review for publication in a journal, so I am afraid the reviewers
> might have trouble to install the package.
> 
> 
> Does anyone knows if this is going to be fixed soon?
> 
> 
> Thanks very much in advance,
> 
> 
> Andrea
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Why can't NAMESPACE be a strict subset of DESCRIPTION Imports?

[Dan Tenenbaum]

- Original Message -
> From: "Martin Morgan" 
> To: "McDavid, Andrew" , "bioc-devel" 
> 
> Sent: Tuesday, October 4, 2016 2:09:27 PM
> Subject: Re: [Bioc-devel] Why can't NAMESPACE be a strict subset of 
> DESCRIPTION Imports?

> On 10/04/2016 05:07 PM, McDavid, Andrew wrote:
>> BiocCheck throws a warning when a package is listed as Imports: in 
>> DESCRIPTION
>> but not used in the NAMESPACE.  This may happen when a developer uses the 
>> fully
>> qualified names of objects within a package.  I am unclear as to the 
>> rationale
>> for this warning.
>>
> 
> agree it's wrong. can you point to an example? Martin
> 

https://bioconductor.org/spb_reports/MAST_buildreport_20160929192258.html#zin1_check_anchor

* Checking DESCRIPTION/NAMESPACE consistency...
* WARNING: Import parallel, reshape2 in NAMESPACE as well as
  DESCRIPTION.

Dan



>> Per Hadley:
>>
>> It's common for packages to be listed in Imports in DESCRIPTION, but not in
>> NAMESPACE. In fact, this is what I recommend: list the package in DESCRIPTION
>> so that it's installed, then always refer to it explicitly with pkg::fun().
>> Unless there is a strong reason not to, it's better to be explicit. It's a
>> little more work to write, but a lot easier to read when you come back to the
>> code in the future.
>>
>> Per R extensions:
>>
>> If a package only needs a few objects from another package it can use a fully
>> qualified variable reference in the code instead of a formal import. A fully
>> qualified reference to the function f in package foo is of the form foo::f.
>>
>> -Andrew
>>
>>
>>  [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
> 
> 
> This email message may contain legally privileged and/or...{{dropped:2}}
> 
> ___
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Re: [Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine

[Dan Tenenbaum]

- Original Message -
> From: "Hervé Pagès" <hpa...@fredhutch.org>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
> Cc: "Philipp Angerer" <philipp.ange...@helmholtz-muenchen.de>, "bioc-devel" 
> <bioc-devel@r-project.org>
> Sent: Tuesday, October 4, 2016 10:16:34 AM
> Subject: Re: [Bioc-devel] tokay1 (windows) build server cannot use the 
> nbconvertR vignette engine

> On 10/04/2016 09:56 AM, Dan Tenenbaum wrote:
>>
>>
>> - Original Message -
>>> From: "Hervé Pagès" <hpa...@fredhutch.org>
>>> To: "Philipp Angerer" <philipp.ange...@helmholtz-muenchen.de>, "bioc-devel"
>>> <bioc-devel@r-project.org>
>>> Sent: Tuesday, October 4, 2016 9:23:29 AM
>>> Subject: Re: [Bioc-devel] tokay1 (windows) build server cannot use the
>>> nbconvertR vignette engine
>>
>>> Hi Philipp,
>>>
>>> On 10/04/2016 12:13 AM, Angerer, Philipp via Bioc-devel wrote:
>>>> Hi,
>>>>
>>>> Looking at my package’s build report, the devel version isn’t built 
>>>> anymore on
>>>> windows:
>>>> http://bioconductor.org/checkResults/devel/bioc-LATEST/destiny/tokay1-buildsrc.html
>>>>
>>>> The release version is built just fine with moscato2:
>>>> http://bioconductor.org/checkResults/release/bioc-LATEST/destiny/moscato2-buildsrc.html
>>>>
>>>> It would be really nice if this could be fixed. Usually running “jupyter
>>>> nbconvert --help” successfully means that nbconvertR will work.
>>>
>>> The error says:
>>>
>>>   Either IPython 3+ or Jupyter has to be installed, but neither could
>>>   be called.
>>>
>>> But neither Jupyter or IPython 3+ is installed on tokay1 at the moment.
>>> Which one should we install?
>>>
>>> Note that packages with special requirements should list them in the
>>> SystemRequirements field of the DESCRIPTION file. Also it would be great
>>> if you could provide an INSTALL file in the top-level folder of the
>>> package where you explain the installation process of these
>>> requirements.
>>>
>>
>> Note that ipython/jupyter are requirements not of destiny but of the CRAN
>> package nbconvertR, which does list those dependencies in its
>> SystemDependencies field.
>> https://cran.r-project.org/web/packages/nbconvertR/index.html
>> SystemRequirements:  pandoc, ipython (>= 3.0) or jupyter, ipython/jupyter
>> notebook optional dependencies, pywin32 (on windows)
> 
> Good to know, thanks Dan! That makes testing on tokay1 easier:
> 
>   > library(nbconvertR)
>   > path <- system.file('doc', 'test-vignette.ipynbmeta',
> package='nbconvertR')
>   > nbconvert(path, 'pdf')
>   Error in get.binary() :
> Either IPython 3+ or Jupyter has to be installed, but neither could
> be called.
> 
> I'll work on this.
> 
> @Philipp: no need to add anything to SystemRequirements or to add an
> INSTALL file to your package. I take this back.
> 

Although, since you (Philipp) are the maintainer of the nbconvertR package, you 
may want to create an INSTALL file in that package. It's up to you.

Dan



> Cheers,
> H.
> 
>>
>> Dan
>>
>>
>>> Thanks,
>>> H.
>>>
>>>>
>>>> Best, Philipp
>>>>
>>>>
>>>>
>>>>
>>>> Helmholtz Zentrum Muenchen
>>>>
>>>> Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)
>>>>
>>>> Ingolstaedter Landstr. 1
>>>>
>>>> 85764 Neuherberg
>>>>
>>>> www.helmholtz-muenchen.de
>>>>
>>>> Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe
>>>>
>>>> Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen
>>>>
>>>> Registergericht: Amtsgericht Muenchen HRB 6466
>>>>
>>>> USt-IdNr: DE 129521671
>>>>
>>>>
>>>>[[alternative HTML version deleted]]
>>>>
>>>> ___
>>>> Bioc-devel@r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>
>>> --
>>> Hervé Pagès
>>>
>>> Program in Computational Biology
>>> Division of Public Health Sciences
>>> Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N, M1-B514
>>> P.O. Box 19024
>>> Seattle, WA 98109-1024
>>>
>>> E-mail: hpa...@fredhutch.org
>>> Phone:  (206) 667-5791
>>> Fax:(206) 667-1319
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> --
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319

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Re: [Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine

[Dan Tenenbaum]

- Original Message -
> From: "Hervé Pagès" 
> To: "Philipp Angerer" , "bioc-devel" 
> 
> Sent: Tuesday, October 4, 2016 9:23:29 AM
> Subject: Re: [Bioc-devel] tokay1 (windows) build server cannot use the 
> nbconvertR vignette engine

> Hi Philipp,
> 
> On 10/04/2016 12:13 AM, Angerer, Philipp via Bioc-devel wrote:
>> Hi,
>>
>> Looking at my package’s build report, the devel version isn’t built anymore 
>> on
>> windows:
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/destiny/tokay1-buildsrc.html
>>
>> The release version is built just fine with moscato2:
>> http://bioconductor.org/checkResults/release/bioc-LATEST/destiny/moscato2-buildsrc.html
>>
>> It would be really nice if this could be fixed. Usually running “jupyter
>> nbconvert --help” successfully means that nbconvertR will work.
> 
> The error says:
> 
>   Either IPython 3+ or Jupyter has to be installed, but neither could
>   be called.
> 
> But neither Jupyter or IPython 3+ is installed on tokay1 at the moment.
> Which one should we install?
> 
> Note that packages with special requirements should list them in the
> SystemRequirements field of the DESCRIPTION file. Also it would be great
> if you could provide an INSTALL file in the top-level folder of the
> package where you explain the installation process of these
> requirements.
> 

Note that ipython/jupyter are requirements not of destiny but of the CRAN 
package nbconvertR, which does list those dependencies in its 
SystemDependencies field. 
https://cran.r-project.org/web/packages/nbconvertR/index.html
SystemRequirements: pandoc, ipython (>= 3.0) or jupyter, ipython/jupyter 
notebook optional dependencies, pywin32 (on windows)

Dan


> Thanks,
> H.
> 
>>
>> Best, Philipp
>>
>>
>>
>>
>> Helmholtz Zentrum Muenchen
>>
>> Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)
>>
>> Ingolstaedter Landstr. 1
>>
>> 85764 Neuherberg
>>
>> www.helmholtz-muenchen.de
>>
>> Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe
>>
>> Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen
>>
>> Registergericht: Amtsgericht Muenchen HRB 6466
>>
>> USt-IdNr: DE 129521671
>>
>>
>>  [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
> 
> --
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] SSL connect error on package build machine

[Dan Tenenbaum]

Seems like that was a transient error. I was able to kick off another build 
that did not have this problem.

https://github.com/Bioconductor/Contributions/issues/155#issuecomment-250036650

Dan


- Original Message -
> From: "Tyler Smith" 
> To: "bioc-devel" 
> Sent: Tuesday, September 27, 2016 2:05:08 PM
> Subject: [Bioc-devel] SSL connect error on package build machine

> Hi,
> 
> I've just submitted a new package. The automated build generated an
> error which I think (?) is a problem on one of the build servers (SSL
> connect error in querying the bioc-devel list). I'm not sure if I'm far
> enough along in the process for my assigned human to be alerted to this,
> or if they'll be waiting until bioc-issue-bot gives me a clean bill of
> health before they take a look at things. If the latter, can someone on
> the list help me resolve this?
> 
> https://github.com/Bioconductor/Contributions/issues/155#issuecomment-249995539
> 
> Thanks,
> 
> Tyler
> 
> --
> plantarum.ca
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] msPurity build fail on Mac OS X (morelia)

[Dan Tenenbaum]

One thing I notice is that the crash does not happen every time. I have 
successfully built the package on morelia by hand with "R CMD build".

Similarly I can source the stangled vignette without a crash sometimes. But 
when it does crash, this is what I see:

> source("msPurity-vignette.R", echo=TRUE, max=Inf)

> ## 
> library(msPurity)
Loading required package: Rcpp

> msmsPths <- list.files(system.file("extdata", "lcms", "mzML", 
> package="msPurityData"), full.names = TRUE, pattern = "MSMS")

> msPths <- list.files(system.file("extdata", "lcms", "mzML", 
> package="msPurityData"), full.names = TRUE, pattern = "LCMS_")

> ## 
> pa <- purityA(msmsPths)

 *** caught segfault ***
address 0x2980297, cause 'memory not mapped'

Traceback:
 1: .External(list(name = "CppMethod__invoke_notvoid", address = , dll = list(name = "Rcpp", path = 
"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/libs/Rcpp.so",
 dynamicLookup = TRUE, handle = , info 
= ), numParameters = -1L), , 
, .pointer, ...)
 2: object@backend$getPeakList(x)
 3: FUN(X[[i]], ...)
 4: lapply(X = X, FUN = FUN, ...)
 5: sapply(scans, function(x) object@backend$getPeakList(x)$peaks, simplify 
= FALSE)
 6: sapply(scans, function(x) object@backend$getPeakList(x)$peaks, simplify 
= FALSE)
 7: .local(object, ...)
 8: mzR::peaks(mr)
 9: mzR::peaks(mr)
10: getscans(filepth)
11: assessPuritySingle(filepth = pa@fileList[[i]], mostIntense = mostIntense,   
  nearest = nearest, offsets = offsets, plotP = plotP, plotdir = plotdir, 
interpol = interpol, iwNorm = iwNorm, iwNormFun = iwNormFun, ilim = ilim)
12: eval(expr, envir, enclos)
13: eval(xpr, envir = envir)
14: doTryCatch(return(expr), name, parentenv, handler)
15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
16: tryCatchList(expr, classes, parentenv, handlers)
17: tryCatch(eval(xpr, envir = envir), error = function(e) e)
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
20: tryCatchList(expr, classes, parentenv, handlers)
21: tryCatch({repeat {args <- nextElem(it)if (obj$verbose) 
{cat(sprintf("evaluation # %d:\n", i))print(args)   
 }for (a in names(args)) assign(a, args[[a]], pos = envir, 
inherits = FALSE)r <- tryCatch(eval(xpr, envir = envir), error = 
function(e) e)if (obj$verbose) {cat("result of evaluating 
expression:\n")print(r)}
tryCatch(accumulator(list(r), i), error = function(e) {cat("error 
calling combine function:\n")print(e)NULL}) 
   i <- i + 1}}, error = function(e) {if 
(!identical(conditionMessage(e), "StopIteration")) 
stop(simpleError(conditionMessage(e), expr))})
22: e$fun(obj, substitute(ex), parent.frame(), e$data)
23: operator(foreach::foreach(i = 1:length(pa@fileList), .packages = "mzR"),
 assessPuritySingle(filepth = pa@fileList[[i]], mostIntense = mostIntense,  
   nearest = nearest, offsets = offsets, plotP = plotP, plotdir = 
plotdir, interpol = interpol, iwNorm = iwNorm, iwNormFun = iwNormFun, 
ilim = ilim))
24: purityA(msmsPths)
25: eval(expr, envir, enclos)
26: eval(ei, envir)
27: withVisible(eval(ei, envir))
28: source("msPurity-vignette.R", echo = TRUE, max = Inf)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats graphics  grDevices utils datasets  methods
[8] base

other attached packages:
[1] xcms_1.49.6 Biobase_2.33.3  ProtGenerics_1.5.1
[4] BiocGenerics_0.19.2 mzR_2.7.4   msPurity_0.99.6
[7] Rcpp_0.12.7

loaded via a namespace (and not attached):
 [1] sapa_2.0-2 magrittr_1.5   ifultools_2.0-4
 [4] MASS_7.3-45splines_3.3.1  BiocParallel_1.7.8
 [7] lattice_0.20-34foreach_1.4.3  splus2R_1.2-2
[10] stringr_1.1.0  fastcluster_1.1.21 plyr_1.8.4
[13] tools_3.3.1grid_3.3.1 snow_0.4-1
[16] iterators_1.0.8survival_2.39-5multtest_2.29.0
[19] doSNOW_1.0.14  Matrix_1.2-7.1 RColorBrewer_1.1-2
[22] reshape2_1.4.1 S4Vectors_0.11.16  codetools_0.2-14
[25] MassSpecWavelet_1.39.0 stringi_1.1.1  compiler_3.3.1
[28] stats4_3.3.1   RANN_2.5

- Original Message -
> From: "Thomas Lawson" 
> To: "Martin Morgan" 
> Cc: 

Re: [Bioc-devel] Trouble checking out svn with username and password

[Dan Tenenbaum]

Your username is b.nelms

(note the dot).

Dan


- Original Message -
> From: "Brad Nelms" 
> To: "bioc-devel" 
> Sent: Saturday, September 3, 2016 1:23:18 PM
> Subject: [Bioc-devel] Trouble checking out svn with username and password

> Hi all,
> 
> I'm trying to checkout a package that was recently accepted to Bioconductor
> ('CellMapperData'), but am unable to check this out using my provided svn
> credentials. If I type:
> 
> svn co
> https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/CellMapperData
> --username "bnelms" --password xxx
> 
> where 'xxx' is my svn password. I get the following error:
> 
> svn: E170013: Unable to connect to a repository at URL '
> https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/CellMapperData'
> svn: E175013: Access to
> '/bioc-data/trunk/experiment/pkgs/CellMapperData' forbidden
> 
> I have also tried using my full email as my username (
> bnelms.resea...@gmail.com), but then I get this error:
> 
> svn co
> https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/CellMapperData
> --username "bnelms.resea...@gmail.com" --password xxx
> svn: E170013: Unable to connect to a repository at URL '
> https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/CellMapperData'
> svn: E175002: Unexpected server error 500 'Internal Server Error' on
> '/bioc-data/trunk/experiment/pkgs/CellMapperData'
> 
> I can checkout the package using readonly as the password and username:
> 
> svn co
> https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/CellMapperData
> --username "readonly" --password readonly
> ACellMapperData/vignettes
> ACellMapperData/man
> .
> Checked out revision 3880.
> 
> I see there was a similar bioc-devel question last May (
> https://stat.ethz.ch/pipermail/bioc-devel/2016-May/009226.html), but it is
> not clear to me what solved the problem for that user. My svn version can
> access https. What can I do to resolve this issue?
> 
> Thanks in advance for your help!
> Brad
> 
>   [[alternative HTML version deleted]]
> 
> ___
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Re: [Bioc-devel] commit changes with scenario 1

[Dan Tenenbaum]

- Original Message -
> From: "Karim Mezhoud" <kmezh...@gmail.com>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
> Cc: "bioc-devel" <bioc-devel@r-project.org>
> Sent: Tuesday, August 16, 2016 8:33:39 AM
> Subject: Re: [Bioc-devel] commit changes with scenario 1

> Thanks Dr Dan,
> I have multiple files to commit. How can I specify multiple files names?
> 
> git commit -m " resolve prblm" -a "file1.R, file2.R"
> 

You don't need to specify filenames if you use -a. If you do specify filenames 
you should not qute them or put commas in them.

git commit -m 'resolve prblm' file1.R file2.R

Dan



> Thanks
> karim
> 
> 
> On Mon, Aug 8, 2016 at 6:33 PM, Dan Tenenbaum <dtene...@fredhutch.org>
> wrote:
> 
>>
>>
>> - Original Message -
>> > From: "Karim Mezhoud" <kmezh...@gmail.com>
>> > To: "bioc-devel" <bioc-devel@r-project.org>
>> > Sent: Tuesday, August 2, 2016 2:53:53 PM
>> > Subject: [Bioc-devel] commit changes with scenario 1
>>
>> > I am trying to commit some changes to bioCancer
>> > <https://github.com/Bioconductor-mirror/bioCancer>. the issue is no
>> changes
>> > added to commit.
>> >
>> > Please, here is commands. Thanks
>> >
>> >   -  git clone https://github.com/Bioconductor-mirror/bioCancer
>> >   - cd bioCancer/
>> >   - ../update_remotes.sh
>> >
>> >
>> > Already on 'master'
>> > Your branch is up-to-date with 'origin/master'.
>> > Rebuilding
>> > .git/svn/refs/remotes/git-svn/.rev_map.bc3139a8-67e5-0310-
>> 9ffc-ced21a209358
>> > ...
>> > r117706 = 3d3efd35ec0406c4aaa4be764cf4ccb36a77d132
>> > Done rebuilding
>> > .git/svn/refs/remotes/git-svn/.rev_map.bc3139a8-67e5-0310-
>> 9ffc-ced21a209358
>> > Current branch master is up to date.
>> > Commit to git as normal, when you want to push your commits to svn
>> >  1. `git svn rebase` to get the latest SVN changes.
>> >  2. `git svn dcommit --add-author-from` to commit your changes to SVN.
>> >
>> >
>> >
>> >   - Change manually  vignette.Rmd file
>> >   - git commit -m "just vignette"
>>
>> In your git commit command you are not specifying a file to commit.
>> You should either add the -a flag to commit all changed files (which have
>> already been added) or specify the file(s) you want to commit on the
>> command line.
>>
>> Dan
>>
>>
>>
>>
>> >
>> > On branch master
>> > Your branch is up-to-date with 'origin/master'.
>> > Changes not staged for commit:
>> >modified:   vignettes/bioCancer.Rmd
>> >
>> > no changes added to commit
>> >
>> >   - git svn rebase
>> >
>> > vignettes/bioCancer.Rmd: needs update
>> > update-index --refresh: command returned error: 1
>> >
>> >
>> >
>> >   - git svn dcommit --add-author-from
>> >
>> > vignettes/bioCancer.Rmd: needs update
>> > update-index --refresh: command returned error: 1
>> >
>> >   [[alternative HTML version deleted]]
>> >
>> > ___
>> > Bioc-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?

[Dan Tenenbaum]

- Original Message -
> From: "Martin Morgan" <martin.mor...@roswellpark.org>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "lcollado" <lcoll...@jhu.edu>
> Cc: "Jeff Leek" <jtl...@gmail.com>, "bioc-devel" <bioc-devel@r-project.org>, 
> "Andrew Jaffe" <andreweja...@gmail.com>,
> "Ben Langmead" <lang...@cs.jhu.edu>, "Abhi Nellore" <anell...@gmail.com>
> Sent: Friday, August 12, 2016 4:43:59 PM
> Subject: Re: [Bioc-devel] Debugging build error on Linux machine: is it using 
> rtracklayer >= 1.33.11?

> On 08/12/2016 03:27 PM, Dan Tenenbaum wrote:
>> Well, I wrote my email to you on August 9th and the latest build report is 
>> from
>> Aug 10 and we see the same error as before.
>>
>> I just manually went to zin1 and was able to remove /tmp/udcCache without 
>> having
>> to be a superuser, I could do it as the user that the build system runs as
>> (biocbuild).
>>
>> I then rebuilt the recount package (successfully, btw) and it created the
>> /tmp/udcCache directory again (but again it was removable without superuser
>> powers).
>>
>> So I am not sure what is going on. Hopefully the next build will not have 
>> this
>> error. Maybe when I touched it last time the build was already in progress 
>> and
>> what I did came too late to affect the build.
>>
>> Anyway it would be good to know which package is creating that /tmp/udcCache
>> directory. Ideally that package would instead use tmpdir() and then the
>> directory would be removed when recount is done building, and this issue 
>> would
>> never come up again.
>>
> 
> Only rtracklayer references this. it might not be such a good idea to
> use tempdir(), because then the cache wouldn't be available for use
> during the builds... in what sense was it a permissions issue?
> 




When I initially went onto zin1 and installed and then stangled and sourced the 
vignette I saw some sort of permissions error with this directory. 
Unfortunately I did not save the exact error message.

When I initially tried

rm -rf /tmp/udcCache

...as the biocbuild user I got a permission denied error.

I should have investigated further to see which file(s) could not be deleted by 
biocbuild and what their permissions/ownership were but instead I just removed 
the entire directory as superuser.

So there was a permissions issue which caused the problem Leonardo reported.


Dan


> Martin
> 
>> Dan
>>
>>
>> - Original Message -
>>> From: "lcollado" <lcoll...@jhu.edu>
>>> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
>>> Cc: "Jeff Leek" <jtl...@gmail.com>, "bioc-devel" <bioc-devel@r-project.org>,
>>> "Andrew Jaffe" <andreweja...@gmail.com>,
>>> "Ben Langmead" <lang...@cs.jhu.edu>, "Abhi Nellore" <anell...@gmail.com>
>>> Sent: Friday, August 12, 2016 10:44:20 AM
>>> Subject: Re: [Bioc-devel] Debugging build error on Linux machine: is it 
>>> using
>>> rtracklayer >= 1.33.11?
>>
>>> Thanks Dan for finding the /tmp/udcCache error and fixing it! I assume
>>> that recount will build properly next time.
>>>
>>>
>>> The error related to SRP009615-results.Rmd is likely related to
>>> https://github.com/leekgroup/recount/blob/master/vignettes/Makefile.
>>> I'm using that Makefile trick to include the HTML output of a
>>> regionReport::DESeq2Report() created via
>>> https://github.com/leekgroup/recount/blame/master/vignettes/recount-quickstart.Rmd#L343-L359
>>> which re-writes SRP009615-results.Rmd. regionReport::DESeq2Report()
>>> specifies the `software` variable which is then used when rendering
>>> the Rmd file. Given that it works well on the OS build machine, I
>>> suspect it'll work well now with Linux thanks to the /tmp/udcCache
>>> issue you resolved. If you use R CMD build from a clean `recount` dir,
>>> it should all work.
>>>
>>> Best,
>>> Leo
>>>
>>> On Tue, Aug 9, 2016 at 2:30 PM, Dan Tenenbaum <dtene...@fredhutch.org> 
>>> wrote:
>>>> Actually it looks like it was a permissions issue with the directory
>>>> /tmp/udcCache. I removed this directory (as superuser) and that error no 
>>>> longer
>>>> happens.
>>>>
>>>> Now I get a different error which seems unrelated:
>>>>
>>>> ...
>>>> * creating vignettes ...

