[Bioc-devel] BiocCheck not passing at test check phase

[Dan Tenenbaum]

You found a bug in BiocCheck!

Now fixed in version 1.7.2 in devel.

Please update from git (https://github.com/Bioconductor/BiocCheck), svn (https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocCheck) or wait till tomorrow afternoon and install it with biocLite().

Thanks,
Dan


----- Original Message -----
> From: "Marcel Ramos" <mramos09 at gmail.com>
> To: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Tuesday, February 9, 2016 11:54:17 AM
> Subject: [Bioc-devel] BiocCheck not passing at test check phase

> Hi everyone,
> I am running into trouble when running BiocCheck from within RStudio and
> the command line. This check is for a package that would be going into the
> development branch. After running BiocCheck::BiocCheck("biocMultiAssay"), I
> get the following error:
> 
> * Checking unit tests...
> Warning in file(filename, "r") :
>  cannot open file '/tmp/RtmpLUhaD5/MultiAssayExperiment.R': No such file
> or directory
> Error in file(filename, "r") : cannot open the connection
> Calls: <Anonymous> ... BiocCheck -> parseFiles -> parseFile -> parse -> file
> Execution halted
> 
> After looking into the temp folder, I see that the file referenced in the
> error is actually the *vignette* file (after re-running the check with a
> renamed vignette file). The check tries to open the vignette file as an R
> file but it is unable to read the file with the right (or wrong) extension.
> The file in question "MultiAssayExperiment.Rmd.R" which was created in the
> temp folder by the check process. The original vignette file is an Rmd file
> named "MultiAssayExperiment.Rmd". I'm not sure how this file is included in
> the tests phase of the checks.
> 
> Thank you in advance for your help.
> 
> P.S. GitHub Repository: https://www.github.com/vjcitn/biocMultiAssay
> Regular check is passing.
> 
> Regards,
> Marcel Ramos
> 
> sessionInfo()
> R Under development (unstable) (2015-11-25 r69695)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 15.04
> 
> locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> LC_TIME=en_US.UTF-8
> [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8
> LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C
> 
> [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
> LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] biocMultiAssay_0.5.0
> 
> loaded via a namespace (and not attached):
> [1] graph_1.49.1                XVector_0.11.4              knitr_1.12.3
> 
> [4] zlibbioc_1.17.0             IRanges_2.5.24
> GenomicRanges_1.23.13
> [7] BiocGenerics_0.17.3         devtools_1.10.0
> BiocCheck_1.7.1
> [10] getopt_1.20.0               R6_2.1.2
> GenomeInfoDb_1.7.6
> [13] httr_1.1.0                  tools_3.3.0
> biocViews_1.39.4
> [16] SummarizedExperiment_1.1.18 parallel_3.3.0              Biobase_2.31.3
> 
> [19] RBGL_1.47.0                 digest_0.6.9                optparse_1.3.2
> 
> [22] S4Vectors_0.9.27            bitops_1.0-6
> codetools_0.2-14
> [25] rsconnect_0.4.1.11          RCurl_1.95-4.7              RUnit_0.4.31
> 
> [28] memoise_1.0.0               BiocInstaller_1.21.3        stats4_3.3.0
> 
> [31] XML_3.98-1.3
> 
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> 
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