Hi Daniel, I have the same issue with my package (new contribution). I just finish reviewing the package with the modifications requested.
I am having a warning because R CMD check is exceeding 5 min, but this is happening only in the Windows machine. In Linux and OSX the check finishes in <= 4min, while in Windows takes ~6min. http://bioconductor.org/spb_reports/maser_buildreport_20180425114748.html Not sure how to proceed from here. Thanks, Diogo On Thu, Apr 26, 2018 at 9:52 AM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > We have been working on the minfi package lately, with a move to a > DelayedArray backend. > > Right now there are some weird issues regarding timings in R CMD check. > Leaving aside the issue that the tests (now disabled) and examples are too > slow, we get some very weird behaviour. > > An example is the current (soon to be replace) build report of minfi 1.25.2 > which prints > > Examples with CPU or elapsed time > 5s > user system elapsed > preprocessFunnorm 99.388 0.632 148.554 > combineArrays 64.104 2.120 68.329 > bumphunter 62.540 1.392 64.107 > preprocessNoob 43.944 0.016 44.955 > preprocessQuantile 33.968 0.064 36.547 > getAnnotation 31.072 0.024 31.126 > compartments 18.668 0.188 18.871 > minfiQC 10.124 6.628 1102.929 > getSex 10.536 0.012 10.561 > read.metharray 7.504 2.116 82.713 > read.metharray.exp 9.076 0.032 10.592 > mapToGenome-methods 4.648 0.548 163.648 > mdsPlot 0.340 0.204 14.901 > > > on Tokay (Linux). Note minfiQC which has an elapsed time which is crazy > high compared to user+system. Previous build report (which I didn't save) > had a timeout on all platforms with a semingly similar behaviour but with > the getSex function. The code did not change in the meantime. For today's > build we only see this on Linux, but yesterday all platforms were affected. > > This is likely to be very hard to debug. But I am thinking memory issues: > this example requires loading an annotation package and a data package, > both of which are "big". How much RAM does the machines have and are > multiple R CMD check's run concurrently? > > Best, > Kasper > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
