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

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

2024-02-28 Thread Shian Su via Bioc-devel

I believe that devtools just uses remotes under the hood, so it should work.

Shian

On 29 Feb 2024, at 11:42, Ruff, Sergej  wrote:

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 are already asking your end users to install {devtools}
(really {remotes}) first in order to install your package anyway, ie:

Instead of asking them to do this:

R> install.packages("remote")
R> remotes::install_github("klausjung-hannover/bootGSEA")


You should instead ask them to:

R> install.packages("BiocManager")
R> BiocManager::install("klausjung-hannover/bootGSEA")


HTH,
-steve

On Feb 28, 2024 at 6:22:48 AM, "Ruff, Sergej" 
wrote:

library(devtools)
install_github("klausjung-hannover/bootGSEA")

This command was used. Does it mean, I just need to provide instructions
to use Biocmanager:install() for teh End-users?

I want to make the installation process as smooth as possible. Meaning
there should be no need to install something else ideally.


Von: Vincent Carey 
Gesendet: Mittwoch, 28. Februar 2024 15:20:49
An: Ruff, Sergej
Cc: bioc-devel@r-project.org
Betreff: [EXTERN] Re: [Bioc-devel] R package on Github uses Bioconductor
depenencies and cant be installed.

What command was used?  BiocManager::install should resolve the
dependencies
whereas straight use of install.packages would not.

On Wed, Feb 28, 2024 at 9:07 AM Ruff, Sergej mailto:sergej.r...@tiho-hannover.de>> wrote:
Hello,


I have an R package on  Github that uses Bioconductor dependencies:


https://github.com/klausjung-hannover/bootGSEA/blob/main/DESCRIPTION


One reviewer recently sent me a message that he can´t install the package.

Itried installing the package on a new device and got the following error:


Installing package into
‘/home/sergejruff/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
ERROR: dependencies ‘topGO’, ‘ReactomePA’, ‘org.Mm.eg.db’ are not
available for package ‘bootGSEA’
* removing ‘/home/sergejruff/R/x86_64-pc-linux-gnu-library/4.3/bootGSEA’
Warning messages:
1: packages ‘org.Mm.eg.db’, ‘ReactomePA’, ‘topGO’ are not available for
this version of R

Versions of

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

2024-02-28 Thread Ruff, Sergej

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 are already asking your end users to install {devtools}
(really {remotes}) first in order to install your package anyway, ie:

Instead of asking them to do this:

R> install.packages("remote")
R> remotes::install_github("klausjung-hannover/bootGSEA")


You should instead ask them to:

R> install.packages("BiocManager")
R> BiocManager::install("klausjung-hannover/bootGSEA")


HTH,
-steve

On Feb 28, 2024 at 6:22:48 AM, "Ruff, Sergej" 
wrote:

library(devtools)
install_github("klausjung-hannover/bootGSEA")

This command was used. Does it mean, I just need to provide instructions
to use Biocmanager:install() for teh End-users?

I want to make the installation process as smooth as possible. Meaning
there should be no need to install something else ideally.


Von: Vincent Carey 
Gesendet: Mittwoch, 28. Februar 2024 15:20:49
An: Ruff, Sergej
Cc: bioc-devel@r-project.org
Betreff: [EXTERN] Re: [Bioc-devel] R package on Github uses Bioconductor
depenencies and cant be installed.

What command was used?  BiocManager::install should resolve the
dependencies
whereas straight use of install.packages would not.

On Wed, Feb 28, 2024 at 9:07 AM Ruff, Sergej mailto:sergej.r...@tiho-hannover.de>> wrote:
Hello,


I have an R package on  Github that uses Bioconductor dependencies:


https://github.com/klausjung-hannover/bootGSEA/blob/main/DESCRIPTION


One reviewer recently sent me a message that he can´t install the package.

Itried installing the package on a new device and got the following error:


Installing package into
‘/home/sergejruff/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
ERROR: dependencies ‘topGO’, ‘ReactomePA’, ‘org.Mm.eg.db’ are not
available for package ‘bootGSEA’
* removing ‘/home/sergejruff/R/x86_64-pc-linux-gnu-library/4.3/bootGSEA’
Warning messages:
1: packages ‘org.Mm.eg.db’, ‘ReactomePA’, ‘topGO’ are not available for
this version of R

Versions of these packages for your version of R might be available
elsewhere,
see the ideas at

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

2024-02-28 Thread Shian Su via Bioc-devel

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 are already asking your end users to install {devtools}
(really {remotes}) first in order to install your package anyway, ie:

Instead of asking them to do this:

R> install.packages("remote")
R> remotes::install_github("klausjung-hannover/bootGSEA")


You should instead ask them to:

R> install.packages("BiocManager")
R> BiocManager::install("klausjung-hannover/bootGSEA")


HTH,
-steve

On Feb 28, 2024 at 6:22:48 AM, "Ruff, Sergej" 
wrote:

library(devtools)
install_github("klausjung-hannover/bootGSEA")

This command was used. Does it mean, I just need to provide instructions
to use Biocmanager:install() for teh End-users?

