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
