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

[Marcel Ramos]

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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