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CHECK report for chipseq on tokay1

This page was generated on 2018-04-12 13:19:44 -0400 (Thu, 12 Apr 2018).

Package 222/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chipseq 1.28.0
Bioconductor Package Maintainer
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/chipseq
Branch: RELEASE_3_6
Last Commit: 7e2cc6e
Last Changed Date: 2017-10-30 12:39:26 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: chipseq
Version: 1.28.0
Command: rm -rf chipseq.buildbin-libdir chipseq.Rcheck && mkdir chipseq.buildbin-libdir chipseq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chipseq.buildbin-libdir chipseq_1.28.0.tar.gz >chipseq.Rcheck\00install.out 2>&1 && cp chipseq.Rcheck\00install.out chipseq-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=chipseq.buildbin-libdir --install="check:chipseq-install.out" --force-multiarch --no-vignettes --timings chipseq_1.28.0.tar.gz
StartedAt: 2018-04-11 22:52:34 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:57:21 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 287.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: chipseq.Rcheck
Warnings: 4

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf chipseq.buildbin-libdir chipseq.Rcheck && mkdir chipseq.buildbin-libdir chipseq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chipseq.buildbin-libdir chipseq_1.28.0.tar.gz >chipseq.Rcheck\00install.out 2>&1 && cp chipseq.Rcheck\00install.out chipseq-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=chipseq.buildbin-libdir --install="check:chipseq-install.out" --force-multiarch --no-vignettes --timings chipseq_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/chipseq.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.28.0'
* 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-3.6-bioc/tmpdir/Rtmpu6r6R9/R.INSTALL2664462e62e9/chipseq/man/estimate.mean.fraglen.Rd:56: missing file link 'IntegerList-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpu6r6R9/R.INSTALL2664462e62e9/chipseq/man/islandDepthPlot.Rd:17: missing file link 'RleList-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpu6r6R9/R.INSTALL2664462e62e9/chipseq/man/peakCutoff.Rd:17: missing file link 'RleList-class'
See 'C:/Users/biocbuild/bbs-3.6-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<-'
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-3.6-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 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 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 5.68   0.24     6.5
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
diffPeakSummary 7.68   0.33    8.00
chipseqFilter   1.34   0.59    5.27
* 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-3.6-bioc/meat/chipseq.Rcheck/00check.log'
for details.



Installation output

chipseq.Rcheck/00install.out


install for i386

* installing *source* package 'chipseq' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c rlesumprod.c -o rlesumprod.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o chipseq.dll tmp.def rlesumprod.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/chipseq.buildbin-libdir/chipseq/libs/i386
** R
** data
** inst
** preparing 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-3.6-bioc/tmpdir/Rtmpu6r6R9/R.INSTALL2664462e62e9/chipseq/man/estimate.mean.fraglen.Rd:56: missing file link 'IntegerList-class'
    islandDepthPlot                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpu6r6R9/R.INSTALL2664462e62e9/chipseq/man/islandDepthPlot.Rd:17: missing file link 'RleList-class'
    laneSubsample                           html  
    peakCutoff                              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpu6r6R9/R.INSTALL2664462e62e9/chipseq/man/peakCutoff.Rd:17: missing file link 'RleList-class'
    peakSummary-methods                     html  
    subsetSummary                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'chipseq' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c rlesumprod.c -o rlesumprod.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o chipseq.dll tmp.def rlesumprod.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/chipseq.buildbin-libdir/chipseq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chipseq' as chipseq_1.28.0.zip
* DONE (chipseq)
In R CMD INSTALL
In R CMD INSTALL

Tests output


Example timings

chipseq.Rcheck/examples_i386/chipseq-Ex.timings

nameusersystemelapsed
chipseqFilter1.270.694.66
coverageplot0.160.000.16
cstest0.920.040.97
diffPeakSummary5.680.246.50
estimate.mean.fraglen2.790.263.06
islandDepthPlot1.470.111.58
laneSubsample0.920.111.03
peakCutoff1.430.131.55

chipseq.Rcheck/examples_x64/chipseq-Ex.timings

nameusersystemelapsed
chipseqFilter1.340.595.27
coverageplot0.180.000.75
cstest0.700.000.71
diffPeakSummary7.680.338.00
estimate.mean.fraglen3.00.53.5
islandDepthPlot2.000.122.12
laneSubsample1.610.081.69
peakCutoff1.510.131.64