I want to make the installation process as smooth as possible. Meaning
there should be no need to install something else ideally.


Von: Vincent Carey 
Gesendet: Mittwoch, 28. Februar 2024 15:20:49
An: Ruff, Sergej
Cc: bioc-devel@r-project.org
Betreff: [EXTERN] Re: [Bioc-devel] R package on Github uses Bioconductor
depenencies and cant be installed.

What command was used?  BiocManager::install should resolve the
dependencies
whereas straight use of install.packages would not.

On Wed, Feb 28, 2024 at 9:07 AM Ruff, Sergej mailto:sergej.r...@tiho-hannover.de>> wrote:
Hello,


I have an R package on  Github that uses Bioconductor dependencies:


https://github.com/klausjung-hannover/bootGSEA/blob/main/DESCRIPTION


One reviewer recently sent me a message that he can´t install the package.

Itried installing the package on a new device and got the following error:


Installing package into
‘/home/sergejruff/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
ERROR: dependencies ‘topGO’, ‘ReactomePA’, ‘org.Mm.eg.db’ are not
available for package ‘bootGSEA’
* removing ‘/home/sergejruff/R/x86_64-pc-linux-gnu-library/4.3/bootGSEA’
Warning messages:
1: packages ‘org.Mm.eg.db’, ‘ReactomePA’, ‘topGO’ are not available for
this version of R

Versions of these packages for your version of R might be available
elsewhere,
see the ideas at

https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
2: In i.p(...) :
installation of package
‘/tmp/Rtmpnq6hVG/filed7528253e49/bootGSEA_1.0.tar.gz’ had non-zero exit
status


The CRAN dependencies install fine but Bioconductor packages refuse to
install.


Is there a way to solve the problem?


I use the following command:


library(devtools)

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

2024-02-28 Thread Ruff, Sergej

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 
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 are already asking your end users to install {devtools}
> (really {remotes}) first in order to install your package anyway, ie:
>
> Instead of asking them to do this:
>
> R> install.packages("remote")
> R> remotes::install_github("klausjung-hannover/bootGSEA")
>
>
> You should instead ask them to:
>
> R> install.packages("BiocManager")
> R> BiocManager::install("klausjung-hannover/bootGSEA")
>
>
> HTH,
> -steve
>
> On Feb 28, 2024 at 6:22:48 AM, "Ruff, Sergej" 
> wrote:
>
> > library(devtools)
> > install_github("klausjung-hannover/bootGSEA")
> >
> > This command was used. Does it mean, I just need to provide instructions
> > to use Biocmanager:install() for teh End-users?
> >
> > I want to make the installation process as smooth as possible. Meaning
> > there should be no need to install something else ideally.
> >
> > 
> > Von: Vincent Carey 
> > Gesendet: Mittwoch, 28. Februar 2024 15:20:49
> > An: Ruff, Sergej
> > Cc: bioc-devel@r-project.org
> > Betreff: [EXTERN] Re: [Bioc-devel] R package on Github uses Bioconductor
> > depenencies and cant be installed.
> >
> > What command was used?  BiocManager::install should resolve the
> > dependencies
> > whereas straight use of install.packages would not.
> >
> > On Wed, Feb 28, 2024 at 9:07 AM Ruff, Sergej  > > wrote:
> > Hello,
> >
> >
> > I have an R package on  Github that uses Bioconductor dependencies:
> >
> >
> > https://github.com/klausjung-hannover/bootGSEA/blob/main/DESCRIPTION
> >
> >
> > One reviewer recently sent me a message that he can´t install the package.
> >
> > Itried installing the package on a new device and got the following error:
> >
> >
> > Installing package into
> > ‘/home/sergejruff/R/x86_64-pc-linux-gnu-library/4.3’
> > (as ‘lib’ is unspecified)
> > ERROR: dependencies ‘topGO’, ‘ReactomePA’, ‘org.Mm.eg.db’ are not
> > available for package ‘bootGSEA’
> > * removing ‘/home/sergejruff/R/x86_64-pc-linux-gnu-library/4.3/bootGSEA’
> > Warning messages:
> > 1: packages ‘org.Mm.eg.db’, ‘ReactomePA’, ‘topGO’ are not available for
> > this version of R
> >
> > Versions of these packages for your version of R might be available
> > elsewhere,
> > see the ideas at
> >
> > https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
> > 2: In i.p(...) :
> >  installation of package
> > ‘/tmp/Rtmpnq6hVG/filed7528253e49/bootGSEA_1.0.tar.gz’ had non-zero exit
> > status
> >
> >
> > The CRAN dependencies install fine but Bioconductor packages refuse to
> > install.
> >
> >
> > Is there a way to solve the problem?
> >
> >
> > I use the following command:
> >
> >
> > library(devtools)
> > install_github("klausjung-hannover/bootGSEA")
> >
> >
> > I read that I should use biocView to the description file, but i couldn´t
> > find a good source where someone explains why thats right or what biocView
> > does?
> >
> > Could someone help me with my problem and explain if adding Biocview helps
> > and more importantly why?
> >
> >
> > Best, Sergej
> >
> >[[alternative HTML version deleted]]
> >
> >

