[Bioc-devel] split on IRanges semantic change 3.3->3.4

Dear All, I ran into the following change in behaviour between the 3.3 and 3.4 Bioconductor releases. The following code returns TRUE for 3.3 and FALSE for 3.4 library(GenomicRanges) ir <- IRanges(sample(100),sample(100)+100) ir2 <- unlist(split(ir, ceiling(1:100 / 10))) all(ir==ir2) The

[Bioc-devel] Implementation of vmatchPattern Indels

Good day, I notice that with.indels has been a parameter to vmatchPattern for almost a decade but is only a stub. I am hoping that this suggestion could put it into future development plans so the underlying functionality could be implemented soon. It could be a useful option for preprocessing

Re: [Bioc-devel] biconductor build error and warning

Thank you so much Dan!! From: Dan Tenenbaum Sent: Sunday, December 4, 2016 1:41:59 PM To: Dwivedi, Bhakti Cc: bioc-devel Subject: Re: [Bioc-devel] biconductor build error and warning - Original Message - > From: "Bhakti Dwivedi"

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

I don't really understand your question. But, create an inst/extdata directory: md inst md inst\extdata ... add your files to inst\extdata ... git add inst\extdata git commit git push Dan - Original Message - > From: "Jurat Shayidin" > To: "Dan Tenenbaum"

[Bioc-devel] biconductor build error and warning

Could anyone please help me with the below two bioconductor build error and warnings? I am getting the below ERROR Bioconductor build msg on Mac OS X (https://github.com/Bioconductor/Contributions/issues/202) installing the package to build vignettes ERROR: dependency HH is not available for

[Bioc-devel] pdflatex not found on oaxaca (Mac OS X Mavericks (10.9.5)/x86_64) - R CMD check fails

Hi, I'm stuck in the submission process and encounter the following error when CHECK is performed (on oaxaca): * checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. * checking PDF version of manual without hyperrefs or index

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

Dear Dan : Thanks again for your kind help. I did clean up my package git working tree, make every commit readable, tractable. I've read about R writing extension manual and that helped a lot. Many thanks to Herve' insightful answer to overcome file permission issue, R CMD check working perfectly