[Bioc-devel] seq2pathway install and build error

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Thu Sep 17 16:37:10 CEST 2020

In your git repository, you have in the DESCRIPTION file

seq2pathway master$ tail -n 1 DESCRIPTION
Built: R 3.5.2

So R thinks the package was built for a version that is not compatible with the current version.

There are additional lines that don't belong in the 'source' version of your DESCRIPTION file, I think the following should be removed

-Packaged: 2019-02-27 20:41:28 UTC; jennifersun Packaged: 2018-10-31 00:33:19 UTC; biocbuild
-git_url: https://git.bioconductor.org/packages/seq2pathway
-git_branch: master
-git_last_commit: 4ed0bbc
-git_last_commit_date: 2020-08-18
-Date/Publication: 2020-04-27
-Built: R 3.5.2

and generally it looks like what you've done is downloaded the 'source' tarball and used that to populate your git repository -- directories


need to be removed.

It seems also like there are files that shouldn't be included, including several copies (in different folders) of .DS_store, .Rhistory, and .Rapp.history. You should remove these, and perhaps add a '.gitignore' file to the top-level of your repository to flag these as files that should be ignored by git in the future

Remove these, and things should be back on track...


On 9/16/20, 12:33 PM, "Bioc-devel on behalf of Yuxi Sun" <bioc-devel-bounces using r-project.org on behalf of ysun11 using uchicago.edu> wrote:


    We are writing on behalf of the development team for the Bioconductor
    package seq2pathway. There are two problems we are encountering that we
    wish to seek some insights from the team.

    1) Our Windows installation throws this error message:

    Warning: *** someone has corrupted the Built field in package 'seq2pathway' ***
    * installing *binary* package 'seq2pathway' ...
    cp: unknown option -- )
    Try '/usr/bin/cp --help' for more information.
    ERROR: installing binary package failed
    * removing 'C:/Users/biocbuild/bbs-3.12-bioc/meat/seq2pathway.buildbin-libdir/seq2pathway'

    Would anyone kindly help us understand the implications of this error

    2) When we run R CMD build on Linux and Mac machines, there is an error
    message when creating vignette:

    Warning: package ‘seq2pathway’ is not available (for R version 4.0.0)

    Error: processing vignette 'seq2pathwaypackage.Rnw' failed with diagnostics:

     chunk 1 (label = setup)

    Error : package or namespace load failed for ‘seq2pathway’:

     package ‘seq2pathway’ was installed before R 4.0.0: please re-install it

    How should we fix this problem?

    Thanks and regards,


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