[Bioc-devel] build_vignette

[Kenneth Condon]

Hi,

I am creating my first package and have run into an issue when building the
vignette with devtools::build_vignette() in Rstudio.

In a nutshell, I add_vignette() , make a few edits, build_vignette, view
the redered html.

That is all fine until I try to make more edits to the .Rmd file.

As soon as I try to build_vignette()  and overwrite the current vignettes,
all that happens is the .Rmd file is deleted, and the newly edited .html +
.R files remain in the vignettes folder (not copied to inst/docs).

I wouldn't mind this, but for the deletion of the .Rmd file

So is build_vignette designed to just be run once on a complette .Rmd file?
How do I view the redered edits I make? Do people just use pandoc?

Regards,
Kenneth.

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Re: [Bioc-devel] Bioc-devel changes and SummarizedExperiment class

[Leonard Goldstein]

Thanks Hervé!

Leonard


On Tue, Apr 10, 2018 at 11:03 AM, Hervé Pagès  wrote:

> Hi Leonard,
>
> This should be fixed in SGSeq 1.13.6 (see commit
> 5dc16968f7ea1a4b59595ebaabacca9a76699b80).
>
> Cheers,
> H.
>
>
> On 04/04/2018 09:23 AM, Leonard Goldstein wrote:
>
>> Hi Hervé,
>>
>> Some recent changes in bioc-devel are causing trouble with
>> SummarizedExperiment objects if the rowRanges slot inherits from
>> GRangesList. Please see example below.
>>
>> Thanks in advance for your help.
>>
>> Leonard
>>
>> --
>>
>>> library(SGSeq)
>>>
>>> ## SGVariants object inherits from GRangesList
>>>
>>
>>
>> is(sgv_pred)
>>>
>>   [1] "SGVariants" "GRangesList"
>>   [3] "Paths"  "GenomicRangesList"
>>   [5] "CompressedRangesList"   "GenomicRanges_OR_GRangesList"
>>   [7] "RangesList" "CompressedList"
>>   [9] "GenomicRanges_OR_GenomicRangesList" "List"
>> [11] "Vector" "list_OR_List"
>> [13] "Annotated"
>>
>>>
>>> ## example counts
>>>
>>
>>
>> counts <- matrix(1:2, ncol = 1)
>>>
>>> ## creating SummarizedExperiment object fails
>>>
>>
>>
>> SummarizedExperiment(assays = list(counts), rowRanges = sgv_pred)
>>>
>> class: RangedSummarizedExperiment
>> dim: 2 1
>> metadata(0):
>> assays(1): ''
>> Error in .local(object, ..., verbose) : unused argument (check = FALSE)
>>
>>>
>>> ## works after coercing to GRangestList
>>>
>>
>>
>> SummarizedExperiment(assays = list(counts), rowRanges = as(sgv_pred,
>>>
>> "GRangesList"))
>> class: RangedSummarizedExperiment
>> dim: 2 1
>> metadata(0):
>> assays(1): ''
>> rownames: NULL
>> rowData names(20): from to ... variantType variantName
>> colnames: NULL
>> colData names(0):
>>
>>>
>>> sessionInfo()
>>>
>> R Under development (unstable) (2017-10-20 r73567)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)
>>
>> Matrix products: default
>> BLAS:
>> /gnet/is2/p01/apps/R/3.5.0-20171105-devel/x86_64-linux-2.6-
>> rhel6/lib64/R/lib/libRblas.so
>> LAPACK:
>> /gnet/is2/p01/apps/R/3.5.0-20171105-devel/x86_64-linux-2.6-
>> rhel6/lib64/R/lib/libRlapack.so
>>
>> locale:
>>   [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
>>   [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>>   [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>>   [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
>>   [9] LC_ADDRESS=C   LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats4parallel  stats graphics  grDevices utils datasets
>> [8] methods   base
>>
>> other attached packages:
>>   [1] SGSeq_1.13.5SummarizedExperiment_1.9.16
>>   [3] DelayedArray_0.5.23 BiocParallel_1.13.3
>>   [5] matrixStats_0.53.1  Biobase_2.39.2
>>   [7] Rsamtools_1.31.3Biostrings_2.47.12
>>   [9] XVector_0.19.9  GenomicRanges_1.31.23
>> [11] GenomeInfoDb_1.15.5 IRanges_2.13.28
>> [13] S4Vectors_0.17.39   BiocGenerics_0.25.3
>>
>> loaded via a namespace (and not attached):
>>   [1] Rcpp_0.12.16  compiler_3.5.0
>>   [3] GenomicFeatures_1.31.10   prettyunits_1.0.2
>>   [5] bitops_1.0-6  tools_3.5.0
>>   [7] zlibbioc_1.25.0   progress_1.1.2
>>   [9] biomaRt_2.35.13   digest_0.6.15
>> [11] bit_1.1-13RSQLite_2.1.0
>> [13] memoise_1.1.0 lattice_0.20-35
>> [15] pkgconfig_2.0.1   igraph_1.2.1
>> [17] Matrix_1.2-13 DBI_0.8
>> [19] GenomeInfoDbData_1.1.0rtracklayer_1.39.9
>> [21] httr_1.3.1stringr_1.3.0
>> [23] bit64_0.9-8   grid_3.5.0
>> [25] R6_2.2.2  AnnotationDbi_1.41.4
>> [27] XML_3.98-1.10 blob_1.1.1
>> [29] magrittr_1.5  GenomicAlignments_1.15.13
>> [31] RUnit_0.4.31  assertthat_0.2.0
>> [33] stringi_1.1.7 RCurl_1.95-4.10
>>
>>>
>>>
>>>
>> [[alternative HTML version deleted]]
>>
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>> gk0XNxCYLZKHMRS-PnHD2znDDwj1P-Eiu7P4aUSuI=qjwH7TgvfYKGtMDC
>> I77_VVUw8S-5PA6ctju8Jb3erUQ=
>>
>>
> --
> 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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[Bioc-devel] RELEASE_3_6 branch frozen at 3:00pm EST today

[Turaga, Nitesh]

Hello Maintainers,

The commits to RELEASE_3_6 will be blocked at 3:00pm EST today.

