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CHECK report for GeneGeneInteR on tokay2

This page was generated on 2019-10-16 12:36:22 -0400 (Wed, 16 Oct 2019).

Package 630/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneGeneInteR 1.10.0
Mathieu Emily , Magalie Houee-Bigot
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/GeneGeneInteR
Branch: RELEASE_3_9
Last Commit: c4d5d33
Last Changed Date: 2019-05-02 11:54:03 -0400 (Thu, 02 May 2019)
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 [ WARNINGS ] 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

Summary

Package: GeneGeneInteR
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneGeneInteR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GeneGeneInteR_1.10.0.tar.gz
StartedAt: 2019-10-16 03:54:36 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:03:01 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 504.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GeneGeneInteR.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:GeneGeneInteR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GeneGeneInteR_1.10.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GeneGeneInteR.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 'GeneGeneInteR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneGeneInteR' version '1.10.0'
* 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 'GeneGeneInteR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpY7QXZX/R.INSTALL202c5a9a61e7/GeneGeneInteR/man/importFile.Rd:42: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GeneGeneInteR.Rcheck/00install.out' for details.
* 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 ... 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/GeneGeneInteR/libs/i386/GeneGeneInteR.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/GeneGeneInteR/libs/x64/GeneGeneInteR.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' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/GeneGeneInteR.Rcheck/00check.log'
for details.



Installation output

GeneGeneInteR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GeneGeneInteR_1.10.0.tar.gz && rm -rf GeneGeneInteR.buildbin-libdir && mkdir GeneGeneInteR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneGeneInteR.buildbin-libdir GeneGeneInteR_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GeneGeneInteR_1.10.0.zip && rm GeneGeneInteR_1.10.0.tar.gz GeneGeneInteR_1.10.0.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  478k  100  478k    0     0  2180k      0 --:--:-- --:--:-- --:--:-- 2248k

install for i386

* installing *source* package 'GeneGeneInteR' ...
** 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 chclust.cpp -o chclust.o
chclust.cpp: In function 'bool Conslink(long int, double**, double**)':
chclust.cpp:82:28: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
 #define dc(a,b)  (((a) > (b)) ? (DPtr[(a)-1][(b)-1]) : (DPtr[(b)-1][(a)-1]))
                            ^
chclust.cpp:306:18: note: in expansion of macro 'dc'
       diag[i] =  dc(i,i+1);
                  ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o GeneGeneInteR.dll tmp.def chclust.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/GeneGeneInteR.buildbin-libdir/00LOCK-GeneGeneInteR/00new/GeneGeneInteR/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 'GeneGeneInteR'
    finding HTML links ... done
    CCA.test                                html  
    CLD.test                                html  
    GBIGM.test                              html  
    GGI                                     html  
    KCCA.test                               html  
    PCA.test                                html  
    PLSPM.test                              html  
    data.SNP                                html  
    gates.test                              html  
    gene.pair                               html  
    importFile                              html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpY7QXZX/R.INSTALL202c5a9a61e7/GeneGeneInteR/man/importFile.Rd:42: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    imputeSnpMatrix                         html  
    minP.test                               html  
    plot.GGInetwork                         html  
    print.GGItest                           html  
    selectSnps                              html  
    snpMatrixScour                          html  
    summary.GGInetwork                      html  
    summary.GGItest                         html  
    tProd.test                              html  
    tTS.test                                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 'GeneGeneInteR' ...
** 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 chclust.cpp -o chclust.o
chclust.cpp: In function 'bool Conslink(long int, double**, double**)':
chclust.cpp:82:28: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
 #define dc(a,b)  (((a) > (b)) ? (DPtr[(a)-1][(b)-1]) : (DPtr[(b)-1][(a)-1]))
                            ^
chclust.cpp:306:18: note: in expansion of macro 'dc'
       diag[i] =  dc(i,i+1);
                  ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o GeneGeneInteR.dll tmp.def chclust.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/GeneGeneInteR.buildbin-libdir/GeneGeneInteR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneGeneInteR' as GeneGeneInteR_1.10.0.zip
* DONE (GeneGeneInteR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GeneGeneInteR' successfully unpacked and MD5 sums checked

Tests output


Example timings

GeneGeneInteR.Rcheck/examples_i386/GeneGeneInteR-Ex.timings

nameusersystemelapsed
CCA.test2.260.072.36
CLD.test1.560.241.79
GBIGM.test4.290.614.92
GGI1.750.172.03
KCCA.test000
PCA.test0.070.000.07
PLSPM.test2.780.002.79
gates.test0.450.000.46
importFile0.550.000.95
imputeSnpMatrix1.040.021.14
minP.test0.830.010.84
plot.GGInetwork0.160.020.18
print.GGItest0.030.000.03
selectSnps0.000.000.06
snpMatrixScour0.120.000.12
summary.GGInetwork0.020.000.02
summary.GGItest0.030.000.03
tProd.test0.530.000.53
tTS.test0.580.000.58

GeneGeneInteR.Rcheck/examples_x64/GeneGeneInteR-Ex.timings

nameusersystemelapsed
CCA.test2.030.042.06
CLD.test1.270.001.26
GBIGM.test3.530.093.63
GGI1.190.011.22
KCCA.test000
PCA.test0.030.000.03
PLSPM.test2.330.002.33
gates.test0.290.021.76
importFile0.360.000.36
imputeSnpMatrix0.860.020.91
minP.test0.780.010.79
plot.GGInetwork0.080.020.10
print.GGItest0.030.000.03
selectSnps0.020.000.02
snpMatrixScour0.050.000.04
summary.GGInetwork0.000.010.02
summary.GGItest0.030.000.03
tProd.test0.420.020.44
tTS.test0.370.000.37