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

Disabling SIP should not be done anywhere. Every page I've read on this topic strongly discourages doing this. - Original Message - > From: "Hervé Pagès" > To: "cstrato" , "Dan Tenenbaum" > Cc: "bioc-devel"

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

Also relying on [DY]LD_LIBRARY_PATH is considered bad practice and has been discouraged for years. xps is the only Bioconductor package that relies on these variables for its configure/build process. H. On 04/20/2017 03:24 PM, Dan Tenenbaum wrote: Disabling SIP should not be done anywhere.

Re: [Bioc-devel] Object not found in vignette

Oh... I think I forget to add... Thanks a lot. Ti-Tai ��: Michael Lawrence [lawrence.mich...@gene.com] 寄件日期: 2017年4月21日 上午 06:12 至: 王棣台 副本: Hervé Pagès; bioc-devel@r-project.org 主旨: Re: [Bioc-devel] Object not found in vignette Did you "svn add" the

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:

Re: [Bioc-devel] Object not found in vignette

Did you "svn add" the file? On Thu, Apr 20, 2017 at 3:10 PM, 王棣台 wrote: > I find that my data file will not change after I did any commit. > That might be the problem. > Is there anything I forget to do? > > Ti-Tai > > 從: Hervé Pagès

Re: [Bioc-devel] Object not found in vignette

I find that my data file will not change after I did any commit. That might be the problem. Is there anything I forget to do? Ti-Tai ��: Hervé Pagès [hpa...@fredhutch.org] 寄件日期: 2017年4月21日 上午 06:00 至: 王棣台; bioc-devel@r-project.org 主旨: Re: [Bioc-devel]

Re: [Bioc-devel] Object not found in vignette

Okay, I will try to commit it again. Ti-Tai ��: Hervé Pagès [hpa...@fredhutch.org] 寄件日期: 2017年4月21日 上午 06:00 至: 王棣台; bioc-devel@r-project.org 主旨: Re: [Bioc-devel] Object not found in vignette Also recently you bumped the version from 1.1.* to 1.2.* then

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

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://support.bioconductor.org/p/90056/#90247 This means, that users of xps seem to be willing to

Re: [Bioc-devel] Object not found in vignette

Also recently you bumped the version from 1.1.* to 1.2.* then went back to 1.1.* again. As a result the version that is available via biocLite() is 1.2.2, as reflected on the package landing page: https://bioconductor.org/packages/3.5/bioc/html/anamiR.html Any change you do to your package

Re: [Bioc-devel] Object not found in vignette

No, I definitely have committed it since version 1.1.8 and I can see it right now in my anamiR/data files. Ti-Tai ��: Hervé Pagès [hpa...@fredhutch.org] 寄件日期: 2017年4月21日 上午 05:53 至: 王棣台; bioc-devel@r-project.org 主旨: Re: [Bioc-devel] Object not found in

Re: [Bioc-devel] Object not found in vignette

On 04/20/2017 02:50 PM, 王棣台 wrote: I put in the anamiR/data/ Just like other data I used in the vignette. As I said, I don't see it there. According to data(package="anamiR"), the data sets available in your package are: Data sets in package ‘anamiR’: egSymb A table with

Re: [Bioc-devel] Object not found in vignette

it should be in my package since anamiR version 1.1.8 That is weird. Ti-Tai ��: Hervé Pagès [hpa...@fredhutch.org] 寄件日期: 2017年4月21日 上午 05:49 至: 王棣台; bioc-devel@r-project.org 主旨: Re: [Bioc-devel] Object not found in vignette On 04/20/2017 02:45 PM, Hervé

Re: [Bioc-devel] Object not found in vignette

I put in the anamiR/data/ Just like other data I used in the vignette. Ti-Tai ��: Hervé Pagès [hpa...@fredhutch.org] 寄件日期: 2017年4月21日 上午 05:45 至: 王棣台; bioc-devel@r-project.org 主旨: Re: [Bioc-devel] Object not found in vignette On 04/20/2017 02:36 PM, 王棣台

Re: [Bioc-devel] Object not found in vignette

On 04/20/2017 02:45 PM, Hervé Pagès wrote: On 04/20/2017 02:36 PM, 王棣台 wrote: That missing object is a list format data generated by myself, so I don't think it would be about Depends, Imports, or Suggests. Except this one, other generated data can be found. And where did you put this data

Re: [Bioc-devel] Object not found in vignette

On 04/20/2017 02:36 PM, 王棣台 wrote: That missing object is a list format data generated by myself, so I don't think it would be about Depends, Imports, or Suggests. Except this one, other generated data can be found. And where did you put this data set so that data(table_pre) can find it? H.

