Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2018-11-07 14:57:49 -0500 (Wed, 07 Nov 2018).
Package 731/1636 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
htSeqTools 1.31.0 Oscar Reina
| malbec2 | Linux (Ubuntu 18.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: htSeqTools |
Version: 1.31.0 |
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:htSeqTools.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings htSeqTools_1.31.0.tar.gz |
StartedAt: 2018-11-07 04:32:41 -0500 (Wed, 07 Nov 2018) |
EndedAt: 2018-11-07 04:36:21 -0500 (Wed, 07 Nov 2018) |
EllapsedTime: 219.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: htSeqTools.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:htSeqTools.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings htSeqTools_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/htSeqTools.Rcheck’ * using R Under development (unstable) (2018-10-16 r75448) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘htSeqTools/DESCRIPTION’ ... OK * this is package ‘htSeqTools’ version ‘1.31.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘multicore’ Depends: includes the non-default packages: 'BiocGenerics', 'Biobase', 'S4Vectors', 'IRanges', 'MASS', 'BSgenome', 'GenomeInfoDb', 'GenomicRanges' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 for sufficient/correct file permissions ... OK * checking whether package ‘htSeqTools’ can be installed ... WARNING Found the following significant warnings: Note: possible error in 'countHitsWindow(x, chrLengths = chrLengths, ': unused argument (chrLengths = chrLengths) Note: possible error in 'extendRanges(x, seqLen = seqLen, ': unused argument (chrLength = chrLength) See ‘/home/biocbuild/bbs-3.9-bioc/meat/htSeqTools.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ A package should be listed in only one of these fields. * 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 * 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 dependencies in R code ... NOTE 'library' or 'require' call to ‘parallel’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Package in Depends field not imported from: ‘Biobase’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported object imported by a ':::' call: ‘S4Vectors:::decodeRle’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE countHitsWindow,GRanges: possible error in countHitsWindow(x, chrLengths = chrLengths, windowSize = windowSize): unused argument (chrLengths = chrLengths) countHitsWindow,GRanges: no visible binding for global variable ‘chrLengths’ enrichedPeaks,RangedData-IRangesList-IRangesList: no visible global function definition for ‘pvec’ enrichedPeaks,RangedData-IRangesList-missing: no visible global function definition for ‘pvec’ extendRanges,GRanges: possible error in extendRanges(x, seqLen = seqLen, chrLength = chrLength, mc.cores = mc.cores): unused argument (chrLength = chrLength) extendRanges,GRanges: no visible binding for global variable ‘chrLength’ extendRanges,GRangesList: possible error in extendRanges(x, seqLen = seqLen, chrLength = chrLength, mc.cores = mc.cores): unused argument (chrLength = chrLength) extendRanges,GRangesList: no visible binding for global variable ‘chrLength’ findPeakHeight,RangedData-IRangesList-IRangesList: no visible global function definition for ‘pvec’ Undefined global functions or variables: chrLength chrLengths pvec * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed giniCoverage 5.961 0.048 6.017 * 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, 4 NOTEs See ‘/home/biocbuild/bbs-3.9-bioc/meat/htSeqTools.Rcheck/00check.log’ for details.
htSeqTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL htSeqTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘htSeqTools’ ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading Note: possible error in 'countHitsWindow(x, chrLengths = chrLengths, ': unused argument (chrLengths = chrLengths) Note: possible error in 'countHitsWindow(x, chrLengths = chrLengths, ': unused argument (chrLengths = chrLengths) Note: possible error in 'countHitsWindow(x, chrLengths = chrLengths, ': unused argument (chrLengths = chrLengths) Note: possible error in 'extendRanges(x, seqLen = seqLen, ': unused argument (chrLength = chrLength) Note: possible error in 'extendRanges(x, seqLen = seqLen, ': unused argument (chrLength = chrLength) Note: possible error in 'extendRanges(x, seqLen = seqLen, ': unused argument (chrLength = chrLength) Note: possible error in 'extendRanges(x, seqLen = seqLen, ': unused argument (chrLength = chrLength) Note: possible error in 'extendRanges(x, seqLen = seqLen, ': unused argument (chrLength = chrLength) Note: possible error in 'extendRanges(x, seqLen = seqLen, ': unused argument (chrLength = chrLength) ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (htSeqTools)
htSeqTools.Rcheck/htSeqTools-Ex.timings
name | user | system | elapsed | |
alignPeaks | 0.216 | 0.032 | 0.249 | |
cmds | 1.553 | 0.028 | 1.777 | |
cmdsFit-class | 0.001 | 0.000 | 0.001 | |
cmdsFit | 0 | 0 | 0 | |
countHitsWindow | 0.067 | 0.000 | 0.067 | |
coverageDiff | 0.15 | 0.00 | 0.15 | |
enrichedChrRegions | 2.283 | 0.064 | 2.356 | |
enrichedPeaks | 1.077 | 0.008 | 1.088 | |
enrichedRegions | 0.269 | 0.000 | 0.269 | |
extendRanges | 0.181 | 0.000 | 0.182 | |
fdrEnrichedCounts | 0.121 | 0.000 | 0.133 | |
filterDuplReads | 0.316 | 0.000 | 0.316 | |
findPeakHeight | 1.020 | 0.000 | 1.022 | |
giniCoverage | 5.961 | 0.048 | 6.017 | |
gridCover-class | 0 | 0 | 0 | |
htSample | 0.521 | 0.004 | 0.527 | |
islandCounts | 0.438 | 0.000 | 0.440 | |
listOverlap | 0.005 | 0.000 | 0.005 | |
mergeRegions | 0.04 | 0.00 | 0.04 | |
plot-methods | 0 | 0 | 0 | |
plotChrRegions | 0.011 | 0.000 | 0.011 | |
regionsCoverage | 0 | 0 | 0 | |
rowLogRegLRT | 0.001 | 0.000 | 0.002 | |
ssdCoverage | 0.240 | 0.016 | 0.256 | |
stdPeakLocation | 0.212 | 0.004 | 0.217 | |