Oscar Reina
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/htSeqTools |
| Branch: RELEASE_3_7 |
| Last Commit: f8ef34c |
| Last Changed Date: 2018-06-11 09:07:43 -0400 (Mon, 11 Jun 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:23:43 -0400 (Wed, 17 Oct 2018).
| Package 699/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| htSeqTools 1.28.3 Oscar Reina
| malbec2 | Linux (Ubuntu 16.04.1 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: 1.28.3 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:htSeqTools.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings htSeqTools_1.28.3.tar.gz |
| StartedAt: 2018-10-16 01:11:14 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 01:13:58 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 163.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: htSeqTools.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:htSeqTools.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings htSeqTools_1.28.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/htSeqTools.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.28.3’
* 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-3.7-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 5.528 0.02 5.555
* 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-3.7-bioc/meat/htSeqTools.Rcheck/00check.log’
for details.
htSeqTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL htSeqTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-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 | 0.144 | 0.000 | 0.146 | |
| cmds | 1.256 | 0.012 | 1.286 | |
| cmdsFit-class | 0.000 | 0.000 | 0.001 | |
| cmdsFit | 0.000 | 0.000 | 0.001 | |
| countHitsWindow | 0.052 | 0.000 | 0.055 | |
| coverageDiff | 0.112 | 0.000 | 0.112 | |
| enrichedChrRegions | 1.256 | 0.076 | 1.334 | |
| enrichedPeaks | 0.796 | 0.016 | 0.810 | |
| enrichedRegions | 0.204 | 0.008 | 0.212 | |
| extendRanges | 0.156 | 0.008 | 0.162 | |
| fdrEnrichedCounts | 0.116 | 0.008 | 0.126 | |
| filterDuplReads | 0.224 | 0.000 | 0.227 | |
| findPeakHeight | 0.852 | 0.000 | 0.852 | |
| giniCoverage | 5.528 | 0.020 | 5.555 | |
| gridCover-class | 0 | 0 | 0 | |
| htSample | 0.236 | 0.012 | 0.249 | |
| islandCounts | 0.264 | 0.000 | 0.266 | |
| listOverlap | 0.004 | 0.000 | 0.006 | |
| mergeRegions | 0.032 | 0.004 | 0.036 | |
| plot-methods | 0.000 | 0.000 | 0.001 | |
| plotChrRegions | 0.008 | 0.000 | 0.010 | |
| regionsCoverage | 0 | 0 | 0 | |
| rowLogRegLRT | 0.000 | 0.000 | 0.002 | |
| ssdCoverage | 0.196 | 0.012 | 0.210 | |
| stdPeakLocation | 0.212 | 0.004 | 0.216 | |