Re: [Bioc-devel] Object not found in vignette

That missing object is a list format data generated by myself, so I don't think it would be about Depends, Imports, or Suggests. Except this one, other generated data can be found. Ti-Tai ��: Hervé Pagès [hpa...@fredhutch.org] 寄件日期: 2017年4月21日 上午 05:16 至:

Re: [Bioc-devel] Object not found in vignette

Hi, The name of my package is anamiR. it is an object which I try to use in vignette as an example data. Ti-Tai Wang ��: Hervé Pagès [hpa...@fredhutch.org] 寄件日期: 2017年4月21日 上午 05:16 至: 王棣台; bioc-devel@r-project.org 主旨: Re: [Bioc-devel] Object not found

Re: [Bioc-devel] Object not found in vignette

Why don't you give us the name of your package so we can look at it? I suspect something is missing in your Depends, Imports, or Suggests field. Works for you because you have the missing package installed on your machine but not on the build machine because the package is missing there. The

[Bioc-devel] Object not found in vignette

Hi all, I kept getting the same Error from BUILD REPORT: Error: processing vignette 'IntroductionToanamiR.Rmd' failed with diagnostics: object 'table_pre' not found However, I did confirm my package with R CMD BUILD and CHECK before committing, and there was no errors and warnings. I really

Re: [R-pkg-devel] Issue with including vignettes without building package

Perhaps you could add a Makefile with a rule that compiles the vignettes into the inst/doc directory? This might avoid the build process. - Zhian N. Kamvar, Ph. D. Postdoctoral Researcher (Everhart Lab) Department of Plant Pathology University of Nebraska-Lincoln > On Apr 20, 2017, at

Re: [R-pkg-devel] Issue with including vignettes without building package

To rephrase my needs, I need to find a way to create the file /Meta/vignette.rds at install, not build, as all other files for the vignettes to run are being installed properly. Has anyone managed to do that? For now my horrible hack is to have a function calling the vignette through a call to

Re: [R-pkg-devel] Issue with including vignettes without building package

Thanks but I don't think so, that would imply them to rebuild the vignettes, which is exactly what I want to avoid. Without knitr cached chunk it would take forever on their laptops and they would also need to install tons of packages... ++ On 20 April 2017 at 21:01, Sven E Templer

Re: [Rd] Problems with S4 methods dispatching on `...` (aka dotsMethods)

Thanks for pointing out these issues. I have a fix that I will commit soon. Btw, I would never have seen the post on Stack Overflow. It's best to report bugs on the bugzilla. Michael On Thu, Apr 20, 2017 at 8:30 AM, Andrzej Oleś wrote: > Hi all, > > I recently

Re: [Bioc-devel] Vignette update after change in git mirror repo

Hi, Maia. The git mirror is not used for building packages. Instead, you will need to commit to svn for changes to show up on Bioconductor. See here for details of working with git and svn together. https://www.bioconductor.org/developers/how-to/git-mirrors/ If I misunderstood what you are

[Bioc-devel] Vignette update after change in git mirror repo

How long does it take for the html vignette to update after a change in the git mirror has taken place? I changed my code in the git mirror a few days ago, and the html vignette hasn't incorporated these changes yet. Thanks in advance for your help. Maia [[alternative HTML version

Re: [R-pkg-devel] Issue with including vignettes without building package

Hi Alex, what if you run devtools::install_github(build_vignettes = TRUE) on your students computer? See ?devtools::install Best, Sven > On 20. Apr 2017, at 15:09, Alexandre Courtiol > wrote: > > Dear all, > > I am using a package for teaching: > my

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

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

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

Hi Christian, Disabling 'csrutil disable' might help xps on veracruz2 but that 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

Re: [Rd] Intel MKL compiling issue

There is nothing here indicating any kind of error, so no way to give any insights And please do follow the posting guide, including not posting HTML. FWIW, I have tested R 3.4.0 RC (sic) with MKL 11.3, which is later than your 2013 ... (on x86_64 Fedora 24). On 20/04/2017 10:39, jing

[Rd] Problems with S4 methods dispatching on `...` (aka dotsMethods)

Hi all, I recently encountered some unexpected behavior with S4 generics dispatching on `...`, which I described in http://stackoverflow.com/questions/43499203/use-callnextmethod-with-dotsmethods TL;DR: `callNextMethod()` doesn't work in methods dispatching on `...`, and arguments of such

Re: [Rd] system/system2 and open file descriptors

In S+ on Unix-alikes we dealt with this issue by using fcntl(fd, F_SETFD, 1) to set the close-on-exec flag on a file descriptor as soon as we opened it. Bill Dunlap TIBCO Software wdunlap tibco.com On Wed, Apr 19, 2017 at 8:40 PM, Winston Chang wrote: > In addition to

Re: [R-pkg-devel] R CMD check not finding my vignettes

Hi guys, Thanks very much for all of your comments. I now have a good sense of what the possibilities are, and I will think about what works best for my package. Cheers, David On 20 April 2017 at 14:42, Duncan Murdoch wrote: > On 20/04/2017 4:57 AM, Brian G.

