[Bioc-devel] Issue with lme4/Matrix in BioC 3.19 R 4.4

[Hoffman, Gabriel via Bioc-devel]

Due to a known issue 
(https://github.com/lme4/lme4/issues/775#issuecomment-2024392388) running 
lme4::lmer() fails in BioC 3.19 using R 4.4 2024-03-18 r86148 on the build site 
because of a discrepancy between the Matrix version and the version used when 
lme4 is compiled.

The solution is to update to Matrix 1.7 and then recompile lme4 from source.  
This will resolve the package failures in BioC 3.19

Best,
Gabriel




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Re: [Bioc-devel] Bioconductor package devel site not updating

[Hoffman, Gabriel]

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[Bioc-devel] Bioconductor package devel site not updating

[Hoffman, Gabriel]

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Re: [Bioc-devel] Bioconductor package build fails

[Hoffman, Gabriel]

uNVkNJulowod64k0PTDC5BHZkk
>=KuNqEpeopBuZGxLxcykyI2_IwkJE_oSorni83Ae717E=c5XRWImsmPTHqu8vDjbP_MZ-k
>E4pZylRmN0EZMQIqlA= prabclus_2.2-6   rlang_0.2.2
>
>  [67] pkgconfig_2.0.2  bitops_1.0-6 evaluate_0.12
>
>  [70] lattice_0.20-35  purrr_0.2.5  bindr_0.1.1
>
>  [73] GenomicAlignments_1.16.0 htmlwidgets_1.3  labeling_0.3
>
>  [76] bit_1.1-14   tidyselect_0.2.5 plyr_1.8.4
>
>  [79] magrittr_1.5 R6_2.3.0 gplots_3.0.1
>
>  [82] Hmisc_4.1-1  DBI_1.0.0pillar_1.3.0
>
>  [85] whisker_0.3-2foreign_0.8-71   withr_2.1.2
>
>  [88] mgcv_1.8-24  survival_2.42-6  RCurl_1.95-4.11
>
>  [91] nnet_7.3-12  tibble_1.4.2 crayon_1.3.4
>
>  [94] KernSmooth_2.23-15   rmarkdown_1.10   viridis_0.5.1
>
>  [97] locfit_1.5-9.1   grid_3.5.1   sva_3.28.0
>
>[100] data.table_1.11.8blob_1.1.1   diptest_0.75-7
>
>[103] digest_0.6.18xtable_1.8-3 munsell_0.5.0
>
>[106] viridisLite_0.3.0
> >
>
>
>On 10/11/2018 11:38 AM, Hoffman, Gabriel wrote:
>> I am the developer of the variancePartition package, and I recently
>>made some very small changes to the documentation of my package.  The
>>latest version 1.10.3 builds correctly on Bioconductor's Windows and OS
>>X machines but fails on Ubuntu:
>> 
>> 
>>https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_chec
>>kResults_release_bioc-2DLATEST_variancePartition_malbec2-2Dbuildsrc.html&
>>d=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKa
>>aPhzWA=zy-TmtsjB4a5Mwg313kvmlN0-6yO-6JDYZsT1nV6cCw=RBYxTA_a5mlzemSuuk
>>87tom-Q10dMclvh6KjhOGULDw=
>> 
>> The code in the package has been stable, and I am not able to reproduce
>>the error on by Ubuntu machine 14.04.5 LTS with R 3.5.1.
>> 
>> The issue has something to do with multithreading using doParallel.
>>The error is:
>> 
>> Warning in socketConnection("localhost", port = port, server = TRUE,
>>blocking = TRUE,  :
>>port 11104 cannot be opened
>> Quitting from lines 102-154 (variancePartition.Rnw)
>> Error: processing vignette 'variancePartition.Rnw' failed with
>>diagnostics:
>> cannot open the connection
>> Execution halted
>> 
>> With the Bioconductor 3.7 Freeze coming, I�m concerned about getting
>>stuck with a broken package.
>> 
>> Thanks,
>>   - Gabriel
>> 
>>  [[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=BK7q3XeAvimeWd
>>GbWY_wJYbW0WYiZvSXAJJKaaPhzWA=zy-TmtsjB4a5Mwg313kvmlN0-6yO-6JDYZsT1nV6c
>>Cw=5WZzTZGK1jX2QI5fKn_INmjLYyv876INVFqftwFxlT4=
>> 
>
>-- 
>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] Bioconductor package build fails

[Hoffman, Gabriel]

I am the developer of the variancePartition package, and I recently made some 
very small changes to the documentation of my package.  The latest version 
1.10.3 builds correctly on Bioconductor's Windows and OS X machines but fails 
on Ubuntu:

http://bioconductor.org/checkResults/release/bioc-LATEST/variancePartition/malbec2-buildsrc.html

The code in the package has been stable, and I am not able to reproduce the 
error on by Ubuntu machine 14.04.5 LTS with R 3.5.1.

