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CHECK report for ChIPseqR on tokay2

This page was generated on 2019-10-16 12:23:02 -0400 (Wed, 16 Oct 2019).

Package 264/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPseqR 1.38.0
Peter Humburg
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ChIPseqR
Branch: RELEASE_3_9
Last Commit: e745192
Last Changed Date: 2019-05-02 11:53:13 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPseqR
Version: 1.38.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ChIPseqR_1.38.0.tar.gz
StartedAt: 2019-10-16 02:37:31 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:43:50 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 378.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ChIPseqR.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ChIPseqR_1.38.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ChIPseqR.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChIPseqR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPseqR' version '1.38.0'
* 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 'ChIPseqR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpukusxb/R.INSTALL1ad019007e91/ChIPseqR/man/strandPileup.Rd:29: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpukusxb/R.INSTALL1ad019007e91/ChIPseqR/man/strandPileup.Rd:46: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
  Warning: replacing previous import 'BiocGenerics::image' by 'graphics::image' when loading 'ChIPseqR'
  Warning: replacing previous import 'S4Vectors::head' by 'utils::head' when loading 'ChIPseqR'
  Warning: replacing previous import 'S4Vectors::tail' by 'utils::tail' when loading 'ChIPseqR'
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ChIPseqR.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* 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 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-3.9-bioc/R/library/ChIPseqR/libs/i386/ChIPseqR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/ChIPseqR/libs/x64/ChIPseqR.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 or elapsed time > 5s
                    user system elapsed
alignFeature       14.69   5.33   20.01
RLEBindScore-class  7.68   0.25    7.92
callBindingSites    7.39   0.34    7.74
simpleNucCall       7.42   0.27    7.69
BindScore           7.38   0.17    7.54
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
alignFeature       11.92   5.17   17.10
BindScore           7.20   0.23    7.43
RLEBindScore-class  5.99   0.36    6.34
callBindingSites    5.05   0.19    5.23
* 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/ChIPseqR.Rcheck/00check.log'
for details.



Installation output

ChIPseqR.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ChIPseqR_1.38.0.tar.gz && rm -rf ChIPseqR.buildbin-libdir && mkdir ChIPseqR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPseqR.buildbin-libdir ChIPseqR_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ChIPseqR_1.38.0.zip && rm ChIPseqR_1.38.0.tar.gz ChIPseqR_1.38.0.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 42444  100 42444    0     0   669k      0 --:--:-- --:--:-- --:--:--  753k

install for i386

* installing *source* package 'ChIPseqR' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c startScore.c -o startScore.o
startScore.c: In function '_ratioStat_pois':
startScore.c:66:15: warning: unused variable 'tmp_stat' [-Wunused-variable]
  double stat, tmp_stat;
               ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o ChIPseqR.dll tmp.def startScore.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/ChIPseqR.buildbin-libdir/00LOCK-ChIPseqR/00new/ChIPseqR/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'BiocGenerics::image' by 'graphics::image' when loading 'ChIPseqR'
Warning: replacing previous import 'S4Vectors::head' by 'utils::head' when loading 'ChIPseqR'
Warning: replacing previous import 'S4Vectors::tail' by 'utils::tail' when loading 'ChIPseqR'
** help
*** installing help indices
  converting help for package 'ChIPseqR'
    finding HTML links ... done
    BindScore                               html  
    ChIPseqR-package                        html  
    RLEBindScore-class                      html  
    finding level-2 HTML links ... done

    RLEReadCounts-class                     html  
    ReadCounts                              html  
    accessors                               html  
    alignFeature                            html  
    callBindingSites                        html  
    compress-BindScore                      html  
    compress-ReadCounts                     html  
    compress-methods                        html  
    decompress-methods                      html  
    decompress                              html  
    exportBindSequence                      html  
    getBindCor                              html  
    getBindLen                              html  
    getCutoff                               html  
    internal                                html  
    pickPeak                                html  
    plot-BindScore                          html  
    plot-ReadCounts                         html  
    plotReads                               html  
    plotWindow                              html  
    pos2gff                                 html  
    simpleNucCall                           html  
    startScore                              html  
    strandPileup                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpukusxb/R.INSTALL1ad019007e91/ChIPseqR/man/strandPileup.Rd:29: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpukusxb/R.INSTALL1ad019007e91/ChIPseqR/man/strandPileup.Rd:46: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
    windowCounts                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'BiocGenerics::image' by 'graphics::image' when loading 'ChIPseqR'
Warning: replacing previous import 'S4Vectors::head' by 'utils::head' when loading 'ChIPseqR'
Warning: replacing previous import 'S4Vectors::tail' by 'utils::tail' when loading 'ChIPseqR'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'BiocGenerics::image' by 'graphics::image' when loading 'ChIPseqR'
Warning: replacing previous import 'S4Vectors::head' by 'utils::head' when loading 'ChIPseqR'
Warning: replacing previous import 'S4Vectors::tail' by 'utils::tail' when loading 'ChIPseqR'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'ChIPseqR' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c startScore.c -o startScore.o
startScore.c: In function '_ratioStat_pois':
startScore.c:66:15: warning: unused variable 'tmp_stat' [-Wunused-variable]
  double stat, tmp_stat;
               ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o ChIPseqR.dll tmp.def startScore.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/ChIPseqR.buildbin-libdir/ChIPseqR/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::image' by 'graphics::image' when loading 'ChIPseqR'
Warning: replacing previous import 'S4Vectors::head' by 'utils::head' when loading 'ChIPseqR'
Warning: replacing previous import 'S4Vectors::tail' by 'utils::tail' when loading 'ChIPseqR'
* MD5 sums
packaged installation of 'ChIPseqR' as ChIPseqR_1.38.0.zip
* DONE (ChIPseqR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ChIPseqR' successfully unpacked and MD5 sums checked

Tests output


Example timings

ChIPseqR.Rcheck/examples_i386/ChIPseqR-Ex.timings

nameusersystemelapsed
BindScore7.380.177.54
ChIPseqR-package000
RLEBindScore-class7.680.257.92
RLEReadCounts-class0.030.000.03
ReadCounts0.010.000.02
alignFeature14.69 5.3320.01
callBindingSites7.390.347.74
pos2gff000
simpleNucCall7.420.277.69
strandPileup0.020.000.01
windowCounts0.080.000.08

ChIPseqR.Rcheck/examples_x64/ChIPseqR-Ex.timings

nameusersystemelapsed
BindScore7.200.237.43
ChIPseqR-package000
RLEBindScore-class5.990.366.34
RLEReadCounts-class0.030.010.05
ReadCounts0.030.000.03
alignFeature11.92 5.1717.10
callBindingSites5.050.195.23
pos2gff000
simpleNucCall4.640.274.91
strandPileup000
windowCounts0.090.000.09