Oscar Reina
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/htSeqTools |
| Branch: RELEASE_3_8 |
| Last Commit: 613ed18 |
| Last Changed Date: 2018-10-30 11:42:09 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:29:25 -0400 (Sat, 13 Apr 2019).
| Package 738/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| htSeqTools 1.30.0 Oscar Reina
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: htSeqTools |
| Version: 1.30.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:htSeqTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings htSeqTools_1.30.0.tar.gz |
| StartedAt: 2019-04-13 03:05:03 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 03:10:27 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 323.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: htSeqTools.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:htSeqTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings htSeqTools_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/htSeqTools.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'htSeqTools/DESCRIPTION' ... OK
* this is package 'htSeqTools' version '1.30.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 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 'C:/Users/biocbuild/bbs-3.8-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
* 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
* 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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
giniCoverage 5.15 0.49 5.63
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
giniCoverage 7.56 0.07 7.62
* 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
'C:/Users/biocbuild/bbs-3.8-bioc/meat/htSeqTools.Rcheck/00check.log'
for details.
htSeqTools.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/htSeqTools_1.30.0.tar.gz && rm -rf htSeqTools.buildbin-libdir && mkdir htSeqTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=htSeqTools.buildbin-libdir htSeqTools_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL htSeqTools_1.30.0.zip && rm htSeqTools_1.30.0.tar.gz htSeqTools_1.30.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1505k 100 1505k 0 0 9129k 0 --:--:-- --:--:-- --:--:-- 9349k
install for i386
* 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
converting help for package 'htSeqTools'
finding HTML links ... done
alignPeaks html
cmds html
cmdsFit-class html
cmdsFit html
countHitsWindow html
coverageDiff html
enrichedChrRegions html
enrichedPeaks html
enrichedRegions html
extendRanges html
fdrEnrichedCounts html
filterDuplReads html
findPeakHeight html
giniCoverage html
gridCover-class html
htSample html
islandCounts html
listOverlap html
mergeRegions html
plot-methods html
plotChrRegions html
regionsCoverage html
rowLogRegLRT html
ssdCoverage html
stdPeakLocation html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'htSeqTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'htSeqTools' as htSeqTools_1.30.0.zip
* DONE (htSeqTools)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'htSeqTools' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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htSeqTools.Rcheck/examples_i386/htSeqTools-Ex.timings
|
htSeqTools.Rcheck/examples_x64/htSeqTools-Ex.timings
|