Re: [Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?

[Dan Tenenbaum]

Well, I wrote my email to you on August 9th and the latest build report is from 
Aug 10 and we see the same error as before.

I just manually went to zin1 and was able to remove /tmp/udcCache without 
having to be a superuser, I could do it as the user that the build system runs 
as (biocbuild).

I then rebuilt the recount package (successfully, btw) and it created the 
/tmp/udcCache directory again (but again it was removable without superuser 
powers).

So I am not sure what is going on. Hopefully the next build will not have this 
error. Maybe when I touched it last time the build was already in progress and 
what I did came too late to affect the build.

Anyway it would be good to know which package is creating that /tmp/udcCache 
directory. Ideally that package would instead use tmpdir() and then the 
directory would be removed when recount is done building, and this issue would 
never come up again.

Dan


- Original Message -
> From: "lcollado" <lcoll...@jhu.edu>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
> Cc: "Jeff Leek" <jtl...@gmail.com>, "bioc-devel" <bioc-devel@r-project.org>, 
> "Andrew Jaffe" <andreweja...@gmail.com>,
> "Ben Langmead" <lang...@cs.jhu.edu>, "Abhi Nellore" <anell...@gmail.com>
> Sent: Friday, August 12, 2016 10:44:20 AM
> Subject: Re: [Bioc-devel] Debugging build error on Linux machine: is it using 
> rtracklayer >= 1.33.11?

> Thanks Dan for finding the /tmp/udcCache error and fixing it! I assume
> that recount will build properly next time.
> 
> 
> The error related to SRP009615-results.Rmd is likely related to
> https://github.com/leekgroup/recount/blob/master/vignettes/Makefile.
> I'm using that Makefile trick to include the HTML output of a
> regionReport::DESeq2Report() created via
> https://github.com/leekgroup/recount/blame/master/vignettes/recount-quickstart.Rmd#L343-L359
> which re-writes SRP009615-results.Rmd. regionReport::DESeq2Report()
> specifies the `software` variable which is then used when rendering
> the Rmd file. Given that it works well on the OS build machine, I
> suspect it'll work well now with Linux thanks to the /tmp/udcCache
> issue you resolved. If you use R CMD build from a clean `recount` dir,
> it should all work.
> 
> Best,
> Leo
> 
> On Tue, Aug 9, 2016 at 2:30 PM, Dan Tenenbaum <dtene...@fredhutch.org> wrote:
>> Actually it looks like it was a permissions issue with the directory
>> /tmp/udcCache. I removed this directory (as superuser) and that error no 
>> longer
>> happens.
>>
>> Now I get a different error which seems unrelated:
>>
>> ...
>> * creating vignettes ... ERROR
>> Quitting from lines 2-32 (SRP009615-results.Rmd)
>> Error: processing vignette 'SRP009615-results.Rmd' failed with diagnostics:
>> object 'software' not found
>> Execution halted
>>
>>
>> Probably because of line 20:
>>
>> Basic `r software` results exploration
>>
>> `r software` is interpreted as a chunk of code to be executed by R.
>>
>>
>> Dan
>>
>>
>> - Original Message -
>>> From: "Dan Tenenbaum" <dtene...@fredhutch.org>
>>> To: "lcollado" <lcoll...@jhu.edu>
>>> Cc: "Jeff Leek" <jtl...@gmail.com>, "bioc-devel" <bioc-devel@r-project.org>,
>>> "Andrew Jaffe" <andreweja...@gmail.com>,
>>> "Ben Langmead" <lang...@cs.jhu.edu>, "Abhi Nellore" <anell...@gmail.com>
>>> Sent: Tuesday, August 9, 2016 11:46:32 AM
>>> Subject: Re: [Bioc-devel] Debugging build error on Linux machine: is it 
>>> using
>>> rtracklayer >= 1.33.11?
>>
>>> 1.33.11 is the latest version in svn.
>>>
>>> https://www.bioconductor.org/checkResults/3.4/bioc-LATEST/zin1-R-instpkgs.html
>>> will tell you (with a reasonable degree of accuracy) which version of which
>>> package is installed on zin1, it reports that it has version 1.33.11 
>>> installed.
>>>
>>> The issue with recount looks like it's a (hopefully transient) UCSC 
>>> connection
>>> problem.
>>>
>>> Dan
>>>
>>>
>>> - Original Message -
>>>> From: "lcollado" <lcoll...@jhu.edu>
>>>> To: "bioc-devel" <bioc-devel@r-project.org>
>>>> Cc: "Jeff Leek" <jtl...@gmail.com>, "Andrew Jaffe" 
>>>> <andreweja...@gmail.com>,
>>>> "Ben Langmead" <lang...@cs.jhu.edu>, "Abhi
>>>> Nellor

Re: [Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?

[Dan Tenenbaum]

Actually it looks like it was a permissions issue with the directory 
/tmp/udcCache. I removed this directory (as superuser) and that error no longer 
happens.

Now I get a different error which seems unrelated:

...
* creating vignettes ... ERROR
Quitting from lines 2-32 (SRP009615-results.Rmd)
Error: processing vignette 'SRP009615-results.Rmd' failed with diagnostics:
object 'software' not found
Execution halted


Probably because of line 20:

Basic `r software` results exploration

`r software` is interpreted as a chunk of code to be executed by R.


Dan


- Original Message -
> From: "Dan Tenenbaum" <dtene...@fredhutch.org>
> To: "lcollado" <lcoll...@jhu.edu>
> Cc: "Jeff Leek" <jtl...@gmail.com>, "bioc-devel" <bioc-devel@r-project.org>, 
> "Andrew Jaffe" <andreweja...@gmail.com>,
> "Ben Langmead" <lang...@cs.jhu.edu>, "Abhi Nellore" <anell...@gmail.com>
> Sent: Tuesday, August 9, 2016 11:46:32 AM
> Subject: Re: [Bioc-devel] Debugging build error on Linux machine: is it using 
> rtracklayer >= 1.33.11?

> 1.33.11 is the latest version in svn.
> 
> https://www.bioconductor.org/checkResults/3.4/bioc-LATEST/zin1-R-instpkgs.html
> will tell you (with a reasonable degree of accuracy) which version of which
> package is installed on zin1, it reports that it has version 1.33.11 
> installed.
> 
> The issue with recount looks like it's a (hopefully transient) UCSC connection
> problem.
> 
> Dan
> 
> 
> - Original Message -
>> From: "lcollado" <lcoll...@jhu.edu>
>> To: "bioc-devel" <bioc-devel@r-project.org>
>> Cc: "Jeff Leek" <jtl...@gmail.com>, "Andrew Jaffe" <andreweja...@gmail.com>,
>> "Ben Langmead" <lang...@cs.jhu.edu>, "Abhi
>> Nellore" <anell...@gmail.com>
>> Sent: Tuesday, August 9, 2016 11:33:50 AM
>> Subject: [Bioc-devel] Debugging build error on Linux machine: is it using
>>  rtracklayer >= 1.33.11?
> 
>> Hi,
>> 
>> Currently the build for `recount` is failing in the Linux build
>> machine
>> http://www.bioconductor.org/checkResults/3.4/bioc-LATEST/recount/zin1-buildsrc.html.
>> It's been failing with the same error message for a while. The build
>> message ends with:
>> 
>> Setting options('download.file.method.GEOquery'='auto')
>> Setting options('GEOquery.inmemory.gpl'=FALSE)
>> trying URL 'http://duffel.rail.bio/recount/SRP009615/rse_gene.Rdata'
>> Content type 'application/octet-stream' length 1383643 bytes (1.3 MB)
>> ==
>> downloaded 1.3 MB
>> 
>> Quitting from lines 400-406 (recount-quickstart.Rmd)
>> Error: processing vignette 'recount-quickstart.Rmd' failed with diagnostics:
>> UCSC library operation failed
>> Execution halted
>> 
>> 
>> The lines of code from the recount vignette this refers to are:
>> 
>> ## Define expressed regions for study SRP009615, only for chromosome Y
>> regions <- expressed_regions('SRP009615', 'chrY', cutoff = 5L,
>>maxClusterGap = 3000L)
>> 
>> ## Briefly explore the resulting regions
>> regions
>> 
>> 
>> 
>> The UCSC error is something I've seen in previous versions of
>> rtracklayer, which have been addressed in rtracklayer 1.33.11. recount
>> version 0.99.25 (which is the one from the build report) had under
>> suggests rtracklayer (>= 1.33.11). I thought that this would mean that
>> the build would fail if rtracklayer below version 1.33.11 was being
>> used. I'm no longer sure, which is why in recount version 0.99.27 I
>> moved rtracklayer to imports to test this. The latest build report
>> shows that rtracklayer 1.33.11 did build correctly in the Linux
>> machine.
>> 
>> 
>> Everything seems to be working fine in my local tests and in R Travis
>> https://travis-ci.org/leekgroup/recount/builds/150995800. Below is
>> some code showing that everything is working as expected in my local
>> Linux test. So I'm a tad confused and can't reproduce this issue when
>> using rtracklayer version 1.33.11. Which is why I'm guessing that
>> somehow the Linux build machine is not using rtracklayer >= 1.33.11.
>> 
>> 
>> 
>> 
>> ## The url redirects as expected to the correct url
>>> rtracklayer:::expandURL('http://duffel.rail.bio/recount/SRP009615/rse_gene.Rdata')
>> [1] "http://idies.jhu.edu/recount/data/SRP009615/rse_gene.Rdata;
>>> library('recount')
>> Loading required package: SummarizedExperiment
>> Lo

Re: [Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?

[Dan Tenenbaum]

1.33.11 is the latest version in svn.

https://www.bioconductor.org/checkResults/3.4/bioc-LATEST/zin1-R-instpkgs.html 
will tell you (with a reasonable degree of accuracy) which version of which 
package is installed on zin1, it reports that it has version 1.33.11 installed.

The issue with recount looks like it's a (hopefully transient) UCSC connection 
problem.

Dan


- Original Message -
> From: "lcollado" 
> To: "bioc-devel" 
> Cc: "Jeff Leek" , "Andrew Jaffe" , 
> "Ben Langmead" , "Abhi
> Nellore" 
> Sent: Tuesday, August 9, 2016 11:33:50 AM
> Subject: [Bioc-devel] Debugging build error on Linux machine: is it using 
> rtracklayer >= 1.33.11?

> Hi,
> 
> Currently the build for `recount` is failing in the Linux build
> machine
> http://www.bioconductor.org/checkResults/3.4/bioc-LATEST/recount/zin1-buildsrc.html.
> It's been failing with the same error message for a while. The build
> message ends with:
> 
> Setting options('download.file.method.GEOquery'='auto')
> Setting options('GEOquery.inmemory.gpl'=FALSE)
> trying URL 'http://duffel.rail.bio/recount/SRP009615/rse_gene.Rdata'
> Content type 'application/octet-stream' length 1383643 bytes (1.3 MB)
> ==
> downloaded 1.3 MB
> 
> Quitting from lines 400-406 (recount-quickstart.Rmd)
> Error: processing vignette 'recount-quickstart.Rmd' failed with diagnostics:
> UCSC library operation failed
> Execution halted
> 
> 
> The lines of code from the recount vignette this refers to are:
> 
> ## Define expressed regions for study SRP009615, only for chromosome Y
> regions <- expressed_regions('SRP009615', 'chrY', cutoff = 5L,
>maxClusterGap = 3000L)
> 
> ## Briefly explore the resulting regions
> regions
> 
> 
> 
> The UCSC error is something I've seen in previous versions of
> rtracklayer, which have been addressed in rtracklayer 1.33.11. recount
> version 0.99.25 (which is the one from the build report) had under
> suggests rtracklayer (>= 1.33.11). I thought that this would mean that
> the build would fail if rtracklayer below version 1.33.11 was being
> used. I'm no longer sure, which is why in recount version 0.99.27 I
> moved rtracklayer to imports to test this. The latest build report
> shows that rtracklayer 1.33.11 did build correctly in the Linux
> machine.
> 
> 
> Everything seems to be working fine in my local tests and in R Travis
> https://travis-ci.org/leekgroup/recount/builds/150995800. Below is
> some code showing that everything is working as expected in my local
> Linux test. So I'm a tad confused and can't reproduce this issue when
> using rtracklayer version 1.33.11. Which is why I'm guessing that
> somehow the Linux build machine is not using rtracklayer >= 1.33.11.
> 
> 
> 
> 
> ## The url redirects as expected to the correct url
>> rtracklayer:::expandURL('http://duffel.rail.bio/recount/SRP009615/rse_gene.Rdata')
> [1] "http://idies.jhu.edu/recount/data/SRP009615/rse_gene.Rdata;
>> library('recount')
> Loading required package: SummarizedExperiment
> Loading required package: GenomicRanges
> Loading required package: stats4
> Loading required package: BiocGenerics
> Loading required package: parallel
> 
> Attaching package: ‘BiocGenerics’
> 
> The following objects are masked from ‘package:parallel’:
> 
>clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
>clusterExport, clusterMap, parApply, parCapply, parLapply,
>parLapplyLB, parRapply, parSapply, parSapplyLB
> 
> The following objects are masked from ‘package:stats’:
> 
>IQR, mad, xtabs
> 
> The following objects are masked from ‘package:base’:
> 
>anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
>duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
>is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
>paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
>Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
>unique, unsplit, which, which.max, which.min
> 
> Loading required package: S4Vectors
> 
> Attaching package: ‘S4Vectors’
> 
> The following objects are masked from ‘package:base’:
> 
>colMeans, colSums, expand.grid, rowMeans, rowSums
> 
> Loading required package: IRanges
> Loading required package: GenomeInfoDb
> Loading required package: Biobase
> Welcome to Bioconductor
> 
>Vignettes contain introductory material; view with
>'browseVignettes()'. To cite Bioconductor, see
>'citation("Biobase")', and for packages 'citation("pkgname")'.
> 
> Setting options('download.file.method.GEOquery'='auto')
> Setting options('GEOquery.inmemory.gpl'=FALSE)
>>
>> ## Define expressed regions for study SRP009615, only for chromosome Y
>> regions <- expressed_regions('SRP009615', 'chrY', cutoff = 5L,
> + maxClusterGap = 3000L)
> 2016-08-09 14:16:59 loadCoverage: loading BigWig file
> 

Re: [Bioc-devel] commit changes with scenario 1

[Dan Tenenbaum]

- Original Message -
> From: "Karim Mezhoud" 
> To: "bioc-devel" 
> Sent: Tuesday, August 2, 2016 2:53:53 PM
> Subject: [Bioc-devel] commit changes with scenario 1

> I am trying to commit some changes to bioCancer
> . the issue is no changes
> added to commit.
> 
> Please, here is commands. Thanks
> 
>   -  git clone https://github.com/Bioconductor-mirror/bioCancer
>   - cd bioCancer/
>   - ../update_remotes.sh
> 
> 
> Already on 'master'
> Your branch is up-to-date with 'origin/master'.
> Rebuilding
> .git/svn/refs/remotes/git-svn/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358
> ...
> r117706 = 3d3efd35ec0406c4aaa4be764cf4ccb36a77d132
> Done rebuilding
> .git/svn/refs/remotes/git-svn/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358
> Current branch master is up to date.
> Commit to git as normal, when you want to push your commits to svn
>  1. `git svn rebase` to get the latest SVN changes.
>  2. `git svn dcommit --add-author-from` to commit your changes to SVN.
> 
> 
> 
>   - Change manually  vignette.Rmd file
>   - git commit -m "just vignette"

In your git commit command you are not specifying a file to commit. 
You should either add the -a flag to commit all changed files (which have 
already been added) or specify the file(s) you want to commit on the command 
line.

Dan




> 
> On branch master
> Your branch is up-to-date with 'origin/master'.
> Changes not staged for commit:
>modified:   vignettes/bioCancer.Rmd
> 
> no changes added to commit
> 
>   - git svn rebase
> 
> vignettes/bioCancer.Rmd: needs update
> update-index --refresh: command returned error: 1
> 
> 
> 
>   - git svn dcommit --add-author-from
> 
> vignettes/bioCancer.Rmd: needs update
> update-index --refresh: command returned error: 1
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] bioconductor/metabolomics Docker image available

[Dan Tenenbaum]

- Original Message -
> From: "Steffen Neumann" <sneum...@ipb-halle.de>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
> Cc: "bioc-devel" <bioc-devel@r-project.org>
> Sent: Wednesday, July 27, 2016 5:02:22 AM
> Subject: bioconductor/metabolomics Docker image available

> Hi Dan and BioC community!
> 
> I now cleaned up my Bioconductor/bioc_docker
> and opened a pull request to add a Metabolomics
> Bioconductor [1].
> 
> This works on our Jenkins installation, where I regularly
> build the devel_metabolomics [2] and release [3] images.
> 
> The image for the previous devel version (BioC-3.3) does build,
> but the image for the old release version (BioC-3.2) does not,
> due to the mzR issue on new gcc we talked about a few months ago.
> 
> If you want, I can send a second pull request
> and modify bioc_docker/config.yml to use the current
> versions 3.3 for release, and 3.4 for devel.
> 

Yes, please do this.

> A more general question, what is the current docker strategy
> for Bioconductor. Are they build/tested on a regular basis ?

Built daily, but not tested.


> Are failure reported to package maintainers, or should they ?

Failure is not reported to anyone, it probably should be.

> Should the docker images be part of the regular checkResults report ?

I think they should be in a separate report, but perhaps one that lives under 
/checkResults.

Dan

> 
> Yours,
> Steffen
> 
> [1] https://github.com/Bioconductor/bioc_docker/pull/4
> [2] http://phenomenal-h2020.eu/jenkins/job/bioc_docker_devel_metabolomics/
> [3] http://phenomenal-h2020.eu/jenkins/job/bioc_docker_release_metabolomics
> 
> 
> --
> IPB HalleAG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann  http://www.IPB-Halle.DE
> Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
> 06120 Halle                       +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409

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Re: [Bioc-devel] shrunken vignette

[Dan Tenenbaum]

It can be changed if we can identify the problem.

Bioconductor package developers should be using the devel version of 
Bioconductor in order to identify problems like this.

Dan


- Original Message -
> From: "Anand MT" <anand...@hotmail.com>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "Kasper Daniel Hansen" 
> <kasperdanielhan...@gmail.com>
> Cc: "bioc-devel" <bioc-devel@r-project.org>
> Sent: Saturday, July 16, 2016 6:37:01 PM
> Subject: RE: [Bioc-devel] shrunken vignette

> Hi Dan and Kasper,
> Thank you. I will add sessionInfo. vignette built with R CMD build also looks
> good with cleaner toc. Maybe its the devel BiocStyle level as suggested. So no
> way to change it now?
> 
>> Date: Fri, 15 Jul 2016 20:46:01 -0700
>> From: dtene...@fredhutch.org
>> To: kasperdanielhan...@gmail.com
>> CC: anand...@hotmail.com; bioc-devel@r-project.org
>> Subject: Re: [Bioc-devel] shrunken vignette
>> 
>> Also note that the build system does not use devtools to build vignettes, it
>> uses R CMD build.
>> 
>> 
>> - Original Message -
>> > From: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com>
>> > To: "Anand MT" <anand...@hotmail.com>
>> > Cc: "bioc-devel" <bioc-devel@r-project.org>
>> > Sent: Friday, July 15, 2016 8:43:00 PM
>> > Subject: Re: [Bioc-devel] shrunken vignette
>> 
>> > If you add a sessionInfo() section to your document (which I highly
>> > recommend) you'll probably realize the two versions are using different
>> > versions of BiocStyle (anything in devel uses BiocStyle level).  The
>> > default layout is changing, and I am sure comments or bug reports are
>> > welcome.  For example, as rendered right now I would agree the TOC sucks.
>> > 
>> > Best,
>> > Kasper
>> > 
>> > On Fri, Jul 15, 2016 at 9:53 PM, Anand MT <anand...@hotmail.com> wrote:
>> > 
>> >> Hi all,
>> >> My package 'maftools' finally found its homepage today. But when I checked
>> >> the vignette, it has been shrunken. It appears to be html vignette is
>> >> center aligned rather than left aligned. It makes things cluttered and and
>> >> toc looks messy.
>> >> Vignette is here:
>> >> http://bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/maftools.html
>> >> When I build it manually on my computer with devtools::build_vignettes()
>> >> it looks like this. http://poisonalien.github.io   - A much cleaner look.
>> >> Do I need to change any thing in markdown file?
>> >> Meta data on my vignette markdown looks like this.
>> >> ---title: "maftools : Summarize, Analyze and Visualize MAF files"author:
>> >> "Anand Mayakonda"date: "`r Sys.Date()`"output:
>> >> BiocStyle::html_document2vignette: >  %\VignetteIndexEntry{Summarize,
>> >> Analyze and Visualize MAF files}  %\VignetteEngine{knitr::rmarkdown}
>> >> %\VignetteEncoding{UTF-8}---
>> >>
>> >> Thank you.
>> >>
>> >> [[alternative HTML version deleted]]
>> >>
>> >> ___
>> >> Bioc-devel@r-project.org mailing list
>> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >>
>> > 
>> >[[alternative HTML version deleted]]
>> > 
>> > ___
>> > Bioc-devel@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] shrunken vignette

[Dan Tenenbaum]

Also note that the build system does not use devtools to build vignettes, it 
uses R CMD build.


- Original Message -
> From: "Kasper Daniel Hansen" 
> To: "Anand MT" 
> Cc: "bioc-devel" 
> Sent: Friday, July 15, 2016 8:43:00 PM
> Subject: Re: [Bioc-devel] shrunken vignette

> If you add a sessionInfo() section to your document (which I highly
> recommend) you'll probably realize the two versions are using different
> versions of BiocStyle (anything in devel uses BiocStyle level).  The
> default layout is changing, and I am sure comments or bug reports are
> welcome.  For example, as rendered right now I would agree the TOC sucks.
> 
> Best,
> Kasper
> 
> On Fri, Jul 15, 2016 at 9:53 PM, Anand MT  wrote:
> 
>> Hi all,
>> My package 'maftools' finally found its homepage today. But when I checked
>> the vignette, it has been shrunken. It appears to be html vignette is
>> center aligned rather than left aligned. It makes things cluttered and and
>> toc looks messy.
>> Vignette is here:
>> http://bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/maftools.html
>> When I build it manually on my computer with devtools::build_vignettes()
>> it looks like this. http://poisonalien.github.io   - A much cleaner look.
>> Do I need to change any thing in markdown file?
>> Meta data on my vignette markdown looks like this.
>> ---title: "maftools : Summarize, Analyze and Visualize MAF files"author:
>> "Anand Mayakonda"date: "`r Sys.Date()`"output:
>> BiocStyle::html_document2vignette: >  %\VignetteIndexEntry{Summarize,
>> Analyze and Visualize MAF files}  %\VignetteEngine{knitr::rmarkdown}
>> %\VignetteEncoding{UTF-8}---
>>
>> Thank you.
>>
>> [[alternative HTML version deleted]]
>>
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Re: [Bioc-devel] BioC check error for flowClust on windows

[Dan Tenenbaum]

When you don't see a specific error message, it's often a hint that R actually 
crashed (popped up a dialog box that you can't see in the build report. 

And indeed that is the case here. 

I can reproduce it easily as follows: 

R --arch i386 

library(flowClust) 
example(flowClust) 

It works fine under the default (x64) architecture. Did you test it under i386? 

