[Bioc-devel] Single Package Builder for New Package Submission

[Kern, Lori]

The updates are complete.  The Single Package Builder is now using Bioc 3.15 and R 4.2 for new package submissions.

We have identified a bug in BiocCheck that will cause current packages to fail in BiocCheckGitClone on the Single Package Builder Report.  That looks similar to the following:


===============================

 BiocCheckGitClone('spbtest3')

===============================


/usr/bin/tar: /home/pkgbuild/packagebuilder/workers/jobs/51/spbtest3_20211129101146/spbtest3: Cannot read: Is a directory /usr/bin/tar: At beginning of tape, quitting now /usr/bin/tar: Error is not recoverable: exiting now Warning in untar(pkgname, exdir = tmp_dir) :   /usr/bin/tar -xf '/home/pkgbuild/packagebuilder/workers/jobs/51/spbtest3_20211129101146/spbtest3' -C '/tmp/RtmpTIAZO0/fileadac1b5fa962' returned error code 2 This is BiocCheckGitClone version 1.31.13. BiocCheckGitClone is a work in progress. Output and severity of issues may change. * Checking valid files... * Checking DESCRIPTION... * Checking if DESCRIPTION is well formatted... Warning in read.dcf(file.path(package_dir, "DESCRIPTION")) :   cannot open compressed file '/tmp/RtmpTIAZO0/fileadac1b5fa962/spbtest3/DESCRIPTION', probable reason 'No such file or directory'     * ERROR: DESCRIPTION is malformed.     cannot open the connection

We are working on the patch right now.  In the meantime you can ignore this ERROR.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Kern, Lori <Lori.Shepherd using RoswellPark.org>
Sent: Monday, November 29, 2021 7:26 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Single Package Builder for New Package Submission

We will be making updates to the Single Package Builder for New Package Submissions throughout the morning.  This will cause some intermittent downtime on the build on commit feature of new submission review process.   We appreciate your patience while we update.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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