Best,

Nitesh 


> On Apr 10, 2018, at 5:03 PM, Turaga, Nitesh  
> wrote:
> 
> Hello Maintainers,
> 
> We are going to block pushes to the RELEASE_3_6 branch tomorrow at 15:00 EST. 
> Maintainers who were planning to commit have until tomorrow 15:00 EST (3pm 
> EST) to fix any outstanding issues they have. 
> 
> NOTE: Once the builds are done, the Bioconductor RELEASE_3_6 branch will be 
> frozen forever.
> 
> Best regards,
> 
> Nitesh Turaga
> Bioconductor Core Team



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Re: [Bioc-devel] update schedule of packages

[Hervé Pagès]

Hi,

As stated on https://bioconductor.org/, Bioconductor has two releases
each year. See the release dates of all the releases so far here:

  https://bioconductor.org/about/release-announcements/

As you can see, there is generally one release in Spring and one in
Fall.

H.

On 04/11/2018 08:02 AM, Minoo Ashtiani wrote:

Hi there,


Thanks for publishing my package on Bioconductor. Just one more question, is 
the updating schedule of Bioconductor only each year on April?


We are planing to submit the paper of the package on a journal. We wanted to 
know if we can make some editions in the package according to the journal 
reviewers comments in the future before next April or not?


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1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
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Re: [Bioc-devel] Unable to access repository

[Turaga, Nitesh]

We have no keys for 'j.saezrodriguez’.

I have added you to DrugVsDisease. You should have access now. Your key is 
under the name c.pacini.

Best,

Nitesh 

> On Apr 11, 2018, at 12:48 PM, Clare Pacini  wrote:
> 
> Hi Nitesh,
> 
> There was a query about ssh keys for this package and another that I am 
> maintainer on. See email chain below. I think I have been accidentally 
> removed from DrugVsDisease would you be able to fix this given the 
> information in the attached ?
> 
> Thanks
> 
> Clare
> 
> —
> 
> 
> From: "Obenchain, Valerie" 
> Subject: Re: Bioconductor package access
> Date: 6 February 2018 at 22:23:39 GMT
> To: Clare Pacini 
> Cc: "saezrodrig...@ebi.ac.uk" 
> 
> On 02/06/2018 02:19 PM, Obenchain, Valerie wrote:
>> Thanks Clare.
>> 
>> I have change the ssh key over to c.pacini and will add your github username 
>> to the new account. You should now have access to both packages with that 
>> key.
>> 
>> Now that the key is moved over, j.saezrodriguz will have no access. Julio, 
>> please go to the link below and add your github username or ssh key. Be sure 
>> to use the email saezrodrig...@ebi.ac.uk and username j.saezrodriguz.
> 
> Oops, forgot the 'e'.  I meant 'j.saezrodriguez'.
> 
> Valerie
>> 
>> https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform
>> 
>> Valerie
>> 
>> 
>> 
>> 
>> 
>> 
>> On 02/06/2018 01:48 PM, Clare Pacini wrote:
>>> Hi Valerie,
>>> 
>>> Thanks for your email. Yes I would like to keep access to both packages, 
>>> Julio will require access just to DrugVsDisease.
>>> The ssh key is mine and my GitHub username is clarepacini.
>>> 
>>> Thanks,
>>> 
>>> Clare
 On 6 Feb 2018, at 21:18, Obenchain, Valerie 
  wrote:
 
 Hi Clare,
 
 There is some confusion between credentials for users c.pacini and 
 j.saezrodriguz. A number of combinations of usernames, emails and ssh keys 
 for these 2 users were entered in the Google Sheet. We also have 
 historical data for these users from svn. I'd like to clean this up if 
 possible.
 
 1) accounts 
 
 Do you want accounts for both c.pacini and j.saezrodriguez? For each 
 account, we need several pieces of information. Here is what we currently 
 have:
 
 username : c.pacini
 email: clarepac...@gmail.com
 github username: none
 ssh keys: none
 
 username: j.saezrodriguez
 email: saezrodrig...@ebi.ac.uk
 github username: none
 ssh keys: ssh-rsa B3NzaC1yc2EA ... 5pTvNvU2MiGd1BaJw== 
 clarepac...@gmail.com
 
 2) package access
 
 Currently user c.pacini has access to covEB and user j.saezrodriguez has 
 access to DrugVsDisease. Is this correct? Because we only have keys for 
 j.saezrodriguez and none for c.pacini, no one can access covEB.
 
 If you are both active maintainers you should have separate accounts and 
 both be listed on both packages. If you have a github usernames please 
 provide those so we can get ssh keys from there.
 
 Let me know if you have questions.
 
 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.
>>> 
>> 
>> 
> 
> 
> 
> 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. 
> 
> 
>> On 11 Apr 2018, at 17:40, Turaga, Nitesh  
>> wrote:
>> 
>> Hi, 
>> 
>> The only key available on that package is “j.saezrodriguez”, and there is no 
>> key available with that username.
>> 
>> I’m not sure how you’ve had previous access to this package after we’ve 
>> moved the Git repository. 
>> 
>> Can you upload a key under the username: clarepacini, and please have Julio 
>> Saez-Rodriguez provide confirmation regarding access. It might be useful for 
>> Julio to provide a key too.
>> 
>> Best,
>> 
>> Nitesh 
>> 
>> 
>> 
>>> On Apr 10, 2018, at 7:23 AM, Clare Pacini  wrote:
>>> 
>>> Hi all,
>>> 
>>> I am 

Re: [Bioc-devel] Unable to access repository

[Turaga, Nitesh]

Hi, 

The only key available on that package is “j.saezrodriguez”, and there is no 
key available with that username.

I’m not sure how you’ve had previous access to this package after we’ve moved 
the Git repository. 

Can you upload a key under the username: clarepacini, and please have Julio 
Saez-Rodriguez provide confirmation regarding access. It might be useful for 
Julio to provide a key too.

Best,

Nitesh 



> On Apr 10, 2018, at 7:23 AM, Clare Pacini  wrote:
> 
> Hi all,
> 
> I am the maintainer for DrugVsDisease package and am trying to push new 
> changes. However, I am getting the following error:
> 
> Permission denied (publickey).
> fatal: Could not read from remote repository.
> 
> Please make sure you have the correct access rights
> and the repository exists.
> 
> I have previously provided an ssh key for my GitHub account with username 
> clarepacini and have been able to push changes previously. I am unsure as to 
> what has changed/what else I need to do?
> 
> Thanks
> 
> Clare
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Unable to access repository

[Clare Pacini]

Hi Nitesh,

There was a query about ssh keys for this package and another that I am 
maintainer on. See email chain below. I think I have been accidentally removed 
from DrugVsDisease would you be able to fix this given the information in the 
attached ?

