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

[Dan Tenenbaum]

----- 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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