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CHECK report for dSimer on tokay1

This page was generated on 2019-04-13 11:26:44 -0400 (Sat, 13 Apr 2019).

Package 438/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dSimer 1.8.0
Peng Ni
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/dSimer
Branch: RELEASE_3_8
Last Commit: 78df868
Last Changed Date: 2018-10-30 11:42:01 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 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
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: dSimer
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dSimer.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings dSimer_1.8.0.tar.gz
StartedAt: 2019-04-13 01:55:08 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:02:04 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 416.4 seconds
RetCode: 0
Status:  OK  
CheckDir: dSimer.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dSimer.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings dSimer_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/dSimer.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'dSimer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dSimer' version '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'dSimer' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.7Mb
* 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-3.8-bioc/R/library/dSimer/libs/i386/dSimer.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
Examples with CPU or elapsed time > 5s
                      user system elapsed
get_GOterm2GeneAssos 27.23   1.28   28.54
FunSim               12.40   0.13   12.53
plot_net             11.85   0.09   11.96
plot_heatmap         11.54   0.24   11.76
HypergeometricTest    8.84   0.13    8.97
PSB                   8.83   0.00    8.83
x2y_conv2_y2x         5.22   0.00    5.22
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
get_GOterm2GeneAssos 40.20   3.31   43.53
FunSim               15.82   0.14   15.95
plot_heatmap         14.97   0.36   15.32
PSB                  14.38   0.00   14.38
plot_net             12.39   0.33   12.75
HypergeometricTest   12.54   0.13   12.67
x2y_conv2_y2x         6.02   0.00    6.02
* 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-3.8-bioc/meat/dSimer.Rcheck/00check.log'
for details.



Installation output

dSimer.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/dSimer_1.8.0.tar.gz && rm -rf dSimer.buildbin-libdir && mkdir dSimer.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dSimer.buildbin-libdir dSimer_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL dSimer_1.8.0.zip && rm dSimer_1.8.0.tar.gz dSimer_1.8.0.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 3193k  100 3193k    0     0  43.2M      0 --:--:-- --:--:-- --:--:-- 45.8M

install for i386

* installing *source* package 'dSimer' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BOG.cpp -o BOG.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c GO2GeneAssos.cpp -o GO2GeneAssos.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ICod.cpp -o ICod.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c PSB.cpp -o PSB.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_dSimer_init.c -o R_dSimer_init.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Sun.cpp -o Sun.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o dSimer.dll tmp.def BOG.o GO2GeneAssos.o ICod.o PSB.o R_dSimer_init.o RcppExports.o Sun.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/dSimer.buildbin-libdir/dSimer/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'dSimer'
    finding HTML links ... done
    BOG                                     html  
    CosineDFV                               html  
    FunSim                                  html  
    HumanNet_sample                         html  
    HypergeometricTest                      html  
    ICod                                    html  
    InformationContent                      html  
    LLSn2List                               html  
    Normalize                               html  
    PPI_HPRD                                html  
    PSB                                     html  
    Separation                              html  
    Separation2Similarity                   html  
    Sun_annotation                          html  
    Sun_function                            html  
    Sun_topology                            html  
    d2g_fundo_entrezid                      html  
    d2g_fundo_symbol                        html  
    d2g_separation                          html  
    d2go_sample                             html  
    d2s_hsdn                                html  
    d2s_hsdn_sample                         html  
    dSimer-package                          html  
    get_GOterm2GeneAssos                    html  
    go2g_sample                             html  
    graphlet_sig_hprd                       html  
    interactome                             html  
    jaccardindex                            html  
    orbit_dependency_count                  html  
    plot_bipartite                          html  
    plot_heatmap                            html  
    plot_net                                html  
    plot_topo                               html  
    setWeight                               html  
    weight                                  html  
    x2y_conv2_y2x                           html  
    x2y_df2list                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'dSimer' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BOG.cpp -o BOG.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c GO2GeneAssos.cpp -o GO2GeneAssos.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ICod.cpp -o ICod.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c PSB.cpp -o PSB.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_dSimer_init.c -o R_dSimer_init.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Sun.cpp -o Sun.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o dSimer.dll tmp.def BOG.o GO2GeneAssos.o ICod.o PSB.o R_dSimer_init.o RcppExports.o Sun.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/dSimer.buildbin-libdir/dSimer/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dSimer' as dSimer_1.8.0.zip
* DONE (dSimer)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'dSimer' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

dSimer.Rcheck/examples_i386/dSimer-Ex.timings

nameusersystemelapsed
BOG4.780.034.82
CosineDFV0.140.010.15
FunSim12.40 0.1312.53
HumanNet_sample0.020.010.03
HypergeometricTest8.840.138.97
ICod1.020.081.09
InformationContent0.110.080.19
LLSn2List0.060.010.08
Normalize000
PPI_HPRD0.110.030.14
PSB8.830.008.83
Separation2.920.253.17
Separation2Similarity000
Sun_annotation0.110.100.20
Sun_function000
Sun_topology0.230.110.35
d2g_fundo_entrezid0.060.100.17
d2g_fundo_symbol0.070.110.17
d2g_separation0.110.070.17
d2go_sample000
d2s_hsdn0.110.010.13
d2s_hsdn_sample000
get_GOterm2GeneAssos27.23 1.2828.54
go2g_sample0.080.020.10
graphlet_sig_hprd0.120.000.12
interactome0.440.140.58
jaccardindex000
orbit_dependency_count000
plot_bipartite0.200.060.27
plot_heatmap11.54 0.2411.76
plot_net11.85 0.0911.96
plot_topo0.240.060.29
setWeight000
weight000
x2y_conv2_y2x5.220.005.22
x2y_df2list0.020.000.01

dSimer.Rcheck/examples_x64/dSimer-Ex.timings

nameusersystemelapsed
BOG4.420.034.46
CosineDFV0.300.030.33
FunSim15.82 0.1415.95
HumanNet_sample0.030.000.03
HypergeometricTest12.54 0.1312.67
ICod0.930.101.04
InformationContent0.070.130.20
LLSn2List0.110.000.11
Normalize000
PPI_HPRD0.190.020.20
PSB14.38 0.0014.38
Separation2.780.263.04
Separation2Similarity000
Sun_annotation0.030.110.14
Sun_function000
Sun_topology0.220.080.30
d2g_fundo_entrezid0.060.090.16
d2g_fundo_symbol0.110.100.20
d2g_separation0.080.060.14
d2go_sample000
d2s_hsdn0.110.000.11
d2s_hsdn_sample0.010.000.02
get_GOterm2GeneAssos40.20 3.3143.53
go2g_sample0.150.000.14
graphlet_sig_hprd0.140.000.14
interactome0.700.240.94
jaccardindex000
orbit_dependency_count0.000.010.01
plot_bipartite0.170.090.27
plot_heatmap14.97 0.3615.32
plot_net12.39 0.3312.75
plot_topo0.250.210.46
setWeight000
weight0.000.010.01
x2y_conv2_y2x6.020.006.02
x2y_df2list000