Thanks

Clare

—


From: "Obenchain, Valerie" 
Subject: Re: Bioconductor package access
Date: 6 February 2018 at 22:23:39 GMT
To: Clare Pacini 
Cc: "saezrodrig...@ebi.ac.uk" 

On 02/06/2018 02:19 PM, Obenchain, Valerie wrote:
> Thanks Clare.
> 
> I have change the ssh key over to c.pacini and will add your github username 
> to the new account. You should now have access to both packages with that key.
> 
> Now that the key is moved over, j.saezrodriguz will have no access. Julio, 
> please go to the link below and add your github username or ssh key. Be sure 
> to use the email saezrodrig...@ebi.ac.uk  and 
> username j.saezrodriguz.

Oops, forgot the 'e'.  I meant 'j.saezrodriguez'.

Valerie
> 
> https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform
>  
> 
> 
> Valerie
> 
> 
> 
> 
> 
> 
> On 02/06/2018 01:48 PM, Clare Pacini wrote:
>> Hi Valerie,
>> 
>> Thanks for your email. Yes I would like to keep access to both packages, 
>> Julio will require access just to DrugVsDisease.
>> The ssh key is mine and my GitHub username is clarepacini.
>> 
>> Thanks,
>> 
>> Clare
>>> On 6 Feb 2018, at 21:18, Obenchain, Valerie 
>>> >> > wrote:
>>> 
>>> Hi Clare,
>>> 
>>> There is some confusion between credentials for users c.pacini and 
>>> j.saezrodriguz. A number of combinations of usernames, emails and ssh keys 
>>> for these 2 users were entered in the Google Sheet. We also have historical 
>>> data for these users from svn. I'd like to clean this up if possible.
>>> 
>>> 1) accounts 
>>> 
>>> Do you want accounts for both c.pacini and j.saezrodriguez? For each 
>>> account, we need several pieces of information. Here is what we currently 
>>> have:
>>> 
>>> username : c.pacini
>>> email: clarepac...@gmail.com 
>>> github username: none
>>> ssh keys: none
>>> 
>>> username: j.saezrodriguez
>>> email: saezrodrig...@ebi.ac.uk 
>>> github username: none
>>> ssh keys: ssh-rsa B3NzaC1yc2EA ... 5pTvNvU2MiGd1BaJw== 
>>> clarepac...@gmail.com 
>>> 
>>> 2) package access
>>> 
>>> Currently user c.pacini has access to covEB and user j.saezrodriguez has 
>>> access to DrugVsDisease. Is this correct? Because we only have keys for 
>>> j.saezrodriguez and none for c.pacini, no one can access covEB.
>>> 
>>> If you are both active maintainers you should have separate accounts and 
>>> both be listed on both packages. If you have a github usernames please 
>>> provide those so we can get ssh keys from there.
>>> 
>>> Let me know if you have questions.
>>> 
>>> 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.
>> 
> 


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. 


> On 11 Apr 2018, at 17:40, Turaga, Nitesh  
> wrote:
> 
> Hi, 
> 
> The only key available on that package is “j.saezrodriguez”, and there is no 
> key available with that username.
> 
> I’m not sure how you’ve had previous access to this package after we’ve moved 
> the Git repository. 
> 
> Can you upload a key under the username: clarepacini, and please have Julio 
> Saez-Rodriguez provide confirmation regarding access. It might be useful for 
> Julio to provide a key too.
> 
> Best,
> 
> Nitesh 
> 
> 
> 
>> On Apr 10, 2018, at 7:23 AM, Clare Pacini  wrote:
>> 
>> Hi all,
>> 
>> I am the maintainer for DrugVsDisease package and am trying to push new 
>> changes. However, I am getting the following error:
>> 
>> 

Re: [Bioc-devel] BiocCheck error

[Aimin Yan]

Martin,

Thank you. yes, you are right.
Now it works, I also changed outputs to tempfile() or tempdir().

Aimin


On Tue, Apr 10, 2018 at 6:07 PM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:

> Hi Aimin -- the problem is that your vignette has two VignetteEngine
> commands in it
>
> PathwaySplice/vignettes master$ grep VignetteEngine *
> tutorial.Rmd:  %\VignetteEngine{knitr::rmarkdown}
> tutorial.Rmd:  %\VignetteEngine{knitr::knitr}
>
> Also, please avoid writing to files in the user system, replace 'C:/temp'
> with tempfile() or dir = tempfile(); dir.create(dir) in code like the
> following
>
> PathwaySplice master$ grep -r "C:/" *
> man/runPathwaySplice.Rd: output.file='C:/temp/test.csv')
> man/runPathwaySplice.Rd: output.file='C:/temp/test.csv')
> man/enrichmentMap.Rd:  label.node.by.index = TRUE,
> output.file.dir='C:/temp')
> man/enrichmentMap.Rd:  label.node.by.index = FALSE,
> output.file.dir='C:/temp')}
> man/compareResults.Rd:compareResults(20, res.adj, res.unadj,
> gene.based.table, type.boxplot='Only3',output.dir='C:/TEMP')
> R/Run_pathwaysplice.R:#' output.file='C:/temp/test.csv')
> R/Run_pathwaysplice.R:#' output.file='C:/temp/test.csv')
> R/Run_pathwaysplice.R:#'   label.node.by.index = TRUE,
> output.file.dir='C:/temp')
> R/Run_pathwaysplice.R:#'   label.node.by.index =
> FALSE, output.file.dir='C:/temp')}
> R/Run_pathwaysplice.R:#' compareResults(20, res.adj, res.unadj,
> gene.based.table, type.boxplot='Only3',output.dir='C:/TEMP')
>
> Martin
>
>
> On 04/10/2018 04:39 PM, Aimin Yan wrote:
>
>> I used "R CMD check PathwaySplice_1.3.0.tar.gz", and get it passed
>> without errors and warnings.
>>
>> However I get the following error when I use "R CMD BiocCheck
>> PathwaySplice_1.3.0.tar.gz"
>>
>> R CMD BiocCheck PathwaySplice_1.3.0.tar.gz
>>
>> This is BiocCheck version 1.15.8. BiocCheck is a work in progress.
>>
>> Output and severity of issues may change. Installing package...
>>
>> * Checking for version number mismatch...
>>
>> * Checking if other packages can import this one...
>>
>> * Checking to see if we understand object initialization...
>>
>>  * NOTE: Consider clarifying how 12 object(s) are initialized. Maybe
>>
>>they are part of a data set loaded with data(), or perhaps part
>>
>>of an object referenced in with() or within().
>>
>>  object (function)
>>
>>winMenuAddItem (.onAttach)
>>
>>ggplot (compareResults2)
>>
>>aes (compareResults2)
>>
>>random_sampling_200k (compareResults2)
>>
>>PValue (compareResults2)
>>
>>PathwaySplice (compareResults2)
>>
>>geom_point (compareResults2)
>>
>>geom_smooth (compareResults2)
>>
>>labs (compareResults2)
>>
>>scale_colour_manual (compareResults2)
>>
>>scale_shape_manual (compareResults2)
>>
>>get.col.scale (netplot)
>>
>> * Checking vignette directory...
>>
>>  This is a software package
>>
>> Error in vapply(vigdircontents, vigHelper, logical(1), builder = desc) :
>>
>>values must be length 1,
>>
>>   but FUN(X[[1]]) result is length 2
>>
>> Calls:  ... BiocCheck -> checkVignetteDir -> checkVigBuilder ->
>> vapply
>>
>> Execution halted
>>
>>
>>
>> Any idea about this?
>>
>>
>> Here is my sessionInfo()
>>
>> https://gist.github.com/aiminy/764718da9b9eeedd6f5eea196ce956b4
>>
>> Thank you,
>>
>> Aimin
>>
>> [[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 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
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>