Re: [Rd] ask.yes.no() function

On 20/04/2017 9:13 AM, Dirk Eddelbuettel wrote: On 20 April 2017 at 09:33, Michael Sumner wrote: | Perhaps worth pointing out "yesno" as a candidate: | | https://CRAN.R-project.org/package=yesno | Not really as i) base R will not have dependencies

Re: [Rd] ask.yes.no() function

On 20 April 2017 at 09:33, Michael Sumner wrote: | Perhaps worth pointing out "yesno" as a candidate: | | https://CRAN.R-project.org/package=yesno | Not really as i) base R will not have dependencies outside of it ii) more importantly, Duncan

Re: [Rd] c() documentation after change; 'recursive' in "base" methods

> Suharto Anggono Suharto Anggono via R-devel > on Wed, 19 Apr 2017 22:50:41 + writes: > In R 3.4.0 RC, argument list of 'c' as S4 generic function has become > (x, ...) . > However, "S4 methods" section in documentation of 'c' (c.Rd) is not

Re: [Bioc-devel] Bioconductor 3.5 release: potential deprecations

Hi Roel, Thank you for working on the package. The builds start at 5pm EST daily. If it's helpful, you can see which R version, compilers and compiler flags are used for each build machine by clicking the name at the top left of the report:

Re: [R-pkg-devel] How to fix errors in R headers when uploading my package to win-builer

I figured it out as header clash. Putting #include R headers after Windows headers works for me. GSC 于2017年4月18日周二 上午9:54写道： > That link is deprecated, new link to log: > https://win-builder.r-project.org/I3u4Z9BbLHsC/ . > > GSC 于2017年4月17日周一 下午10:47写道： > >> I

Re: [Rd] R 3.4 has broken C++11 support

indeed. Makeconf isn’t in the right spot, so the correct vars aren’t set. thank you all and sorry for the noise! Von: "Ista Zahn" An: "Angerer, Philipp" CC: "Dirk Eddelbuettel" , "Martyn Plummer"

Re: [Rd] ask.yes.no() function

Perhaps worth pointing out "yesno" as a candidate: https://CRAN.R-project.org/package=yesno Cheers, Mike On Wed, 19 Apr 2017 at 21:55 Duncan Murdoch wrote: As described in

Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta

On 04/20/2017 03:08 AM, Michael Stadler wrote: Dear Martin, I've now spend a day trying to resolve this. To make a long story short: I could get bowtie 1.1.1 (currently used in Rbowtie 1.15.1) to compile and work under macOS Sierra. I tried updating bowtie, but: - bowtie 1.2 has a bug that

Re: [R-pkg-devel] R CMD check not finding my vignettes

David, I'd suggest creating a vignette for each of HTML and PDF, and including a source file that contains the common code. e.g. have a pdf header and an html header file, and then include the 'main' Rmd as a child doc from each header Rmd. This way R CMD build could build both pdf and html

Re: [R-pkg-devel] R CMD check not finding my vignettes

Hi Duncan, Thank you very much for taking the time to look at this. I tried rebuilding the tar file so as to include only the .Rmd files, not the HTML files, in 'vignettes': drwxr-xr-x 0 david staff 0 20 Apr 09:21 huxtable/vignettes/ -rw-r--r-- 0 david staff1633 6 Apr 16:26

Re: [Rd] Default R-3.4.0 RC CXXFLAGS without -O2 on x86_64-linux-gnu with g++-5.4.0 causes WARNING from stl_list.h

This is fixed in R-rc_2017-04-19_r72555.tar.gz If you are affected by this issue then please test the RC tarball. This is the last chance to detect problems (including those created by the last-minute patch) before the release of R 3.4.0. Martyn On Wed, 2017-04-19 at 12:19 +, Neumann,

Re: [Bioc-devel] Bioconductor 3.5 release: potential deprecations

Dear Valerie, We're working on MutationalPatterns as you can see (we've had our last changes pushed into the SVN repository just two days ago). Due to the timezone differences between Europe and the US, we seem to be missing out the starting point of a new build round. So, at which time do you

Re: [R-pkg-devel] Interplay between knitr() and View()

Dear Roy, In case you create a HTML vignette you can use datatable() from the DT package. That creates a dynamic table in the output. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team

Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta

Dear Martin, I've now spend a day trying to resolve this. To make a long story short: I could get bowtie 1.1.1 (currently used in Rbowtie 1.15.1) to compile and work under macOS Sierra. I tried updating bowtie, but: - bowtie 1.2 has a bug that prevents it from using multiple threads, which I