[Bioc-devel] BiocCheck Local and Single Package Builder Discrepancy

----- Original Message -----
From: "David Kuo" <dkuo at cbio.mskcc.org>
To: "bioc-devel" <bioc-devel at r-project.org>
Sent: Friday, April 1, 2016 1:13:47 PM
Subject: [Bioc-devel] BiocCheck Local and Single Package Builder Discrepancy
Hi,

I'm observing different results from executing BiocCheck, version 1.7.9 locally
and the build output.

The tar.gz output locally shows no Warnings and outputs this:
======================================
* Checking for support site registration...
* Maintainer is registered at support site!

The Single Package Builder, on the other hand, outputs this from the same
tar.gz:
======================================
* Checking for bioc-devel mailing list subscription...
   * REQUIRED: Maintainer should subscribe to the bioc-devel mailing
     list. Subscribe here:
     https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
* Maintainer is registered at support site!

There doesn't seem to be a check on on the local version of BiocCheck that
matches the Single Package Builder version 
Yes, that's correct. As mentioned in the vignette, this check requires special credentials that are available on the build machines but not to end users.
and thus, we're struggling to fix
this mailing list subscription warning. Also puzzling to us is that the
Maintainer has the same email attached to an older version of our package
(MMDiff).

The maintainer for MMDiff2 is G.Schweikert at ed.ac.uk. I just checked manually and it does not look like that address is subscribed. Although I do see that gschweik at staffmail.ed.ac.uk is subscribed, so maybe change the package DESCRIPTION file to match that address?

Dan
Any help or guidance would be greatly appreciated.

Thanks,
David

sessionInfo()
R Under development (unstable) (2016-03-28 r70390)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.4 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
methods
[9] base

other attached packages:
[1] MMDiff2_0.99.6        BiocCheck_1.7.9       Biobase_2.31.3
[4] Rsamtools_1.23.6      Biostrings_2.39.12    XVector_0.11.7
[7] GenomicRanges_1.23.25 GenomeInfoDb_1.7.6    IRanges_2.5.40
[10] S4Vectors_0.9.44      BiocGenerics_0.17.3   httr_1.1.0

loaded via a namespace (and not attached):
[1] Rcpp_0.12.4                 formatR_1.3
[3] plyr_1.8.3                  BiocInstaller_1.21.4
[5] RColorBrewer_1.1-2          bitops_1.0-6
[7] tools_3.4.0                 zlibbioc_1.17.1
[9] digest_0.6.9                jsonlite_0.9.19
[11] lattice_0.20-33             memoise_1.0.0
[13] gtable_0.2.0                BSgenome_1.39.4
[15] graph_1.49.1                shiny_0.13.2
[17] curl_0.9.6                  stringr_1.0.0
[19] rtracklayer_1.31.9          knitr_1.12.3
[21] devtools_1.10.0             locfit_1.5-9.1
[23] grid_3.4.0                  getopt_1.20.0
[25] optparse_1.3.2              R6_2.1.2
[27] XML_3.98-1.4                RBGL_1.47.0
[29] BiocParallel_1.5.21         magrittr_1.5
[31] ggplot2_2.1.0               htmltools_0.3.5
[33] scales_0.4.0                codetools_0.2-14
[35] biocViews_1.39.8            GenomicAlignments_1.7.20
[37] RUnit_0.4.31                SummarizedExperiment_1.1.22
[39] xtable_1.8-2                mime_0.4
[41] colorspace_1.2-6            httpuv_1.3.3
[43] stringi_1.0-1               RCurl_1.95-4.8
[45] munsell_0.4.3
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