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Re: [Bioc-devel] vignette problems

[Martin Morgan]

On 04/11/2018 10:47 AM, campos wrote:

Hi Martin,

when I run git status I get this:

On branch master
Your branch is up-to-date with 'origin/master'.
nothing to commit, working directory clean

shouldn't I see that my version in my machine is some commits behind?

  $git remote -v
origin    g...@git.bioconductor.org:packages/STAN (fetch)
origin    g...@git.bioconductor.org:packages/STAN (push)


maybe your version is current; I have

~/b/git/STAN master$ git log --oneline -n10
06dbdae Merge remote-tracking branch 'upstream/master'
6e070d4 version 2.7.3
b8e2123 make destructors for polymorhpic base classes virtual
18ac6ba mismatch new[] / delete[]
985768b restore EmissionFactory::createEmissionFunctionMixed
8b749db provide return value for non-void functions
26ca36e update poor printf statements
0bb83ab clear 'unused variable' -Wall -pedantic warnings
a3b7666 remove vignette product STAN-knitr.R
1c4f140 upgrade version 2.7.3

if you don't, then I guess `git pull` or more pedantically `git fetch 
origin; git merge origin/master master`.


Martin



Thanks a lot,

Rafa


On 11.04.2018 16:43, Martin Morgan wrote:



On 04/11/2018 09:58 AM, campos wrote:

Hi Martin,

thank you very much for your time and effort!

I pulled the branch to my computer updated the DESCRIPTION file and 
pushed the changes. That should be enough right?


actually I seemed to have messed up the git commit, but I fixed it 
from my end; you should git pull and not worry about pushing any 
further commits for the moment.




Best,

Rafa

PS: If you ever stop by Cologne please let me know. I owe you a beer 
or two!


tasty!

Martin




On 10.04.2018 23:44, Martin Morgan wrote:

Hi --

I'm not sure what you mean; the 'devel' builld report does not 
include mac (the build system experienced problems with disk space 
last night, so the build did not complete)


https://bioconductor.org/checkResults/devel/bioc-LATEST/STAN/

and STAN failed in Release

https://bioconductor.org/checkResults/release/bioc-LATEST/STAN/


HOWEVER, I spent some time with your package. First, I compiled it 
with compiler flages -Wall -pedantic, which makes the compiler quite 
sensitive. I did this by creating, on my Linux, a file


    $ cat ~/.R/Makevars
    CFLAGS = -g -O0 -Wall -pedantic
    CXXFLAGS = -g -O0 -Wall -pedantic

and then installing the package from the source directory

    STAN master$ rm -f src/*o && R CMD INSTALL .

There were a number of minor issues (unused variables, incorrect 
printf formatting [and use of printf() rather than Rprintf()]) as 
well as somewhat more substantial problems (virtual destructors for 
polymorphic base classes); a few problems remain, of the form


    RWrapper.cpp:950:5: warning: control reaches end of non-void 
function [-Wreturn-type]

 }

where the problem is obvious -- no return value if parallel != 0 -- 
but also innocuous, since it seems from inspection that in fact this 
function is always invoked with parallel == 0


    HMM* createHMM(int parallel, int K, InitialProbability* 
initProb, TransitionMatrix* transMat, EmissionFunction** myEmissions)

    {
    if(parallel == 0)
    {
    return new HMM(K, initProb, transMat, myEmissions);
    }
    }

You should fix these problems, e.g., by removing the parallel 
argument from the function and body. After cleaning up as best I 
could, I install the package again and ran the vignette through 
valgrind


    STAN master$ R CMD INSTALL .
    ...
    STAN master$ cd vignettes
    STAN/vignettes master$ R CMD Stangle STAN-knitr.Rnw
    STAN/vignettes master$ R CMD Stangle STAN-knitr.Rnw
    STAN/vignettes master$ R -d valgrind -f STAN-knitr.R

leading to an about mismatched new[] / delete[] -- memory allocated 
by 'new x[]' must be deleted with 'delete[]', but the package code 
had simply 'delete'.


With these changes, the vignette builds without segfaulting or 
valgrind errors on my machine, and on the Mac builder; I did not 
check the full build and check of the package.


