date:20240228

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 these

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

https://cran.r-project.org/doc/manuals/r-patched/R-

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)
install_github("klausjung-hannover/boo

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] TADCompare, permissions denied

2024-02-28 Thread Mikhail Dozmorov

Thank you, solved. Another reminder that Docker containers don't have
access to the ~/.ssh folder. Pushing from the local terminal after
debugging in a container helps.

Thanks,
Mikhail

On Wed, Feb 28, 2024 at 8:42 AM Kern, Lori 
wrote:

> Everything looks correct on our configuration.  You might need to add a
> new ssh key to your BiocCredentials account.  Or since there are multiple
> keys on your account already, explicitly state the correct ssh key you
> would like to use .
>
>
> 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
> Mikhail Dozmorov 
> *Sent:* Wednesday, February 28, 2024 8:36 AM
> *To:* bioc-devel 
> *Subject:* [Bioc-devel] TADCompare, permissions denied
>
> I'm trying to push fixes for
>
> https://secure-web.cisco.com/1gTfFROxVBHZNIvNeHURcWxcDfldi3nsGs93V7hourmSWcnlL0k0cSLr_WO7fNoy78PEpV7edyoPDutmeTWRR6NYRBzNMRUi5DyN6tJTlu2C88HP4EfAj8UKHXIY9hsgcWgJf-rKfXc3DJJV-Oaqwzd3IDmchipQfFgOVHyAiGZMj2dmHBviUcN5aq4Bf5fnUfbp5fgDGQVXsMnN5GAuKqJaSbVeGypdoDLbqi_516zxe3M3axM6tINOkFCryo_vQ3ElgwoRGw3y3xkyCqjz1pvO-8ZkrW3h31QhX5S_9cR2lAiAfqBenSaWrBE24QOTb/https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.19%2Fbioc-LATEST%2FTADCompare%2Fnebbiolo1-buildsrc.html
> git remote -v
> biocg...@git.bioconductor.org:packages/TADCompare.git (fetch)
> biocg...@git.bioconductor.org:packages/TADCompare.git (push)
>
> E.g., for git fetch --all, I'm getting
> 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.
>
> Please, help
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
>
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>
>
> This email message may contain legally privileged and/or confidential
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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}}
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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>
> ___
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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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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] R package on Github uses Bioconductor depenencies and cant be installed.

2024-02-28 Thread Vincent Carey

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
>

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

2024-02-28 Thread Kern, Lori via Bioc-devel

Bioconductor packages need to be installed with BiocManager.  If you do 
BiocManager::install("klausjung-hannover/bootGSEA")  That should also find 
Bioconductor package dependencies.



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: Wednesday, February 28, 2024 8:59 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] R package on Github uses Bioconductor depenencies and 
cant be installed.

Hello,


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


https://secure-web.cisco.com/1mWRxOSlvd9QbWzcsR4ms_SdfUVeG_NS-4PWZehnLBuUGioIAl5-RzQtpIkRALKPMLukxikylL8LraUMueJUB_hjkYjGBv5vn2XFI16WqyL6qFglYE8sNL6Wx1diKBpC90DfA3CUP1BTgC-Mj74Ud0zf-QG42jLhkliViAaeWQzfmichedi3YXRAMaqH1uYP9OIswTrYrnlTimoU8cK6fLnjD7ogMSjw1Mc3WoExDgDPDyQV3Iptdk_1EhabzC-Y7gvtDk0QDzmNuc1MSfbER0terLnJBPqttea34jhLRTKUN1oc5tlEAF2UZPtaaBfxO/https%3A%2F%2Fgithub.com%2Fklausjung-hannover%2FbootGSEA%2Fblob%2Fmain%2FDESCRIPTION


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://secure-web.cisco.com/1h1CY3ac_CGJrKAEZ5jVkjq35qYN2XCsfI6LGP-42NkgSoTaRx83wf-QIHGIoBR3sVmpGJ40cqAUfYKg4kT6EFSSPmi9kyzZL7wfBaouyo8vPc_Kt-avJX6NQbTC5xiLtwnezxo7QZ_gUSX0EYm39MuNl8KU_NfvfXUK6b6HzfjtgIaK5CIGmsfQfd8s26K5DXbRR0nC2AyZJOQEok_SXHUdXxGeoT62N1f-Bx-a8Fsad8sfz2j2kxYsKeuYj7YuhHts9lk_35FzqV2ebiQhklvgwrrtEn4jpnImnI0EDtGD3dxngOUFQpp1Jpkf7ZFBK/https%3A%2F%2Fcran.r-project.org%2Fdoc%2Fmanuals%2Fr-patched%2FR-admin.html%23Installing-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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[Bioc-devel] R package on Github uses Bioconductor depenencies and cant be installed.

2024-02-28 Thread Ruff, Sergej

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] TADCompare, permissions denied

2024-02-28 Thread Kern, Lori via Bioc-devel

Everything looks correct on our configuration.  You might need to add a new ssh 
key to your BiocCredentials account.  Or since there are multiple keys on your 
account already, explicitly state the correct ssh key you would like to use .



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 Mikhail 
Dozmorov 
Sent: Wednesday, February 28, 2024 8:36 AM
To: bioc-devel 
Subject: [Bioc-devel] TADCompare, permissions denied

I'm trying to push fixes for
https://secure-web.cisco.com/1gTfFROxVBHZNIvNeHURcWxcDfldi3nsGs93V7hourmSWcnlL0k0cSLr_WO7fNoy78PEpV7edyoPDutmeTWRR6NYRBzNMRUi5DyN6tJTlu2C88HP4EfAj8UKHXIY9hsgcWgJf-rKfXc3DJJV-Oaqwzd3IDmchipQfFgOVHyAiGZMj2dmHBviUcN5aq4Bf5fnUfbp5fgDGQVXsMnN5GAuKqJaSbVeGypdoDLbqi_516zxe3M3axM6tINOkFCryo_vQ3ElgwoRGw3y3xkyCqjz1pvO-8ZkrW3h31QhX5S_9cR2lAiAfqBenSaWrBE24QOTb/https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.19%2Fbioc-LATEST%2FTADCompare%2Fnebbiolo1-buildsrc.html
git remote -v
biocg...@git.bioconductor.org:packages/TADCompare.git (fetch)
biocg...@git.bioconductor.org:packages/TADCompare.git (push)

E.g., for git fetch --all, I'm getting
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.

Please, help

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[Bioc-devel] TADCompare, permissions denied

2024-02-28 Thread Mikhail Dozmorov

I'm trying to push fixes for
https://master.bioconductor.org/checkResults/3.19/bioc-LATEST/TADCompare/nebbiolo1-buildsrc.html.
git remote -v
biocg...@git.bioconductor.org:packages/TADCompare.git (fetch)
biocg...@git.bioconductor.org:packages/TADCompare.git (push)

E.g., for git fetch --all, I'm getting
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.

Please, help

[[alternative HTML version deleted]]

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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] TADCompare, permissions denied

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] R package on Github uses Bioconductor depenencies and cant be installed.

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

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

Re: [Bioc-devel] TADCompare, permissions denied

[Bioc-devel] TADCompare, permissions denied

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