Re: [Bioc-devel] What can I do if a depended package is not installed in Bioconductor build server
Thank you for your helpful response, Valerie. My main concern was that the issue would persist which could make my package unsuitable for bioconductor 3.9 release next year. However, it does not seem to be the case from your explanation. For now I will focus on making sure my package works well with Linux and Windows, and worry about Mac later. Sincerely, Anh On Thu, Nov 8, 2018 at 12:55 PM Obenchain, Valerie < valerie.obench...@roswellpark.org> wrote: > Hi Anh, > > We don't build CRAN packages from source on the Windows and Mac builders > but instead install the binaries. Building all CRAN packages from source > would require installation and maintenance of many more system > dependencies. We may decide to support this in the future but currently > it's not done. > > There is no R 3.6 El Capitan binary for devtools available which is why > it's not installed on merida2: > >https://cran.r-project.org/web/packages/devtools/index.html > > Actually none of the CRAN packages have el-capitan R 3.6 binaries yet: > >https://cran.r-project.org/bin/macosx/el-capitan/contrib/3.6/ > > We hope the binaries will be built soon. You could make a request for > this on the R-SIG-MAC mailing list: > >https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > Valerie > > > On 11/8/18 10:16 AM, Anh N Tran wrote: > > Hello, > > > > I noticed that multiple packages currently have errors because 'devtools' > > was not installed on merida2. I wonder if the issue will go away > eventually > > or we will have to make changes to our packages to pass the check. > > > > For my HPAanalyze package specifically, merida2 also didn't have the > > XLConnect package and gave me errors. I worked around that by replacing > > XLConnect with openxlsx, which was actually a positive change for my > > package. However, devtools is a lot harder to replace as it is an > integral > > part of my package development workflow. > > > > May you help me to understand how packages are installed in the build > > servers, and what I can do to fix the problem, please? > > > > Thank you, > > Anh Tran. > > > > [[alternative HTML version deleted]] > > > > ___ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] What can I do if a depended package is not installed in Bioconductor build server
Hi Anh, We don't build CRAN packages from source on the Windows and Mac builders but instead install the binaries. Building all CRAN packages from source would require installation and maintenance of many more system dependencies. We may decide to support this in the future but currently it's not done. There is no R 3.6 El Capitan binary for devtools available which is why it's not installed on merida2: https://cran.r-project.org/web/packages/devtools/index.html Actually none of the CRAN packages have el-capitan R 3.6 binaries yet: https://cran.r-project.org/bin/macosx/el-capitan/contrib/3.6/ We hope the binaries will be built soon. You could make a request for this on the R-SIG-MAC mailing list: https://stat.ethz.ch/mailman/listinfo/r-sig-mac Valerie On 11/8/18 10:16 AM, Anh N Tran wrote: > Hello, > > I noticed that multiple packages currently have errors because 'devtools' > was not installed on merida2. I wonder if the issue will go away eventually > or we will have to make changes to our packages to pass the check. > > For my HPAanalyze package specifically, merida2 also didn't have the > XLConnect package and gave me errors. I worked around that by replacing > XLConnect with openxlsx, which was actually a positive change for my > package. However, devtools is a lot harder to replace as it is an integral > part of my package development workflow. > > May you help me to understand how packages are installed in the build > servers, and what I can do to fix the problem, please? > > Thank you, > Anh Tran. > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] What can I do if a depended package is not installed in Bioconductor build server
Hello, I noticed that multiple packages currently have errors because 'devtools' was not installed on merida2. I wonder if the issue will go away eventually or we will have to make changes to our packages to pass the check. For my HPAanalyze package specifically, merida2 also didn't have the XLConnect package and gave me errors. I worked around that by replacing XLConnect with openxlsx, which was actually a positive change for my package. However, devtools is a lot harder to replace as it is an integral part of my package development workflow. May you help me to understand how packages are installed in the build servers, and what I can do to fix the problem, please? Thank you, Anh Tran. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] submitting a tiny data package (GmapGenome.Hsapiens.rCRS)
What's the best/fastest way to do this? The package (MTseeker) will happily build and install it for the user via the indexMTgenome() function, but since I test for its presence prior to running examples, it seems like I might as well have it available through BioC. Thanks, --t [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocManager and local Bioconductor mirror
Let's continue this on github at
https://github.com/Bioconductor/BiocManager/issues/31
On 11/8/18, 6:31 AM, "Martin Morgan" wrote:
I'm not sure why this does not work.
