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This page was generated on 2021-09-13 15:06:22 -0400 (Mon, 13 Sep 2021).

CHECK results for CSAR on tokay2

To the developers/maintainers of the CSAR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CSAR.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 415/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CSAR 1.44.0  (landing page)
Jose M Muino
Snapshot Date: 2021-09-12 04:50:10 -0400 (Sun, 12 Sep 2021)
git_url: https://git.bioconductor.org/packages/CSAR
git_branch: RELEASE_3_13
git_last_commit: 3eef45f
git_last_commit_date: 2021-05-19 11:44:30 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: CSAR
Version: 1.44.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CSAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CSAR_1.44.0.tar.gz
StartedAt: 2021-09-12 21:05:31 -0400 (Sun, 12 Sep 2021)
EndedAt: 2021-09-12 21:09:41 -0400 (Sun, 12 Sep 2021)
EllapsedTime: 249.8 seconds
RetCode: 0
Status:   OK  
CheckDir: CSAR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CSAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CSAR_1.44.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CSAR.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CSAR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CSAR' version '1.44.0'
* 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 'CSAR' 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
mappedReads2Nhits: no visible global function definition for
  'chromosome'
mappedReads2Nhits: no visible global function definition for 'position'
Undefined global functions or variables:
  chromosome position
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... 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-3.13-bioc/R/library/CSAR/libs/i386/CSAR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/CSAR/libs/x64/CSAR.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
getThreshold           12.23   0.03   12.27
CSAR-package           11.80   0.06   11.86
getPermutatedWinScores 10.97   0.00   10.98
permutatedWinScores    10.64   0.03   10.69
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
getThreshold           14.31   0.05   14.36
CSAR-package           13.87   0.06   13.94
getPermutatedWinScores 13.61   0.05   13.65
permutatedWinScores    13.15   0.03   13.17
* 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-3.13-bioc/meat/CSAR.Rcheck/00check.log'
for details.



Installation output

CSAR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CSAR_1.44.0.tar.gz && rm -rf CSAR.buildbin-libdir && mkdir CSAR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CSAR.buildbin-libdir CSAR_1.44.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CSAR_1.44.0.zip && rm CSAR_1.44.0.tar.gz CSAR_1.44.0.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
100 25544  100 25544    0     0   199k      0 --:--:-- --:--:-- --:--:--  201k

install for i386

* installing *source* package 'CSAR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c CSAR.c -o CSAR.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o CSAR.dll tmp.def CSAR.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/CSAR.buildbin-libdir/00LOCK-CSAR/00new/CSAR/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CSAR'
    finding HTML links ... done
    CSAR-package                            html  
    ChIPseqScore                            html  
    distance2Genes                          html  
    genesWithPeaks                          html  
    getPermutatedWinScores                  html  
    getThreshold                            html  
    loadMappedReads                         html  
    mappedReads2Nhits                       html  
    permutatedWinScores                     html  
    sampleSEP3_test                         html  
    score2wig                               html  
    sigWin                                  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 'CSAR' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c CSAR.c -o CSAR.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o CSAR.dll tmp.def CSAR.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/CSAR.buildbin-libdir/CSAR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CSAR' as CSAR_1.44.0.zip
* DONE (CSAR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'CSAR' successfully unpacked and MD5 sums checked

Tests output


Example timings

CSAR.Rcheck/examples_i386/CSAR-Ex.timings

nameusersystemelapsed
CSAR-package11.80 0.0611.86
ChIPseqScore303
distance2Genes4.090.024.11
genesWithPeaks4.190.004.19
getPermutatedWinScores10.97 0.0010.98
getThreshold12.23 0.0312.27
loadMappedReads000
mappedReads2Nhits1.330.001.33
permutatedWinScores10.64 0.0310.69
sampleSEP3_test000
score2wig3.090.003.09
sigWin3.820.003.81

CSAR.Rcheck/examples_x64/CSAR-Ex.timings

nameusersystemelapsed
CSAR-package13.87 0.0613.94
ChIPseqScore3.630.003.62
distance2Genes4.840.004.85
genesWithPeaks4.810.014.83
getPermutatedWinScores13.61 0.0513.65
getThreshold14.31 0.0514.36
loadMappedReads000
mappedReads2Nhits1.530.001.53
permutatedWinScores13.15 0.0313.17
sampleSEP3_test000
score2wig3.510.013.54
sigWin4.50.04.5