The changes are summarized in the following commits:

    STAN master$ git log --oneline
    a719f42 version bump
    b8e2123 make destructors for polymorhpic base classes virtual
    18ac6ba mismatch new[] / delete[]
    985768b restore EmissionFactory::createEmissionFunctionMixed
    8b749db provide return value for non-void functions
    26ca36e update poor printf statements
    0bb83ab clear 'unused variable' -Wall -pedantic warnings
    a3b7666 remove vignette product STAN-knitr.R

You should pull these down to your local git repository, e.g., for 
me I have


    STAN master$ git remote -v
    origin    g...@git.bioconductor.org:packages/STAN (fetch)
    origin    g...@git.bioconductor.org:packages/STAN (push)

So I would

    STAN master$ git pull origin master

to incorporate the changes.

It would be good to port these changes to the RELEASE_3_6 branch; 
remember to bump the version of the RELEASE_3_6 branch to 2.6.1.


Unfortunately, I pushed the changes after 

[Bioc-devel] update schedule of packages

[Minoo Ashtiani]

Hi there,


Thanks for publishing my package on Bioconductor. Just one more question, is 
the updating schedule of Bioconductor only each year on April?


We are planing to submit the paper of the package on a journal. We wanted to 
know if we can make some editions in the package according to the journal 
reviewers comments in the future before next April or not?


[[alternative HTML version deleted]]

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Re: [Bioc-devel] vignette problems

[Martin Morgan]

On 04/11/2018 09:58 AM, campos wrote:

Hi Martin,

thank you very much for your time and effort!

I pulled the branch to my computer updated the DESCRIPTION file and 
pushed the changes. That should be enough right?


actually I seemed to have messed up the git commit, but I fixed it from 
my end; you should git pull and not worry about pushing any further 
commits for the moment.




Best,

Rafa

PS: If you ever stop by Cologne please let me know. I owe you a beer or 
two!


tasty!

Martin




On 10.04.2018 23:44, Martin Morgan wrote:

Hi --

I'm not sure what you mean; the 'devel' builld report does not include 
mac (the build system experienced problems with disk space last night, 
so the build did not complete)


  https://bioconductor.org/checkResults/devel/bioc-LATEST/STAN/

and STAN failed in Release

  https://bioconductor.org/checkResults/release/bioc-LATEST/STAN/


HOWEVER, I spent some time with your package. First, I compiled it 
with compiler flages -Wall -pedantic, which makes the compiler quite 
sensitive. I did this by creating, on my Linux, a file


    $ cat ~/.R/Makevars
    CFLAGS = -g -O0 -Wall -pedantic
    CXXFLAGS = -g -O0 -Wall -pedantic

and then installing the package from the source directory

    STAN master$ rm -f src/*o && R CMD INSTALL .

There were a number of minor issues (unused variables, incorrect 
printf formatting [and use of printf() rather than Rprintf()]) as well 
as somewhat more substantial problems (virtual destructors for 
polymorphic base classes); a few problems remain, of the form


    RWrapper.cpp:950:5: warning: control reaches end of non-void 
function [-Wreturn-type]

 }

where the problem is obvious -- no return value if parallel != 0 -- 
but also innocuous, since it seems from inspection that in fact this 
function is always invoked with parallel == 0


    HMM* createHMM(int parallel, int K, InitialProbability* initProb, 
TransitionMatrix* transMat, EmissionFunction** myEmissions)

    {
    if(parallel == 0)
    {
    return new HMM(K, initProb, transMat, myEmissions);
    }
    }

You should fix these problems, e.g., by removing the parallel argument 
from the function and body. After cleaning up as best I could, I 
install the package again and ran the vignette through valgrind


    STAN master$ R CMD INSTALL .
    ...
    STAN master$ cd vignettes
    STAN/vignettes master$ R CMD Stangle STAN-knitr.Rnw
    STAN/vignettes master$ R CMD Stangle STAN-knitr.Rnw
    STAN/vignettes master$ R -d valgrind -f STAN-knitr.R

leading to an about mismatched new[] / delete[] -- memory allocated by 
'new x[]' must be deleted with 'delete[]', but the package code had 
simply 'delete'.


With these changes, the vignette builds without segfaulting or 
valgrind errors on my machine, and on the Mac builder; I did not check 
the full build and check of the package.


The changes are summarized in the following commits:

    STAN master$ git log --oneline
    a719f42 version bump
    b8e2123 make destructors for polymorhpic base classes virtual
    18ac6ba mismatch new[] / delete[]
    985768b restore EmissionFactory::createEmissionFunctionMixed
    8b749db provide return value for non-void functions
    26ca36e update poor printf statements
    0bb83ab clear 'unused variable' -Wall -pedantic warnings
    a3b7666 remove vignette product STAN-knitr.R

You should pull these down to your local git repository, e.g., for me 
I have


    STAN master$ git remote -v
    origin    g...@git.bioconductor.org:packages/STAN (fetch)
    origin    g...@git.bioconductor.org:packages/STAN (push)

So I would

    STAN master$ git pull origin master

to incorporate the changes.

It would be good to port these changes to the RELEASE_3_6 branch; 
remember to bump the version of the RELEASE_3_6 branch to 2.6.1.


Unfortunately, I pushed the changes after tonight's builds started, so 
the effect of the changes will not be reported until Thursday 
mid-morning, Eastern time, if the build system does not have problems.


Martin

On 04/10/2018 02:14 PM, campos wrote:

Hi Martin,

it seems like mac is ok now. What has changed??

Thank you very much,

Rafael


On 10.04.2018 11:33, Martin Morgan wrote:



On 04/10/2018 05:27 AM, campos wrote:

Hi Martin,

Thank you very much, I am a bit concerned about the option of:


Last Changed Date: 2018-04-05 09:37:37 -0400 (Thu, 05 Apr 2018)

I did a change yesterday and push it, why isn't it visible?


Notice that at the top of the build report it says

  This page was generated on 2018-04-09 09:50:05 -0400 (Mon, 09 Apr 
2018).


  Snapshot Date: 2018-04-08 16:45:28 -0400 (Sun, 08 Apr 2018)

If you pushed after the snapshot date then your changes are not yet 
visible.


Martin



Best,

Rafa




On 09.04.2018 16:44, Martin Morgan wrote:

I'll try to provide you with a pull request addressing issues. Martin

On 04/09/2018 08:42 AM, campos wrote:

Dear devel team,

I am still puzzled with the problems with mac compiling. I am 

Re: [Bioc-devel] vignette problems

[campos]

Aha! now I see all the changes!

so, now everything should be fine and it should run on mac as well right?

here: 
https://bioconductor.org/checkResults/3.7/bioc-LATEST/STAN/malbec2-checksrc.html


there is only the linux and windows machine, there is no info about the 
mac.