Here's the build report url, BTW: 

https://bioconductor.org/checkResults/devel/bioc-LATEST/flowClust/moscato1-checksrc.html
 

By debugging the flowClust() function I can see that the crash happens after 
invoking .flowClustK() via mclapply(). 

Dan 

> From: "Mike" 
> To: "bioc-devel" 
> Sent: Friday, July 15, 2016 1:53:37 PM
> Subject: [Bioc-devel] BioC check error for flowClust on windows

> Hi,

> Here is the CHECK report for flowClust on moscato1. There is not pacific
> error message on that page and I can't reproduce it on my local windows.

> Mike

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Re: [Bioc-devel] GenRank package build error 0.99.4

[Dan Tenenbaum]

- Original Message -
> From: "Chakravarthi Kanduri" 
> To: "bioc-devel" 
> Sent: Tuesday, July 12, 2016 12:37:29 PM
> Subject: Re: [Bioc-devel] GenRank package build error 0.99.4

> Dear Bioconductor developers,
> 
> The latest build of GenRank package (development version) shows error
> (http://bioconductor.org/checkResults/devel/bioc-LATEST/GenRank/).
> 
> The package was built successfully on my local computer and on Travis,
> but fails on Bioconductor build system. When I checked the error report,
> it says:
> 
> * creating vignettes ... ERROR
> Quitting from lines 44-48 (GenRank_Vignette.Rmd)
> Error: processing vignette 'GenRank_Vignette.Rmd' failed with diagnostics:
> no lines available in input
> Execution halted
> 
> I checked those lines in the vignette. I used an input file in an
> example, which is stored in inst/extdata/ in the package. This worked
> fine with the previous versions of the package, but fails now. Could you
> suggest a turnaround? Thanks.
> 

There is no file inst/extdata/CE_toydata.txt which is what you are trying to 
read in on line 45 of the vignette.
Could it be that you forgot to add it to the commit?

Try 'svn st' or 'git status' to see if it has been added.

Dan


> Regards,
> Chakri
> 
> 
> 
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Re: [Bioc-devel] build error only occurs in window system

[Dan Tenenbaum]

Don't bother. The issue is a long-standing one and very difficult to reproduce 
which is why it has not been fixed. It happens sporadically so the solution is 
to wait for the next day's build and it will clear itself up.

Dan


On July 7, 2016 11:05:22 AM PDT, "Ou, Jianhong"  
wrote:
>Hi Julie,
>
>You could try to install windows 10 in a virtualBox for debugging.
>
>virtualBox: https://www.virtualbox.org/wiki/Downloads
>
>Windows 10:
>https://www.microsoft.com/en-us/software-download/windows10/
>
>Yours Sincerely,
>
>Jianhong Ou
>
>TEL: 508-856-5379
>LRB 608
>Bioinformatician of Bioinformatics core at
>Department of Molecular, Cell and Cancer Biology
>UMASS Medical School
>364 Plantation Street Worcester,
>MA 01605
>
>Confidentiality Notice:
>This e-mail message, including any attachments, is for the sole use of
>the
>intended recipient(s) and may contain confidential, proprietary and
>privileged information. Any unauthorized review, use, disclosure or
>distribution is prohibited. If you are not the intended recipient,
>please
>contact the sender immediately and destroy or permanently delete all
>copies of the original message.
>
>
>
>
>
>
>On 7/7/16 1:15 PM, "Bioc-devel on behalf of Zhu, Lihua (Julie)"
>
>wrote:
>
>>Dan,
>>
>>I recently noticed that GUIDEseq page has a error build status at
>>http://bioconductor.org/packages/release/bioc/html/GUIDEseq.html.
>Oddly,
>>the error only occurs in the window server.
>>
>>Is this something related to the window server solvable by the core
>team,
>>or should I change something to make it work? I am preparing a
>>manuscript. It would  not look good if the reviewers see a red error
>>status on the page.
>>
>>Could you please help me? Many thanks!
>>
>>Best regards,
>>
>>Julie
>>
>>
>> running command 
>>'"C:\Users\BIOCBU�1\AppData\Local\Programs\MIKTEX�1.9\miktex\bin\texify.ex
>>e" --quiet --pdf "GUIDEseq.tex" --max-iterations=20 -I
>>"E:/biocbld/bbs-3.3-bioc/R/share/texmf/tex/latex" -I
>>"E:/biocbld/bbs-3.3-bioc/R/share/texmf/bibtex/bst"' had status 1
>>Error in find_vignette_product(name, by = "texi2pdf", engine = engine)
>:
>>  Failed to locate the 'texi2pdf' output file (by engine
>'utils::Sweave')
>>for vignette with name 'GUIDEseq'. The following files exist in
>directory
>>'.': 'GUIDEseq-concordance.tex', 'GUIDEseq.Rnw', 'GUIDEseq.tex',
>>'gRNA-PlusMinusPeaksMerged.bed', 'gRNA-PlusMinusPeaksMerged.xls',
>>'gRNA-peaks.xls', 'gRNAHEK293_site4_chr13.bamReadSummary.xls',
>>'mergedPeaks.bed', 'offTargetsInPeakRegions.xls'
>>Calls:  -> find_vignette_product
>>Execution halted
>>Confidentiality Notice:\ This e-mail message, including
>...{{dropped:11}}
>>
>
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Re: [Bioc-devel] NotNeeded in build report RSS feeds

[Dan Tenenbaum]

We didn't (intentionally anyway) change anything with the RSS feeds. We'll look 
into it.
Dan


- Original Message -
> From: "lcollado" <lcoll...@jhu.edu>
> To: "Antti Honkela" <antti.honk...@hiit.fi>
> Cc: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" 
> <bioc-devel@r-project.org>
> Sent: Wednesday, June 29, 2016 7:19:26 AM
> Subject: Re: [Bioc-devel] NotNeeded in build report RSS feeds

> Hi,
> 
> I don't think this has anything to do with "NotNeeded". The RSS feed
> did indeed change around the time BioC 3.3 was released and I have
> also been getting daily RSS updates, even if they are "No build
> problems for package XYZ" (with the same status the day before).
> 
> My guess is that the RSS feed was changed to add daily updates before
> 3.3's release just to make sure all issues were solved before the
> release. And now that things are a bit more static it'd be nice to
> have the RSS feed to return to "on change".
> 
> Best,
> Leo
> 
> On Wed, Jun 29, 2016 at 9:24 AM, Antti Honkela <antti.honk...@hiit.fi> wrote:
>> Hi Dan,
>>
>> I follow the RSS feed on Feedly and for some time now it has shown two
>> updates every day: "NotNeeded in Release" and "NotNeeded in Devel". Up to
>> approximately 2 months ago I only saw updates when the status changed, but
>> since then there have been these two daily non-updates which add a lot of
>> noise.
>>
>> It seems that the whole NotNeeded thing was introduced in RSS reports
>> sometime last autumn and as far as I can tell it has generated a lot of
>> noise e.g. when the build machine names changes etc. but no useful
>> information.
>>
>> As the NotNeeded state does not seem something a package maintainer needs to
>> care about, perhaps you could ignore it when generating the RSS and revert
>> to the "No build problems for X" report?
>>
>>
>> Thanks!
>>
>> Antti
>>
>>
>>
>> On 28 Jun 2016, at 22:16, Dan Tenenbaum wrote:
>>
>>> Hi Antti,
>>>
>>> I'm not sure I follow. NotNeeded is a status seen in the INSTALL phase of
>>> the build, and it means your package did not need to be installed because no
>>> other package built by the build system depends on it.
>>>
>>> This status should not change from one day to the next. (It would change
>>> if someone were to depend on your package.)
>>>
>>> But the basic behavior of the RSS feeds is supposed to be to only notify
>>> you when there is a change in build status. So you should not get new feeds
>>> when the build status stays the same.
>>>
>>> Dan
>>>
>>>
>>> - Original Message -
>>>>
>>>> From: "Antti Honkela" <antti.honk...@hiit.fi>
>>>> To: "bioc-devel" <bioc-devel@r-project.org>
>>>> Sent: Tuesday, June 28, 2016 4:45:12 AM
>>>> Subject: [Bioc-devel] NotNeeded in build report RSS feeds
>>>
>>>
>>>> Would it be possible to change the build report RSS feed generation to
>>>> treat "NotNeeded" similarly as "OK"?
>>>>
>>>> This would make the feed more useful for spotting real problems.
>>>>
>>>>
>>>> Thanks!
>>>>
>>>> Antti
>>>>
>>>> ___
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>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
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Re: [Bioc-devel] NotNeeded in build report RSS feeds

[Dan Tenenbaum]

We didn't (intentionally anyway) change anything with the RSS feeds. We'll look 
into it.
Dan


- Original Message -
> From: "lcollado" <lcoll...@jhu.edu>
> To: "Antti Honkela" <antti.honk...@hiit.fi>
> Cc: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" 
> <bioc-devel@r-project.org>
> Sent: Wednesday, June 29, 2016 7:19:26 AM
> Subject: Re: [Bioc-devel] NotNeeded in build report RSS feeds

> Hi,
> 
> I don't think this has anything to do with "NotNeeded". The RSS feed
> did indeed change around the time BioC 3.3 was released and I have
> also been getting daily RSS updates, even if they are "No build
> problems for package XYZ" (with the same status the day before).
> 
> My guess is that the RSS feed was changed to add daily updates before
> 3.3's release just to make sure all issues were solved before the
> release. And now that things are a bit more static it'd be nice to
> have the RSS feed to return to "on change".
> 
> Best,
> Leo
> 
> On Wed, Jun 29, 2016 at 9:24 AM, Antti Honkela <antti.honk...@hiit.fi> wrote:
>> Hi Dan,
>>
>> I follow the RSS feed on Feedly and for some time now it has shown two
>> updates every day: "NotNeeded in Release" and "NotNeeded in Devel". Up to
>> approximately 2 months ago I only saw updates when the status changed, but
>> since then there have been these two daily non-updates which add a lot of
>> noise.
>>
>> It seems that the whole NotNeeded thing was introduced in RSS reports
>> sometime last autumn and as far as I can tell it has generated a lot of
>> noise e.g. when the build machine names changes etc. but no useful
>> information.
>>
>> As the NotNeeded state does not seem something a package maintainer needs to
>> care about, perhaps you could ignore it when generating the RSS and revert
>> to the "No build problems for X" report?
>>
>>
>> Thanks!
>>
>> Antti
>>
>>
>>
>> On 28 Jun 2016, at 22:16, Dan Tenenbaum wrote:
>>
>>> Hi Antti,
>>>
>>> I'm not sure I follow. NotNeeded is a status seen in the INSTALL phase of
>>> the build, and it means your package did not need to be installed because no
>>> other package built by the build system depends on it.
>>>
>>> This status should not change from one day to the next. (It would change
>>> if someone were to depend on your package.)
>>>
>>> But the basic behavior of the RSS feeds is supposed to be to only notify
>>> you when there is a change in build status. So you should not get new feeds
>>> when the build status stays the same.
>>>
>>> Dan
>>>
>>>
>>> - Original Message -
>>>>
>>>> From: "Antti Honkela" <antti.honk...@hiit.fi>
>>>> To: "bioc-devel" <bioc-devel@r-project.org>
>>>> Sent: Tuesday, June 28, 2016 4:45:12 AM
>>>> Subject: [Bioc-devel] NotNeeded in build report RSS feeds
>>>
>>>
>>>> Would it be possible to change the build report RSS feed generation to
>>>> treat "NotNeeded" similarly as "OK"?
>>>>
>>>> This would make the feed more useful for spotting real problems.
>>>>
>>>>
>>>> Thanks!
>>>>
>>>> Antti
>>>>
>>>> ___
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>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>> ___
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Re: [Bioc-devel] NotNeeded in build report RSS feeds

[Dan Tenenbaum]

Hi Antti,

I'm not sure I follow. NotNeeded is a status seen in the INSTALL phase of the 
build, and it means your package did not need to be installed because no other 
package built by the build system depends on it. 

This status should not change from one day to the next. (It would change if 
someone were to depend on your package.)

But the basic behavior of the RSS feeds is supposed to be to only notify you 
when there is a change in build status. So you should not get new feeds when 
the build status stays the same.

Dan


- Original Message -
> From: "Antti Honkela" 
> To: "bioc-devel" 
> Sent: Tuesday, June 28, 2016 4:45:12 AM
> Subject: [Bioc-devel] NotNeeded in build report RSS feeds

> Would it be possible to change the build report RSS feed generation to
> treat "NotNeeded" similarly as "OK"?
> 
> This would make the feed more useful for spotting real problems.
> 
> 
> Thanks!
> 
> Antti
> 
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Re: [Bioc-devel] Confusion on biocLite() with github and annotation data repo

[Dan Tenenbaum]

I think you need to add the 

dependencies=TRUE

argument which gets passed to devtools::install_github() and thence to 
devtools::install().

Dan


- Original Message -
> From: "Martin Morgan" 
> To: "James W. MacDonald" , "Sean Davis" 
> 
> Cc: "bioc-devel" 
> Sent: Tuesday, June 28, 2016 8:11:26 AM
> Subject: Re: [Bioc-devel] Confusion on biocLite() with github and annotation 
> data repo

> On 06/28/2016 10:56 AM, James W. MacDonald wrote:
>> I had a similar experience, where the dependencies were not found upon
>> installation. I didn't do anything to fix it - instead it seemed that just
>> re-running biocLite after the initial failed install ended up working.
> 
> Installing from github delegates to devtools::install_github, and that
> the annotation repository is not found. So something like
> 
> > options(repos=BiocInstaller::biocinstallRepos())
> > biocLite("jmacdon/BiocAnno2016")
> 
> I think the code is trying to do that, though
> 
> https://github.com/Bioconductor-mirror/BiocInstaller/blob/master/R/biocLite.R#L72
> 
> so don't really understand why it fails...
> 
> Martin
> 
>>
>> Maybe the same will work for you?
>>
>> Best,
>>
>> Jim
>>
>>
>>
>> On Mon, Jun 27, 2016 at 5:03 PM, Davis, Sean (NIH/NCI) [E] <
>> sdav...@mail.nih.gov> wrote:
>>
>>> I am trying to install from Jim’s annotation workflow from github (
>>> https://github.com/jmacdon/BiocAnno2016), but biocLite() fails because it
>>> cannot find annotation data packages.  I *can* go back and install the
>>> annotation data package with a separate call to biocLite().  Is this
>>> expected behavior?  If so, is it possible and desirable to install from
>>> github and have it “do the right thing” to get Bioc dependencies?
>>>
>>> Thanks,
>>> Sean
>>>
>>>
 biocLite('jmacdon/BiocAnno2016',dependencies=TRUE,build_vignettes=TRUE)
>>> BioC_mirror: https://bioconductor.org
>>> Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.0 (2016-05-03).
>>> Installing github package(s) ‘jmacdon/BiocAnno2016’
>>> Downloading GitHub repo jmacdon/BiocAnno2016@master
>>> from URL https://api.github.com/repos/jmacdon/BiocAnno2016/zipball/master
>>> Installing BiocAnno2016
>>> Skipping 7 unavailable packages: BSgenome.Hsapiens.UCSC.hg19,
>>> EnsDb.Hsapiens.v79, EnsDb.Mmusculus.v79, Homo.sapiens,
>>> hugene20sttranscriptcluster.db, org.Hs.eg.db,
>>> TxDb.Hsapiens.UCSC.hg19.knownGene
>>> Skipping 19 packages ahead of CRAN: AnnotationDbi, AnnotationHub, Biobase,
>>> BiocGenerics, BiocParallel, biomaRt, Biostrings, BSgenome,
>>> GenomicAlignments, GenomicRanges, interactiveDisplayBase, IRanges,
>>> rmarkdown, Rsamtools, rtracklayer, S4Vectors, SummarizedExperiment,
>>> XVector, zlibbioc
>>> '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file
>>> --no-environ  \
>>>--no-save --no-restore --quiet CMD build  \
>>>
>>> '/private/var/folders/21/b_rp6qyj1_b1j5cp8qby0tnrgn/T/Rtmpq8yntE/devtools32fa3fcc4899/jmacdon-BiocAnno2016-7317126'
>>> \
>>>--no-resave-data --no-manual
>>>
>>> * checking for file
>>> ‘/private/var/folders/21/b_rp6qyj1_b1j5cp8qby0tnrgn/T/Rtmpq8yntE/devtools32fa3fcc4899/jmacdon-BiocAnno2016-7317126/DESCRIPTION’
>>> ... OK
>>> * preparing ‘BiocAnno2016’:
>>> * checking DESCRIPTION meta-information ... OK
>>> * installing the package to process help pages
>>>---
>>> ERROR: dependencies ‘EnsDb.Hsapiens.v79’, ‘Homo.sapiens’,
>>> ‘EnsDb.Mmusculus.v79’ are not available for package ‘BiocAnno2016’
>>> * removing
>>> ‘/private/var/folders/21/b_rp6qyj1_b1j5cp8qby0tnrgn/T/RtmpBduTCP/Rinst33cf24872f4e/BiocAnno2016’
>>>---
>>> ERROR: package installation failed
>>> Error: Command failed (1)
 biocLite('Homo.sapiens')
>>> BioC_mirror: https://bioconductor.org
>>> Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.0 (2016-05-03).
>>> Installing package(s) ‘Homo.sapiens’
>>> installing the source package ‘Homo.sapiens’
>>>
>>> trying URL '
>>> https://bioconductor.org/packages/3.3/data/annotation/src/contrib/Homo.sapiens_1.3.1.tar.gz
>>> '
>>> Content type 'application/x-gzip' length 1617 bytes
>>> ==
>>> downloaded 1617 bytes
>>>
>>> * installing *source* package ‘Homo.sapiens’ ...
>>> ** R
>>> ** data
>>> ** preparing package for lazy loading
>>> Warning: package ‘GenomicRanges’ was built under R version 3.3.1
>>> ** help
>>> *** installing help indices
>>> ** building package indices
>>> ** testing if installed package can be loaded
>>> Warning: package ‘GenomicRanges’ was built under R version 3.3.1
>>> * DONE (Homo.sapiens)
>>>
>>> The downloaded source packages are in
>>>
>>> ‘/private/var/folders/21/b_rp6qyj1_b1j5cp8qby0tnrgn/T/Rtmpq8yntE/downloaded_packages’
>>> Old packages: 'airway', 'BiocStyle', 'ComplexHeatmap', 'dendextend',
>>> 'DESeq2',
>>>'devtools', 'docopt', 

Re: [Bioc-devel] git svn dcommit

[Dan Tenenbaum]

My understanding is that this happens if you ever had non-linear commit history 
in your github repository (i.e. more than one branch changed and then were 
merged together), or if you used the old git/svn bridge. As far as I understand 
it, the only solution (in the near term) is to cherry pick the commits you 
want, a la

https://bioconductor.org/developers/how-to/git-mirrors/#dealing-with-prior-history--merge-conflicts

And this has to be done every time you want to sync git to svn.

Dan


- Original Message -
> From: "Kasper Daniel Hansen" 
> To: "bioc-devel" 
> Sent: Wednesday, June 22, 2016 6:11:24 PM
> Subject: [Bioc-devel] git svn dcommit

> So I have made some updates to minfi and they are "safe" in Github.  I now
> want to commit them to Bioconductor.  I get pretty strange results,
> although I never really understand what is going on.
> 
> 1. I clone a fresh copy of minfi from Github.
> 2. I do
> # bash update_remotes.sh
> (using proper path of course)
> 3. I do
> # git checkout devel
> # git svn rebase
> # git merge master --log
> without any hiccups, and all seems to work so far.
> 
> Then I do
>  # git svn dcommit --add-author-from
> 
> and hell starts (see output below).  What is kind of weird is that now it
> wants me to do 241 (!) rebase.  And it starts to involve commits or
> changes in files that haven't been touch for months.  This is really pretty
> weird, given that I have completed the previous steps fine.
> 
> Any idea?  Otherwise I hope I can get special help at Stanford in a few
> days ...
> 
> Best,
> Kasper
> 
> 
> 
> 
> 
> 
> $ git svn dcommit --add-author-from
> Committing to
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/minfi ...
> M DESCRIPTION
> 
> ERROR from SVN:
> Item is out of date: Item '/trunk/madman/Rpacks/minfi/DESCRIPTION' is out
> of date
> W: 85e070dd7d7825132ca3e6399f2e4dc19195b627 and refs/remotes/git-svn-devel
> differ, using rebase:
> :100644 100644 0025283098af2a8f4376b1300533a4c5aabaea7b
> 8ac95ea78753b0a25d97c5debecbc6b2ead04ac0 M DESCRIPTION
> :100644 100644 64a40f0b2655c7953ff154b42d6fa849e14462d3
> 92430c671d00d2131f5dc59cd3dbaa54679b585a M NAMESPACE
> :04 04 732260942165586cd80d15ad9aa923e0969f604f
> 5098b8e0b0cabed337857680555df1ea6dc853f8 M R
> :04 04 655f45f8ddd850a62a643151b73711c12ca0c5bb
> 9e9250da0089f89b9fb9ab986c617dbe66a3aab2 M inst
> :04 04 3b781c09f0472bdff07ee734418b1bc263a31bd9
> 0f59f20b6cc89eaeeb94626a4445e3da26cef08f M man
> :04 04 dd0723ff2712c2882b81fafc1eb2de441e86
> 83da824cbedf66e528e93ba03abf4adb7e243669 M vignettes
> First, rewinding head to replay your work on top of it...
> Applying: updated citation information
> Using index info to reconstruct a base tree...
> .git/rebase-apply/patch:34: trailing whitespace.
> beanplot,
> .git/rebase-apply/patch:35: trailing whitespace.
> RColorBrewer,
> .git/rebase-apply/patch:36: trailing whitespace.
> nor1mix,
> .git/rebase-apply/patch:37: trailing whitespace.
> siggenes,
> .git/rebase-apply/patch:38: trailing whitespace.
> limma,
> warning: squelched 287 whitespace errors
> warning: 292 lines add whitespace errors.
> Falling back to patching base and 3-way merge...
> Auto-merging vignettes/minfi.bib
> CONFLICT (add/add): Merge conflict in vignettes/minfi.bib
> Auto-merging man/utils.Rd
> CONFLICT (add/add): Merge conflict in man/utils.Rd
> Auto-merging man/read.450k.sheet.Rd
> CONFLICT (add/add): Merge conflict in man/read.450k.sheet.Rd
> Auto-merging man/read.450k.exp.Rd
> CONFLICT (add/add): Merge conflict in man/read.450k.exp.Rd
> Auto-merging man/read.450k.Rd
> CONFLICT (add/add): Merge conflict in man/read.450k.Rd
> Auto-merging man/preprocessQuantile.Rd
> CONFLICT (add/add): Merge conflict in man/preprocessQuantile.Rd
> Auto-merging man/mdsPlot.Rd
> CONFLICT (add/add): Merge conflict in man/mdsPlot.Rd
> Auto-merging man/getAnnotation.Rd
> CONFLICT (add/add): Merge conflict in man/getAnnotation.Rd
> Auto-merging man/estimateCellCounts.Rd
> CONFLICT (add/add): Merge conflict in man/estimateCellCounts.Rd
> Auto-merging man/densityBeanPlot.Rd
> CONFLICT (add/add): Merge conflict in man/densityBeanPlot.Rd
> Auto-merging man/cpgCollapse.Rd
> CONFLICT (add/add): Merge conflict in man/cpgCollapse.Rd
> Auto-merging man/bumphunter.Rd
> CONFLICT (add/add): Merge conflict in man/bumphunter.Rd
> Auto-merging man/blockFinder.Rd
> CONFLICT (add/add): Merge conflict in man/blockFinder.Rd
> Auto-merging man/RGChannelSet-class.Rd
> CONFLICT (add/add): Merge conflict in man/RGChannelSet-class.Rd
> Auto-merging man/GenomicRatioSet-class.Rd
> CONFLICT (add/add): Merge conflict in man/GenomicRatioSet-class.Rd
> Auto-merging man/GenomicMethylSet-class.Rd
> CONFLICT (add/add): Merge conflict in man/GenomicMethylSet-class.Rd
> Auto-merging inst/unitTests/test_preprocess.R
> CONFLICT (add/add): Merge conflict in inst/unitTests/test_preprocess.R
> Auto-merging inst/NEWS.Rd
> CONFLICT 

Re: [Bioc-devel] notify out-dated branches

[Dan Tenenbaum]

- Original Message -
> From: "Yu, Guangchuang" 
> To: "bioc-devel" 
> Sent: Wednesday, June 8, 2016 1:44:12 AM
> Subject: [Bioc-devel] notify out-dated branches

> Dear all,
> 
> I found many peoples still using (and asking questions of) out-dated branch
> of Bioconductor packages that are no longer maintained.
> 
> I think it would be great to have a message notifying them when they are
> browsing the web page of out-dated branches, just like we have a message
> for devel branch.
> 
> For example, for BioC 3.2, a message like:
> 
> This is the BioC 3.2 version of XXX_pkg; for the current stable release
> version, see XXX_pkg_url.
> 
> would be helpful.
> 

We have implemented your suggestion for package landing pages for old versions 
2.8 through 3.2.
For technical reasons, it will take a little longer to implement this for 
versions prior to 2.8.

