segmentSeq 2.4.0
Thomas J. Hardcastle
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/segmentSeq | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf segmentSeq.buildbin-libdir segmentSeq.Rcheck && mkdir segmentSeq.buildbin-libdir segmentSeq.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=segmentSeq.buildbin-libdir segmentSeq_2.4.0.tar.gz >segmentSeq.Rcheck\00install.out 2>&1 && cp segmentSeq.Rcheck\00install.out segmentSeq-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=segmentSeq.buildbin-libdir --install="check:segmentSeq-install.out" --force-multiarch --no-vignettes --timings segmentSeq_2.4.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/segmentSeq.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'segmentSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'segmentSeq' version '2.4.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'segmentSeq' can be installed ... OK
* checking installed package size ... NOTE
installed size is 10.0Mb
sub-directories of 1Mb or more:
extdata 9.2Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'GenomicRanges' which was already attached by Depends.
Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.chrProcessing: no visible global function definition for 'seqlengths'
.chrProcessing: no visible global function definition for 'seqlevels'
.classifyNulls : <anonymous>: no visible global function definition for
'seqlengths'
.constructMethNulls: no visible global function definition for
'seqlevels'
.constructNullPriors: no visible global function definition for
'seqlevels'
.constructNulls: no visible global function definition for 'seqlevels'
.findMethChunks: no visible global function definition for 'seqlevels'
.getCounts: no visible global function definition for 'seqlevels'
.getCounts : <anonymous>: no visible global function definition for
'clusterCall'
.getCounts : <anonymous>: no visible global function definition for
'parLapplyLB'
.getLocLikelihoods: no visible global function definition for
'clusterExport'
.getLocLikelihoods: no visible global function definition for
'parRapply'
.getMethylatedCounts: no visible global function definition for
'seqlevels'
.getMethylatedCounts: no visible global function definition for
'clusterEvalQ'
.getOverlaps: no visible global function definition for 'seqlevels'
.getOverlaps : <anonymous>: no visible global function definition for
'clusterExport'
.getOverlaps : <anonymous>: no visible global function definition for
'clusterCall'
.getOverlaps : <anonymous>: no visible global function definition for
'parApply'
.getOverlaps: no visible global function definition for 'clusterEvalQ'
.lociLikelihoods: no visible global function definition for 'abind'
.partheuristicSeg: no visible global function definition for
'seqlevels'
.partheuristicSeg : <anonymous>: no visible global function definition
for 'seqlengths'
.partheuristicSeg : <anonymous>: no visible global function definition
for 'seqlevels'
.plotSampleMeth: no visible global function definition for 'seqlengths'
.processPosts: no visible global function definition for 'clusterEvalQ'
.processPosts: no visible global function definition for 'seqlevels'
.processPosts : <anonymous>: no visible global function definition for
'seqlengths'
.processTags: no visible global function definition for 'seqlevels'
.processTags: no visible global function definition for 'seqlengths'
.processTags: no visible global function definition for 'seqlengths<-'
.squeezeAlign: no visible global function definition for 'seqlevels'
.subProfile: no visible global function definition for 'seqlevels'
findChunks: no visible global function definition for 'seqlevels'
plotGenome: no visible global function definition for 'seqlevels'
plotGenome: no visible global function definition for 'seqlevels<-'
processAD: no visible global function definition for 'seqlevels'
readBAM: no visible global function definition for 'Seqinfo'
readBAM : <anonymous>: no visible global function definition for
'scanBam'
readBAM : <anonymous>: no visible global function definition for
'ScanBamParam'
readBAM : <anonymous>: no visible global function definition for
'seqlevels'
readGeneric: no visible global function definition for 'Seqinfo'
readGeneric : <anonymous>: no visible global function definition for
'seqlevels'
readMeths: no visible binding for global variable 'seqlevels'
readMeths : <anonymous>: no visible global function definition for
'seqlevels<-'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'plotMethDistribution':
plotMethDistribution
Code: function(meth, samples, bw = 0.001, subtract, chrs,
centromeres, add = FALSE, col, ylim = NULL, legend =
TRUE, ...)
Docs: function(meth, samples, bw = 0.001, subtract, chrs,
centromeres, add = FALSE, col, legend = TRUE, ...)
Argument names in code not in docs:
ylim
Mismatches in argument names:
Position: 9 Code: ylim Docs: legend
Position: 10 Code: legend Docs: ...
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [112s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
classifySeg 39.31 0.03 39.36
readMeths 13.69 0.39 14.07
lociLikelihoods 12.20 0.00 12.21
heuristicSeg 9.55 0.00 9.55
plotGenome 5.86 0.00 5.93
** running examples for arch 'x64' ... [139s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
classifySeg 50.40 0.00 50.41
lociLikelihoods 17.03 0.01 17.05
heuristicSeg 16.02 0.02 16.03
readMeths 12.79 0.33 13.12
plotGenome 7.51 0.00 7.51
getCounts 5.39 0.00 5.43
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/segmentSeq.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'segmentSeq' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'segmentSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'segmentSeq' as segmentSeq_2.4.0.zip
* DONE (segmentSeq)