[Bioc-devel] Bioconductor Devel Build Machines Set to Daily Build Schedule, Release Set to MWF

2024-03-07 Thread Jennifer Wokaty 
In preparation for the next release, the 3.19 devel builders will run daily 
except for Saturday. The release builders will run Monday, Wednesday, and 
Friday.

R has also been updated on the release and devel builders.

We'll also add the following flag to the Renviron.bioc for the devel Linux 
builder to catch ordered comparisons on language objects:

_R_COMPARE_LANG_OBJECTS=eqonly

For more information, see 
https://stat.ethz.ch/pipermail/r-devel/2024-March/083254.html.

Jennifer Wokaty (they/them)

Waldron Lab at CUNY SPH
Bioconductor Core Team

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Re: [Bioc-devel] [EXTERN] Re: R package on Github uses Bioconductor depenencies and cant be installed.

2024-03-07 Thread Kern, Lori via Bioc-devel 
It looks like a permission denied ERROR. Perhaps  R was installed as root and 
you do not have access to write to the default R install directory.  You should 
install to a directory you do have write permissions by setting a lib argument 
or by setting the .libPaths()


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Ruff, Sergej 

Sent: Thursday, March 7, 2024 7:51 AM
To: Shian Su 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] [EXTERN] Re: R package on Github uses Bioconductor 
depenencies and cant be installed.

Hello,


I tried using biocManager:install but it doesnt seem to work. I am using Ubuntu 
and I get the following error when installing


installing to /usr/lib/R/library/00LOCK-survival/00new/survival/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (survival)

The downloaded source packages are in
‘/tmp/RtmpFjeZ5j/downloaded_packages’
Updating HTML index of packages in '.Library'
Warning messages:
1: In i.p(...) : installation of package ‘igraph’ had non-zero exit status
2: In i.p(...) :
  installation of package ‘graphlayouts’ had non-zero exit status
3: In i.p(...) :
  installation of package ‘tidygraph’ had non-zero exit status
4: In i.p(...) : installation of package ‘ggraph’ had non-zero exit status
5: In i.p(...) :
  installation of package ‘enrichplot’ had non-zero exit status
6: In i.p(...) :
  installation of package ‘ReactomePA’ had non-zero exit status
7: In i.p(...) :
  installation of package ‘clusterProfiler’ had non-zero exit status
8: In i.p(...) :
  installation of package 
‘/tmp/RtmpFjeZ5j/file631b384ef274/bootGSEA_1.0.tar.gz’ had non-zero exit status
9: In file.create(f.tg) :
  cannot create file '/usr/share/R/doc/html/packages.html', reason 'Permission 
denied'
10: In make.packages.html(.Library) : cannot update HTML package index


I get a similar error when using Windows.


Von: Bioc-devel  im Auftrag von Ruff, Sergej 

Gesendet: Donnerstag, 29. Februar 2024 01:42:00
An: Shian Su
Cc: bioc-devel@r-project.org
Betreff: Re: [Bioc-devel] [EXTERN] Re: R package on Github uses Bioconductor 
depenencies and cant be installed.

Does it apply only to the remotes package or also to devtools::install_git 
function?


Sergej


Von: Shian Su 
Gesendet: Donnerstag, 29. Februar 2024 01:39:18
An: Ruff, Sergej
Cc: bioc-devel@r-project.org
Betreff: [EXTERN] Re: [Bioc-devel] [EXTERN] Re: R package on Github uses 
Bioconductor depenencies and cant be installed.

Sorry if this is spam, I think my last message got bounced because my mail 
client converted the GitHub link into a nice jpg.