We try to make sure that search engines do not index old package landing pages, 
but 
people sometimes still link to a particular version of a package landing page 
in publications, etc.
As Martin points out, it's best to use the "short URL" of the package, for 
example:

https://bioconductor.org/packages/a4/

If you click on that page and go to the bottom you will see a line saying
"Package Short Url". And then if you mouse over the short url it says

"Canonical url for use in publications, etc., will always redirect to current 
release version (or devel if package is not in release yet).".

Thanks,
Dan



> Best wishes,
> Guangchuang
> --
> --~--~-~--~~~---~--~~
> Guangchuang Yu, PhD Candidate
> State Key Laboratory of Emerging Infectious Diseases
> School of Public Health
> The University of Hong Kong
> Hong Kong SAR, China
> www: https://guangchuangyu.github.io
> -~--~~~~--~~--~--~---
> 
>   [[alternative HTML version deleted]]
> 
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] Permission denied warning when building vignette

[Dan Tenenbaum]

I can't reproduce this.

One thing you can do is try and reproduce it in an interactive session in order 
to get more information.

So install your package:

R CMD INSTALL ASAFE

Then do the following:

cd ASAFE/vignettes
R CMD Stangle ASAFE.Rmd

This will produce a file called ASAFE.R containing just the R code from your 
vignette, you can then start R and do:


source("ASAFE.R", echo=TRUE, max=Inf)

Then see if the code fails again in the same place. If it does fail you can use 
traceback() and debug() and other tools to find the error.
Be sure that traceback() is the first command you run after the error.
Also at this point you can run sessionInfo() to see what you have installed. If 
you still have trouble and return to this list for help you should include the 
sessionInfo() and traceback() output. 

Dan




- Original Message -
> From: "Qian Sophia Zhang" 
> To: "bioc-devel" 
> Sent: Tuesday, June 7, 2016 11:22:29 AM
> Subject: [Bioc-devel] Permission denied warning when building vignette

> Dear Bioc-devel list people,
> 
> I am baffled about this 1 WARNING when I run “R CMD check ASAFE_0.99.0.tar.gz”
> and would be grateful if anyone could help me get rid of it.
> 
> Excerpt from attached log file:
> 
> "* checking re-building of vignette outputs ... WARNING
> Error in re-building vignettes:
>  ...
> Warning in file(file, ifelse(append, "a", "w")) :
>  cannot open file 'ASAFE.R': Permission denied
> Quitting from lines 163-172 (ASAFE.Rmd)
> Error: processing vignette 'ASAFE.Rmd' failed with diagnostics:
> cannot open the connection
> Execution halted”
> 
> I don’t have a file called ASAFE.R. I looked at lines 163-172 of ASAFE.Rmd. 
> Here
> are lines 162-172 in vim:
> 
> 162 ```{r}
> 163
> 164 # Making the rsID column row names
> 165
> 166 row.names(adm_ancestries) <- adm_ancestries[,1]
> 167 row.names(adm_genotypes) <- adm_genotypes[,1]
> 168
> 169 adm_ancestries <- adm_ancestries[,-1]
> 170 adm_genotypes <- adm_genotypes[,-1]
> 171
> 172 ```
> 
> I think adm_ancestries and adm_genotypes are successfully exported data 
> objects
> because they are used earlier in the vignette and no warning occurred then.
> Hence, I don’t see why I’m getting a warning from these lines.
> 
> The tar.gz file can be found here:
> 
> https://github.com/BiostatQian/ASAFE/raw/master/ASAFE_0.99.0.tar.gz
> 
> Thanks,
> Qian
> 
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] New Package Submission Process

[Dan Tenenbaum]

I put the wrong link in my announcement--the instructions for submitting a new 
package are at:

https://github.com/Bioconductor/Contributions

Dan



- Original Message -
> From: "Dan Tenenbaum" <dtene...@fredhutch.org>
> To: "bioc-devel" <bioc-devel@r-project.org>
> Sent: Monday, June 6, 2016 10:52:05 AM
> Subject: Re: [Bioc-devel] New Package Submission Process

> The new GitHub-based new package contribution system is up and running.
> 
> To contribute a Bioconductor package, file a new issue at
> 
> https://github.com/Bioconductor/Contributions/issues/new
> 
> 
> Read the full instructions here:
> 
> https://github.com/Bioconductor/Contributions/issues/new
> 
> as well as the updated package submission page:
> 
> http://bioconductor.org/developers/package-submission/
> 
> The old issue/package tracker is still up, but adding new packages is 
> disabled.
> 
> Please post questions/issues to bioc-devel.
> 
> Dan
> 
> 
> 
> - Original Message -
>> From: "Valerie Obenchain" <valerie.obench...@roswellpark.org>
>> To: "bioc-devel" <bioc-devel@r-project.org>
>> Sent: Tuesday, May 31, 2016 5:43:41 AM
>> Subject: [Bioc-devel] New Package Submission Process
> 
>> Package developers,
>> 
>> On June 6 we will transition to our new 'package tracker' on github. The
>> new system will enable a more public review process where community
>> members (not just the assigned reviewer) can give technical and
>> scientific input during the review.  More background in this post:
>> 
>>https://support.bioconductor.org/p/76472
>> 
>> Over the next week, we'll post instructions for the new submission
>> process on the web site and announce when access to the old tracker is
>> shut off. Reviews that are in-progress in the old tracker will continue
>> there and not be transferred to the new system.
>> 
>> Valerie
>> 
>> 
>> 
>> This email message may contain legally privileged and/or confidential
>> information.  If you are not the intended recipient(s), or the employee or
>> agent responsible for the delivery of this message to the intended
>> recipient(s), you are hereby notified that any disclosure, copying,
>> distribution, or use of this email message is prohibited.  If you have 
>> received
>> this message in error, please notify the sender immediately by e-mail and
>> delete this email message from your computer. Thank you.
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] New Package Submission Process

[Dan Tenenbaum]

The new GitHub-based new package contribution system is up and running.

To contribute a Bioconductor package, file a new issue at

https://github.com/Bioconductor/Contributions/issues/new


Read the full instructions here:

https://github.com/Bioconductor/Contributions/issues/new

as well as the updated package submission page:

http://bioconductor.org/developers/package-submission/

The old issue/package tracker is still up, but adding new packages is disabled.

Please post questions/issues to bioc-devel.

Dan



- Original Message -
> From: "Valerie Obenchain" 
> To: "bioc-devel" 
> Sent: Tuesday, May 31, 2016 5:43:41 AM
> Subject: [Bioc-devel] New Package Submission Process

> Package developers,
> 
> On June 6 we will transition to our new 'package tracker' on github. The
> new system will enable a more public review process where community
> members (not just the assigned reviewer) can give technical and
> scientific input during the review.  More background in this post:
> 
>https://support.bioconductor.org/p/76472
> 
> Over the next week, we'll post instructions for the new submission
> process on the web site and announce when access to the old tracker is
> shut off. Reviews that are in-progress in the old tracker will continue
> there and not be transferred to the new system.
> 
> Valerie
> 
> 
> 
> This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited.  If you have 
> received
> this message in error, please notify the sender immediately by e-mail and
> delete this email message from your computer. Thank you.
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

___
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Re: [Bioc-devel] Cannot update the release in svn

[Dan Tenenbaum]

- Original Message -
> From: "Tiphaine Martin" <tiphaine.mar...@kcl.ac.uk>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
> Cc: "bioc-devel" <Bioc-devel@r-project.org>
> Sent: Thursday, June 2, 2016 2:28:44 PM
> Subject: Re: [Bioc-devel] Cannot update the release in svn

> Sorry to answer only now, but I was busy to finish a paper in time.
> 
> So I did it as you said and everything goes well.
> and the function "git svn dcommit --add-author-from"
> finished by
> "...
>   M   R/AnalyseFile.R
> r118127 = 3f9d47140ab77cf30381c5afa24007967ce3a615
> (refs/remotes/git-svn-release-3.3)
> No changes between 7019708a1dcfbe8759b8107fcb20823167d43c08 and
> refs/remotes/git-svn-release-3.3
> Resetting to the latest refs/remotes/git-svn-release-3.3
> "
> So I did then 2 last commands
> git checkout  version-1.4.3_release-3.3
> git merge  release-3.3
> 
> But I didn't see modification on my fork of gitHub and when I go back to
> "release-3.3" (I run git checkout release-3.3), I have this message
> Switched to branch 'release-3.3'
> Your branch is ahead of 'bioc/release-3.3' by 7 commits.
>  (use "git push" to publish your local commits)
> 
> Should I push them on the remote or something else ?

I think (and Jim (cc'd) can correct me if I am wrong)) that you can just say 
"git push" and the push will go to your own repository's 'release-3.3' branch. 

git may tell you that there is no upstream branch and you can just paste the 
command that it suggests in order to fix this.

Dan



> Thanks
> 
> Tiphaine
> 
> 
> Tiphaine Martin
> PhD Research Student | King's College
> The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular
> Medicine Division
> St Thomas' Hospital
> 4th Floor, Block D, South Wing
> SE1 7EH, London
> United Kingdom
> 
> email : tiphaine.mar...@kcl.ac.uk
> Fax: +44 (0) 207 188 6761
> 
> 
> From: Dan Tenenbaum <dtene...@fredhutch.org>
> Sent: 30 May 2016 02:36
> To: Martin, Tiphaine
> Cc: bioc-devel
> Subject: Re: [Bioc-devel] Cannot update the release in svn
> 
> - Original Message -
>> From: "Tiphaine Martin" <tiphaine.mar...@kcl.ac.uk>
>> To: "bioc-devel" <Bioc-devel@r-project.org>
>> Sent: Sunday, May 29, 2016 2:54:20 PM
>> Subject: [Bioc-devel] Cannot update the release in svn
> 
>> Hi,
>>
>>
>> I cleaned my gitHub repository to have now the repository coMET in my gitHub 
>> as
>> the fork of coMET from bioconductor.
>>
>> I followed the directive from
>> http://bioconductor.org/developers/how-to/git-mirrors/
>>
>> as I need to correct bug in the current release
>>
>>
>> but when I try to run
>>
>>  1.  git svn rebase to get the latest SVN changes.
>>
>> I have an error message
>>
>>
>> git svn rebase
>>
>> Authentication realm: <https://hedgehog.fhcrc.org:443> The bioconductor
>> Subversion Repository
>>
>> Password for 'tiphaine':
>>
>> Can't create session: Unable to connect to a repository at URL
>> 'https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET':
>> Unexpected server error 500 'Internal Server Error' on
>> '/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET' at
>> /usr/share/perl5/Git/SVN.pm line 712.
>>
>>
>> So I cannot push my update in SVN.
>>
>>
>> Can you tell me if the bug is still on my side or on the side of svn of
>> bioconductor? and what I need to do to push my update.
>>
> 
> "git svn" relies on svn's authentication mechanisms. So svn has to already 
> know
> about your credentials.
> 
> Also, note that your svn username is 't.martin', not 'tiphaine' (which I guess
> is the username that you are logged into your computer as).
> 
> So you need to let svn know about your credentials, so do something like this:
> 
> svn log --limit 1 --username t.martin
> https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET
> 
> This will prompt for your svn password and might also ask you if it is ok to
> store your credentials on your computer in cleartext. You should answer 'y' to
> the questions it asks you.
> 
> After doing this you should be able to successfully run the 'git svn rebase'
> command.
> 
> Dan
> 
> 
>>
>> Regards,
>>
>> Tiphaine
>>
>>
>>
>> 
>> Tiphaine Martin
>> PhD Research Student | King's College
>> The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular
>> Medicine Division
>> St Thomas' Hospital
>> 4th Floor, Block D, South Wing
>> SE1 7EH, London
>> United Kingdom
>>
>> email : tiphaine.mar...@kcl.ac.uk
>> Fax: +44 (0) 207 188 6761
>>
>>   [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] there is no package called 'zlibbioc' on WINDOWS

[Dan Tenenbaum]

It's a problem on the server itself. It will not be present in today's build 
report which should be up in half an hour or so.

This is an intermittent problem, not a continuous one.

Dan


- Original Message -
> From: "Hartley, Stephen (NIH/NHGRI) [F]" <stephen.hart...@nih.gov>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "Monther Alhamdoosh" 
> <m.hamdo...@gmail.com>, "bioc-devel"
> <bioc-devel@r-project.org>
> Sent: Wednesday, June 1, 2016 12:11:27 PM
> Subject: RE: [Bioc-devel] there is no package called 'zlibbioc' on WINDOWS

> It looks like the zlibbioc package still won't load on moscato2. This is 
> causing
> something a ton of packages to fail at build (almost half?).
> 
> Does anyone have any idea what the issue is? Is it a problem with a patch to 
> the
> zlibbioc package, or a problem on the server itself?
> 
> -Steve
> 
> -Original Message-
> From: Dan Tenenbaum [mailto:dtene...@fredhutch.org]
> Sent: Thursday, May 26, 2016 9:03 PM
> To: Monther Alhamdoosh; bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] there is no package called 'zlibbioc' on WINDOWS
> 
> It's an as yet unknown problem with the build system. It's very likely that it
> will resolve itself in tonight's builds.
> 
> Dan
> 
> 
> On May 26, 2016 5:04:43 PM PDT, Monther Alhamdoosh <m.hamdo...@gmail.com> 
> wrote:
>>Hi developers,
>>
>>Our package named EGSEA seems to fail to be built on Windows as it
>>depends on "gage" which depends on zlibbioc. The problem appears in the
>>release branch and not in the devel branch.
>>
>>Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck =
>>vI[[i]])
>>:
>>
>>there is no package called 'zlibbioc'
>>
>>ERROR: lazy loading failed for package 'gage'
>>
>>Cheers,
>>Monther
>>
>>  [[alternative HTML version deleted]]
>>
>>___
>>Bioc-devel@r-project.org mailing list
>>https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
>   [[alternative HTML version deleted]]
> 
> ___
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Re: [Bioc-devel] Cannot update the release in svn

[Dan Tenenbaum]

- Original Message -
> From: "Tiphaine Martin" 
> To: "bioc-devel" 
> Sent: Sunday, May 29, 2016 2:54:20 PM
> Subject: [Bioc-devel] Cannot update the release in svn

> Hi,
> 
> 
> I cleaned my gitHub repository to have now the repository coMET in my gitHub 
> as
> the fork of coMET from bioconductor.
> 
> I followed the directive from
> http://bioconductor.org/developers/how-to/git-mirrors/
> 
> as I need to correct bug in the current release
> 
> 
> but when I try to run
> 
>  1.  git svn rebase to get the latest SVN changes.
> 
> I have an error message
> 
> 
> git svn rebase
> 
> Authentication realm:  The bioconductor
> Subversion Repository
> 
> Password for 'tiphaine':
> 
> Can't create session: Unable to connect to a repository at URL
> 'https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET':
> Unexpected server error 500 'Internal Server Error' on
> '/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET' at
> /usr/share/perl5/Git/SVN.pm line 712.
> 
> 
> So I cannot push my update in SVN.
> 
> 
> Can you tell me if the bug is still on my side or on the side of svn of
> bioconductor? and what I need to do to push my update.
> 

"git svn" relies on svn's authentication mechanisms. So svn has to already know 
about your credentials.

Also, note that your svn username is 't.martin', not 'tiphaine' (which I guess 
is the username that you are logged into your computer as).

So you need to let svn know about your credentials, so do something like this:

svn log --limit 1 --username t.martin 
https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET

This will prompt for your svn password and might also ask you if it is ok to 
store your credentials on your computer in cleartext. You should answer 'y' to 
the questions it asks you.

After doing this you should be able to successfully run the 'git svn rebase' 
command.

Dan


> 
> Regards,
> 
> Tiphaine
> 
> 
> 
> 
> Tiphaine Martin
> PhD Research Student | King's College
> The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular
> Medicine Division
> St Thomas' Hospital
> 4th Floor, Block D, South Wing
> SE1 7EH, London
> United Kingdom
> 
> email : tiphaine.mar...@kcl.ac.uk
> Fax: +44 (0) 207 188 6761
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] there is no package called 'zlibbioc' on WINDOWS

[Dan Tenenbaum]

It's an as yet unknown problem with the build system. It's very likely that it 
will resolve itself in tonight's builds. 

Dan


On May 26, 2016 5:04:43 PM PDT, Monther Alhamdoosh  wrote:
>​Hi developers,
>
>Our package named EGSEA seems to fail to be built on Windows​ as it
>depends
>on "gage" which depends on zlibbioc. The problem appears in the release
>branch and not in the devel branch.
>
>Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck =
>vI[[i]])
>:
>
>there is no package called 'zlibbioc'
>
>ERROR: lazy loading failed for package 'gage'
>
>Cheers,
>Monther
>
>   [[alternative HTML version deleted]]
>
>___
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>https://stat.ethz.ch/mailman/listinfo/bioc-devel

[[alternative HTML version deleted]]

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Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX

[Dan Tenenbaum]

- Original Message -
> From: "Aaron Lun" <a...@wehi.edu.au>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
> Cc: "bioc-devel" <bioc-devel@r-project.org>
> Sent: Tuesday, May 24, 2016 11:04:59 AM
> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX

> Yep, works on my machine as well. Seems like it would be a pain to have
> to do it manually every time csaw (or deepSNV, or diffHic) gets
> re-installed, though.
> 
> I should stress that I didn't do anything special to my R installation
> to get it to install packages in a different place. As far as I know,
> that's just what R decided to do by itself. (I never run R with sudo
> permissions, so it wouldn't be able to put packages in the central R
> installation folder anyway.)
> 
> So I think it's worth seriously thinking about whether this scenario
> should be supported; a user (i.e., me) would reasonably expect that BioC
> packages would work off the bat on this "standard" setting. Perhaps the
> csaw.so library can be built with static linkage to the libhts.a?
> 
> Or maybe I'm just spouting rubbish here. I don't know, I never do any
> serious work on a Mac.
> 

Martin just provided a fix that worked in my testing--Rhtslib now links 
statically against htslib.
I have committed the fix and bumped the version of all packages that depend 
directly on Rhtslib, in release and devel.

Thanks,
Dan



> Cheers,
> 
> Aaron
> 
> 
> On 24/05/16 18:42, Dan Tenenbaum wrote:
>>
>>
>> - Original Message -
>>> From: "Dan Tenenbaum" <dtene...@fredhutch.org>
>>> To: "Aaron Lun" <a...@wehi.edu.au>
>>> Cc: "bioc-devel" <bioc-devel@r-project.org>
>>> Sent: Tuesday, May 24, 2016 9:38:01 AM
>>> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX
>>
>>> - Original Message -
>>>> From: "Dan Tenenbaum" <dtene...@fredhutch.org>
>>>> To: "Aaron Lun" <a...@wehi.edu.au>
>>>> Cc: "bioc-devel" <bioc-devel@r-project.org>
>>>> Sent: Tuesday, May 24, 2016 8:51:30 AM
>>>> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX
>>>
>>>> - Original Message -
>>>>> From: "Aaron Lun" <a...@wehi.edu.au>
>>>>> To: "bioc-devel" <bioc-devel@r-project.org>
>>>>> Sent: Tuesday, May 24, 2016 8:06:13 AM
>>>>> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX
>>>>
>>>>> Dear Martin and List,
>>>>>
>>>>> I have a problem with linking to Rhtslib on Mac OSX when my R installation
>>>>> directory differs from the package installation directory. Trying to load 
>>>>> csaw
>>>>> (Bioc release version) gives me:
>>>>>
>>>>>> require(csaw)
>>>>> # ... whole lot of dependencies...
>>>>> Loading required package: csaw
>>>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>>>>   unable to load shared object
>>>>>   '/Users/lun01/Library/R/3.3/library/csaw/libs/csaw.so':
>>>>>   dlopen(/Users/lun01/Library/R/3.3/library/csaw/libs/csaw.so, 6): 
>>>>> Library not
>>>>>   loaded:
>>>>>   
>>>>> /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/lib/libhts.0.dylib
>>>>>   Referenced from: /Users/lun01/Library/R/3.3/library/csaw/libs/csaw.so
>>>>>   Reason: image not found
>>>>>
>>>>> ... which is because my Rhtslib shared library is sitting instead at
>>>>> /Users/lun01/Library/R/3.3/library/Rhtslib/lib/libhts.0.dylib (along with 
>>>>> all
>>>>> my other non-recommended, non-base packages). I presume this linking 
>>>>> failure
>>>>> occurs because the Makevars file (which would normally indicate where the
>>>>> shared library is living) doesn't get run when installing a prebuilt 
>>>>> binary?
>>>>> The same issue occurs with deepSNV, which is the other package that links 
>>>>> to
>>>>> Rhtslib.
>>>>
>>>>
>>>> I can't reproduce this issue after installing the binaries of csaw and 
>>>> Rhtslib.
>>>> I believe that htslib is statically linked inside of Rhtslib so you don't 
>>>> need
>>>> your own installation of htslib on your machine in order to us

[Bioc-devel] building packages that depend on openssl (was Re: problems linking to Rhtslib on Mac OSX)

[Dan Tenenbaum]

[renamed the thread]

- Original Message -
> From: "Jason Serviss" <jason.serv...@ki.se>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
> Cc: "Aaron Lun" <a...@wehi.edu.au>, "bioc-devel" <bioc-devel@r-project.org>
> Sent: Tuesday, May 24, 2016 11:32:17 AM
> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX

> Dan,
> 
> Thanks for the input. Yes, maybe it is a different problem altogether. If it 
> is
> more convenient I can start another “thread” to keep the issues separated…
> 
> Due to the fact that I am running R-devel, as far as I am aware, all (?)
> packages need to be installed from source. I have carefully followed the
> instructions for installing openssl on my system and testing the installation
> with:
> 

Why are you using R-devel? Bioconductor (even its devel version) does not use 
R-devel.
So your question may not really be a Bioconductor question.

If you are intending to work with the devel version of Bioconductor (3.4) it 
runs on R.3.3.0.
CRAN binaries are available for that version of R. Bioconductor is not yet 
providing Mac binaries for Bioconductor 3.4 due to an ill-timed hardware crash, 
but we are working on getting them building agains oon.

So...first, decide whether you really need R-devel. If so, you could try 
installing the R-3.3.0 binaries of git2r and openssl. They may work.
If they don't (and I see now that you tried this already without luck) you 
might want to talk to the maintainer of openssl about this, which is 
incidentally not a Bioconductor package.

