Hi Fabricio,
If your package requires external software/libraries/tools in order to
pass 'R CMD build' and 'R CMD check', then please list them in the
SystemRequirements field of your DESCRIPTION file. In addition, we
kindly ask you to provide an INSTALL file in the top-level folder of
your package source tree that documents how to install these external
deps on all the supported platforms.
BTW I'm not sure that KnowSeq or ORFik have external system
requirements. I don't see that they have a SystemRequirements field.
Only openPrimeR has one but it's not clear to me that the package
actually needs all the things listed there e.g. for example MAFFT is
listed but we don't have it on the build machines.
FWIW most packages avoid having to depend on external tools like
SRAtoolkit, STAR or salmon by assuming that this step of the analysis
was already taken care of, and by focusing on the downstream analysis.
These packages often include the output of the upstream analysis as a
small dataset and start from there.
Hope this helps,
Best,
H.
On 23/08/2021 07:10, Fabricio de Almeida wrote:
Dear Bioc developers,
I am writing a package that contains external dependencies, and I'd like to
know what are the best practices to submit this kind of package to Bioconductor.
The external dependencies are standard RNA-seq analysis algorithms, such as
SRAtoolkit, STAR and salmon. I have seen other Bioc packages with external
dependencies, such as KnowSeq
(https://bioconductor.org/packages/release/bioc/html/KnowSeq.html), ORFik
(https://www.bioconductor.org/packages/release/bioc/html/ORFik.html), and
openPrimeR
(https://bioconductor.org/packages/release/bioc/html/openPrimeR.html), but it
is not clear how they handle the dependencies in the Bioconductor build system.
I have a conda environment containing all the dependencies + R 4.1.0, which
works fine. However, conda is not the best option, as some dependencies may not
exist in all OS, particularly in Windows.
Perhaps a Docker container with the dependencies in an Ubuntu OS would ensure
reproducibility in all platforms, but what should I do for the package to pass
all checks in the Bioc build system?
Any help is appreciated.
Best,
=========================
Fabr�cio de Almeida Silva
Undergraduate degree in Biological Sciences (UENF)
MSc. candidate in Plant Biotechnology (PGBV/UENF - RJ/Brazil)
Laborat�rio de Qu�mica e Fun��o de Prote�nas e Pept�deos (LQFPP/CBB/UENF -
RJ/Brazil)
Personal website: https://almeidasilvaf.github.io
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