chipseq 1.26.0
Bioconductor Package Maintainer
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/chipseq | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf chipseq.buildbin-libdir chipseq.Rcheck && mkdir chipseq.buildbin-libdir chipseq.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chipseq.buildbin-libdir chipseq_1.26.0.tar.gz >chipseq.Rcheck\00install.out 2>&1 && cp chipseq.Rcheck\00install.out chipseq-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=chipseq.buildbin-libdir --install="check:chipseq-install.out" --force-multiarch --no-vignettes --timings chipseq_1.26.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/chipseq.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'chipseq/DESCRIPTION' ... OK
* this is package 'chipseq' version '1.26.0'
* 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 'chipseq' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'methods' 'BiocGenerics' 'IRanges' 'GenomicRanges' 'ShortRead'
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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.genomicContext: no visible global function definition for
'transcripts'
.genomicContext: no visible global function definition for 'cdsBy'
.genomicContext: no visible global function definition for
'threeUTRsByTranscript'
.genomicContext: no visible global function definition for
'fiveUTRsByTranscript'
.genomicContext: no visible global function definition for
'intronsByTranscript'
.nearestTss: no visible global function definition for 'transcripts'
.nearestTss: no visible global function definition for 'seqlevels<-'
.nearestTss: no visible global function definition for 'seqlevels'
applyPosByChrAndStrand: no visible global function definition for
'seqnames'
correlation.estimate: no visible binding for global variable 'mu'
correlation.estimate: no visible binding for global variable 'corr'
correlationProfile : <anonymous>: no visible global function definition
for 'subseq'
coverage.estimate: no visible binding for global variable 'mu'
coverage.estimate: no visible binding for global variable 'covered'
islandDepthPlot: no visible binding for global variable 'depth'
islandDepthPlot : <anonymous>: no visible global function definition
for 'panel.lines'
islandDepthPlot : <anonymous>: no visible global function definition
for 'panel.xyplot'
laneSubsample: no visible global function definition for 'seqnames'
laneSubsample: no visible global function definition for 'GRangesList'
subsetSummary: no visible global function definition for 'seqlengths'
subsetSummary: no visible global function definition for 'GRanges'
subsetSummary: no visible global function definition for 'seqnames'
subsetSummary: no visible global function definition for 'seqlengths<-'
estimate.mean.fraglen,GRanges: no visible global function definition
for 'seqnames'
Undefined global functions or variables:
GRanges GRangesList cdsBy corr covered depth fiveUTRsByTranscript
intronsByTranscript mu panel.lines panel.xyplot seqlengths
seqlengths<- seqlevels seqlevels<- seqnames subseq
threeUTRsByTranscript transcripts
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic 'densityCorr' and siglist 'GenomicRanges'
generic 'densityCorr' and siglist 'list'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'estimate.mean.fraglen':
densityCorr
Code: function(x, ...)
Docs: function(x, shift = seq(0, 500, 5), center = FALSE, width =
seqLen * 2L, seqLen = 100L, maxDist = 500L, ...)
Argument names in docs not in code:
shift center width seqLen maxDist
Mismatches in argument names:
Position: 2 Code: ... Docs: shift
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'library' or 'require' call not declared from: 'BSgenome.Mmusculus.UCSC.mm9'
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/chipseq.buildbin-libdir/chipseq/libs/i386/chipseq.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
diffPeakSummary 5.71 0.25 5.95
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
diffPeakSummary 6.81 0.21 7.03
chipseqFilter 1.07 0.80 5.54
* 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: 3 WARNINGs, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/chipseq.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'chipseq' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c rlesumprod.c -o rlesumprod.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o chipseq.dll tmp.def rlesumprod.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/chipseq.buildbin-libdir/chipseq/libs/i386
** R
** data
** 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 'chipseq' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c rlesumprod.c -o rlesumprod.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o chipseq.dll tmp.def rlesumprod.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/chipseq.buildbin-libdir/chipseq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chipseq' as chipseq_1.26.0.zip
* DONE (chipseq)