But if you don't need R-devel, then you don't have to do anything special, just:
biocLite(c("git2r","openssl"))

Dan


> 
> openssl version -a
> 
> gives:
> 
> OpenSSL 1.1.0-pre6-dev  xx XXX 
> built on: reproducible build, date unspecified
> platform: darwin64-x86_64-cc
> compiler: cc -DDSO_DLFCN -DHAVE_DLFCN_H -DNDEBUG -DOPENSSL_THREADS
> -DOPENSSL_NO_STATIC_ENGINE -DOPENSSL_PIC -DOPENSSL_IA32_SSE2
> -DOPENSSL_BN_ASM_MONT -DOPENSSL_BN_ASM_MONT5 -DOPENSSL_BN_ASM_GF2m -DSHA1_ASM
> -DSHA256_ASM -DSHA512_ASM -DMD5_ASM -DAES_ASM -DVPAES_ASM -DBSAES_ASM
> -DGHASH_ASM -DECP_NISTZ256_ASM -DPOLY1305_ASM 
> -DOPENSSLDIR="\"/usr/local/ssl\""
> -DENGINESDIR="\"/usr/local/lib/engines\""
> OPENSSLDIR: "/usr/local/ssl"
> ENGINESDIR: "/usr/local/lib/engines”
> 
> Since I am also experiencing the same problem with git2r, I don’t think that 
> in
> my case the problem is isolated to openssl but I am struggling to identify 
> what
> it is specifically. I can download the .zip file for either of the packages 
> and
> install with R CMD INSTALL -no-test-load and see that the files (openssl.so 
> and
> git2r.so) are present in the libs directory but then library(git2r) or
> library(openssl) generates the same warning. I also tried reinstalling the
> previous version of Xcode and command line tools, thinking as mentioned
> previously that the problem could lie there, but to no avail.
> 
> Jason
> 
> 
> On 24 May 2016, at 19:48, Dan Tenenbaum
> <dtene...@fredhutch.org<mailto:dtene...@fredhutch.org>> wrote:
> 
> 
> 
> - Original Message -
> From: "Jason Serviss" <jason.serv...@ki.se<mailto:jason.serv...@ki.se>>
> To: "Aaron Lun" <a...@wehi.edu.au<mailto:a...@wehi.edu.au>>
> Cc: "bioc-devel" <bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>>
> Sent: Tuesday, May 24, 2016 8:20:18 AM
> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX
> 
> I can confirm that I am experiencing similar problems on OSX with several 
> other
> packages at the moment (openssl and git2r), I know that Xcode just updated and
> am not sure if this is causing some of the problems (potentially some update
> with their command line tools?)...
> 
> install.packages('openssl', type=‘source’)
> ...
> ** testing if installed package can be loaded
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
> unable to load shared object
> '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/openssl/libs/openssl.so':
> dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/openssl/libs/openssl.so,
> 6): Symbol not found: _ERR_free_strings
> Referenced from:
> /Library/Frameworks/R.framework/Versions/3.4/Resources/library/openssl/libs/openssl.so
> Expected in: flat namespace
> in
> /Library/Frameworks/R.framework/Versions/3.4/Resources/library/openssl/libs/openssl.so
> Error: loading failed
> Execution halted
> 
> install.packages(‘git2r', type=‘source’)
> …
> ** testing if installed package can be loaded
> Error in dyn.load(file, DL

Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX

[Dan Tenenbaum]

- Original Message -
> From: "Dan Tenenbaum" <dtene...@fredhutch.org>
> To: "Aaron Lun" <a...@wehi.edu.au>
> Cc: "bioc-devel" <bioc-devel@r-project.org>
> Sent: Tuesday, May 24, 2016 9:38:01 AM
> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX

> - Original Message -
>> From: "Dan Tenenbaum" <dtene...@fredhutch.org>
>> To: "Aaron Lun" <a...@wehi.edu.au>
>> Cc: "bioc-devel" <bioc-devel@r-project.org>
>> Sent: Tuesday, May 24, 2016 8:51:30 AM
>> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX
> 
>> - Original Message -
>>> From: "Aaron Lun" <a...@wehi.edu.au>
>>> To: "bioc-devel" <bioc-devel@r-project.org>
>>> Sent: Tuesday, May 24, 2016 8:06:13 AM
>>> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX
>> 
>>> Dear Martin and List,
>>> 
>>> I have a problem with linking to Rhtslib on Mac OSX when my R installation
>>> directory differs from the package installation directory. Trying to load 
>>> csaw
>>> (Bioc release version) gives me:
>>> 
>>>> require(csaw)
>>> # ... whole lot of dependencies...
>>> Loading required package: csaw
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>>  unable to load shared object
>>>  '/Users/lun01/Library/R/3.3/library/csaw/libs/csaw.so':
>>>  dlopen(/Users/lun01/Library/R/3.3/library/csaw/libs/csaw.so, 6): Library 
>>> not
>>>  loaded:
>>>  
>>> /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/lib/libhts.0.dylib
>>>  Referenced from: /Users/lun01/Library/R/3.3/library/csaw/libs/csaw.so
>>>  Reason: image not found
>>> 
>>> ... which is because my Rhtslib shared library is sitting instead at
>>> /Users/lun01/Library/R/3.3/library/Rhtslib/lib/libhts.0.dylib (along with 
>>> all
>>> my other non-recommended, non-base packages). I presume this linking failure
>>> occurs because the Makevars file (which would normally indicate where the
>>> shared library is living) doesn't get run when installing a prebuilt binary?
>>> The same issue occurs with deepSNV, which is the other package that links to
>>> Rhtslib.
>> 
>> 
>> I can't reproduce this issue after installing the binaries of csaw and 
>> Rhtslib.
>> I believe that htslib is statically linked inside of Rhtslib so you don't 
>> need
>> your own installation of htslib on your machine in order to use it.If you 
>> look
>> at the Mac tarball
>> (https://bioconductor.org/packages/release/bioc/bin/macosx/mavericks/contrib/3.3/Rhtslib_1.4.2.tgz)
>> untar it and go to the Rhtslib/lib directory you see the following files:
>> 
>> libhts.0.dylib
>> libhts.a
>> libhts.dylib
>> 
>> ...in addition to Rhtslib.so which is in Rhtslib/libs.
>> 
> 
> Actually I can induce issues if I install Rhtslib in a different library
> directory, which is what you were saying. Will look into this a little.


The following seems to fix it:

cd ~/Library/R/3.3/csaw/libs
# change dtenenba to your username in the below
sudo install_name_tool -change 
"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/lib/libhts.0.dylib"
 "/Users/dtenenba/Library/R/3.3/Rhtslib/lib/libhts.0.dylib" csaw.so

(the sudo may not be necessary)

Then I can 
require(csaw) 

and it works.

I'm not sure if there is something that the bioc group should be doing about 
thiswe'll discuss it when we meet soon.

Dan



> Dan
> 

> 
>> Dan
>> 
>> 
>> 
>>> 
>>> Any thoughts? I don't usually use Macs, so I don't know exactly what goes on
>>> during package installation, or whether my setup (i.e., with different
>>> package/R locations) is atypical or not.
>>> 
>>> Aaron
>>> 
>>>> sessionInfo()
>>> R version 3.3.0 (2016-05-03)
>>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>>> Running under: OS X 10.10.5 (Yosemite)
>>> 
>>> locale:
>>> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>>> 
>>> attached base packages:
>>> [1] stats4parallel  stats graphics  grDevices utils datasets
>>> [8] methods   base
>>> 
>>> other attached packages:
>>> [1] SummarizedExperiment_1.2.2 Biobase_2.32.0
>>> [3] GenomicRanges_1.24.0   GenomeInfoDb_1.8.1
>>> [5] IRanges_2.6.0  S4Vector

Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX

[Dan Tenenbaum]

- Original Message -
> From: "Aaron Lun" 
> To: "bioc-devel" 
> Sent: Tuesday, May 24, 2016 8:06:13 AM
> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX

> Dear Martin and List,
> 
> I have a problem with linking to Rhtslib on Mac OSX when my R installation
> directory differs from the package installation directory. Trying to load csaw
> (Bioc release version) gives me:
> 
>> require(csaw)
> # ... whole lot of dependencies...
> Loading required package: csaw
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared object
>  '/Users/lun01/Library/R/3.3/library/csaw/libs/csaw.so':
>  dlopen(/Users/lun01/Library/R/3.3/library/csaw/libs/csaw.so, 6): Library not
>  loaded:
>  
> /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/lib/libhts.0.dylib
>  Referenced from: /Users/lun01/Library/R/3.3/library/csaw/libs/csaw.so
>  Reason: image not found
> 
> ... which is because my Rhtslib shared library is sitting instead at
> /Users/lun01/Library/R/3.3/library/Rhtslib/lib/libhts.0.dylib (along with all
> my other non-recommended, non-base packages). I presume this linking failure
> occurs because the Makevars file (which would normally indicate where the
> shared library is living) doesn't get run when installing a prebuilt binary?
> The same issue occurs with deepSNV, which is the other package that links to
> Rhtslib.


I can't reproduce this issue after installing the binaries of csaw and Rhtslib. 
I believe that htslib is statically linked inside of Rhtslib so you don't need 
your own installation of htslib on your machine in order to use it.If you look 
at the Mac tarball 
(https://bioconductor.org/packages/release/bioc/bin/macosx/mavericks/contrib/3.3/Rhtslib_1.4.2.tgz)
 untar it and go to the Rhtslib/lib directory you see the following files:

libhts.0.dylib
libhts.a
libhts.dylib

...in addition to Rhtslib.so which is in Rhtslib/libs.

Dan



> 
> Any thoughts? I don't usually use Macs, so I don't know exactly what goes on
> during package installation, or whether my setup (i.e., with different
> package/R locations) is atypical or not.
> 
> Aaron
> 
>> sessionInfo()
> R version 3.3.0 (2016-05-03)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X 10.10.5 (Yosemite)
> 
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
> 
> attached base packages:
> [1] stats4parallel  stats graphics  grDevices utils datasets
> [8] methods   base
> 
> other attached packages:
> [1] SummarizedExperiment_1.2.2 Biobase_2.32.0
> [3] GenomicRanges_1.24.0   GenomeInfoDb_1.8.1
> [5] IRanges_2.6.0  S4Vectors_0.10.1
> [7] BiocGenerics_0.18.0BiocInstaller_1.22.2
> 
> loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.34.3XVector_0.12.0  edgeR_3.14.0
> [4] GenomicAlignments_1.8.0 zlibbioc_1.18.0 BiocParallel_1.6.2
> [7] tools_3.3.0 DBI_0.4-1   Rhtslib_1.4.2
> [10] rtracklayer_1.32.0  bitops_1.0-6RCurl_1.95-4.8
> [13] biomaRt_2.28.0  RSQLite_1.0.0   limma_3.28.5
> [16] GenomicFeatures_1.24.2  Biostrings_2.40.1   Rsamtools_1.24.0
> [19] XML_3.98-1.4
> __
> 
> The information in this email is confidential and inte...{{dropped:6}}

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Re: [Bioc-devel] workflow builds on windows but not on mac and linux

[Dan Tenenbaum]

Hi,

The problem on linux has been fixed, but now there's another problem. It is 
running out of memory when building your workflow.

The problem on mac is that R-3.2.x is not compatible with the newest knitr 
(1.13), so the recommendation is to downgrade to knitr 1.12 or upgrade to 
R-3.3.0.
The workflow builders will update to R-3.3.0 soon, so this issue will go away 
then.

In the meantime, I did try and downgrade the machine to knitr 1.12 but the 
workflow build code rightfully updated everything before building so that had 
no effect.

Both of these new build results are here:

http://docbuilder.bioconductor.org:8080/job/maEndToEnd/8/

Dan


- Original Message -
> From: "Bernd Klaus" 
> To: "bioc-devel" 
> Sent: Monday, May 23, 2016 3:33:24 AM
> Subject: [Bioc-devel] workflow builds on windows but not on mac and linux

> Dear all,
> 
> I recently took up developing a workflow again (matEndToEnd).
> 
> http://docbuilder.bioconductor.org:8080/job/maEndToEnd/
> 
> While it builds fine on windows (winbuilder1) I get error message on
> linux (master) and mac (vagrantmac) that I cannot really trace down.
> 
> 1.) On vagrantmac, it gives
> 
> 
>> * creating vignettes ... ERROR
>> Quitting from lines 36-43 (MA-Workflow.Rmd)
>>  Error: processing vignette 'MA-Workflow.Rmd' failed with diagnostics:
>> unused arguments (filename, stop_on_error != 2)
> 
> http://docbuilder.bioconductor.org:8080/job/maEndToEnd/label=vagrantmac/lastBuild/console
> 
> 
> Some searching revealed that this might be related to using a version
> of knitr that is too old:
> 
> http://stackoverflow.com/questions/37241578/getting-a-parser-all-error-in-r-when-using-knitr-for-converting-a-basic-rmd-file
> 
>  
> 2.) On master the error is:
> 
> 
>> * installing the package to build vignettes
>> * creating vignettes ... ERROR
>> Error : .onLoad failed in loadNamespace() for 'BiocInstaller', details:
>>   call: url(paste0(.protocol(), "//bioconductor.org/BiocInstaller.dcf"))
>>   error: https:// URLs are not supported
>> Quitting from lines 76-109 (MA-Workflow.Rmd)
> 
> http://docbuilder.bioconductor.org:8080/job/maEndToEnd/label=master/lastBuild/console
> 
> 
> potentially "old" package versions are a problem here as well?
> 
> (All servers still seem to still use Bioc 3.2 in principle, but
> maybe there is some mixup between old and new? )
> 
> 
> Thanks a lot and best wishes,
> 
> Bernd
> 
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] test coverage not shown

[Dan Tenenbaum]

It looks like something has changed at codecov. I have contacted them and asked 
them for guidance about the issue.
Thanks,
Dan


- Original Message -
> From: "Ramon Diaz-Uriarte" 
> To: "bioc-devel" 
> Cc: "ramon diaz" 
> Sent: Friday, May 20, 2016 2:11:29 AM
> Subject: [Bioc-devel] test coverage not shown

> Dear All,
> 
> For both Bioc 3.3 and Bioc 3.4, test coverage is shown as "unknown" for (at
> least some) packages that do have tests. (As an example, one package I
> maintain:
> https://www.bioconductor.org/packages/release/bioc/html/OncoSimulR.html and
> https://www.bioconductor.org/packages/devel/bioc/html/OncoSimulR.html).
> 
> 
> Best,
> 
> 
> R.
> 
> 
> --
> Ramon Diaz-Uriarte
> Department of Biochemistry, Lab B-25
> Facultad de Medicina
> Universidad Autónoma de Madrid
> Arzobispo Morcillo, 4
> 28029 Madrid
> Spain
> 
> Phone: +34-91-497-2412
> 
> Email: rdia...@gmail.com
>   ramon.d...@iib.uam.es
> 
> http://ligarto.org/rdiaz
> 
> ___
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Re: [Bioc-devel] New package submission warning

[Dan Tenenbaum]

You can ignore these warnings. Those build machines need to be updated to the 
devel version of Bioconductor but there are several other things that need to 
happen before we can do that.

Dan


- Original Message -
> From: "Brad Nelms" 
> To: "bioc-devel" 
> Sent: Friday, May 20, 2016 1:11:38 PM
> Subject: [Bioc-devel] New package submission warning

> Hi,
> I'm trying to submit two packages to Bioconductor ('GSE64985' and
> 'E.MTAB.62'), but am receiving this warning from BiocCheck:
> 
> * Checking version number validity...
>* RECOMMENDED: y of x.y.z version should be even in release
> 
> The version number of my packages are 0.99.x, which is required for new
> packages. I have been unable to find any information about why I am
> receiving this error, perhaps there is something I need to change so that
> BiocCheck recognizes the submission as a devel package rather than a
> release package? Is there a mistake in how I am submitting my packages?
> 
> Thanks,
> Brad
> 
>   [[alternative HTML version deleted]]
> 
> ___
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Re: [Bioc-devel] Version numbers incremented?

[Dan Tenenbaum]

For the record, here is the log message:

Version bump to trigger package rebuilding now that purl()'ing issue
has been correctly identified. knitr does not create purl()'ed
(Stangle equivalent) .R files if _R_CHECK_TIMINGS_ is set, which
the build system was setting. Now it's not set, so these .R files are
now created. See https://github.com/yihui/knitr/issues/1212 for more.

Dan


- Original Message -
> From: "Kasper Daniel Hansen" 
> To: "Ulrich Bodenhofer" 
> Cc: "bioc-devel" , "msa" , 
> keb...@bioinf.jku.at
> Sent: Tuesday, May 17, 2016 7:15:35 AM
> Subject: Re: [Bioc-devel] Version numbers incremented?

> Ulrich, "svn log" does not help you here?
> 
> On Tue, May 17, 2016 at 9:12 AM, Ulrich Bodenhofer > wrote:
> 
>> Thanks, Leonardo! Yes, all my four packages use knitr, while the other
>> eight packages I mentioned use Sweave. So my question is answered and the
>> issue is closed, thanks again! I just wanted to know what happened, since I
>> could not find an explaination why the version numbers have been bumped.
>>
>> Best regards,
>> Ulrich
>>
>>
>> On 05/17/2016 02:17 PM, Leonardo Collado Torres wrote:
>>
>>> Hi,
>>>
>>> Does your package use knitr for creating the vignettes? If so, it must
>>> be because of
>>> https://github.com/lcolladotor/derfinder/commit/c70ede92fb14e83a0fe0032353f7f897ff55b5d5
>>> (the equivalent commit for your package).
>>>
>>> Best,
>>> Leonardo
>>>
>>> On Tue, May 17, 2016 at 4:18 AM, Ulrich Bodenhofer
>>>  wrote:
>>>
 Hi all,

 I just noticed that the version numbers of many (yet not all) packages
 have
 recently been incremented from x.y.0 to x.y.2 both in the devel and in
 the
 release branch. Actually, this affected all four packages I am
 maintaining,
 but strangely none of the other eight packages that are maintained by
 other
 members of my group. As it seems to me, the only change was the version
 number in the DESCRIPTION file itself. What is the reason for that? I'm
 sorry if this subject has been covered already and if I should know
 that. At
 least I could not find any information on the bioc-devel list.

 Thanks in advance and best regards,
 Ulrich

>>>
>> ___
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] \donttest and the "80% of man pages documenting exported objects must have runnable examples" rule

[Dan Tenenbaum]

- Original Message -
> From: "Richard Cotton" 
> To: "bioc-devel" 
> Sent: Sunday, May 15, 2016 4:45:09 AM
> Subject: [Bioc-devel] \donttest and the "80% of man pages documenting 
> exported objects must have runnable examples" rule

> I have a package with a lot of examples in exported functions marked
> as \donttest.
> 
> BiocCheck doesn't count these functions towards the target of having
> 80% of exported objects with runnable examples.  I do have more than
> 80% runnable examples; it's just that BiocCheck can't see them.  (For
> background, the package is mostly about file import, and it takes a
> second or two to import the sample files included in the package.
> Having examples that run for a couple of seconds is fine for users,
> but makes package testing very slow (once dozens of the example are
> run).
> 
> This check is considered REQUIRED to be solved, so I'd like to know if
> it's OK to include an explanation about the use of \donttest during
> submission, or if my pacakge will just get rejected outright.
> 


Ultimately, humans make all decisions about package inclusion. 
So you will have a chance to discuss your package with someone.

DAn


> --
> Regards,
> Richie
> 
> Learning R
> 4dpiecharts.com
> 
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Re: [Bioc-devel] new download stats

[Dan Tenenbaum]

- Original Message -
> From: "bioc-devel" 
> To: "bioc-devel" , "Hervé Pagès" 
> 
> Sent: Thursday, May 12, 2016 5:27:17 PM
> Subject: Re: [Bioc-devel] new download stats

> Hervé,
> Thanks for the update, it looks great!
> Here is one problem though. I noticed that the original download stats link 
> has
> change too. For my pathview package, it was:
> http://bioconductor.org/packages/stats/bioc/pathview.html
> now changed to:
> https://bioconductor.org/packages/stats/bioc/pathview/
>   

I made the old url work for now, just for your package...until we can decide 
what to do about this. 
It's just a copy of the file at 
http://bioconductor.org/packages/stats/bioc/pathview.html , with the url paths 
adjusted,
it won't be updated the next time the scripts are run, but hopefully by then we 
will have a solution in place.

Dan


> I happened to include the old link in a submitted grant application as an
> objective impact metric for the Pathview project. And now the old one is not
> used any more, and my application suddenly look bad now because the supportive
> evidence claimed does not even exist. Not sure how that may affect our grant
> application.
> can we still keep the old URL or at least make it a alias to the new one? 
> Thank
> you!
> Weijun
> 
> 
> On Thu, 5/12/16, Hervé Pagès  wrote:
> 
> Subject: [Bioc-devel] new download stats
> To: "bioc-devel@r-project.org" 
> Date: Thursday, May 12, 2016, 1:55 PM
> 
> Hi,
> 
> We've refactored the download stats a little:
> 
>    https://bioconductor.org/packages/stats/
> 
> 2 new visible features are (1) yearly stats since 2009 to
> present
> and (2) downloadable stats in tabulated format (.tab
> extension,
> import in R with 'read.table(, header=TRUE)').
> 
> Feedback welcome.
> 
> Cheers,
> H.
> 
> PS: Updated stats for annotation and experiment packages
> coming soon.
> 
> --
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
> 
> ___
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> mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
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Re: [Bioc-devel] GEOquery for Bioc devel

[Dan Tenenbaum]

Thanks Sean!

It looks like it does build and check. But the last commit was made after the 
daily deadline (4:20PM Seattle time) so this won't be available via biocLite() 
till Tuesday sometime. It can be installed via git or svn in the meantime.

Dan


- Original Message -
> From: "Sean Davis" <seand...@gmail.com>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
> Cc: "Vincent Carey" <st...@channing.harvard.edu>, "bioc-devel" 
> <bioc-devel@r-project.org>
> Sent: Sunday, May 8, 2016 5:00:41 PM
> Subject: Re: [Bioc-devel] GEOquery for Bioc devel

> Hi, all.
> 
> Sorry for the hiccup.  The problem appears to have stemmed from NCBI GEO
> switching to using https for GEO data tables.  This is not a highly-used
> feature, but it was enough to break the build.  It should be fixed (cross
> fingers) in Devel.  If fixed in devel, I will backport to release.
> 
> Sean
> 
>> On May 8, 2016, at 11:52 AM, Dan Tenenbaum <dtene...@fredhutch.org> wrote:
>> 
>> GEOquery is available in release (3.3), though not the most recent version.
>> Hopefully release and not devel is being used in the edX class; the devel
>> builds are not yet stable, but should be later today. In any case, it's
>> early-cycle devel.
>> 
>> Dan
>> 
>> 
>> - Original Message -
>>> From: "Dan Tenenbaum" <dtene...@fredhutch.org>
>>> To: "Vincent Carey" <st...@channing.harvard.edu>
>>> Cc: "bioc-devel" <bioc-devel@r-project.org>
>>> Sent: Sunday, May 8, 2016 8:49:09 AM
>>> Subject: Re: [Bioc-devel] GEOquery for Bioc devel
>> 
>>> Maybe. If the package does not build for many days on end, it's more than
>>> flakiness and one wonders if the service is usable at all.
>>> Tests that indicate this seem appropriate to me, though I agree false 
>>> positives
>>> can be annoying.
>>> Dan
>>> 
>>> 
>>> - Original Message -
>>>> From: "Vincent Carey" <st...@channing.harvard.edu>
>>>> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
>>>> Cc: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com>, "bioc-devel"
>>>> <bioc-devel@r-project.org>
>>>> Sent: Sunday, May 8, 2016 8:46:57 AM
>>>> Subject: Re: [Bioc-devel] GEOquery for Bioc devel
>>> 
>>>> Hmm.  Very important piece of software so we should try to remedy this.  I
>>>> had assigned some GEOquery problems in the edX class and there were some
>>>> people who could not get getGEO to work, but the problem seemed
>>>> intermittent.  There was a workaround posted on the support site which
>>>> involved separate steps for assay and platform data acquisition; ultimately
>>>> the solution data object was just made available directly.
>>>> 
>>>> Can/should we make the build/distribution process robust to data server
>>>> flakiness?  The user may encounter intermittent problems, but the software
>>>> should still be available IMHO.
>>>> Reduce server-dependent tests and examples?
>>>> 
>>>> On Sun, May 8, 2016 at 11:08 AM, Dan Tenenbaum <dtene...@fredhutch.org>
>>>> wrote:
>>>> 
>>>>> It has not built since the devel (3.4) builds started. Apparently GEO has
>>>>> been pretty flaky.
>>>>> Dan
>>>>> 
>>>>> 
>>>>> - Original Message -
>>>>>> From: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com>
>>>>>> To: "bioc-devel" <bioc-devel@r-project.org>
>>>>>> Sent: Sunday, May 8, 2016 5:54:59 AM
>>>>>> Subject: [Bioc-devel] GEOquery for Bioc devel
>>>>> 
>>>>>> I don't see GEOquery for Bioc devel.  Is that a mistake somehow?
>>>>>> 
>>>>>>  [[alternative HTML version deleted]]
>>>>>> 
>>>>>> ___
>>>>>> Bioc-devel@r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>> 
>>>>> ___
>>>>> Bioc-devel@r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> 
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
>> ___
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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel

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[Bioc-devel] Mac builds in bioconductor devel

[Dan Tenenbaum]

Hi all,

You may have noticed that there are no Mac builds in the new devel 
(Bioconductor 3.4) build report. 