Thousand thanks again Martin, you have been of great help.

Best,

Rafael


On 11.04.2018 16:52, Martin Morgan wrote:



On 04/11/2018 10:47 AM, campos wrote:

Hi Martin,

when I run git status I get this:

On branch master
Your branch is up-to-date with 'origin/master'.
nothing to commit, working directory clean

shouldn't I see that my version in my machine is some commits behind?

  $git remote -v
origin    g...@git.bioconductor.org:packages/STAN (fetch)
origin    g...@git.bioconductor.org:packages/STAN (push)


maybe your version is current; I have

~/b/git/STAN master$ git log --oneline -n10
06dbdae Merge remote-tracking branch 'upstream/master'
6e070d4 version 2.7.3
b8e2123 make destructors for polymorhpic base classes virtual
18ac6ba mismatch new[] / delete[]
985768b restore EmissionFactory::createEmissionFunctionMixed
8b749db provide return value for non-void functions
26ca36e update poor printf statements
0bb83ab clear 'unused variable' -Wall -pedantic warnings
a3b7666 remove vignette product STAN-knitr.R
1c4f140 upgrade version 2.7.3

if you don't, then I guess `git pull` or more pedantically `git fetch 
origin; git merge origin/master master`.


Martin



Thanks a lot,

Rafa


On 11.04.2018 16:43, Martin Morgan wrote:



On 04/11/2018 09:58 AM, campos wrote:

Hi Martin,

thank you very much for your time and effort!

I pulled the branch to my computer updated the DESCRIPTION file and 
pushed the changes. That should be enough right?


actually I seemed to have messed up the git commit, but I fixed it 
from my end; you should git pull and not worry about pushing any 
further commits for the moment.




Best,

Rafa

PS: If you ever stop by Cologne please let me know. I owe you a 
beer or two!


tasty!

Martin




On 10.04.2018 23:44, Martin Morgan wrote:

Hi --

I'm not sure what you mean; the 'devel' builld report does not 
include mac (the build system experienced problems with disk space 
last night, so the build did not complete)


https://bioconductor.org/checkResults/devel/bioc-LATEST/STAN/

and STAN failed in Release

https://bioconductor.org/checkResults/release/bioc-LATEST/STAN/


HOWEVER, I spent some time with your package. First, I compiled it 
with compiler flages -Wall -pedantic, which makes the compiler 
quite sensitive. I did this by creating, on my Linux, a file


    $ cat ~/.R/Makevars
    CFLAGS = -g -O0 -Wall -pedantic
    CXXFLAGS = -g -O0 -Wall -pedantic

and then installing the package from the source directory

    STAN master$ rm -f src/*o && R CMD INSTALL .

There were a number of minor issues (unused variables, incorrect 
printf formatting [and use of printf() rather than Rprintf()]) as 
well as somewhat more substantial problems (virtual destructors 
for polymorphic base classes); a few problems remain, of the form


    RWrapper.cpp:950:5: warning: control reaches end of non-void 
function [-Wreturn-type]

 }

where the problem is obvious -- no return value if parallel != 0 
-- but also innocuous, since it seems from inspection that in fact 
this function is always invoked with parallel == 0


    HMM* createHMM(int parallel, int K, InitialProbability* 
initProb, TransitionMatrix* transMat, EmissionFunction** myEmissions)

    {
    if(parallel == 0)
    {
    return new HMM(K, initProb, transMat, myEmissions);
    }
    }

You should fix these problems, e.g., by removing the parallel 
argument from the function and body. After cleaning up as best I 
could, I install the package again and ran the vignette through 
valgrind


    STAN master$ R CMD INSTALL .
    ...
    STAN master$ cd vignettes
    STAN/vignettes master$ R CMD Stangle STAN-knitr.Rnw
    STAN/vignettes master$ R CMD Stangle STAN-knitr.Rnw
    STAN/vignettes master$ R -d valgrind -f STAN-knitr.R

leading to an about mismatched new[] / delete[] -- memory 
allocated by 'new x[]' must be deleted with 'delete[]', but the 
package code had simply 'delete'.


With these changes, the vignette builds without segfaulting or 
valgrind errors on my machine, and on the Mac builder; I did not 
check the full build and check of the package.


The changes are summarized in the following commits:

    STAN master$ git log --oneline
    a719f42 version bump
    b8e2123 make destructors for polymorhpic base classes virtual
    18ac6ba mismatch new[] / delete[]
    985768b restore EmissionFactory::createEmissionFunctionMixed
    8b749db provide return value for non-void functions
    26ca36e update poor printf statements
    0bb83ab clear 'unused variable' -Wall -pedantic warnings
    a3b7666 remove vignette product STAN-knitr.R

You should pull these down to your local git repository, e.g., for 
me I have


    STAN 

Re: [Bioc-devel] vignette problems

[campos]

Hi Martin,

when I run git status I get this:

On branch master
Your branch is up-to-date with 'origin/master'.
nothing to commit, working directory clean

shouldn't I see that my version in my machine is some commits behind?

 $git remote -v
origin    g...@git.bioconductor.org:packages/STAN (fetch)
origin    g...@git.bioconductor.org:packages/STAN (push)

Thanks a lot,

Rafa


On 11.04.2018 16:43, Martin Morgan wrote:



On 04/11/2018 09:58 AM, campos wrote:

Hi Martin,

thank you very much for your time and effort!

I pulled the branch to my computer updated the DESCRIPTION file and 
pushed the changes. That should be enough right?


actually I seemed to have messed up the git commit, but I fixed it 
from my end; you should git pull and not worry about pushing any 
further commits for the moment.




Best,

Rafa

PS: If you ever stop by Cologne please let me know. I owe you a beer 
or two!


tasty!

