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CHECK report for CSAR on tokay1

This page was generated on 2018-04-12 13:19:58 -0400 (Thu, 12 Apr 2018).

Package 313/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CSAR 1.30.0
Jose M Muino
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/CSAR
Branch: RELEASE_3_6
Last Commit: a366b21
Last Changed Date: 2017-10-30 12:39:28 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CSAR
Version: 1.30.0
Command: rm -rf CSAR.buildbin-libdir CSAR.Rcheck && mkdir CSAR.buildbin-libdir CSAR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CSAR.buildbin-libdir CSAR_1.30.0.tar.gz >CSAR.Rcheck\00install.out 2>&1 && cp CSAR.Rcheck\00install.out CSAR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CSAR.buildbin-libdir --install="check:CSAR-install.out" --force-multiarch --no-vignettes --timings CSAR_1.30.0.tar.gz
StartedAt: 2018-04-11 23:17:10 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:20:58 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 228.2 seconds
RetCode: 0
Status:  OK  
CheckDir: CSAR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf CSAR.buildbin-libdir CSAR.Rcheck && mkdir CSAR.buildbin-libdir CSAR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CSAR.buildbin-libdir CSAR_1.30.0.tar.gz >CSAR.Rcheck\00install.out 2>&1 && cp CSAR.Rcheck\00install.out CSAR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CSAR.buildbin-libdir --install="check:CSAR-install.out" --force-multiarch --no-vignettes --timings CSAR_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CSAR.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.30.0'
* 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-3.6-bioc/meat/CSAR.buildbin-libdir/CSAR/libs/i386/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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
CSAR-package           11.02   0.08   11.09
getThreshold            9.47   0.05    9.51
getPermutatedWinScores  8.52   0.03    8.55
permutatedWinScores     8.54   0.01    8.56
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
CSAR-package           11.97   0.07   12.13
getThreshold           10.29   0.03   10.33
getPermutatedWinScores 10.16   0.02   10.17
permutatedWinScores    10.03   0.01   10.05
* 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-3.6-bioc/meat/CSAR.Rcheck/00check.log'
for details.



Installation output

CSAR.Rcheck/00install.out


install for i386

* installing *source* package 'CSAR' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c CSAR.c -o CSAR.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o CSAR.dll tmp.def CSAR.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/CSAR.buildbin-libdir/CSAR/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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
In R CMD INSTALL

install for x64

* installing *source* package 'CSAR' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c CSAR.c -o CSAR.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o CSAR.dll tmp.def CSAR.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/CSAR.buildbin-libdir/CSAR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CSAR' as CSAR_1.30.0.zip
* DONE (CSAR)
In R CMD INSTALL
In R CMD INSTALL

Tests output


Example timings

CSAR.Rcheck/examples_i386/CSAR-Ex.timings

nameusersystemelapsed
CSAR-package11.02 0.0811.09
ChIPseqScore2.470.022.48
distance2Genes3.790.013.80
genesWithPeaks3.430.053.48
getPermutatedWinScores8.520.038.55
getThreshold9.470.059.51
loadMappedReads000
mappedReads2Nhits1.080.001.08
permutatedWinScores8.540.018.56
sampleSEP3_test000
score2wig2.890.022.91
sigWin2.820.002.81

CSAR.Rcheck/examples_x64/CSAR-Ex.timings

nameusersystemelapsed
CSAR-package11.97 0.0712.13
ChIPseqScore3.210.003.21
distance2Genes3.630.003.63
genesWithPeaks3.700.013.72
getPermutatedWinScores10.16 0.0210.17
getThreshold10.29 0.0310.33
loadMappedReads000
mappedReads2Nhits1.300.021.31
permutatedWinScores10.03 0.0110.05
sampleSEP3_test000
score2wig3.150.023.17
sigWin3.600.013.61