search for: checksrc

...viously be no problem. One more issue: While I have always received this warning on my WinXP installation, for some lucky reason the warning did until now not appear on the Bioconductor Windows server, see BioC 2.6 with R-2.11.1: http://bioconductor.org/checkResults/2.6/bioc-LATEST/xps/liverpool-checksrc.html However, for some reason on BioC 2.7 running R-2.12.0 this warning does appear, see: http://bioconductor.org/checkResults/2.7/bioc-LATEST/xps/liverpool-checksrc.html For this reason I would appreciate if there would be a possibility to suppress this warning message. Thank you in advance....

...39; script gets also confused sometimes on Windows in a random way. It seems that sometimes (maybe 1% of the times) running 'R CMD check' is actually running another script, not the 'check' script, e.g., here http://bioconductor.org/checkResults/2.7/bioc-LATEST/geneplotter/gewurz-checksrc.html the output of the command looks like if 'R CMD build' was run instead of 'R CMD check'. Here http://bioconductor.org/checkResults/2.7/bioc-LATEST/lumi/gewurz-checksrc.html it looks like if 'R CMD Rd2txt' was run. Same here http://bioconductor.org/checkResults/2.7/...

...p://www.ebi.ac.uk/microarray-as/ae/files/E-TABM-25/E-TABM-25.raw.1.zip', tempfile()) sometimes gets 52% (according to the dialog box) of the way through, and then pauses or, when running R CMD check, truncates (see http://bioconductor.org/checkResults/devel/bioc-LATEST/ArrayExpress/moscato1-checksrc.html). I tried options(internet.info=0, timeout=600), without effect; the messages from internet.info are the same on successful and failed downloads. Thank you, Martin -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Locatio...

...data, shouldn't it reinstall the package in order to be able to do this correctly? Here is why. There is this new warning in 'R CMD check' that complains about files not of a type allowed in a 'data' directory: http://bioconductor.org/checkResults/2.8/bioc-LATEST/Icens/lamb1-checksrc.html The Icens package also has .R files under data/ with things like: bet <- matrix(scan("CMVdata", quiet=TRUE),nc=5,byr=TRUE) i.e. the R code needs to access some of the text files located in the data/ folder. So in order to get rid of this warning I tried to move those text fi...

Hi Mr Tierney, I have noticed an error message from R 1.12.x's CMD check for a while (apparently prof Ripley completely rewrote CMD check in R 1.12+) e.g.: http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/lamb2-checksrc.html ---------------- * checking R code for possible problems ... NOTE Warning: non-unique value when setting 'row.names': ?new? Error in `row.names<-.data.frame`(`*tmp*`, value = c("1", "new", "new" : duplicate 'row.names' are not allowed Calls:...

Hi, Warnings issued at installation time are not reported by 'R CMD check'. Some of them are really important and telling something very useful to the developer. See for example this warning: http://bioconductor.org/checkResults/2.9/bioc-LATEST/globaltest/wilson2-checksrc.html Actually, there is no formal warning reported by 'R CMD check' for this package but if you scroll down the report and look at the output produced during installation (globaltest.Rcheck/00install.out), you'll see this: * installing *source* package ?globaltest? ... ** R *...

...tGeneric in namespaceImportFrom should use named arguments because impenv, an environment, will be assigned to the mustFind arg which is most likely not desired. An example where this seems to show up is in the check reports for GOstats: http://bioconductor.org/checkResults/1.9/gopher5-GOstats-checksrc.html Here's the snip from the check output (the results may have been updated in the meantime): * checking whether the name space can be loaded with stated dependencies ... WARNING Loading required package: methods Error in if (mustFind) stop(gettextf("no generic function fou...