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

2024-02-28 Thread Gábor Csárdi

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 are already asking your end users to install {devtools}
> (really {remotes}) first in order to install your package anyway, ie:
>
> Instead of asking them to do this:
>
> R> install.packages("remote")
> R> remotes::install_github("klausjung-hannover/bootGSEA")
>
>
> You should instead ask them to:
>
> R> install.packages("BiocManager")
> R> BiocManager::install("klausjung-hannover/bootGSEA")
>
>
> HTH,
> -steve
>
> On Feb 28, 2024 at 6:22:48 AM, "Ruff, Sergej" 
> wrote:
>
> > library(devtools)
> > install_github("klausjung-hannover/bootGSEA")
> >
> > This command was used. Does it mean, I just need to provide instructions
> > to use Biocmanager:install() for teh End-users?
> >
> > I want to make the installation process as smooth as possible. Meaning
> > there should be no need to install something else ideally.
> >
> > 
> > Von: Vincent Carey 
> > Gesendet: Mittwoch, 28. Februar 2024 15:20:49
> > An: Ruff, Sergej
> > Cc: bioc-devel@r-project.org
> > Betreff: [EXTERN] Re: [Bioc-devel] R package on Github uses Bioconductor
> > depenencies and cant be installed.
> >
> > What command was used?  BiocManager::install should resolve the
> > dependencies
> > whereas straight use of install.packages would not.
> >
> > On Wed, Feb 28, 2024 at 9:07 AM Ruff, Sergej  > > wrote:
> > Hello,
> >
> >
> > I have an R package on  Github that uses Bioconductor dependencies:
> >
> >
> > https://github.com/klausjung-hannover/bootGSEA/blob/main/DESCRIPTION
> >
> >
> > One reviewer recently sent me a message that he can´t install the package.
> >
> > Itried installing the package on a new device and got the following error:
> >
> >
> > Installing package into
> > ‘/home/sergejruff/R/x86_64-pc-linux-gnu-library/4.3’
> > (as ‘lib’ is unspecified)
> > ERROR: dependencies ‘topGO’, ‘ReactomePA’, ‘org.Mm.eg.db’ are not
> > available for package ‘bootGSEA’
> > * removing ‘/home/sergejruff/R/x86_64-pc-linux-gnu-library/4.3/bootGSEA’
> > Warning messages:
> > 1: packages ‘org.Mm.eg.db’, ‘ReactomePA’, ‘topGO’ are not available for
> > this version of R
> >
> > Versions of these packages for your version of R might be available
> > elsewhere,
> > see the ideas at
> >
> > https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
> > 2: In i.p(...) :
> >  installation of package
> > ‘/tmp/Rtmpnq6hVG/filed7528253e49/bootGSEA_1.0.tar.gz’ had non-zero exit
> > status
> >
> >
> > The CRAN dependencies install fine but Bioconductor packages refuse to
> > install.
> >
> >
> > Is there a way to solve the problem?
> >
> >
> > I use the following command:
> >
> >
> > library(devtools)
> > install_github("klausjung-hannover/bootGSEA")
> >
> >
> > I read that I should use biocView to the description file, but i couldn´t
> > find a good source where someone explains why thats right or what biocView
> > does?
> >
> > Could someone help me with my problem and explain if adding Biocview helps
> > and more importantly why?
> >
> >
> > Best, Sergej
> >
> >[[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> > The information in this e-mail is intended only for th...{{dropped:22}}
>
> ___
> 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