One of the build macs died. 

We have ordered replacement hardware and we hope it will arrive soon. Then 
after it is configured, we aim to get Mac builds going again as soon as 
possible.

All of this will probably take at least two weeks. Thanks for your 
understanding.

Thanks,
Dan

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Re: [Bioc-devel] GEOquery for Bioc devel

[Dan Tenenbaum]

GEOquery is available in release (3.3), though not the most recent version. 
Hopefully release and not devel is being used in the edX class; the devel 
builds are not yet stable, but should be later today. In any case, it's 
early-cycle devel.

Dan


- Original Message -
> From: "Dan Tenenbaum" <dtene...@fredhutch.org>
> To: "Vincent Carey" <st...@channing.harvard.edu>
> Cc: "bioc-devel" <bioc-devel@r-project.org>
> Sent: Sunday, May 8, 2016 8:49:09 AM
> Subject: Re: [Bioc-devel] GEOquery for Bioc devel

> Maybe. If the package does not build for many days on end, it's more than
> flakiness and one wonders if the service is usable at all.
> Tests that indicate this seem appropriate to me, though I agree false 
> positives
> can be annoying.
> Dan
> 
> 
> ----- Original Message -
>> From: "Vincent Carey" <st...@channing.harvard.edu>
>> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
>> Cc: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com>, "bioc-devel"
>> <bioc-devel@r-project.org>
>> Sent: Sunday, May 8, 2016 8:46:57 AM
>> Subject: Re: [Bioc-devel] GEOquery for Bioc devel
> 
>> Hmm.  Very important piece of software so we should try to remedy this.  I
>> had assigned some GEOquery problems in the edX class and there were some
>> people who could not get getGEO to work, but the problem seemed
>> intermittent.  There was a workaround posted on the support site which
>> involved separate steps for assay and platform data acquisition; ultimately
>> the solution data object was just made available directly.
>> 
>> Can/should we make the build/distribution process robust to data server
>> flakiness?  The user may encounter intermittent problems, but the software
>> should still be available IMHO.
>> Reduce server-dependent tests and examples?
>> 
>> On Sun, May 8, 2016 at 11:08 AM, Dan Tenenbaum <dtene...@fredhutch.org>
>> wrote:
>> 
>>> It has not built since the devel (3.4) builds started. Apparently GEO has
>>> been pretty flaky.
>>> Dan
>>>
>>>
>>> - Original Message -
>>> > From: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com>
>>> > To: "bioc-devel" <bioc-devel@r-project.org>
>>> > Sent: Sunday, May 8, 2016 5:54:59 AM
>>> > Subject: [Bioc-devel] GEOquery for Bioc devel
>>>
>>> > I don't see GEOquery for Bioc devel.  Is that a mistake somehow?
>>> >
>>> >   [[alternative HTML version deleted]]
>>> >
>>> > ___
>>> > Bioc-devel@r-project.org mailing list
>>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> ___
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Re: [Bioc-devel] GEOquery for Bioc devel

[Dan Tenenbaum]

Maybe. If the package does not build for many days on end, it's more than 
flakiness and one wonders if the service is usable at all.
Tests that indicate this seem appropriate to me, though I agree false positives 
can be annoying.
Dan


- Original Message -
> From: "Vincent Carey" <st...@channing.harvard.edu>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
> Cc: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com>, "bioc-devel" 
> <bioc-devel@r-project.org>
> Sent: Sunday, May 8, 2016 8:46:57 AM
> Subject: Re: [Bioc-devel] GEOquery for Bioc devel

> Hmm.  Very important piece of software so we should try to remedy this.  I
> had assigned some GEOquery problems in the edX class and there were some
> people who could not get getGEO to work, but the problem seemed
> intermittent.  There was a workaround posted on the support site which
> involved separate steps for assay and platform data acquisition; ultimately
> the solution data object was just made available directly.
> 
> Can/should we make the build/distribution process robust to data server
> flakiness?  The user may encounter intermittent problems, but the software
> should still be available IMHO.
> Reduce server-dependent tests and examples?
> 
> On Sun, May 8, 2016 at 11:08 AM, Dan Tenenbaum <dtene...@fredhutch.org>
> wrote:
> 
>> It has not built since the devel (3.4) builds started. Apparently GEO has
>> been pretty flaky.
>> Dan
>>
>>
>> - Original Message -
>> > From: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com>
>> > To: "bioc-devel" <bioc-devel@r-project.org>
>> > Sent: Sunday, May 8, 2016 5:54:59 AM
>> > Subject: [Bioc-devel] GEOquery for Bioc devel
>>
>> > I don't see GEOquery for Bioc devel.  Is that a mistake somehow?
>> >
>> >   [[alternative HTML version deleted]]
>> >
>> > ___
>> > Bioc-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>> ___
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] GEOquery for Bioc devel

[Dan Tenenbaum]

It has not built since the devel (3.4) builds started. Apparently GEO has been 
pretty flaky. 
Dan


- Original Message -
> From: "Kasper Daniel Hansen" 
> To: "bioc-devel" 
> Sent: Sunday, May 8, 2016 5:54:59 AM
> Subject: [Bioc-devel] GEOquery for Bioc devel

> I don't see GEOquery for Bioc devel.  Is that a mistake somehow?
> 
>   [[alternative HTML version deleted]]
> 
> ___
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Re: [Bioc-devel] New package version and BiocCheck

[Dan Tenenbaum]

The package builder attached to the tracker is running on release, not devel. 
It will be like that for a while so just ignore that warning.
Dan


- Original Message -
> From: "Peng Ni" 
> To: "bioc-devel" 
> Sent: Friday, May 6, 2016 7:48:50 PM
> Subject: [Bioc-devel] New package version and BiocCheck

> I'm trying to submit a new package. I have set the version number to 0.99.0 as
> indicated at
> However, I get a warning from BiocCheck 1.6.1 that says:
> 
> * Checking version number validity...
>* RECOMMENDED: y of x.y.z version should be even in release
> 
> I see that the end of the warning says "in release", but I'm don't see a way 
> to
> change the
> package status to development on the Issue tracking website.
> 
> I'm confused. Do I need to change some information in DESCRIPTION? Or did I 
> miss
> something somewhere?
> 
> Can someone point me toward a solution? My package submission is here:
> https://github.com/Bioconductor/ContributionsBeta/issues/7
> 
> Thanks a lot.
> 
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Re: [Bioc-devel] how to declare vignette processing properly

[Dan Tenenbaum]

Yeah, this was because pandoc-citeproc was not installed. So it should go 
away

Dan

- Original Message -
> From: "lcollado" <lcoll...@jhu.edu>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
> Cc: "Vincent Carey" <st...@channing.harvard.edu>, "bioc-devel" 
> <bioc-devel@r-project.org>
> Sent: Friday, May 6, 2016 11:21:33 AM
> Subject: Re: [Bioc-devel] how to declare vignette processing properly

> Hi,
> 
> I had the same error at derfinder's devel build report yesterday
> morning (v1.7.0), and it went away on the build from yesterday
> afternoon (v1.7.1).
> 
> Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if
> (grepl("\\.[Rr]rst$",  :
> 
>  It seems you should call rmarkdown::render() instead of
> knitr::knit2html() because yriMulti.Rmd appears to be an R Markdown v2
> document.
> 
> 
> So I think that it'll go away on the build report for yriMulti. You
> can see at the end of
> http://bioconductor.org/packages/release/bioc/vignettes/regionReport/inst/doc/bumphunterExampleOutput.html#reproducibility
> that BioC uses pandoc version 1.16.0.2
> 
> Best,
> Leo
> 
> On Fri, May 6, 2016 at 1:15 PM, Dan Tenenbaum <dtene...@fredhutch.org> wrote:
>> Is pandoc-citeproc installed?
>>
>>
>> - Original Message -
>>> From: "Vincent Carey" <st...@channing.harvard.edu>
>>> To: "Andrzej Oleś" <andrzej.o...@gmail.com>
>>> Cc: "bioc-devel" <bioc-devel@r-project.org>
>>> Sent: Friday, May 6, 2016 9:44:06 AM
>>> Subject: Re: [Bioc-devel] how to declare vignette processing properly
>>
>>> Thanks Andrzej, can you give a bit more diagnosis?  Is 1.13.1 too old?
>>>
>>> %derby01> pandoc -v
>>>
>>> pandoc 1.13.1
>>>
>>> Compiled with texmath 0.8, highlighting-kate 0.5.11.
>>>
>>> Syntax highlighting is supported for the following languages:
>>>
>>>abc, actionscript, ada, agda, apache, asn1, asp, awk, bash, bibtex,
>>> boo, c,
>>>
>>>changelog, clojure, cmake, coffee, coldfusion, commonlisp, cpp, cs, css,
>>>
>>>curry, d, diff, djangotemplate, dockerfile, dot, doxygen, doxygenlua,
>>> dtd,
>>>
>>>eiffel, email, erlang, fasm, fortran, fsharp, gcc, glsl, gnuassembler,
>>> go,
>>>
>>>haskell, haxe, html, ini, isocpp, java, javadoc, javascript, json, jsp,
>>>
>>>julia, latex, lex, lilypond, literatecurry, literatehaskell, lua, m4,
>>>
>>>makefile, mandoc, markdown, mathematica, matlab, maxima, mediawiki,
>>>
>>>metafont, mips, modelines, modula2, modula3, monobasic, nasm, noweb,
>>>
>>>objectivec, objectivecpp, ocaml, octave, opencl, pascal, perl, php,
>>> pike,
>>>
>>>postscript, prolog, pure, python, r, relaxng, relaxngcompact, rest,
>>> rhtml,
>>>
>>>roff, ruby, rust, scala, scheme, sci, sed, sgml, sql, sqlmysql,
>>>
>>>sqlpostgresql, tcl, tcsh, texinfo, verilog, vhdl, xml, xorg, xslt, xul,
>>>
>>>yacc, yaml, zsh
>>>
>>> Default user data directory: /udd/stvjc/.pandoc
>>>
>>> Copyright (C) 2006-2014 John MacFarlane
>>>
>>> Web:  http://johnmacfarlane.net/pandoc
>>>
>>> This is free software; see the source for copying conditions.
>>>
>>> There is no warranty, not even for merchantability or fitness
>>>
>>> for a particular purpose.
>>>
>>> On Fri, May 6, 2016 at 12:30 PM, Andrzej Oleś <andrzej.o...@gmail.com>
>>> wrote:
>>>
>>>> Hi Vince,
>>>>
>>>> this is most probably due to missing/incorrect pandoc installation.
>>>>
>>>> Cheers,
>>>> Andrzej
>>>>
>>>> On Fri, May 6, 2016 at 6:18 PM, Vincent Carey <st...@channing.harvard.edu>
>>>> wrote:
>>>>
>>>>> this is for the current svn version of yriMulti, from 00check.log
>>>>>
>>>>> * checking re-building of vignette outputs ... WARNING
>>>>>
>>>>> Error in re-building vignettes:
>>>>>
>>>>>   ...
>>>>>
>>>>> Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if
>>>>> (grepl("\\.[Rr]rst$",  :
>>>>>
>>>>>   It seems you should call rmarkdown::render() instead of
&

Re: [Bioc-devel] error message - package GSAR

[Dan Tenenbaum]

This is an issue that was reported 3 years ago 
(http://thr3ads.net/r-devel/2013/04/2193760-Failed-to-locate-the-texi2pdf-output-file)
 and has not been fixed, probably because it is extremely hard to reproduce. It 
tends to happen on random packages from one day to the next. In fact, in 
today's build report which is coming out in a few minutes, the problem does not 
occur.

So you don't need to do anything.

Dan


- Original Message -
> From: "Rahmatallah, Yasir" 
> To: "bioc-devel" 
> Sent: Thursday, May 5, 2016 12:28:35 PM
> Subject: [Bioc-devel] error message - package GSAR

> Hi,
> 
> I'm the maintainer of package GSAR. Last Tuesday's build produced the 
> following
> error message for the Windows platform only
> 
> Warning: running command
> '"C:\Users\BIOCBU?1\AppData\Local\Programs\MIKTEX?1.9\miktex\bin\texify.exe"
> --quiet --pdf "GSAR.tex" --max-iterations=20 -I
> "E:/biocbld/bbs-3.3-bioc/R/share/texmf/tex/latex" -I
> "E:/biocbld/bbs-3.3-bioc/R/share/texmf/bibtex/bst"' had status 1
> Error in find_vignette_product(name, by = "texi2pdf", engine = engine) :
>  Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave') for
>  vignette with name 'GSAR'. The following files exist in directory '.':
>  'Bioconductor.sty', 'GSAR-KCMLplot.pdf', 'GSAR-mst.pdf', 'GSAR-mst2plot.pdf',
>  'GSAR.Rnw', 'GSAR.bib', 'GSAR.tex', 'unsrturl.bst'
> Calls:  -> find_vignette_product
> Execution halted
> 
> It seems that the PDF file of the vignette cannot be found. Since the package
> passes on Linux and Mac platforms, I assume the source of error is not in the
> vignette's .tex file itself. There is no line in the vignette's code that
> changes the working directory and all other files in the directory are being
> listed in the error message. Any idea what caused this error and how to fix 
> it?
> 
> Regards,
> Yasir
> 
> --
> Confidentiality Notice: This e-mail message, including a...{{dropped:10}}
> 
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[Bioc-devel] Bioconductor 3.3 is released

[Dan Tenenbaum]

April 4, 2016

Bioconductors:

We are pleased to announce Bioconductor 3.3, consisting of 1211
software packages, 293 experiment data packages, and 916
up-to-date annotation packages.

There are 107 new software packages, and many updates and improvements
to existing packages; Bioconductor 3.3 is compatible with R 3.3,
and is supported on Linux, 32- and 64-bit Windows, and Mac OS X.  This
release includes an updated Bioconductor [Amazon Machine Image][1]
and [Docker containers][2].

Visit [http://bioconductor.org][3]
for details and downloads.

[1]: http://bioconductor.org/help/bioconductor-cloud-ami/
[2]: http://bioconductor.org/help/docker/
[3]: http://bioconductor.org

Contents


* Getting Started with Bioconductor 3.3
* New Software Packages
* NEWS from new and existing packages
* Packages removed from Bioconductor since the last release

Getting Started with Bioconductor 3.3
==

To update to or install Bioconductor 3.3:

1. Install R 3.3.  Bioconductor 3.3 has been designed expressly
for this version of R.

2. Follow the instructions at
[http://bioconductor.org/install/](http://bioconductor.org/install/) .

New Software Packages
=

There are 107 new packages in this release of Bioconductor.

AneuFinder - This package implements functions for CNV calling, plotting, 
export and analysis from whole-genome single cell sequencing data.

bacon - Bacon can be used to remove inflation and bias often observed in 
epigenome- and transcriptome-wide association studies. To this end bacon 
constructs an empirical null distribution using a Gibbs Sampling algorithm by 
fitting a three-component normal mixture on z-scores.

BadRegionFinder - BadRegionFinder is a package for identifying regions with a 
bad, acceptable and good coverage in sequence alignment data available as bam 
files. The whole genome may be considered as well as a set of target regions. 
Various visual and textual types of output are available.

BasicSTARRseq - Basic peak calling on STARR-seq data based on a method 
introduced in "Genome-Wide Quantitative Enhancer Activity Maps Identified by 
STARR-seq" Arnold et al. Science. 2013 Mar 1;339(6123):1074-7. doi: 
10.1126/science. 1232542. Epub 2013 Jan 17.

BatchQC - Sequencing and microarray samples often are collected or processed in 
multiple batches or at different times. This often produces technical biases 
that can lead to incorrect results in the downstream analysis. BatchQC is a 
software tool that streamlines batch preprocessing and evaluation by providing 
interactive diagnostics, visualizations, and statistical analyses to explore 
the extent to which batch variation impacts the data. BatchQC diagnostics help 
determine whether batch adjustment needs to be done, and how correction should 
be applied before proceeding with a downstream analysis. Moreover, BatchQC 
interactively applies multiple common batch effect approaches to the data, and 
the user can quickly see the benefits of each method. BatchQC is developed as a 
Shiny App. The output is organized into multiple tabs, and each tab features an 
important part of the batch effect analysis and visualization of the data. The 
BatchQC interface has the following analysis groups: Summary, Differential 
Expression, Median Correlations, Heatmaps, Circular Dendrogram, PCA Analysis, 
Shape, ComBat and SVA.

BgeeDB - A package for the annotation and gene expression data download from 
Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, 
mapped to genes by expression patterns.

biomformat - This is an R package for interfacing with the BIOM format. This 
package includes basic tools for reading biom-format files, accessing and 
subsetting data tables from a biom object (which is more complex than a single 
table), as well as limited support for writing a biom-object back to a 
biom-format file. The design of this API is intended to match the python API 
and other tools included with the biom-format project, but with a decidedly "R 
flavor" that should be familiar to R users. This includes S4 classes and 
methods, as well as extensions of common core functions/methods.

BioQC - BioQC performs quality control of high-throughput expression data based 
on tissue gene signatures

biosigner - Feature selection is critical in omics data analysis to extract 
restricted and meaningful molecular signatures from complex and high-dimension 
data, and to build robust classifiers. This package implements a new method to 
assess the relevance of the variables for the prediction performances of the 
classifier. The approach can be run in parallel with the PLS-DA, Random Forest, 
and SVM binary classifiers. The signatures and the corresponding 'restricted' 
models are returned, enabling future predictions on new datasets. A Galaxy 
implementation of the package is available within the Workflow4metabolomics.org 
online infrastructure for computational metabolomics.

cellity 

Re: [Bioc-devel] svn co with username and password

[Dan Tenenbaum]

Never mind, I found it. Please try the checkout again now.
Dan


- Original Message -
> From: "Dan Tenenbaum" <dtene...@fredhutch.org>
> To: "Billy Chang" <billyheungw...@gmail.com>
> Cc: "bioc-devel" <bioc-devel@r-project.org>
> Sent: Wednesday, May 4, 2016 11:59:32 AM
> Subject: Re: [Bioc-devel] svn co with username and password

> Whst is your svn username?
> Dan
> 
> 
> - Original Message -
>> From: "Billy Chang" <billyheungw...@gmail.com>
>> To: "bioc-devel" <bioc-devel@r-project.org>
>> Sent: Wednesday, May 4, 2016 11:58:23 AM
>> Subject: [Bioc-devel] svn co with username and password
> 
>> Dear All,
>> 
>> I recently submitted a package called “GSALightning”. The package has been
>> accepted and I have received the svn credentials. However I am unable to
>> checkout the GSALightning package using my username and password.
>> 
>> If I use the username readonly and password readonly it works:
>> 
>> 
>> $ svn co --username readonly --password readonly
>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSALightning
>> AGSALightning/vignettes
>> AGSALightning/vignettes/vignette.Rmd
>> AGSALightning/data
>> ...
>> Checked out revision 112386.
>> 
>> 
>> But I could not checkout using my given username and password:
>> 
>> 
>> $ svn co --username xxx --password x
>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSALightning
>> svn: E175013: Unable to connect to a repository at URL
>> 'https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSALightning'
>> svn: E175013: Access to
>> 'https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSALightning'
>> forbidden
>> 
>> 
>> The bioconductor help page suggested putting single or double quotes around 
>> the
>> username. This could not resolve the issue neither. All of the following:
>> 
>> 
>> $ svn co --username "xxx" --password x
>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSALightning
>> $ svn co --username 'xxx' --password x
>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSALightning
>> $ svn co --username="xxx" --password x
>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSALightning
>> $ svn co --username='xxx' --password x
>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSALightning
>> 
>> 
>> gives:
>> 
>> 
>> svn: E175013: Unable to connect to a repository at URL
>> 'https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSALightning'
>> svn: E175013: Access to
>> 'https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSALightning'
>> forbidden
>> 
>> 
>> My svn version appears capable of accessing https:
>> 
>> 
>> $ svn --version
>> svn, version 1.7.19 (r1643991)
>>  compiled Feb 24 2015, 19:10:03
>> 
>> Copyright (C) 2014 The Apache Software Foundation.
>> This software consists of contributions made by many people; see the NOTICE
>> file for more information.
>> Subversion is open source software, see http://subversion.apache.org/
>> 
>> The following repository access (RA) modules are available:
>> 
>> * ra_neon : Module for accessing a repository via WebDAV protocol using Neon.
>> - handles 'http' scheme
>> - handles 'https' scheme
>> * ra_svn : Module for accessing a repository using the svn network protocol.
>> - handles 'svn' scheme
>> * ra_local : Module for accessing a repository on local disk.
>> - handles 'file' scheme
>> * ra_serf : Module for accessing a repository via WebDAV protocol using serf.
>> - handles 'http' scheme
>> - handles 'https' scheme
>> 
>> 
>> Please kindly help. Thanks in advance!
>> 
>> Billy Heung Wing Chang
>> Division of Biostatistics
>> Jockey Club School of Public Health and Primary Care
>> The Chinese University of Hong Kong
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

___
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Re: [Bioc-devel] svn co with username and password

[Dan Tenenbaum]

Whst is your svn username?
Dan


- Original Message -
> From: "Billy Chang" 
> To: "bioc-devel" 
> Sent: Wednesday, May 4, 2016 11:58:23 AM
> Subject: [Bioc-devel] svn co with username and password

> Dear All,
> 
> I recently submitted a package called “GSALightning”. The package has been
> accepted and I have received the svn credentials. However I am unable to
> checkout the GSALightning package using my username and password.
> 
> If I use the username readonly and password readonly it works:
> 
> 
> $ svn co --username readonly --password readonly
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSALightning
> AGSALightning/vignettes
> AGSALightning/vignettes/vignette.Rmd
> AGSALightning/data
> ...
> Checked out revision 112386.
> 
> 
> But I could not checkout using my given username and password:
> 
> 
> $ svn co --username xxx --password x
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSALightning
> svn: E175013: Unable to connect to a repository at URL
> 'https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSALightning'
> svn: E175013: Access to
> 'https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSALightning'
> forbidden
> 
> 
> The bioconductor help page suggested putting single or double quotes around 
> the
> username. This could not resolve the issue neither. All of the following:
> 
> 
> $ svn co --username "xxx" --password x
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSALightning
> $ svn co --username 'xxx' --password x
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSALightning
> $ svn co --username="xxx" --password x
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSALightning
> $ svn co --username='xxx' --password x
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSALightning
> 
> 
> gives:
> 
> 
> svn: E175013: Unable to connect to a repository at URL
> 'https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSALightning'
> svn: E175013: Access to
> 'https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSALightning'
> forbidden
> 
> 
> My svn version appears capable of accessing https:
> 
> 
> $ svn --version
> svn, version 1.7.19 (r1643991)
>  compiled Feb 24 2015, 19:10:03
> 
> Copyright (C) 2014 The Apache Software Foundation.
> This software consists of contributions made by many people; see the NOTICE
> file for more information.
> Subversion is open source software, see http://subversion.apache.org/
> 
> The following repository access (RA) modules are available:
> 
> * ra_neon : Module for accessing a repository via WebDAV protocol using Neon.
> - handles 'http' scheme
> - handles 'https' scheme
> * ra_svn : Module for accessing a repository using the svn network protocol.
> - handles 'svn' scheme
> * ra_local : Module for accessing a repository on local disk.
> - handles 'file' scheme
> * ra_serf : Module for accessing a repository via WebDAV protocol using serf.
> - handles 'http' scheme
> - handles 'https' scheme
> 
> 
> Please kindly help. Thanks in advance!
> 
> Billy Heung Wing Chang
> Division of Biostatistics
> Jockey Club School of Public Health and Primary Care
> The Chinese University of Hong Kong
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

___
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Re: [Bioc-devel] 3.3 branch created

[Dan Tenenbaum]

- Original Message -
> From: "lcollado" <lcoll...@jhu.edu>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
> Cc: "bioc-devel" <bioc-devel@r-project.org>
> Sent: Tuesday, May 3, 2016 7:52:50 PM
> Subject: Re: [Bioc-devel] 3.3 branch created

> Hi Dan,
> 
> Everything looks great! Thanks for all the hard work!!
> 
> My one question is regarding when we can resume using
> https://github.com/Bioconductor-mirror/. Right now
> https://github.com/Bioconductor-mirror/derfinder and
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/derfinder/DESCRIPTION
> are off by the version bump commit (to release version numbers).
> 

derfinder (the devel branch) should be ok in git now. Other packages should 
catch up soon.
As for the release branch, I ran into a snag trying to create the new branch in 
git. Will email the list when this is resolved.

