[Bioc-devel] What can I do if a depended package is not installed in Bioconductor build server

Anh N Tran tr@nnh@t@nh89 @ending from gm@il@com
Thu Nov 8 20:27:25 CET 2018

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.


On Thu, Nov 8, 2018 at 12:55 PM Obenchain, Valerie <
Valerie.Obenchain using 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.
> >
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> >
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