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CHECK report for Mulcom on tokay2

This page was generated on 2019-10-16 12:24:12 -0400 (Wed, 16 Oct 2019).

Package 1063/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mulcom 1.34.1
Claudio Isella
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/Mulcom
Branch: RELEASE_3_9
Last Commit: f95b4a7
Last Changed Date: 2019-09-12 07:54:14 -0400 (Thu, 12 Sep 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Mulcom
Version: 1.34.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Mulcom.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Mulcom_1.34.1.tar.gz
StartedAt: 2019-10-16 05:27:37 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:29:37 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 120.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: Mulcom.Rcheck
Warnings: 1

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:Mulcom.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Mulcom_1.34.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Mulcom.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Mulcom/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Mulcom' version '1.34.1'
* 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 'Mulcom' can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... OK
* 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/Mulcom/libs/i386/Mulcom.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/Mulcom/libs/x64/Mulcom.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'Mulcom.Rmd'
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
mulInt 6.94   0.97    7.92
mulOpt 5.75   0.64    6.42
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
mulInt 4.25   1.08    5.33
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/Mulcom.Rcheck/00check.log'
for details.



Installation output

Mulcom.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/Mulcom_1.34.1.tar.gz && rm -rf Mulcom.buildbin-libdir && mkdir Mulcom.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Mulcom.buildbin-libdir Mulcom_1.34.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Mulcom_1.34.1.zip && rm Mulcom_1.34.1.tar.gz Mulcom_1.34.1.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 1119k  100 1119k    0     0  13.9M      0 --:--:-- --:--:-- --:--:-- 15.1M

install for i386

* installing *source* package 'Mulcom' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c mulLibs.cc -o mulLibs.o
mulLibs.cc: In function 'void Single_SimulationC(double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*)':
mulLibs.cc:708:33: warning: statement has no effect [-Wunused-value]
                 current_cluster ;
                                 ^
mulLibs.cc: In function 'void Complete_SimulationC(double*, int*, double*, double*, int*, int*, int*, int*, int*)':
mulLibs.cc:1022:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                  for ( int i = 0 ; i < sss2.size() ; i++ ) {
                                      ^
mulLibs.cc:1023:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                          for ( int j = 0 ; j < harmonic_means.size() ; j++ ) {
                                              ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o Mulcom.dll tmp.def mulLibs.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/Mulcom.buildbin-libdir/00LOCK-Mulcom/00new/Mulcom/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Mulcom'
    finding HTML links ... done
    Affy                                    html  
    AffyIlmn                                html  
    Illumina                                html  
    Ilmn                                    html  
    MULCOM-class                            html  
    MULCOM_P                                html  
    harmonicMean                            html  
    limmaAffySymbols                        html  
    limmaIlmnSymbols                        html  
    mulCAND                                 html  
    mulCalc                                 html  
    mulDELTA                                html  
    mulDiff                                 html  
    mulFSG                                  html  
    mulIndex                                html  
    mulInt                                  html  
    mulMSE                                  html  
    mulOpt                                  html  
    mulOptPars                              html  
    mulOptPlot                              html  
    mulParOpt                               html  
    mulPerm                                 html  
    mulPermC                                html  
    mulSSE                                  html  
    mulScores                               html  
    mulcomGeneListIlmn                      html  
    samAffySymbols                          html  
    samIlmnSymbols                          html  
    samOptPars                              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 'Mulcom' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c mulLibs.cc -o mulLibs.o
mulLibs.cc: In function 'void Single_SimulationC(double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*)':
mulLibs.cc:708:33: warning: statement has no effect [-Wunused-value]
                 current_cluster ;
                                 ^
mulLibs.cc: In function 'void Complete_SimulationC(double*, int*, double*, double*, int*, int*, int*, int*, int*)':
mulLibs.cc:1022:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                  for ( int i = 0 ; i < sss2.size() ; i++ ) {
                                      ^
mulLibs.cc:1023:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                          for ( int j = 0 ; j < harmonic_means.size() ; j++ ) {
                                              ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o Mulcom.dll tmp.def mulLibs.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/Mulcom.buildbin-libdir/Mulcom/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Mulcom' as Mulcom_1.34.1.zip
* DONE (Mulcom)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'Mulcom' successfully unpacked and MD5 sums checked

Tests output


Example timings

Mulcom.Rcheck/examples_i386/Mulcom-Ex.timings

nameusersystemelapsed
MULCOM-class0.400.020.42
MULCOM_P0.350.000.35
mulCAND1.160.051.20
mulCalc0.30.00.3
mulDELTA0.320.000.33
mulDiff1.190.041.23
mulFSG1.190.071.25
mulIndex0.280.000.29
mulInt6.940.977.92
mulOpt5.750.646.42
mulOptPars0.980.031.02
mulOptPlot1.310.071.38
mulParOpt1.430.091.51
mulPerm1.450.001.45
mulPermC0.340.010.36
mulScores0.420.020.44

Mulcom.Rcheck/examples_x64/Mulcom-Ex.timings

nameusersystemelapsed
MULCOM-class0.320.000.32
MULCOM_P0.230.030.26
mulCAND0.890.000.89
mulCalc0.230.020.25
mulDELTA0.210.000.20
mulDiff0.860.030.89
mulFSG0.920.000.92
mulIndex0.190.020.20
mulInt4.251.085.33
mulOpt3.470.624.09
mulOptPars0.830.030.86
mulOptPlot1.340.221.56
mulParOpt1.280.191.47
mulPerm1.170.021.19
mulPermC0.290.000.28
mulScores0.250.010.27