Dan


> Thanks,
> Leo
> 
> On Tue, May 3, 2016 at 5:49 PM, Dan Tenenbaum <dtene...@fredhutch.org> wrote:
>> The BioC 3.3 branch is now ready.
>>
>> Remember, you always have access to 2 versions of your package:
>> the "release" and the "devel" versions.
>>
>> Right now the "release" version of your package (which is not
>> officially released yet but will be tomorrow if
>> everything goes well) is in the 3.3 branch and accessible at:
>>
>> https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/
>>
>> Only bug fixes and documentation improvements should go here.
>>
>> As always the "devel" version of your package is at:
>>
>>  https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/
>>
>> Similarly for experiment packages, where your package is available in devel 
>> at
>>
>> https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/
>>
>> The release branch of it is in:
>>
>> https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_3/experiment/pkgs/
>>
>>
>> Normal development of your package can now resume here.
>>
>> Please let us know if you have any questions.
>>
>>
>> Thanks!
>>
>> Dan
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

___
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[Bioc-devel] 3.3 branch created

[Dan Tenenbaum]

The BioC 3.3 branch is now ready.

Remember, you always have access to 2 versions of your package:
the "release" and the "devel" versions.

Right now the "release" version of your package (which is not
officially released yet but will be tomorrow if
everything goes well) is in the 3.3 branch and accessible at:

https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/

Only bug fixes and documentation improvements should go here.

As always the "devel" version of your package is at:

 https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/

Similarly for experiment packages, where your package is available in devel at

https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/

The release branch of it is in:

https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_3/experiment/pkgs/


Normal development of your package can now resume here.

Please let us know if you have any questions.


Thanks!

Dan

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[Bioc-devel] Bioconductor 3.3 branch to be created today - do not commit during this time

[Dan Tenenbaum]

Hello BioC developers,

We will be creating the Bioconductor 3.3 branch today at 2:15 PM
Seattle time. (21:15 UTC). This is about an hour from now.

Please stop all commits to trunk before 2:15PM and do not resume until
further notice.

We will send another email when it is OK to resume commits. The
process (once it starts) should not take more than an hour.

Thanks!

___
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Re: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

[Dan Tenenbaum]

Well, you can tell your helpdesk that this is going to impact people's work as 
the OS you are using will no longer be supported by R/Bioconductor starting 
with the release this week.

Mavericks was released 3 years ago. It seems reasonable to support it now.

Dan


- Original Message -
> From: "Jianhong Ou" <jianhong...@umassmed.edu>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
> Cc: "bioc-devel" <bioc-devel@r-project.org>
> Sent: Monday, May 2, 2016 12:34:47 PM
> Subject: Re: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

> Hi Dan,
> 
> Thank you for your answer. I hope I can update to Mavericks but our help
> desk just ask me to hold on current OS.
> 
> Yours Sincerely,
> 
> Jianhong Ou
> 
> TEL: 508-856-5379
> LRB 608
> Bioinformatician of Bioinformatics core at
> Department of Molecular, Cell and Cancer Biology
> 364 Plantation Street Worcester,
> MA 01605
> 
> 
> 
> 
> On 5/2/16 3:04 PM, "Dan Tenenbaum" <dtene...@fredhutch.org> wrote:
> 
>>This question should probably go on the support site as it is not about
>>package development.
>>
>>You should update to Mavericks or higher. Earlier versions of Mac OS X
>>are no longer officially supported by R or Bioconductor (that's why a
>>binary is not available).
>>
>>
>>Dan
>>
>>
>>- Original Message -
>>> From: "Jianhong Ou" <jianhong...@umassmed.edu>
>>> To: "bioc-devel" <bioc-devel@r-project.org>
>>> Sent: Monday, May 2, 2016 12:00:09 PM
>>> Subject: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5
>>
>>> Hi,
>>> 
>>> I got error when I update S4Vectors in R 3.3 RC r70564 today. I also
>>>tried
>>> r70549, same error like this
>>> 
>>>> biocLite()
>>> BioC_mirror: https://bioconductor.org
>>> Using Bioconductor 3.3 (BiocInstaller 1.21.6), R 3.3.0 RC (2016-04-28
>>>r70564).
>>> Old packages: 'S4Vectors'
>>> Update all/some/none? [a/s/n]:
>>> a
>>> trying URL
>>> 
>>>'https://bioconductor.org/packages/3.3/bioc/src/contrib/S4Vectors_0.9.52.
>>>tar.gz'
>>> Content type 'application/x-gzip' length 225431 bytes (220 KB)
>>> ==
>>> downloaded 220 KB
>>> 
>>> * installing *source* package �S4Vectors� ...
>>> ** libs
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c AEbufs.c -o AEbufs.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c DataFrame_class.c -o
>>> DataFrame_class.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c Hits_class.c -o Hits_class.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c List_class.c -o List_class.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c R_init_S4Vectors.c -o
>>> R_init_S4Vectors.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c Rle_class.c -o Rle_class.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c Rle_utils.c -o Rle_utils.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c SEXP_utils.c -o SEXP_utils.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c SimpleList_class.c -o
>>> SimpleList_class.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c anyMissing.c -o anyMissing.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c eval_utils.c -o eval_utils.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c hash_utils.c -o hash_utils.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c int_utils.c -o int_utils.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c logical_u

Re: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

[Dan Tenenbaum]

This question should probably go on the support site as it is not about package 
development.

You should update to Mavericks or higher. Earlier versions of Mac OS X are no 
longer officially supported by R or Bioconductor (that's why a binary is not 
available).


Dan


- Original Message -
> From: "Jianhong Ou" 
> To: "bioc-devel" 
> Sent: Monday, May 2, 2016 12:00:09 PM
> Subject: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

> Hi,
> 
> I got error when I update S4Vectors in R 3.3 RC r70564 today. I also tried
> r70549, same error like this
> 
>> biocLite()
> BioC_mirror: https://bioconductor.org
> Using Bioconductor 3.3 (BiocInstaller 1.21.6), R 3.3.0 RC (2016-04-28 r70564).
> Old packages: 'S4Vectors'
> Update all/some/none? [a/s/n]:
> a
> trying URL
> 'https://bioconductor.org/packages/3.3/bioc/src/contrib/S4Vectors_0.9.52.tar.gz'
> Content type 'application/x-gzip' length 225431 bytes (220 KB)
> ==
> downloaded 220 KB
> 
> * installing *source* package �S4Vectors� ...
> ** libs
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c AEbufs.c -o AEbufs.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c DataFrame_class.c -o
> DataFrame_class.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c Hits_class.c -o Hits_class.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c List_class.c -o List_class.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c R_init_S4Vectors.c -o
> R_init_S4Vectors.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c Rle_class.c -o Rle_class.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c Rle_utils.c -o Rle_utils.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c SEXP_utils.c -o SEXP_utils.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c SimpleList_class.c -o
> SimpleList_class.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c anyMissing.c -o anyMissing.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c eval_utils.c -o eval_utils.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c hash_utils.c -o hash_utils.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c int_utils.c -o int_utils.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c logical_utils.c -o logical_utils.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c safe_arithm.c -o safe_arithm.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c sort_utils.c -o sort_utils.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c str_utils.c -o str_utils.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c vector_utils.c -o vector_utils.o
> gcc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup
> -single_module -multiply_defined suppress
> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
> S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o List_class.o
> R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o
> anyMissing.o eval_utils.o hash_utils.o int_utils.o logical_utils.o
> safe_arithm.o sort_utils.o str_utils.o vector_utils.o
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
> -Wl,CoreFoundation
> installing to
> /Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/libs
> ** R
> ** inst
> ** preparing package for lazy loading
> Creating a generic function for �head� from package �utils� in package
> �S4Vectors�
> Creating a generic function for �tail� from package �utils� in package
> �S4Vectors�
> Creating a generic function for �na.omit� from package �stats� in package
> �S4Vectors�
> Creating a generic function for �na.exclude� from package �stats� in package
> �S4Vectors�
> Creating a generic function for �complete.cases� from package �stats� in 
> package
> �S4Vectors�
> Creating a generic function for �transform� from package �base� in package
> �S4Vectors�
> Creating a generic function for �merge� from package �base� in 

Re: [Bioc-devel] can't find an annotation package

[Dan Tenenbaum]

Annotation packages are not in a public repository.

You can get the tarball from the package landing page. Here's the devel (soon 
to be release) version:

https://www.bioconductor.org/packages/devel/data/annotation/html/LowMACAAnnotation.html

Dan


- Original Message -
> From: "Giorgio Melloni" 
> To: "bioc-devel" 
> Sent: Thursday, April 28, 2016 6:11:58 AM
> Subject: [Bioc-devel] can't find an annotation package

> Dear all,
> 
> I was doing some debugging on a package submitted a year ago (LowMACA) that is
> accompanied by an annotation package (LowMACAAnnotation). I am able to svn
> checkout LowMACA here:
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LowMACA , but I
> cannot find a way to checkout the annotation package
> (https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LowMACAAnnotation
> doesn't exist). Are the data packages on a different folder or repository?
> 
> thanks in advance,
> 
> Giorgio
>   [[alternative HTML version deleted]]
> 
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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[Bioc-devel] Updating package NEWS files for Bioconductor 3.3 release announcement (and biocViews)

[Dan Tenenbaum]

Package developers --

Each Bioconductor release is accompanied by release notes that mention
new packages and other significant project developments. For the
forthcoming release we will include release notes for
individual packages, so that users have an easy way to survey changes
in their favorite packages.

To have your package release notes made available in the Bioconductor
release notes, please arrange for your package to include a NEWS.Rd or
NEWS file that can be parsed by the utils::news function (please make sure
this function runs without error on your package, or your package NEWS will
not be included in the release announcement). We'll run
this command over all packages, using a 'query' argument that captures
all updates more recent than the start of the current release cycle.
For instance, Rsamtools in the devel branch is at version "1.23.9", so
we'll get news with

> utils::news(Version >= "1.23.0", "Rsamtools")

Note that both NEWS and NEWS.Rd files are NOT free-form text files, they each 
have 
specific formats they must adhere to. See the Rsamtools NEWS file 
(http://www.bioconductor.org/packages/devel/bioc/news/Rsamtools/NEWS) for an 
example
of the correct format for NEWS.

See ?news for more detail. We will collate these files no later than Friday,
April 29 at 5PM Seattle time.

Also, please make sure your biocViews are up-to-date/valid/relevant. This is 
important 
because this is one of the main ways people will find your package. Refer to:

http://bioconductor.org/developers/how-to/biocViews/


Thanks,
Dan

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Re: [Bioc-devel] prebs failing in devel

[Dan Tenenbaum]

For some reason zlibbioc was unavailable on windows yesterday, but 
GenomicRanges is ok in the build report that will come out later today.

Dan


- Original Message -
> From: "Karolis Uziela" <karolis.uzi...@scilifelab.se>
> To: "Valerie Obenchain" <valerie.obench...@roswellpark.org>, "bioc-devel" 
> <bioc-devel@r-project.org>
> Cc: "Dan Tenenbaum" <dtene...@fredhutch.org>
> Sent: Monday, April 25, 2016 1:02:02 AM
> Subject: Re: prebs failing in devel

> Hi,
> 
> Now the problem with RPA package is fixed. However, PREBS fails to build on
> Windows server because of a problem with GenomicRanges. GenomicRanges fails
> to build on WindowsServer itself. Here is the error:
> 
> ##
> ##
> ###
> ### Running command:
> ###
> ###   rm -rf GenomicRanges.buildbin-libdir && mkdir
> GenomicRanges.buildbin-libdir  && C:\cygwin\bin\curl.exe -O
> http://zin2/BBS/3.3/bioc/src/contrib/GenomicRanges_1.23.27.tar.gz &&
> E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build
> --library=GenomicRanges.buildbin-libdir --merge-multiarch
> GenomicRanges_1.23.27.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe
> CMD INSTALL GenomicRanges_1.23.27.zip  && rm
> GenomicRanges_1.23.27.tar.gz GenomicRanges_1.23.27.zip
> ###
> ##
> ##
> 
> 
> 
> 
> install for i386
> 
> * installing *source* package 'GenomicRanges' ...
> ** libs
> C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include"
> -DNDEBUG-I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include"
> -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include"
> -I"c:/local323/include" -O3 -Wall  -std=gnu99 -mtune=core2 -c
> IRanges_stubs.c -o IRanges_stubs.o
> C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include"
> -DNDEBUG-I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include"
> -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include"
> -I"c:/local323/include" -O3 -Wall  -std=gnu99 -mtune=core2 -c
> R_init_GenomicRanges.c -o R_init_GenomicRanges.o
> C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include"
> -DNDEBUG-I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include"
> -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include"
> -I"c:/local323/include" -O3 -Wall  -std=gnu99 -mtune=core2 -c
> S4Vectors_stubs.c -o S4Vectors_stubs.o
> C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include"
> -DNDEBUG-I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include"
> -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include"
> -I"c:/local323/include" -O3 -Wall  -std=gnu99 -mtune=core2 -c
> transcript_utils.c -o transcript_utils.o
> transcript_utils.c: In function 'tlocs2rlocs':
> transcript_utils.c:143:38: warning: 'end' may be used uninitialized in
> this function [-Wmaybe-uninitialized]
>  return on_minus_strand ? end - tloc : start + tloc;
>  ^
> transcript_utils.c:120:24: note: 'end' was declared here
>  int nexons, j, start, end, width;
>^
> transcript_utils.c:143:38: warning: 'start' may be used uninitialized
> in this function [-Wmaybe-uninitialized]
>  return on_minus_strand ? end - tloc : start + tloc;
>  ^
> transcript_utils.c:120:17: note: 'start' was declared here
>  int nexons, j, start, end, width;
> ^
> C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o
> GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o
> S4Vectors_stubs.o transcript_utils.o -Lc:/local323/lib/i386
> -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
> installing to
> E:/biocbld/bbs-3.3-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/i386
> ** R
> ** inst
> ** preparing package for lazy loading
> Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
>  there is no package called 'zlibbioc'
> ERROR: lazy loading failed for package 'GenomicRanges'
> * removing
> 'E:/biocbld/bbs-3.3-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges'
> Warning: running command 'E:/biocbld/bbs-3.3-bioc/R/bin/i386/Rcmd.exe
> INSTALL --library=GenomicRanges.buildbin-libdir
> GenomicRanges_1.23.27.tar.gz --no-multiarch' had status 1
> 
> 
> On Thu, Apr 21, 2016 at 5:40 PM, Karol

Re: [Bioc-devel] gage fails to build on Windows in devel

[Dan Tenenbaum]

Seems like a hiccup in the build system. In the report that will come out 
today, gage installs OK.
Dan

- Original Message -
> From: "Monther Alhamdoosh" 
> To: "bioc-devel" 
> Sent: Monday, April 25, 2016 2:08:54 AM
> Subject: [Bioc-devel] gage fails to build on Windows in devel

> Hi developers,
> 
> It seems the  gage package  failed to build on Windows with this error
> 
> inst
> ** preparing package for lazy loading
> Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
> :
> there is no package called 'zlibbioc'
> 
> Any clue?
> 
> I recently submitted a package, named EGSEA,  which depends on gage.
> 
> Cheers,
> Monther
> --
> 
> Dr Monther Alhamdoosh, PhD
> Research Scientist
> 
> -sent from phone
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] linking stage excessive runtime issue on windows (was: New package submission)

[Dan Tenenbaum]

- Original Message -
> From: "Thomas Lawson" <thomas.nigel.law...@gmail.com>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
> Cc: "Steffen Neumann" <sneum...@ipb-halle.de>, "bioc-devel" 
> <Bioc-devel@r-project.org>
> Sent: Thursday, April 21, 2016 1:37:15 PM
> Subject: Re: [Bioc-devel] linking stage excessive runtime issue on windows 
> (was: New package submission)

> Hi Steffen/Dan
> 
> Thank you both for your quick responses and help.
> 
> I have just submitted another job and it looks like moscato2 is passing
> now. Which is great! However, I am now missing the mac morelia build
> completely, which is a bit strange
> 
> 
>   - http://staging.bioconductor.org:8000/job/510/
> 
> 
> There also seems to be a submission sent at  April 21 2016, 11:15 am
> (server time) that passed all checks on all systems. I don't think I
> submitted this, I am guessing that this was from Dan testing something out?
> 

Yes.

> 
>   - http://staging.bioconductor.org:8000/job/507/
> 

You should not be looking at reports on staging.bioconductor.org, just the ones 
that are provided to you in the tracker.
According to that 
(https://bioconductor.org/spb_reports/msPurity_0.99.0_buildreport_20160421114005.html),
 the last build was totally clean.

Dan


> 
> Thanks again for your help.
> 
> Kind regards,
> Tom
> 
> 
> 
> On Thu, Apr 21, 2016 at 4:22 PM, Dan Tenenbaum <dtene...@fredhutch.org>
> wrote:
> 
>>
>>
>> - Original Message -
>> > From: "Steffen Neumann" <sneum...@ipb-halle.de>
>> > To: "Thomas Lawson" <thomas.nigel.law...@gmail.com>, "bioc-devel" <
>> Bioc-devel@r-project.org>
>> > Sent: Thursday, April 21, 2016 7:29:50 AM
>> > Subject: Re: [Bioc-devel] linking stage excessive runtime issue on
>> windows (was: New package submission)
>>
>> > Hi Thomas,
>> >
>> > mzR has been in stormy waters since the new Windows toolchain
>> > was used. While now all compile errors are gone:
>> > http://bioconductor.org/checkResults/devel/bioc-LATEST/mzR/
>> >
>> > The build still timeouts on windows, because for reasons completely
>> > unknown to me the linking step into mzR.dll takes a whopping 20 minutes
>> > on windows, and that twice to create the mzR.dll for both i386 and x64.
>> >
>>
>> The package actually INSTALLs in less than 40 minutes (35m23s). And if you
>> look at where it's trying to build, it seems like it's done, and yet still
>> times out. I've seen this before. But also sometimes there are 'real'
>> timeouts in the build phase, where the build is not complete after 40
>> minutes.
>>
>> I don't think this has anything to do with Thomas's issue. I think the
>> single package builder was installing dependencies without
>> INSTALL_opts="--merge-multiarch" which I have added and am trying now.
>>
>> Dan
>>
>>
>> > It is somehow an issue in the mingw compiler. We even tried
>> > an alternative linker (see issue threads linked below).
>> > I don't know if this could be helped with CFLAGS/LDFLAGS.
>> >
>> > => If there is anyone who knows why and if there is any way
>> >   to speed this up, any suggestions would be greatly appreciated.
>> >   This has been a pain for a long time, and I am sorry
>> >   for the turbulences caused.
>> >
>> > Yours,
>> > Steffen
>> >
>> > We track this issue here:
>> > https://github.com/sneumann/mzR/issues/21#issuecomment-87801932
>> >
>> >
>> >
>> >
>> > On Do, 2016-04-21 at 14:37 +0100, Thomas Lawson wrote:
>> >> Hi BioConductor community,
>> >>
>> >> I have recently submitted my new R package into BioConductor tracker
>> >> (issue
>> >> 1455) that carries out some data pre-processing for MS/MS spectra.
>> >>
>> >> I seem to be having trouble with the moscato2 Windows build though.
>> >> The
>> >> package is fine on Linux and Mac but I get an error message (see
>> >> below) for
>> >> windows. Also, I was not receiving the error last night.
>> >>
>> >> It looks like it has something to do with the BioConductor package
>> >> that I
>> >> import called "mzR" and an associated DLL it uses.
>> >>
>> >> The error message:
>> >>
>> >> ---
>> >>

Re: [Bioc-devel] linking stage excessive runtime issue on windows (was: New package submission)

[Dan Tenenbaum]

- Original Message -
> From: "Steffen Neumann" 
> To: "Thomas Lawson" , "bioc-devel" 
> 
> Sent: Thursday, April 21, 2016 7:29:50 AM
> Subject: Re: [Bioc-devel] linking stage excessive runtime issue on windows 
> (was: New package submission)

> Hi Thomas,
> 
> mzR has been in stormy waters since the new Windows toolchain
> was used. While now all compile errors are gone:
> http://bioconductor.org/checkResults/devel/bioc-LATEST/mzR/
> 
> The build still timeouts on windows, because for reasons completely
> unknown to me the linking step into mzR.dll takes a whopping 20 minutes
> on windows, and that twice to create the mzR.dll for both i386 and x64.
> 

The package actually INSTALLs in less than 40 minutes (35m23s). And if you look 
at where it's trying to build, it seems like it's done, and yet still times 
out. I've seen this before. But also sometimes there are 'real' timeouts in the 
build phase, where the build is not complete after 40 minutes.

I don't think this has anything to do with Thomas's issue. I think the single 
package builder was installing dependencies without 
INSTALL_opts="--merge-multiarch" which I have added and am trying now.