As you mentioned, you can just add biocViews: Software to your DESCRIPTION: 
https://secure-web.cisco.com/1wopfqFdwbMQtSarDm0LQ5OAWXDMubuw81X9h1N3RWB4uVHvJx7WgJV8LNWW2WYAMAg3ifiyrGL93M0S19PQvOjQmQxzwCJ02_9ZVOzD6npQcShn2ZOXFHHP-rc6zNEmJ0ibZvSjIFbcbiJAazBDZhkm9ax0TV9qbdt44QTf0VWgl_CJ44bcDnlKZ2hFvj7eUEHRmU4Y0yf3pHla6TM07vw2TTZjTrkQe-Fk14hM0XJ2O7T3293sIhdA6c4AcfhJVuPJvzCxqnvMFTApxxraX7woOU-3np4EDXS5iSrA3r21Sn5U4P8easYdRJ8J-Zfkb/https%3A%2F%2Fgithub.com%2Fr-lib%2Fremotes%2Fissues%2F477
 If you need further explanation then the code is here: 
https://secure-web.cisco.com/1cE54cuJDX8io0J_UdaJEuI1tyCrNkFRdVvlHFN-olu-1QNeet_Xr_yx8g44lO0xcst7dRL61HPQiE3uPKdGV7MzyT2YbUByZiRihhvJRilb3dCjPl855QZRJtGIK3dBwYiimWvQ1-HH-m89pfTjTBB0gd1pLpWWiSFqp3DhUMIvPLz2mOcy_yzoFipxgFmgWQkvBRHCpW3-6DMGaKoPffLnGgEJdxHqeMxYm__dfAKQZX1Yzaa588EPx7w88aXJyctel8kF7E9FNAPcD_H_s_ouWWGAcTZukWntgCZKTR-34qK2hSvDEJl7Xyt-_lbf2/https%3A%2F%2Fgithub.com%2Fr-lib%2Fremotes%2Fblob%2Fb9091cc471ea59471d10981330a868402e1b7bd9%2Finstall-github.R%23L687-L694

Adding the field causes remotes to add BioC to the repo list when installing 
dependencies. I think it's worth doing so your users can use remotes if they 
want and not have to install/use other installation managers.

Shian

On 29 Feb 2024, at 11:24, Ruff, Sergej  wrote:

Thank you,


I am still wondering why everyone on the internet mentions adding "biocView" to 
the DESCRIPTIOn-File. I couldn´t find a source for that but everyone on 
Biostart, Stackoverflow or any other forum keeps mentioning adding biocView.


What does adding biocView do if anything? When should I add BiocView to the 
DESCRIPTION-File?


Von: Gábor Csárdi

Re: [Bioc-devel] [EXTERN] Re: R package on Github uses Bioconductor depenencies and cant be installed.

2024-03-07 Thread Ruff, Sergej 
Hello,


I tried using biocManager:install but it doesnt seem to work. I am using Ubuntu 
and I get the following error when installing


installing to /usr/lib/R/library/00LOCK-survival/00new/survival/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (survival)

The downloaded source packages are in
‘/tmp/RtmpFjeZ5j/downloaded_packages’
Updating HTML index of packages in '.Library'
Warning messages:
1: In i.p(...) : installation of package ‘igraph’ had non-zero exit status
2: In i.p(...) :
  installation of package ‘graphlayouts’ had non-zero exit status
3: In i.p(...) :
  installation of package ‘tidygraph’ had non-zero exit status
4: In i.p(...) : installation of package ‘ggraph’ had non-zero exit status
5: In i.p(...) :
  installation of package ‘enrichplot’ had non-zero exit status
6: In i.p(...) :
  installation of package ‘ReactomePA’ had non-zero exit status
7: In i.p(...) :
  installation of package ‘clusterProfiler’ had non-zero exit status
8: In i.p(...) :
  installation of package 
‘/tmp/RtmpFjeZ5j/file631b384ef274/bootGSEA_1.0.tar.gz’ had non-zero exit status
9: In file.create(f.tg) :
  cannot create file '/usr/share/R/doc/html/packages.html', reason 'Permission 
denied'
10: In make.packages.html(.Library) : cannot update HTML package index


I get a similar error when using Windows.


Von: Bioc-devel  im Auftrag von Ruff, Sergej 

Gesendet: Donnerstag, 29. Februar 2024 01:42:00
An: Shian Su
Cc: bioc-devel@r-project.org
Betreff: Re: [Bioc-devel] [EXTERN] Re: R package on Github uses Bioconductor 
depenencies and cant be installed.

