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" <mramo...@gmail.com> > To: "bioc-devel" <bioc-devel@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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
