Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-14 13:06:09 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for ChIPseqR on tokay2


To the developers/maintainers of the ChIPseqR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPseqR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 306/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPseqR 1.48.0  (landing page)
Peter Humburg
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/ChIPseqR
git_branch: RELEASE_3_14
git_last_commit: c68564e
git_last_commit_date: 2021-10-26 11:54:55 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChIPseqR
Version: 1.48.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ChIPseqR_1.48.0.tar.gz
StartedAt: 2022-01-13 17:00:23 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 17:05:54 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 330.4 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPseqR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ChIPseqR_1.48.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ChIPseqR.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.48.0'
* 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-3.14-bioc/R/library/ChIPseqR/libs/i386/ChIPseqR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.14-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       8.54   3.00   11.55
simpleNucCall      5.85   0.21    6.04
BindScore          5.79   0.25    6.04
RLEBindScore-class 5.61   0.24    5.86
callBindingSites   5.63   0.11    5.73
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
alignFeature       8.12   3.84   11.97
BindScore          6.58   0.22    6.79
RLEBindScore-class 6.12   0.35    6.47
simpleNucCall      4.74   0.27    5.00
* 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-3.14-bioc/meat/ChIPseqR.Rcheck/00check.log'
for details.



Installation output

ChIPseqR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ChIPseqR_1.48.0.tar.gz && rm -rf ChIPseqR.buildbin-libdir && mkdir ChIPseqR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPseqR.buildbin-libdir ChIPseqR_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ChIPseqR_1.48.0.zip && rm ChIPseqR_1.48.0.tar.gz ChIPseqR_1.48.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 21 42522   21  9239    0     0   154k      0 --:--:-- --:--:-- --:--:--  155k
100 42522  100 42522    0     0   391k      0 --:--:-- --:--:-- --:--:--  391k

install for i386

* installing *source* package 'ChIPseqR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/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-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-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-3~1.14-/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-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/ChIPseqR.buildbin-libdir/ChIPseqR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChIPseqR' as ChIPseqR_1.48.0.zip
* DONE (ChIPseqR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ChIPseqR' successfully unpacked and MD5 sums checked

Tests output


Example timings

ChIPseqR.Rcheck/examples_i386/ChIPseqR-Ex.timings

nameusersystemelapsed
BindScore5.790.256.04
ChIPseqR-package000
RLEBindScore-class5.610.245.86
RLEReadCounts-class0.030.010.05
ReadCounts0.020.000.01
alignFeature 8.54 3.0011.55
callBindingSites5.630.115.73
pos2gff0.010.000.02
simpleNucCall5.850.216.04
strandPileup000
windowCounts0.200.000.21

ChIPseqR.Rcheck/examples_x64/ChIPseqR-Ex.timings

nameusersystemelapsed
BindScore6.580.226.79
ChIPseqR-package000
RLEBindScore-class6.120.356.47
RLEReadCounts-class0.030.000.03
ReadCounts0.040.000.03
alignFeature 8.12 3.8411.97
callBindingSites4.130.264.39
pos2gff000
simpleNucCall4.740.275.00
strandPileup000
windowCounts0.180.000.18