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CHECK report for chipseq on riesling1

This page was generated on 2020-10-24 11:04:47 -0400 (Sat, 24 Oct 2020).

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 289/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chipseq 1.39.0
Bioconductor Package Maintainer
Snapshot Date: 2020-10-23 14:40:36 -0400 (Fri, 23 Oct 2020)
URL: https://git.bioconductor.org/packages/chipseq
Branch: master
Last Commit: 5ce3042
Last Changed Date: 2020-04-27 14:19:32 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ WARNINGS ] OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: chipseq
Version: 1.39.0
Command: D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chipseq.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings chipseq_1.39.0.tar.gz
StartedAt: 2020-10-24 01:58:43 -0400 (Sat, 24 Oct 2020)
EndedAt: 2020-10-24 02:02:25 -0400 (Sat, 24 Oct 2020)
EllapsedTime: 222.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: chipseq.Rcheck
Warnings: 4

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chipseq.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings chipseq_1.39.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.12-bioc/meat/chipseq.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.39.0'
* 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: D:/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA1pG76/R.INSTALL2edc2d6f1b17/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: D:/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA1pG76/R.INSTALL2edc2d6f1b17/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: D:/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA1pG76/R.INSTALL2edc2d6f1b17/chipseq/man/peakCutoff.Rd:17: file link 'RleList-class' in package 'IRanges' does not exist and so has been treated as a topic
See 'D:/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 'D:/biocbuild/bbs-3.12-bioc/R/library/chipseq/libs/i386/chipseq.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/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 5.22   0.21    7.03
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
diffPeakSummary 4.75   0.31    6.09
* 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
  'D:/biocbuild/bbs-3.12-bioc/meat/chipseq.Rcheck/00check.log'
for details.



Installation output

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_1.39.0.tar.gz && rm -rf chipseq.buildbin-libdir && mkdir chipseq.buildbin-libdir && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chipseq.buildbin-libdir chipseq_1.39.0.tar.gz && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL chipseq_1.39.0.zip && rm chipseq_1.39.0.tar.gz chipseq_1.39.0.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  26.4M      0 --:--:-- --:--:-- --:--:-- 26.4M

install for i386

* installing *source* package 'chipseq' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.12-bioc/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 -LD:/biocbuild/bbs-3.12-bioc/R/bin/i386 -lR
installing to D:/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: D:/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA1pG76/R.INSTALL2edc2d6f1b17/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: D:/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA1pG76/R.INSTALL2edc2d6f1b17/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: D:/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA1pG76/R.INSTALL2edc2d6f1b17/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"D:/biocbuild/bbs-3.12-bioc/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 -LD:/biocbuild/bbs-3.12-bioc/R/bin/x64 -lR
installing to D:/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_1.39.0.zip
* DONE (chipseq)
* installing to library 'D:/biocbuild/bbs-3.12-bioc/R/library'
package 'chipseq' successfully unpacked and MD5 sums checked

Tests output


Example timings

chipseq.Rcheck/examples_i386/chipseq-Ex.timings

nameusersystemelapsed
chipseqFilter0.500.691.97
coverageplot0.110.000.11
cstest0.270.030.29
diffPeakSummary5.220.217.03
estimate.mean.fraglen2.710.533.92
islandDepthPlot1.190.141.39
laneSubsample0.610.080.95
peakCutoff1.810.172.29

chipseq.Rcheck/examples_x64/chipseq-Ex.timings

nameusersystemelapsed
chipseqFilter0.570.661.51
coverageplot0.060.030.30
cstest0.220.000.36
diffPeakSummary4.750.316.09
estimate.mean.fraglen3.060.393.45
islandDepthPlot1.060.101.17
laneSubsample0.390.060.45
peakCutoff0.690.060.75