Dan


> It is somehow an issue in the mingw compiler. We even tried
> an alternative linker (see issue threads linked below).
> I don't know if this could be helped with CFLAGS/LDFLAGS.
> 
> => If there is anyone who knows why and if there is any way
>   to speed this up, any suggestions would be greatly appreciated.
>   This has been a pain for a long time, and I am sorry
>   for the turbulences caused.
> 
> Yours,
> Steffen
> 
> We track this issue here:
> https://github.com/sneumann/mzR/issues/21#issuecomment-87801932
> 
> 
> 
> 
> On Do, 2016-04-21 at 14:37 +0100, Thomas Lawson wrote:
>> Hi BioConductor community,
>> 
>> I have recently submitted my new R package into BioConductor tracker
>> (issue
>> 1455) that carries out some data pre-processing for MS/MS spectra.
>> 
>> I seem to be having trouble with the moscato2 Windows build though.
>> The
>> package is fine on Linux and Mac but I get an error message (see
>> below) for
>> windows. Also, I was not receiving the error last night.
>> 
>> It looks like it has something to do with the BioConductor package
>> that I
>> import called "mzR" and an associated DLL it uses.
>> 
>> The error message:
>> 
>> ---
>> 
>> Installing package prior to check...
>> 
>> install for i386
>> 
>> * installing *source* package 'msPurity' ...
>> ** R
>> ** inst
>> ** preparing package for lazy loading
>> Error in library.dynam(lib, package, package.lib) :
>>   DLL 'mzR' not found: maybe not installed for this architecture?
>> ERROR: lazy loading failed for package 'msPurity'
>> * removing
>> 'E:/packagebuilder/workers/jobs/msPurity_20160421061423/msPurity.
>> buildbin-libdir/msPurity'
>> Warning: running command 'E:/packagebuilder/R/bin/i386/Rcmd.exe
>> INSTALL
>> --library=msPurity.buildbin-libdir msPurity_0.99.0.tar.gz --no-
>> multiarch'
>> had status 1
>> 
>> ---
>> 
>> For more information see: http://staging.bioconductor.org:8000/job/50
>> 6/
>> 
>> Any help would be really appreciated.
>> 
>> Kind regards,
>> Tom
>> 
>>  [[alternative HTML version deleted]]
>> 
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> --
> IPB HalleAG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann  http://www.IPB-Halle.DE
> Weinberg 3   http://msbi.bic-gh.de
> 06120 Halle  Tel. +49 (0) 345 5582 - 1470
>  +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
> 
> ___
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Re: [Bioc-devel] git-svn-mirror problem committing

[Dan Tenenbaum]

- Original Message -
> From: "Hector Corrada Bravo" 
> To: "bioc-devel" 
> Sent: Monday, April 18, 2016 7:56:06 AM
> Subject: [Bioc-devel] git-svn-mirror problem committing

> I am having issues committing to new package 'epivizrServer'. The error
> reported by 'git svn dcommit' is printed below. Links to github repos below
> as well. Help appreciated!
> 
> Cheers,
> Hector
> 
> Github repos:
> https://github.com/epiviz/epivizrServer
> https://github.com/Bioconductor-mirror/epivizrServer
> 
> git-svn error:
> 
> MacBook-Pro:epivizrServer hcorrada$ git svn dcommit --add-author-from
> Committing to
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/epivizrServer
> ...
> A .Rbuildignore
> 
> ERROR from SVN:
> URL access forbidden for unknown reason: Access to
> '/bioconductor/!svn/txr/116455-1/trunk/madman/Rpacks/epivizrServer/.Rbuildignore'
> forbidden


Looks like an authentication problem. Have you tried it with the --username 
option?

Sometimes it helps to 'seed' the svn authentication first, so do something like:


svn log --limit 1 --username XXX 
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/epivizrServer

Where XXX is your username, then enter the password when prompted. Then try git 
svn dcommit again.

Dan


> W: 938ecad892524e86792329e8d8766686bb1a087f and refs/remotes/git-svn-devel
> differ, using rebase:
> :100644 00 6148565133db357a9890af714348d2e4794c3621
>  D .Rbuildignore
> :100644 00 47a9b8e270f369afab79beeebe32d21901d0ef72
>  D .gitignore
> :100644 100644 2853b00474deb4958f4fbabc63497fcad87fb5f9
> 47e7f18877bb374cb50a1e07ef66da5b4b55de43 M DESCRIPTION
> :04 04 ce9e12e2cac7f4afb237941b7a9a8b2d0f056e71
> 157860d339673d6bc8f68520e1910308b7287648 M R
> :100644 00 9f964990f3272399c497e7e227c082eaf58c6cb3
>  D epivizrServer.Rproj
> :04 04 ecf32c9ff0527398545309b15a04a1bcd93cb9b9
> 34b7a3e62b88729128c8c5fe855a03c8650e22e8 M man
> :04 04 3a49548f078dafd069dfc91ee044b17fcd4c0ba5
> ae055d2e89a3c01789e94cea703b9047a1343bfb M tests
> Current branch devel is up to date.
> ERROR: Not all changes have been committed into SVN, however the committed
> ones (if any) seem to be successfully integrated into the working tree.
> Please see the above messages for details.
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] SVN and GitHub mirror out-of-sync

[Dan Tenenbaum]

Should be caught up now.
Dan


- Original Message -
> From: "Peter Hickey" 
> To: "bioc-devel" 
> Sent: Monday, April 18, 2016 7:00:29 AM
> Subject: Re: [Bioc-devel] SVN and GitHub mirror out-of-sync

> Typo - github version is 1.5.23
> 
> On Mon, 18 Apr 2016 at 09:26 Peter Hickey  wrote:
> 
>> Hi,
>>
>> The current version of GenomicTuples on the official SVN is 1.5.24
>> (
>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicTuples/DESCRIPTION
>> ),
>> however, the version available via the GitHub mirror is only 1.5.21
>> (
>> https://github.com/Bioconductor-mirror/GenomicTuples/blob/master/DESCRIPTION
>> ).
>> Shouldn't the latest version be automatically propagated to the GitHub
>> mirror?
>>
>> Thanks,
>> Pete
>>
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] update versions for 3.3 with to deal with new testthat

[Dan Tenenbaum]

The build system will automatically pick up new versions from CRAN when they 
are available. So yes, packages (in both release and devel) need to be 
compatible with the changes in the new testthat.

Dan


- Original Message -
> From: "Ramon Diaz-Uriarte" 
> To: "bioc-devel" 
> Cc: "ramon diaz" 
> Sent: Thursday, April 14, 2016 6:22:06 AM
> Subject: [Bioc-devel] update versions for 3.3 with to deal with new testthat

> Dear All,
> 
> Before doing something I shouldn't I want to make sure how to proceed:
> 
> a few hours ago, a new version of testthat has been made available in CRAN
> (v. 1.0.0); this version can be more picky with statements such as
> 
> expect_output(out, "some message")
> 
> Now (depending on the details, which I skip here) some of those might fail
> unless we write:
> 
> 
> expect_output(print(out), "some message").
> 
> 
> This change could lead to failures of some tests (it will for my OncoSimulR
> package).
> 
> 
> So my question is:  will new tests of BioC 3.3 use the former testthat
> (0.11) and be frozen at that version, or should we update changes that will
> prevent failures when testthat us updated to version 1.0? I'd just go ahead
> and update, but
> 
> https://www.bioconductor.org/developers/release-schedule/
> 
> indicates that we should only change code if there are show-stopper
> bugs. But whether these are show stopper bugs depends on whether testthat
> will be upgraded to 1.0
> 
> 
> I am inclined to upgrade, but want to make sure that is the right course of
> action.
> 
> 
> Best,
> 
> 
> R.
> 
> 
> 
> 
> --
> Ramon Diaz-Uriarte
> Department of Biochemistry, Lab B-25
> Facultad de Medicina
> Universidad Autónoma de Madrid
> Arzobispo Morcillo, 4
> 28029 Madrid
> Spain
> 
> Phone: +34-91-497-2412
> 
> Email: rdia...@gmail.com
>   ramon.d...@iib.uam.es
> 
> http://ligarto.org/rdiaz
> 
> ___
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Re: [Bioc-devel] moscato2 Windows build error reading IDAT file

[Dan Tenenbaum]

I upgraded to r70462 and I cannot reproduce it now either. I guess it was an 
issue in R-alpha, since fixed.
Sorry for the trouble.

Dan


- Original Message -
> From: "Henrik Bengtsson" <henrik.bengts...@gmail.com>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
> Cc: "Maarten van Iterson" <mviter...@gmail.com>, "bioc-devel" 
> <bioc-devel@r-project.org>
> Sent: Monday, April 11, 2016 4:01:05 PM
> Subject: Re: [Bioc-devel] moscato2 Windows build error reading IDAT file

> I *cannot* reproduce this:
> 
> % R --vanilla
> ## The IDAT file
>> pathname <- system.file(package="minfiData", "extdata", "5723646053",
>> "5723646053_R05C02_Grn.idat")
>> file.info(pathname)$size
> [1] 8091452
>> unname(tools::md5sum(pathname))
> [1] "dfc33fdaf3e91d872be896643a0c837f"
>> packageVersion("minfiData")
> [1] '0.13.0'
> 
> ## Parsing it
>> data <- illuminaio:::readIDAT_nonenc(pathname)
>> str(data)
> List of 12
> $ fileSize : num 8091452
> $ versionNumber: int 3
> $ nFields  : int 19
> $ fields   : num [1:19, 1:3] 1000 102 103 104 107 200 300 400 401 402 ...
>  ..- attr(*, "dimnames")=List of 2
>  .. ..$ : chr [1:19] "nSNPsRead" "IlluminaID" "SD" "Mean" ...
>  .. ..$ : chr [1:3] "fieldCode" "byteOffset" "Bytes"
> $ nSNPsRead: int 622399
> $ Quants   : int [1:622399, 1:3] 455 12883 2451 7650 4579 4955
> 1665 1953 5689 264 ...
>  ..- attr(*, "dimnames")=List of 2
>  .. ..$ : chr [1:622399] "10600313" "10600322" "10600328" "10600336" ...
>  .. ..$ : chr [1:3] "Mean" "SD" "NBeads"
> $ MidBlock : int [1:622399] 10600313 10600322 10600328 10600336
> 10600345 10600353 10600357 10600364 10600366 10600369 ...
> $ RedGreen : int 0
> $ Barcode  : chr "5723646053"
> $ ChipType : chr "BeadChip 12x8"
> $ RunInfo  : chr[0 , 1:5]
>  ..- attr(*, "dimnames")=List of 2
>  .. ..$ : NULL
>  .. ..$ : chr [1:5] "RunTime" "BlockType" "BlockPars" "BlockCode" ...
> $ Unknowns :List of 7
>  ..$ MostlyNull: chr ""
>  ..$ MostlyA   : chr "R05C02"
>  ..$ Unknown.1 : chr ""
>  ..$ Unknown.2 : chr ""
>  ..$ Unknown.3 : chr ""
>  ..$ Unknown.4 : chr ""
>  ..$ Unknown.5 : chr ""
> 
>> sessionInfo()
> R version 3.3.0 beta (2016-04-08 r70447)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 7 x64 (build 7601) Service Pack 1
> 
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
> 
> loaded via a namespace (and not attached):
> [1] base64_1.1illuminaio_0.13.1
> 
> % R CMD config COMPILED_BY
> gcc-4.9.3
> 
> /Henrik
> 
> On Mon, Apr 11, 2016 at 9:21 AM, Dan Tenenbaum <dtene...@fredhutch.org> wrote:
>> The problem seems to have to do with illuminaio and possibly minfiData; it 
>> can
>> be reduced to / reproduced by the following:
>>
>> library(illuminaio)
>> file <-
>> "e:/biocbld/bbs-3.3-bioc/R/library/minfiData/extdata/5723646053/5723646053_R05C02_Grn.idat"
>> illuminaio:::readIDAT_nonenc(file)
>>
>> Specifically the error occurs on line 59 of illuminaio/R/readIDAT_nonenc.R, 
>> in
>> the readString() function inside readIDAT_nonenc().
>>
>> I'll leave it to the maintainer(s) of those packages to trobuleshoot further
>> what the problem is.
>>
>>> traceback()
>> 5: readString(con = con)
>> 4: readField(con = con, field = xx)
>> 3: FUN(X[[i]], ...)
>> 2: lapply(res, function(xx) {
>>where <- fields[xx, "byteOffset"]
>>seek(con, where = where, origin = "start")
>>readField(con = con, field = xx)
>>})
>> 1: illuminaio:::readIDAT_nonenc(file)
>>
>>
>>> sessionInfo()
>> R version 3.3.0 alpha (2016-03-28 r70390)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>> Running under: Windows Server 2008 R2 x64 (build 7601) Service Pack 1
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252
>> [2] LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.

Re: [Bioc-devel] Using Git with Bioconductor SVN repositories

[Dan Tenenbaum]

>From your git log excerpt it looks like there has been some non-linear commit 
>history. svn does not like this.
You may need to follow the instructions here:

https://www.bioconductor.org/developers/how-to/git-mirrors/#dealing-with-prior-history--merge-conflicts

Dan


- Original Message -
> From: "Maarten van Iterson" 
> To: "bioc-devel" 
> Sent: Friday, April 8, 2016 11:26:16 PM
> Subject: [Bioc-devel] Using Git with Bioconductor SVN repositories

> Dear all,
> 
> I'm struggling with using git and the Bioconductor SVN repo of my packages.
> 
> For example, I have a package in devel (bacon) and managed to push changes
> to the svn/trunk of my package using the steps described at:
> 
> https://www.bioconductor.org/developers/how-to/git-mirrors/
> 
> following scenario 2, but after
> 
> git checkout master
> git merge devel
> 
> the decorate output of git log is:
> 
> *   e8e3752 - (HEAD, master) Merge branch 'devel' (22 seconds ago)
> 
>|\
>| * fe340af - (git-svn-devel, devel) fix bug meta-analysis and add trimming
> of test-statistics (in the future) 
> * | 73921c7 - (origin/master, origin/HEAD) fix bug meta-analysis and add
> trimming of test-statistics (15 minutes ago) 
>|/
> * 693fdba - (bioc/master) add ggplot versions of hist and qq add topTable
> function and updating vignette (2 weeks ago) 
> * fc2436f - update markdown file (2 weeks ago) 
> * 52a7818 - add ggplot versions of hist and qq add topTable function and
> updating vignette (2 weeks ago) 
> * 92ed414 - fix typo and add URL and BugReports to DESCR. (2 weeks ago)
> 
> * b45332b - Adding doppelgangR, EpiCluster, PCAN, bacon, SwathXtend (3
> weeks ago) 
> 
> whereas I expect every branch should be in sync.
> The state of my fork is: 1 commit ahead, 1 commit behind
> Bioconductor-mirror:master.  What should I do at this point?
> 
> If followed this scenario before and commit to git and push to GitHub as
> normally but ended up in a state that I only could solve by removing my
> fork from github and start all over again.
> 
> Cheers,
> Maarten
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] import except on Window Machine

[Dan Tenenbaum]

In that output you sent me, it's still using roxygen (via devtools) to create 
the namespace. Try creating it manually and see if you still get the same 
error. 

What does your NAMESPACE look like anyway?

Looking at the NAMESPACE for CRISPRseek, the instances of the 'except' syntax 
look like this:

import(S4Vectors, except=c(fold, values))
import(IRanges, except=values)

So maybe make sure the objects to be excepted are not quoted?

Dan



- Original Message -
> From: "Karim Mezhoud" <kmezh...@gmail.com>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
> Cc: "Lihua Zhu" <julie@umassmed.edu>, "Michael Lawrence" 
> <lawrence.mich...@gene.com>, "bioc-devel"
> <bioc-devel@r-project.org>
> Sent: Monday, April 11, 2016 10:21:42 AM
> Subject: Re: [Bioc-devel] import except on Window Machine

> # ##BUILT &   RELOAD
> ==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer
> 
> * installing to library
> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
> ERROR: failed to lock directory
> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’ for
> modifying
> Try removing
> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/00LOCK-bioCancer’
> 
> Exited with status 3.
> 
>  BUILT SOURCE PACKAGE
> ==> devtools::document(roclets=c('rd', 'collate', 'namespace'))
> 
> Updating bioCancer documentation
> Loading bioCancer
> Documentation completed
> 
> ==> devtools::build()
> 
> '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file
> --no-environ  \
>  --no-save --no-restore CMD build '/Volumes/DATA/radiant/bioCancer'  \
>  --no-resave-data --no-manual
> 
> * checking for file ‘/Volumes/DATA/radiant/bioCancer/DESCRIPTION’ ... OK
> * preparing ‘bioCancer’:
> * checking DESCRIPTION meta-information ... OK
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories
> * building ‘bioCancer_0.99.0.tar.gz’
> 
> [1] "/Volumes/DATA/radiant/bioCancer_0.99.0.tar.gz"
> 
> Source package written to /Volumes/DATA/radiant
> 
> On Mon, Apr 11, 2016 at 6:10 PM, Dan Tenenbaum <dtene...@fredhutch.org>
> wrote:
> 
>> roxygen2 does not support the new syntax. Do you still get the same error
>> if you write your NAMESPACE manually?
>>
>> - Original Message -
>> > From: "Karim Mezhoud" <kmezh...@gmail.com>
>> > To: "Dan Tenenbaum" <dtene...@fredhutch.org>
>> > Cc: "Lihua Zhu" <julie@umassmed.edu>, "Michael Lawrence" <
>> lawrence.mich...@gene.com>, "bioc-devel"
>> > <bioc-devel@r-project.org>
>> > Sent: Monday, April 11, 2016 10:08:15 AM
>> > Subject: Re: [Bioc-devel] import except on Window Machine
>>
>> >> sessionInfo()
>> > R version 3.3.0 beta (2016-04-06 r70435)
>> > Platform: x86_64-apple-darwin13.4.0 (64-bit)
>> > Running under: OS X 10.11.3 (El Capitan)
>> >
>> > locale:
>> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> >
>> >
>> > On Mon, Apr 11, 2016 at 6:07 PM, Dan Tenenbaum <dtene...@fredhutch.org>
>> > wrote:
>> >
>> >> Karim, What is the sessionInfo() in your R-3.3? It might be too old to
>> >> have the new feature. It needs to be at svn rev r70426 or newer.
>> >>
>> >> Dan
>> >>
>> >>
>> >> - Original Message -
>> >> > From: "Karim Mezhoud" <kmezh...@gmail.com>
>> >> > To: "Lihua Zhu" <julie@umassmed.edu>
>> >> > Cc: "Dan Tenenbaum" <dtene...@fredhutch.org>, "Michael Lawrence" <
>> >> lawrence.mich...@gene.com>, "bioc-devel"
>> >> > <bioc-devel@r-project.org>
>> >> > Sent: Monday, April 11, 2016 10:03:52 AM
>> >> > Subject: Re: [Bioc-devel] import except on Window Machine
>> >>
>> >> > Dear Julie,
>> >> > Are you using roxigen2 to edit NAMESPACE file?
>> >> > Are you using R 3.4?
>> >> > Thanks
>> >> >
>> >> > In my case, When I used R 3.3 I get this error:
>> >> >
>> >> >
>> >> > ==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer
>> >> >
>> >> > * installing to library
>> >> > ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
>>

Re: [Bioc-devel] import except on Window Machine

[Dan Tenenbaum]

roxygen2 does not support the new syntax. Do you still get the same error if 
you write your NAMESPACE manually?

- Original Message -
> From: "Karim Mezhoud" <kmezh...@gmail.com>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
> Cc: "Lihua Zhu" <julie@umassmed.edu>, "Michael Lawrence" 
> <lawrence.mich...@gene.com>, "bioc-devel"
> <bioc-devel@r-project.org>
> Sent: Monday, April 11, 2016 10:08:15 AM
> Subject: Re: [Bioc-devel] import except on Window Machine

>> sessionInfo()
> R version 3.3.0 beta (2016-04-06 r70435)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X 10.11.3 (El Capitan)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> 
> On Mon, Apr 11, 2016 at 6:07 PM, Dan Tenenbaum <dtene...@fredhutch.org>
> wrote:
> 
>> Karim, What is the sessionInfo() in your R-3.3? It might be too old to
>> have the new feature. It needs to be at svn rev r70426 or newer.
>>
>> Dan
>>
>>
>> - Original Message -
>> > From: "Karim Mezhoud" <kmezh...@gmail.com>
>> > To: "Lihua Zhu" <julie@umassmed.edu>
>> > Cc: "Dan Tenenbaum" <dtene...@fredhutch.org>, "Michael Lawrence" <
>> lawrence.mich...@gene.com>, "bioc-devel"
>> > <bioc-devel@r-project.org>
>> > Sent: Monday, April 11, 2016 10:03:52 AM
>> > Subject: Re: [Bioc-devel] import except on Window Machine
>>
>> > Dear Julie,
>> > Are you using roxigen2 to edit NAMESPACE file?
>> > Are you using R 3.4?
>> > Thanks
>> >
>> > In my case, When I used R 3.3 I get this error:
>> >
>> >
>> > ==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer
>> >
>> > * installing to library
>> > ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
>> > * installing *source* package ‘bioCancer’ ...
>> > ** R
>> > ** inst
>> > ** preparing package for lazy loading
>> > Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck =
>> vI[[i]])
>> > :
>> >  there is no package called ‘c("dataTableOutput", "renderDataTable")’
>> > ERROR: lazy loading failed for package ‘bioCancer’
>> > * removing
>> >
>> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCancer’
>> > * restoring previous
>> >
>> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCancer’
>> >
>> > Exited with status 1
>> >
>> > When I used R 3.4, I get :
>> >
>> > unfortunately,
>> >
>> > Bioconductor version 3.3 (BiocInstaller 1.21.4), ?biocLite for help
>> > Bioconductor does not yet support R version 3.4.0
>> >
>> >
>> >
>> > On Mon, Apr 11, 2016 at 5:30 PM, Zhu, Lihua (Julie) <
>> julie@umassmed.edu>
>> > wrote:
>> >
>> >> Thanks, Dan!
>> >>
>> >> Best,
>> >>
>> >> Julie
>> >>
>> >> On 4/11/16 12:22 PM, "Dan Tenenbaum" <dtene...@fredhutch.org> wrote:
>> >>
>> >> >The windows machine is still running an older version of R that does
>> not
>> >> >support this NAMESPACE syntax. I will update it this week.
>> >> >Dan
>> >> >
>> >> >
>> >> >- Original Message -
>> >> >> From: "Lihua Zhu" <julie@umassmed.edu>
>> >> >> To: "bioc-devel" <bioc-devel@r-project.org>
>> >> >> Cc: "Michael Lawrence" <lawrence.mich...@gene.com>
>> >> >> Sent: Monday, April 11, 2016 9:18:31 AM
>> >> >> Subject: [Bioc-devel] import except on Window Machine
>> >> >
>> >> >> Michael,
>> >> >>
>> >> >> For some reason,  adding except clause in import in the NAMESPACE
>> file
>> >> >>gives
>> >> >> error on window server, although it runs fine on Linux and Mac OS X.
>> >> >>
>> >> >>
>> >>
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_chec
>> >>
>> >>kResults_devel_bioc-2DLATEST_CRISPRseek_moscato2-2Dbuildsrc.html=BQICaQ
>> >>
>> >>=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ=3IbW-yoIQpGZOKgd4i2bgmPH
>> >>
>> >>hwHHF5gJMlij5cC5bLU=t9rR8WHE_O0PrI0B-0ySt37UGJMdDhnwk0JFoVzS5Cw=lEJWy
>> >> >>zN3zY_O2V1X3QmOZcPD25KidcjhIQMAky52xsA=
>> >> >>
>> >> >> Here is the line that gives error.
>> >> >> import(S4Vectors, except=c(fold, values))
>> >> >>
>> >> >> Did I miss something? Thank!
>> >> >>
>> >> >> Best regards,
>> >> >>
>> >> >> Julie
>> >> >>
>> >> >>
>> >> >>
>> >> >>  [[alternative HTML version deleted]]
>> >> >>
>> >> >> ___
>> >> >> Bioc-devel@r-project.org mailing list
>> >> >>
>> >> >>
>> >>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman
>> >>
>> >>_listinfo_bioc-2Ddevel=BQICaQ=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPl
>> >>
>> >>OmhQ=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU=t9rR8WHE_O0PrI0B-0yS
>> >>
>> >>t37UGJMdDhnwk0JFoVzS5Cw=3ZMFBJ4XMwlGXkfXcB5spcBnnzqBDeqk05sf_TSi88g=
>> >>
>> >> ___
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>> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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