The key is BiocManager::repositories(), which determines the repositories
where R looks for packages. R choose the first repository where it finds the
package (maybe of equivalent version, not exactly sure...). The first argument
to repositories() can be a site repository, so
> BiocManager::repositories("https://ima.repo;)
site_repository
"https://ima.repo;
BioCsoft
"https://bioconductor.org/packages/3.9/bioc;
...
The Bioc repositories themselves are based on getOption("BioC_mirror") and
getOption("repos"), so
> options(BioC_mirror = "https://a.mirror.org;)
> BiocManager::repositories()
BioCsoft
"https://a.mirror.org/packages/3.9/bioc;
BioCann
"https://a.mirror.org/packages/3.9/data/annotation;
...
These can be file paths; we are just delegating to install.packages().
It sounds like this doesn't work, somehow for you. Can you elaborate?
Martin
On 11/8/18, 6:13 AM, "Bioc-devel on behalf of Rainer Johannes"
wrote:
Dear all,
I like the new BiocManager package with its new possibilities to
install specific versions of Bioconductor - but what I miss is the possibility
to specify a local Bioconductor mirror from which to install packages.
Our calculation clusters don't have direct internet access, so I am
mirroring CRAN and Bioconductor to local folders that are accessible by the
cluster. Previously, with BiocInstaller and biocLite.R, I could install
packages from these simply setting options(repos = "")
and options(BioC_mirror = ""). Now, with BiocManager
this does no longer work. Is it possible to specify a local mirror for
BiocManager? And if not - would it be possible to add this possibility?
thanks!
jo
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocManager and local Bioconductor mirror
I'm not sure why this does not work.
The key is BiocManager::repositories(), which determines the repositories where
R looks for packages. R choose the first repository where it finds the package
(maybe of equivalent version, not exactly sure...). The first argument to
repositories() can be a site repository, so
> BiocManager::repositories("https://ima.repo;)
site_repository
"https://ima.repo;
BioCsoft
"https://bioconductor.org/packages/3.9/bioc;
...
The Bioc repositories themselves are based on getOption("BioC_mirror") and
getOption("repos"), so
> options(BioC_mirror = "https://a.mirror.org;)
> BiocManager::repositories()
BioCsoft
"https://a.mirror.org/packages/3.9/bioc;
BioCann
"https://a.mirror.org/packages/3.9/data/annotation;
...
These can be file paths; we are just delegating to install.packages().
It sounds like this doesn't work, somehow for you. Can you elaborate?
Martin
On 11/8/18, 6:13 AM, "Bioc-devel on behalf of Rainer Johannes"
wrote:
Dear all,
I like the new BiocManager package with its new possibilities to install
specific versions of Bioconductor - but what I miss is the possibility to
specify a local Bioconductor mirror from which to install packages.
Our calculation clusters don't have direct internet access, so I am
mirroring CRAN and Bioconductor to local folders that are accessible by the
cluster. Previously, with BiocInstaller and biocLite.R, I could install
packages from these simply setting options(repos = "")
and options(BioC_mirror = ""). Now, with BiocManager
this does no longer work. Is it possible to specify a local mirror for
BiocManager? And if not - would it be possible to add this possibility?
thanks!
jo
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] BiocManager and local Bioconductor mirror
Dear all, I like the new BiocManager package with its new possibilities to install specific versions of Bioconductor - but what I miss is the possibility to specify a local Bioconductor mirror from which to install packages. Our calculation clusters don't have direct internet access, so I am mirroring CRAN and Bioconductor to local folders that are accessible by the cluster. Previously, with BiocInstaller and biocLite.R, I could install packages from these simply setting options(repos = "") and options(BioC_mirror = ""). Now, with BiocManager this does no longer work. Is it possible to specify a local mirror for BiocManager? And if not - would it be possible to add this possibility? thanks! jo ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
