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CHECK report for CSAR on tokay2

This page was generated on 2019-04-09 11:57:42 -0400 (Tue, 09 Apr 2019).

Package 362/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CSAR 1.35.0
Jose M Muino
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/CSAR
Branch: master
Last Commit: bf510c8
Last Changed Date: 2018-10-30 11:54:28 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: CSAR
Version: 1.35.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CSAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CSAR_1.35.0.tar.gz
StartedAt: 2019-04-09 02:04:56 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:09:20 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 264.2 seconds
RetCode: 0
Status:  OK  
CheckDir: CSAR.Rcheck
Warnings: 0

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:CSAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CSAR_1.35.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CSAR.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.35.0'
* 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 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-3.9-bioc/R/library/CSAR/libs/i386/CSAR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-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 or elapsed time > 5s
                        user system elapsed
getThreshold           10.86   0.01   10.87
CSAR-package           10.41   0.00   10.41
getPermutatedWinScores 10.09   0.02   10.11
permutatedWinScores     9.15   0.04    9.17
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
getThreshold           20.00   0.01   20.03
getPermutatedWinScores 18.17   0.07   18.56
permutatedWinScores    17.70   0.05   17.77
CSAR-package           13.41   0.00   13.40
distance2Genes          5.92   0.00    5.92
genesWithPeaks          5.60   0.01    5.61
score2wig               5.22   0.00    5.22
* 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-3.9-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 https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/CSAR_1.35.0.tar.gz && rm -rf CSAR.buildbin-libdir && mkdir CSAR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CSAR.buildbin-libdir CSAR_1.35.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CSAR_1.35.0.zip && rm CSAR_1.35.0.tar.gz CSAR_1.35.0.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 25088  100 25088    0     0   415k      0 --:--:-- --:--:-- --:--:--  471k

install for i386

* installing *source* package 'CSAR' ...
** 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 CSAR.c -o CSAR.o
C:/Rtools/mingw_32/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˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-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:/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 CSAR.c -o CSAR.o
C:/Rtools/mingw_64/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˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/CSAR.buildbin-libdir/CSAR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CSAR' as CSAR_1.35.0.zip
* DONE (CSAR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'CSAR' successfully unpacked and MD5 sums checked

Tests output


Example timings

CSAR.Rcheck/examples_i386/CSAR-Ex.timings

nameusersystemelapsed
CSAR-package10.41 0.0010.41
ChIPseqScore2.690.022.70
distance2Genes3.400.003.41
genesWithPeaks3.740.013.75
getPermutatedWinScores10.09 0.0210.11
getThreshold10.86 0.0110.87
loadMappedReads000
mappedReads2Nhits1.260.001.27
permutatedWinScores9.150.049.17
sampleSEP3_test000
score2wig3.370.013.39
sigWin4.420.024.44

CSAR.Rcheck/examples_x64/CSAR-Ex.timings

nameusersystemelapsed
CSAR-package13.41 0.0013.40
ChIPseqScore3.860.003.86
distance2Genes5.920.005.92
genesWithPeaks5.600.015.61
getPermutatedWinScores18.17 0.0718.56
getThreshold20.00 0.0120.03
loadMappedReads000
mappedReads2Nhits2.360.002.36
permutatedWinScores17.70 0.0517.77
sampleSEP3_test000
score2wig5.220.005.22
sigWin505