Does it apply only to the remotes package or also to devtools::install_git 
function?


Sergej


Von: Shian Su 
Gesendet: Donnerstag, 29. Februar 2024 01:39:18
An: Ruff, Sergej
Cc: bioc-devel@r-project.org
Betreff: [EXTERN] Re: [Bioc-devel] [EXTERN] Re: R package on Github uses 
Bioconductor depenencies and cant be installed.

Sorry if this is spam, I think my last message got bounced because my mail 
client converted the GitHub link into a nice jpg.

As you mentioned, you can just add biocViews: Software to your DESCRIPTION: 
https://github.com/r-lib/remotes/issues/477. If you need further explanation 
then the code is here: 
https://github.com/r-lib/remotes/blob/b9091cc471ea59471d10981330a868402e1b7bd9/install-github.R#L687-L694

Adding the field causes remotes to add BioC to the repo list when installing 
dependencies. I think it's worth doing so your users can use remotes if they 
want and not have to install/use other installation managers.

Shian

On 29 Feb 2024, at 11:24, Ruff, Sergej  wrote:

Thank you,


I am still wondering why everyone on the internet mentions adding "biocView" to 
the DESCRIPTIOn-File. I couldn´t find a source for that but everyone on 
Biostart, Stackoverflow or any other forum keeps mentioning adding biocView.


What does adding biocView do if anything? When should I add BiocView to the 
DESCRIPTION-File?


Von: Gábor Csárdi mailto:csardi.ga...@gmail.com>>
Gesendet: Mittwoch, 28. Februar 2024 19:32:40
An: Martin Morgan
Cc: Steve Lianoglou; Ruff, Sergej; 
bioc-devel@r-project.org
Betreff: Re: [Bioc-devel] [EXTERN] Re: R package on Github uses Bioconductor 
depenencies and cant be installed.

While the remotes package still works, https://github.com/r-lib/pak is
now a better alternative. It also comes with built-in Bioconductor
support:

pak::pkg_install("klausjung-hannover/bootGSEA")

Gabor

On Wed, Feb 28, 2024 at 4:52 PM Martin Morgan  wrote:

Actually BiocManager delegates to remotes, and remotes is only a 'Suggests', so 
the user needs to have both remotes and BiocManager

 pkgs <- c("remotes", "BiocManager")
 pkgs <- setdiff(pkgs, rownames(installed.packages())
 install.packages(pkgs)

and then

 BiocManager::install("/")

or

 remotes::install_github("/", repos = 
BiocManager::repositories())

The `setdiff()` isn't really quite good enough because it wouldn't install an 
updated version of BiocManager or remotes…

From: Bioc-devel  on behalf of Steve 
Lianoglou 
Date: Wednesday, February 28, 2024 at 10:46 AM
To: Ruff, Sergej 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] [EXTERN] Re: R package on Github uses Bioconductor 
depenencies and cant be installed.
As was already mentioned, your easiest path forward is to first ask your
users to install the {BiocManager} package from CRAN, then use that to
install your package.

As it is, you

Re: [Bioc-devel] Access rights for simPIC repository, git fetch error

2024-03-07 Thread Kern, Lori via Bioc-devel 
I would either add a new ssh key or check out the FAQ section at
http://contributions.bioconductor.org/git-version-control.html#faq
specifically, #13, 14, and 15



Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Sagrika Chugh 

Sent: Thursday, March 7, 2024 7:13 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Access rights for simPIC repository, git fetch error

Hi Bioconductor team,

I submitted a package called "simPIC" recently and want to make some
changes as the reviewer suggested.