Martin




On 10.04.2018 23:44, Martin Morgan wrote:

Hi --

I'm not sure what you mean; the 'devel' builld report does not 
include mac (the build system experienced problems with disk space 
last night, so the build did not complete)


https://bioconductor.org/checkResults/devel/bioc-LATEST/STAN/

and STAN failed in Release

https://bioconductor.org/checkResults/release/bioc-LATEST/STAN/


HOWEVER, I spent some time with your package. First, I compiled it 
with compiler flages -Wall -pedantic, which makes the compiler quite 
sensitive. I did this by creating, on my Linux, a file


    $ cat ~/.R/Makevars
    CFLAGS = -g -O0 -Wall -pedantic
    CXXFLAGS = -g -O0 -Wall -pedantic

and then installing the package from the source directory

    STAN master$ rm -f src/*o && R CMD INSTALL .

There were a number of minor issues (unused variables, incorrect 
printf formatting [and use of printf() rather than Rprintf()]) as 
well as somewhat more substantial problems (virtual destructors for 
polymorphic base classes); a few problems remain, of the form


    RWrapper.cpp:950:5: warning: control reaches end of non-void 
function [-Wreturn-type]

 }

where the problem is obvious -- no return value if parallel != 0 -- 
but also innocuous, since it seems from inspection that in fact this 
function is always invoked with parallel == 0


    HMM* createHMM(int parallel, int K, InitialProbability* 
initProb, TransitionMatrix* transMat, EmissionFunction** myEmissions)

    {
    if(parallel == 0)
    {
    return new HMM(K, initProb, transMat, myEmissions);
    }
    }

You should fix these problems, e.g., by removing the parallel 
argument from the function and body. After cleaning up as best I 
could, I install the package again and ran the vignette through 
valgrind


    STAN master$ R CMD INSTALL .
    ...
    STAN master$ cd vignettes
    STAN/vignettes master$ R CMD Stangle STAN-knitr.Rnw
    STAN/vignettes master$ R CMD Stangle STAN-knitr.Rnw
    STAN/vignettes master$ R -d valgrind -f STAN-knitr.R

leading to an about mismatched new[] / delete[] -- memory allocated 
by 'new x[]' must be deleted with 'delete[]', but the package code 
had simply 'delete'.


With these changes, the vignette builds without segfaulting or 
valgrind errors on my machine, and on the Mac builder; I did not 
check the full build and check of the package.


The changes are summarized in the following commits:

    STAN master$ git log --oneline
    a719f42 version bump
    b8e2123 make destructors for polymorhpic base classes virtual
    18ac6ba mismatch new[] / delete[]
    985768b restore EmissionFactory::createEmissionFunctionMixed
    8b749db provide return value for non-void functions
    26ca36e update poor printf statements
    0bb83ab clear 'unused variable' -Wall -pedantic warnings
    a3b7666 remove vignette product STAN-knitr.R

You should pull these down to your local git repository, e.g., for 
me I have


    STAN master$ git remote -v
    origin    g...@git.bioconductor.org:packages/STAN (fetch)
    origin    g...@git.bioconductor.org:packages/STAN (push)

So I would

    STAN master$ git pull origin master

to incorporate the changes.

It would be good to port these changes to the RELEASE_3_6 branch; 
remember to bump the version of the RELEASE_3_6 branch to 2.6.1.


Unfortunately, I pushed the changes after tonight's builds started, 
so the effect of the changes will not be reported until Thursday 
mid-morning, Eastern time, if the build system does not have problems.


Martin

On 04/10/2018 02:14 PM, campos wrote:

Hi Martin,

it seems like mac is ok now. What has changed??

Thank you very much,

Rafael


On 10.04.2018 11:33, Martin Morgan wrote:



On 04/10/2018 05:27 AM, campos wrote:

Hi Martin,

Thank you very much, I am a bit concerned about the option of:


Last Changed Date: 2018-04-05 09:37:37 -0400 (Thu, 05 Apr 2018)

I did a change yesterday and push it, why isn't it visible?


Notice that at the top of the build report it says

  This page was generated on 2018-04-09 09:50:05 -0400 (Mon, 

Re: [Bioc-devel] vignette problems

[campos]

Hi Martin,

thank you very much for your time and effort!

I pulled the branch to my computer updated the DESCRIPTION file and 
pushed the changes. That should be enough right?


Best,

Rafa

PS: If you ever stop by Cologne please let me know. I owe you a beer or two!


On 10.04.2018 23:44, Martin Morgan wrote:

Hi --

I'm not sure what you mean; the 'devel' builld report does not include 
mac (the build system experienced problems with disk space last night, 
so the build did not complete)


  https://bioconductor.org/checkResults/devel/bioc-LATEST/STAN/

and STAN failed in Release

  https://bioconductor.org/checkResults/release/bioc-LATEST/STAN/


HOWEVER, I spent some time with your package. First, I compiled it 
with compiler flages -Wall -pedantic, which makes the compiler quite 
sensitive. I did this by creating, on my Linux, a file


    $ cat ~/.R/Makevars
    CFLAGS = -g -O0 -Wall -pedantic
    CXXFLAGS = -g -O0 -Wall -pedantic

and then installing the package from the source directory

    STAN master$ rm -f src/*o && R CMD INSTALL .

There were a number of minor issues (unused variables, incorrect 
printf formatting [and use of printf() rather than Rprintf()]) as well 
as somewhat more substantial problems (virtual destructors for 
polymorphic base classes); a few problems remain, of the form


    RWrapper.cpp:950:5: warning: control reaches end of non-void 
function [-Wreturn-type]

 }

where the problem is obvious -- no return value if parallel != 0 -- 
but also innocuous, since it seems from inspection that in fact this 
function is always invoked with parallel == 0


    HMM* createHMM(int parallel, int K, InitialProbability* initProb, 
TransitionMatrix* transMat, EmissionFunction** myEmissions)

    {
    if(parallel == 0)
    {
    return new HMM(K, initProb, transMat, myEmissions);
    }
    }

You should fix these problems, e.g., by removing the parallel argument 
from the function and body. After cleaning up as best I could, I 
install the package again and ran the vignette through valgrind


    STAN master$ R CMD INSTALL .
    ...
    STAN master$ cd vignettes
    STAN/vignettes master$ R CMD Stangle STAN-knitr.Rnw
    STAN/vignettes master$ R CMD Stangle STAN-knitr.Rnw
    STAN/vignettes master$ R -d valgrind -f STAN-knitr.R

leading to an about mismatched new[] / delete[] -- memory allocated by 
'new x[]' must be deleted with 'delete[]', but the package code had 
simply 'delete'.


