[Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

[Charles Warden]

Hi,

I recently received error messages for 2 packages.  As a worst-case-scenario, it is acceptable if the sRAP package had to be removed.  However, I need to resolve the issue for the COHCAP package.

This is odd because I don’t think I have updated either package in the last year or so.  In fact, if I check the CHANGES file in the COHCAP package, the last change I manually noted was v1.29.3, which I can see was added to the GitHub version of the code on 3/2/2019:

https://github.com/cwarden45/COHCAP/commits/master/CHANGES

I can successfully install the package, with either the GitHub or Bioconductor instructions.  However, I want to correct the error because I don’t want the Bioconductor package to be removed.

I had some dependency issues on some systems related to the PDF generation (which I would usually ignore).  However, if I run “R CMD build” on an Ubuntu system where I have all dependencies installed, I don’t get any error message:

$ R CMD build COHCAP
* checking for file ‘COHCAP/DESCRIPTION’ ... OK
* preparing ‘COHCAP’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
Warning: ‘inst/doc’ files
    ‘COHCAP.Rnw’, ‘COHCAP.pdf’, ‘COHCAP.R’
  ignored as vignettes have been rebuilt.
  Run R CMD build with --no-build-vignettes to prevent rebuilding.
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘COHCAP_1.33.0.tar.gz’

I am using the development version, which I thought should match what was being tested for the BioC 3.11 error message.

Can you please either tell me what I need to do to reproduce (and then correct) this error, or confirm that it is OK to ignore the e-mails that I have received recently?

Thank You,
Charles

Charles Warden, Bioinformatics Specialist
Integrative Genomics Core
City of Hope National Medical Center
Shamrock Monrovia Building (655 Huntington Dr, Monrovia, CA, 91016)
Room 1086
Internal Ext: 80375 | Direct: 626-218-0375
Work-From-Home Cell: 404-316-0012

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