___

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

2024-02-28 Thread Martin Morgan

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 are already asking your end users to install {devtools}
(really {remotes}) first in order to install your package anyway, ie:

Instead of asking them to do this:

R> install.packages("remote")
R> remotes::install_github("klausjung-hannover/bootGSEA")


You should instead ask them to:

R> install.packages("BiocManager")
R> BiocManager::install("klausjung-hannover/bootGSEA")


HTH,
-steve

On Feb 28, 2024 at 6:22:48 AM, "Ruff, Sergej" 
wrote:

> library(devtools)
> install_github("klausjung-hannover/bootGSEA")
>
> This command was used. Does it mean, I just need to provide instructions
> to use Biocmanager:install() for teh End-users?
>
> I want to make the installation process as smooth as possible. Meaning
> there should be no need to install something else ideally.
>
> 
> Von: Vincent Carey 
> Gesendet: Mittwoch, 28. Februar 2024 15:20:49
> An: Ruff, Sergej
> Cc: bioc-devel@r-project.org
> Betreff: [EXTERN] Re: [Bioc-devel] R package on Github uses Bioconductor
> depenencies and cant be installed.
>
> What command was used?  BiocManager::install should resolve the
> dependencies
> whereas straight use of install.packages would not.
>
> On Wed, Feb 28, 2024 at 9:07 AM Ruff, Sergej  > wrote:
> Hello,
>
>
> I have an R package on  Github that uses Bioconductor dependencies:
>
>
> https://github.com/klausjung-hannover/bootGSEA/blob/main/DESCRIPTION
>
>
> One reviewer recently sent me a message that he can´t install the package.
>
> Itried installing the package on a new device and got the following error:
>
>
> Installing package into
> ‘/home/sergejruff/R/x86_64-pc-linux-gnu-library/4.3’
> (as ‘lib’ is unspecified)
> ERROR: dependencies ‘topGO’, ‘ReactomePA’, ‘org.Mm.eg.db’ are not
> available for package ‘bootGSEA’
> * removing ‘/home/sergejruff/R/x86_64-pc-linux-gnu-library/4.3/bootGSEA’
> Warning messages:
> 1: packages ‘org.Mm.eg.db’, ‘ReactomePA’, ‘topGO’ are not available for
> this version of R
>
> Versions of these packages for your version of R might be available
> elsewhere,
> see the ideas at
>
> https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
> 2: In i.p(...) :
>  installation of package
> ‘/tmp/Rtmpnq6hVG/filed7528253e49/bootGSEA_1.0.tar.gz’ had non-zero exit
> status
>
>
> The CRAN dependencies install fine but Bioconductor packages refuse to
> install.
>
>
> Is there a way to solve the problem?
>
>
> I use the following command:
>
>
> library(devtools)
> install_github("klausjung-hannover/bootGSEA")
>
>
> I read that I should use biocView to the description file, but i couldn´t
> find a good source where someone explains why thats right or what biocView
> does?
>
> Could someone help me with my problem and explain if adding Biocview helps
> and more importantly why?
>
>
> Best, Sergej
>
>[[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> The information in this e-mail is intended only for th...{{dropped:22}}

___
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[[alternative HTML version deleted]]

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

2024-02-28 Thread Steve Lianoglou

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 are already asking your end users to install {devtools}
(really {remotes}) first in order to install your package anyway, ie:

Instead of asking them to do this:

R> install.packages("remote")
R> remotes::install_github("klausjung-hannover/bootGSEA")


You should instead ask them to:

R> install.packages("BiocManager")
R> BiocManager::install("klausjung-hannover/bootGSEA")


HTH,
-steve

On Feb 28, 2024 at 6:22:48 AM, "Ruff, Sergej" 
wrote:

> library(devtools)
> install_github("klausjung-hannover/bootGSEA")
>
> This command was used. Does it mean, I just need to provide instructions
> to use Biocmanager:install() for teh End-users?
>
> I want to make the installation process as smooth as possible. Meaning
> there should be no need to install something else ideally.
>
> 
> Von: Vincent Carey 
> Gesendet: Mittwoch, 28. Februar 2024 15:20:49
> An: Ruff, Sergej
> Cc: bioc-devel@r-project.org
> Betreff: [EXTERN] Re: [Bioc-devel] R package on Github uses Bioconductor
> depenencies and cant be installed.
>
> What command was used?  BiocManager::install should resolve the
> dependencies
> whereas straight use of install.packages would not.
>
> On Wed, Feb 28, 2024 at 9:07 AM Ruff, Sergej  > wrote:
> Hello,
>
>
> I have an R package on  Github that uses Bioconductor dependencies:
>
>
> https://github.com/klausjung-hannover/bootGSEA/blob/main/DESCRIPTION
>
>
> One reviewer recently sent me a message that he can´t install the package.
>
> Itried installing the package on a new device and got the following error:
>
>
> Installing package into
> ‘/home/sergejruff/R/x86_64-pc-linux-gnu-library/4.3’
> (as ‘lib’ is unspecified)
> ERROR: dependencies ‘topGO’, ‘ReactomePA’, ‘org.Mm.eg.db’ are not
> available for package ‘bootGSEA’
> * removing ‘/home/sergejruff/R/x86_64-pc-linux-gnu-library/4.3/bootGSEA’
> Warning messages:
> 1: packages ‘org.Mm.eg.db’, ‘ReactomePA’, ‘topGO’ are not available for
> this version of R
>
> Versions of these packages for your version of R might be available
> elsewhere,
> see the ideas at
>
> https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
> 2: In i.p(...) :
>  installation of package
> ‘/tmp/Rtmpnq6hVG/filed7528253e49/bootGSEA_1.0.tar.gz’ had non-zero exit
> status
>
>
> The CRAN dependencies install fine but Bioconductor packages refuse to
> install.
>
>
> Is there a way to solve the problem?
>
>
> I use the following command:
>
>
> library(devtools)
> install_github("klausjung-hannover/bootGSEA")
>
>
> I read that I should use biocView to the description file, but i couldn´t
> find a good source where someone explains why thats right or what biocView
> does?
>
> Could someone help me with my problem and explain if adding Biocview helps
> and more importantly why?
>
>
> Best, Sergej
>
>[[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> The information in this e-mail is intended only for th...{{dropped:22}}

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

2024-02-28 Thread Ruff, Sergej

library(devtools)
install_github("klausjung-hannover/bootGSEA")

This command was used. Does it mean, I just need to provide instructions to use 
Biocmanager:install() for teh End-users?

I want to make the installation process as smooth as possible. Meaning there 
should be no need to install something else ideally.


Von: Vincent Carey 
Gesendet: Mittwoch, 28. Februar 2024 15:20:49
An: Ruff, Sergej
Cc: bioc-devel@r-project.org
Betreff: [EXTERN] Re: [Bioc-devel] R package on Github uses Bioconductor 
depenencies and cant be installed.

What command was used?  BiocManager::install should resolve the dependencies
whereas straight use of install.packages would not.

On Wed, Feb 28, 2024 at 9:07 AM Ruff, Sergej 
mailto:sergej.r...@tiho-hannover.de>> wrote:
Hello,


I have an R package on  Github that uses Bioconductor dependencies:


https://github.com/klausjung-hannover/bootGSEA/blob/main/DESCRIPTION


One reviewer recently sent me a message that he can´t install the package.

Itried installing the package on a new device and got the following error:


Installing package into ‘/home/sergejruff/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
ERROR: dependencies ‘topGO’, ‘ReactomePA’, ‘org.Mm.eg.db’ are not available for 
package ‘bootGSEA’
* removing ‘/home/sergejruff/R/x86_64-pc-linux-gnu-library/4.3/bootGSEA’
Warning messages:
1: packages ‘org.Mm.eg.db’, ‘ReactomePA’, ‘topGO’ are not available for this 
version of R

Versions of these packages for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
2: In i.p(...) :
  installation of package ‘/tmp/Rtmpnq6hVG/filed7528253e49/bootGSEA_1.0.tar.gz’ 
had non-zero exit status


The CRAN dependencies install fine but Bioconductor packages refuse to install.


Is there a way to solve the problem?


I use the following command:


library(devtools)
install_github("klausjung-hannover/bootGSEA")


I read that I should use biocView to the description file, but i couldn´t find 
a good source where someone explains why thats right or what biocView does?

Could someone help me with my problem and explain if adding Biocview helps and 
more importantly why?


Best, Sergej

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

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

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

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

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

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

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

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

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

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

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