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CHECK report for ChIPseqR on tokay2

This page was generated on 2020-10-17 11:56:15 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ChIPseqR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 286/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPseqR 1.42.0
Peter Humburg
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/ChIPseqR
Branch: RELEASE_3_11
Last Commit: 39fee3a
Last Changed Date: 2020-04-27 14:20:24 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPseqR
Version: 1.42.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ChIPseqR_1.42.0.tar.gz
StartedAt: 2020-10-17 02:31:53 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:38:41 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 408.3 seconds
RetCode: 0
Status:  OK  
CheckDir: ChIPseqR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ChIPseqR_1.42.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ChIPseqR.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 'ChIPseqR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPseqR' version '1.42.0'
* 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 ... OK
* 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 ... NOTE
.fixCounts: no visible global function definition for 'runLength'
.fixCounts: no visible global function definition for 'runValue'
getBindLen: no visible global function definition for 'window'
pickPeak: no visible global function definition for 'start'
pickPeak: no visible global function definition for 'runLength'
pickPeak : <anonymous>: no visible global function definition for
  'window'
[[,BindScore-ANY-numeric: no visible global function definition for
  'window'
decompress,Rle: no visible global function definition for 'runValue'
decompress,RleList : <anonymous>: no visible global function definition
  for 'runValue'
initialize,RLEBindScore : <anonymous>: no visible global function
  definition for 'Rle'
initialize,RLEBindScore : <anonymous>: no visible global function
  definition for 'runValue'
initialize,RLEBindScore : <anonymous>: no visible global function
  definition for 'runValue<-'
plot,RLEReadCounts-missing : <anonymous>: no visible global function
  definition for 'window'
Undefined global functions or variables:
  Rle runLength runValue runValue<- start window
Consider adding
  importFrom("stats", "start", "window")
to your NAMESPACE file.
* 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-3.11-bioc/R/library/ChIPseqR/libs/i386/ChIPseqR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.11-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 (user + system) or elapsed time > 5s
                    user system elapsed
alignFeature       12.46   3.68   16.12
BindScore           7.75   0.27    8.02
RLEBindScore-class  6.89   0.34    7.24
simpleNucCall       6.45   0.24    6.69
callBindingSites    5.36   0.21    5.58
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
alignFeature       12.30   3.41   15.70
BindScore           7.11   0.33    7.44
RLEBindScore-class  6.70   0.30    7.00
simpleNucCall       5.32   0.27    5.58
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-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/3.11/bioc/src/contrib/ChIPseqR_1.42.0.tar.gz && rm -rf ChIPseqR.buildbin-libdir && mkdir ChIPseqR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPseqR.buildbin-libdir ChIPseqR_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ChIPseqR_1.42.0.zip && rm ChIPseqR_1.42.0.tar.gz ChIPseqR_1.42.0.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 42513  100 42513    0     0   730k      0 --:--:-- --:--:-- --:--:--  814k

install for i386

* installing *source* package 'ChIPseqR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw32/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-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/ChIPseqR.buildbin-libdir/00LOCK-ChIPseqR/00new/ChIPseqR/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** 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  
    windowCounts                            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 'ChIPseqR' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw64/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-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/ChIPseqR.buildbin-libdir/ChIPseqR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChIPseqR' as ChIPseqR_1.42.0.zip
* DONE (ChIPseqR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'ChIPseqR' successfully unpacked and MD5 sums checked

Tests output


Example timings

ChIPseqR.Rcheck/examples_i386/ChIPseqR-Ex.timings

nameusersystemelapsed
BindScore7.750.278.02
ChIPseqR-package000
RLEBindScore-class6.890.347.24
RLEReadCounts-class0.040.000.05
ReadCounts0.030.000.03
alignFeature12.46 3.6816.12
callBindingSites5.360.215.58
pos2gff000
simpleNucCall6.450.246.69
strandPileup0.020.000.01
windowCounts0.150.000.16

ChIPseqR.Rcheck/examples_x64/ChIPseqR-Ex.timings

nameusersystemelapsed
BindScore7.110.337.44
ChIPseqR-package000
RLEBindScore-class6.70.37.0
RLEReadCounts-class0.030.000.03
ReadCounts0.050.000.05
alignFeature12.30 3.4115.70
callBindingSites4.650.204.86
pos2gff000
simpleNucCall5.320.275.58
strandPileup000
windowCounts0.170.000.17