I am following the instructions as mentioned here
https://secure-web.cisco.com/1ewkpsBTVEAXYF9LrstZgLo9sVMgZfeGHQQMQvWNGE5KRlrE-pr8Gi5qNnfQyFB7NpM1I9kQl2cyi7ggw9RJcVofNtzfhflM4z6xQ2E-QqD5Jpugpe529jKmTiNPqrMkvJX4R-stHfTlZKixFtDFYBtTBrQzLazRKcGGaEQeBgqVCRemnNK3adhUiLMrRXugyWOB_TYHdB1eL7-_vGPQLX6dWKfbLWnNoCqVdhiL_zuyExUT3bj0mGDaT4-Tpo55FZO1HDz38kATxMSlH3JwHz3-U4hJ2jA6QyojDCw_tRrO29fwPBjjrgrWfrGCC8vwb/https%3A%2F%2Fcontributions.bioconductor.org%2Fgit-version-control.html%23new-package-workflow

But I get an error when i try to fetch using git fetch --all

git fetch --all

Fetching origin

Fetching upstream

g...@git.bioconductor.org: Permission denied (publickey).

fatal: Could not read from remote repository.


Please make sure you have the correct access rights

and the repository exists.

error: could not fetch upstream

This is my remote status:

git remote -v

origin 
https://secure-web.cisco.com/13QKTOQsJtM0rHg-rPur8C-KbOLjZuBodt_Wi7RdUlt0lh3HSzopRBc4qodK_MwsnfA6_icjbc3zD_yt-qqHGcloj8ExKijOCVyJHBXH0fPHDMA1d-s0YGmNTdw0MYU_DEDB_szta220kx0oiWJadQAScL8qrkNOO66u50SdROF0bclo0t-mla0K5Ve6Y28PgN-P-u231vc3aB2WAdhRj8MyLbtypf_lLFTL6XpvehAA2cVgG4UID9Eb9an3wcRYgt_Xgq5P-wi0KG94kAtYWl_PAJGNcgxtVphbl_yUQ-RIVoRAqxQkkeGEebjvAcqLE/https%3A%2F%2Fgithub.com%2Fsagrikachugh%2FsimPIC
 (fetch)

origin 
https://secure-web.cisco.com/13QKTOQsJtM0rHg-rPur8C-KbOLjZuBodt_Wi7RdUlt0lh3HSzopRBc4qodK_MwsnfA6_icjbc3zD_yt-qqHGcloj8ExKijOCVyJHBXH0fPHDMA1d-s0YGmNTdw0MYU_DEDB_szta220kx0oiWJadQAScL8qrkNOO66u50SdROF0bclo0t-mla0K5Ve6Y28PgN-P-u231vc3aB2WAdhRj8MyLbtypf_lLFTL6XpvehAA2cVgG4UID9Eb9an3wcRYgt_Xgq5P-wi0KG94kAtYWl_PAJGNcgxtVphbl_yUQ-RIVoRAqxQkkeGEebjvAcqLE/https%3A%2F%2Fgithub.com%2Fsagrikachugh%2FsimPIC
 (push)

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

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


ssh -T g...@git.bioconductor.org

g...@git.bioconductor.org: Permission denied (publickey).


My Bioconductor git credentials account is already active and I can see
that I have access to my package there but there seems to be some issue
with the keys or permission.

Any advice would be greatly appreciated.

Thanks,
Sagrika

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[Bioc-devel] Access rights for simPIC repository, git fetch error

2024-03-07 Thread Sagrika Chugh 
Hi Bioconductor team,

I submitted a package called "simPIC" recently and want to make some
changes as the reviewer suggested.

I am following the instructions as mentioned here
https://contributions.bioconductor.org/git-version-control.html#new-package-workflow

But I get an error when i try to fetch using git fetch --all

git fetch --all

Fetching origin

Fetching upstream

g...@git.bioconductor.org: Permission denied (publickey).

fatal: Could not read from remote repository.


Please make sure you have the correct access rights

and the repository exists.

error: could not fetch upstream

This is my remote status:

git remote -v

origin https://github.com/sagrikachugh/simPIC (fetch)

origin https://github.com/sagrikachugh/simPIC (push)

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

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


ssh -T g...@git.bioconductor.org

g...@git.bioconductor.org: Permission denied (publickey).


My Bioconductor git credentials account is already active and I can see
that I have access to my package there but there seems to be some issue
with the keys or permission.

Any advice would be greatly appreciated.

Thanks,
Sagrika

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