Bioconductor Package Maintainer
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/chipseq |
| Branch: RELEASE_3_12 |
| Last Commit: 84bcbc0 |
| Last Changed Date: 2020-10-27 10:35:54 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:30:14 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the chipseq package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 289/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| chipseq 1.40.0 (landing page) Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: chipseq |
| Version: 1.40.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chipseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings chipseq_1.40.0.tar.gz |
| StartedAt: 2021-05-06 01:22:41 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 01:28:02 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 321.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: chipseq.Rcheck |
| Warnings: 4 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chipseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings chipseq_1.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/chipseq.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.40.0'
* 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 ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpsT8ePg/R.INSTALL1ed81a5c4e1e/chipseq/man/estimate.mean.fraglen.Rd:48: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpsT8ePg/R.INSTALL1ed81a5c4e1e/chipseq/man/islandDepthPlot.Rd:17: file link 'RleList-class' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpsT8ePg/R.INSTALL1ed81a5c4e1e/chipseq/man/peakCutoff.Rd:17: file link 'RleList-class' in package 'IRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/chipseq.Rcheck/00install.out' for details.
* 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<-'
diffPeakSummary,RleViewsList-RleViewsList: no visible global function
definition for 'GRanges'
estimate.mean.fraglen,GRanges: no visible global function definition
for 'seqnames'
peakSummary,RleViewsList: no visible global function definition for
'GRanges'
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-3.12-bioc/R/library/chipseq/libs/i386/chipseq.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/chipseq/libs/x64/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 use Fortran I/O
nor system RNGs. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
diffPeakSummary 6.53 0.38 6.91
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
diffPeakSummary 5.55 0.33 5.88
* 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: 4 WARNINGs, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/chipseq.Rcheck/00check.log'
for details.
chipseq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/chipseq_1.40.0.tar.gz && rm -rf chipseq.buildbin-libdir && mkdir chipseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chipseq.buildbin-libdir chipseq_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL chipseq_1.40.0.zip && rm chipseq_1.40.0.tar.gz chipseq_1.40.0.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 1706k 100 1706k 0 0 41.3M 0 --:--:-- --:--:-- --:--:-- 42.7M
install for i386
* installing *source* package 'chipseq' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rlesumprod.c -o rlesumprod.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o chipseq.dll tmp.def rlesumprod.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/chipseq.buildbin-libdir/00LOCK-chipseq/00new/chipseq/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'chipseq'
finding HTML links ... done
chipseqFilter html
coverageplot html
cstest html
diffPeakSummary html
estimate.mean.fraglen html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpsT8ePg/R.INSTALL1ed81a5c4e1e/chipseq/man/estimate.mean.fraglen.Rd:48: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
islandDepthPlot html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpsT8ePg/R.INSTALL1ed81a5c4e1e/chipseq/man/islandDepthPlot.Rd:17: file link 'RleList-class' in package 'IRanges' does not exist and so has been treated as a topic
laneSubsample html
peakCutoff html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpsT8ePg/R.INSTALL1ed81a5c4e1e/chipseq/man/peakCutoff.Rd:17: file link 'RleList-class' in package 'IRanges' does not exist and so has been treated as a topic
peakSummary-methods html
subsetSummary html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'chipseq' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rlesumprod.c -o rlesumprod.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o chipseq.dll tmp.def rlesumprod.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/chipseq.buildbin-libdir/chipseq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chipseq' as chipseq_1.40.0.zip
* DONE (chipseq)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'chipseq' successfully unpacked and MD5 sums checked
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chipseq.Rcheck/examples_i386/chipseq-Ex.timings
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chipseq.Rcheck/examples_x64/chipseq-Ex.timings
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