The issue has something to do with multithreading using doParallel.  The error 
is:

Warning in socketConnection("localhost", port = port, server = TRUE, blocking = 
TRUE,  :
  port 11104 cannot be opened
Quitting from lines 102-154 (variancePartition.Rnw)
Error: processing vignette 'variancePartition.Rnw' failed with diagnostics:
cannot open the connection
Execution halted

With the Bioconductor 3.7 Freeze coming, I�m concerned about getting stuck with 
a broken package.

Thanks,
 - Gabriel

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[Bioc-devel] Issue with dependencies on Windows (tokay2)

[Hoffman, Gabriel]

Hi,
I am getting a dependency error in the development branch of my package 
variancePartition when Bioconductor builds my package.

ERROR: dependencies 'pbkrtest', 'lme4' are not available for package 
'variancePartition'

These are standard enough dependencies, especially lme4.  There is no issue on 
OS X or Ubuntu.  My R code has not changed since the Release branch, and that 
builds with no error.

Here is the devel page:
http://bioconductor.org/checkResults/3.7/bioc-LATEST/variancePartition/tokay2-buildsrc.html

Is anyone else having issues on the Windows machine?

Thanks,
- Gabriel

 --

Gabriel Hoffman, Ph.D.



Assistant Professor

Icahn Institute for Genomics and Multiscale Biology

Department of Genetics and Genomic Sciences

Icahn School of Medicine at Mount Sinai



gabriel.hoff...@mssm.edu



1425 Madison Avenue

New York, NY 10029

Icahn Building L3-70B

212-659-1635


http://gabrielhoffman.github.io

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[Bioc-devel] git push to Bioconductor failing

[Hoffman, Gabriel]

Hi,

I am having an issue pushing changes from my git repo to Bioconductor.  I can 
push changes to Github just fine.


Here my push command fails.


> git push upstream

FATAL: W any packages/variancePartition gabrielhoffman DENIED by fallthru

(or you mis-spelled the reponame)

fatal: Could not read from remote repository.


Please make sure you have the correct access rights

and the repository exists.

I have the proper upstream location set


> git remote -v

origin https://github.com/GabrielHoffman/variancePartition.git (fetch)

origin https://github.com/GabrielHoffman/variancePartition.git (push)

upstream g...@git.bioconductor.org:packages/variancePartition (fetch)

upstream g...@git.bioconductor.org:packages/variancePartition (push)


But it seems like I don't have write access to this repo.


> ssh -T g...@git.bioconductor.org | grep variancePartition

 R  packages/variancePartition



I have registered my SSH RSA key with Bioconductor, and I have received the 
emails saying it was approved.  But I still do not have write access.


Do you have any suggestions to debug this?


Thanks,

- Gabriel




--

Gabriel Hoffman, Ph.D.



Assistant Professor

Icahn Institute for Genomics and Multiscale Biology

Department of Genetics and Genomic Sciences

Icahn School of Medicine at Mount Sinai



gabriel.hoff...@mssm.edu



1425 Madison Avenue

New York, NY 10029

Icahn Building L3-70B

212-659-1635


http://gabrielhoffman.github.io

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[Bioc-devel] git push to Bioconductor failing

[Hoffman, Gabriel]

n> git push upstream

FATAL: W any packages/variancePartition gabrielhoffman DENIED by fallthru

(or you mis-spelled the reponame)

fatal: Could not read from remote repository.


Please make sure you have the correct access rights

and the repository exists.



> ssh -T g...@git.bioconductor.org | grep variancePartition

 R   packages/variancePartition





> git remote -v

origin https://github.com/GabrielHoffman/variancePartition.git (fetch)

origin https://github.com/GabrielHoffman/variancePartition.git (push)

upstream g...@git.bioconductor.org:packages/variancePartition (fetch)

upstream g...@git.bioconductor.org:packages/variancePartition (push)

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