With these changes, the vignette builds without segfaulting or 
valgrind errors on my machine, and on the Mac builder; I did not check 
the full build and check of the package.


The changes are summarized in the following commits:

    STAN master$ git log --oneline
    a719f42 version bump
    b8e2123 make destructors for polymorhpic base classes virtual
    18ac6ba mismatch new[] / delete[]
    985768b restore EmissionFactory::createEmissionFunctionMixed
    8b749db provide return value for non-void functions
    26ca36e update poor printf statements
    0bb83ab clear 'unused variable' -Wall -pedantic warnings
    a3b7666 remove vignette product STAN-knitr.R

You should pull these down to your local git repository, e.g., for me 
I have


    STAN master$ git remote -v
    origin    g...@git.bioconductor.org:packages/STAN (fetch)
    origin    g...@git.bioconductor.org:packages/STAN (push)

So I would

    STAN master$ git pull origin master

to incorporate the changes.

It would be good to port these changes to the RELEASE_3_6 branch; 
remember to bump the version of the RELEASE_3_6 branch to 2.6.1.


Unfortunately, I pushed the changes after tonight's builds started, so 
the effect of the changes will not be reported until Thursday 
mid-morning, Eastern time, if the build system does not have problems.


Martin

On 04/10/2018 02:14 PM, campos wrote:

Hi Martin,

it seems like mac is ok now. What has changed??

Thank you very much,

Rafael


On 10.04.2018 11:33, Martin Morgan wrote:



On 04/10/2018 05:27 AM, campos wrote:

Hi Martin,

Thank you very much, I am a bit concerned about the option of:


Last Changed Date: 2018-04-05 09:37:37 -0400 (Thu, 05 Apr 2018)

I did a change yesterday and push it, why isn't it visible?


Notice that at the top of the build report it says

  This page was generated on 2018-04-09 09:50:05 -0400 (Mon, 09 Apr 
2018).


  Snapshot Date: 2018-04-08 16:45:28 -0400 (Sun, 08 Apr 2018)

If you pushed after the snapshot date then your changes are not yet 
visible.


Martin



Best,

Rafa




On 09.04.2018 16:44, Martin Morgan wrote:

I'll try to provide you with a pull request addressing issues. Martin

On 04/09/2018 08:42 AM, campos wrote:

Dear devel team,

I am still puzzled with the problems with mac compiling. I am 
really lost and have no idea how to continue or how to be able to 
check about this problems with my linux machine in order to fix 
it faster. Could you please help me with that??


Best,

Rafael


On 05.04.2018 14:29, Shepherd, 

Re: [Bioc-devel] iGraph depending packages failing on Windows build machines

[Obenchain, Valerie]

Thanks for the report Petr. We'll look into it.

Valerie

On 04/10/2018 04:44 PM, petr smirnov wrote:

I noticed that our Bioconductor package (PharmacoGx) is failing to build on
Windows development, with the error:

 error: DLL 'maps' not found: maybe not installed for this architecture?

A google search brings up the package 'sincell', which has experienced this
error before.

The only dependency that package has is iGraph (CRAN), which we share with
them. Checking some of the build reports, there's a handful of packages
failing with the same issue.

There is also at least one package, 'Mulcom', that is failing with the
error:

Error : package 'maps' is not installed for 'arch = i386'

The CRAN package 'maps' seems to be the one providing the 'maps.dll' file.
There seems to be a successful binary build of the 'maps' package on CRAN
for both the release and prerelease versions of R.

Is this is an issue with the package 'maps' not being successfully
installed on the Windows build system?





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Re: [Bioc-devel] package is not available (for R version 3.4.4)

[Shepherd, Lori]

The IMMAN package is a newly accepted package and still only available in 
Bioconductor 3.7 (devel) - The devel version of Bioconductor is built with R 
3.5.  You would have to update your version of R.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Minoo Ashtiani 

Sent: Wednesday, April 11, 2018 5:40:14 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] package is not available (for R version 3.4.4)

Hi there,

I installed the "IMMAN" package which was built on Bioconductor 3.7 (devel) 
recently. I tried to install it but I faced this

package �IMMAN� is not available (for R version 3.4.4)

Why does it happen and how can i fix it?

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[Bioc-devel] package is not available (for R version 3.4.4)

[Minoo Ashtiani]

Hi there,

I installed the "IMMAN" package which was built on Bioconductor 3.7 (devel) 
recently. I tried to install it but I faced this

package �IMMAN� is not available (for R version 3.4.4)

Why does it happen and how can i fix it?

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[Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

[Elizabeth Purdom]

Hello,

Our package clusterExperiment has suddenly started producing errors in the 
bioconductor devel branch because our unit tests are failing, even though we 
haven’t pushed any changes and they passed previously. We first noticed this on 
April 5th. 

I believe the source of these errors likely do to calls to 
SummarizedExperiment() creating the following messages due to conflicts in 
‘RNeXML’ and ’S4Vectors’ both defining class ‘Annotated':

> Found more than one class "Annotated" in cache; using the first, from 
> namespace 'S4Vectors'
> Also defined by ‘RNeXML’
This is killing a vast number of our tests where we repeatedly use 
‘expect_silent’ calls in our unit tests and SummarizedExperiment calls underlie 
everything.

We had this message issue two years ago 
(https://github.com/epurdom/clusterExperiment/issues/66), when it appeared to 
be a problem with two definitions of the ‘Annotated’ class in two packages that 
are both dependencies of packages we call. At that time, Michael Lawrence 
posted that he would fix the problem, and it was then fixed in later versions 
of bioconductor/R. But it appears to be back.  I am unfortunately unable to get 
the RNeXML package to compile from source on my computer with the current Mac 
OS X development binary which I just downloaded (2018-04-05 r74542), so I 
haven’t been able to completely redo the code that we presented in that earlier 
github issue to confirm it is the exact same problem. I am having to rely on 
the error reports/logs from both Bioconductor and TravisCI (e.g. 2018-04-07 
r74551), where this message shows up everywhere and didn’t before. Thus I’m 
guessing that since they are the same messages from before that the source is 
again the call to SummarizedExperiment. 

I would note that in development version 2018-03-22 r74446, where I was able to 
install all of the packages, I was not getting these messages. 

Thanks,
Elizabeth Purdom
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