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BioC 3.4: CHECK report for dSimer on moscato1

This page was generated on 2016-09-21 03:48:27 -0700 (Wed, 21 Sep 2016).

Package 338/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dSimer 0.99.3
Peng Ni
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/dSimer
Last Changed Rev: 120702 / Revision: 121152
Last Changed Date: 2016-09-03 05:57:55 -0700 (Sat, 03 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: dSimer
Version: 0.99.3
Command: rm -rf dSimer.buildbin-libdir dSimer.Rcheck && mkdir dSimer.buildbin-libdir dSimer.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=dSimer.buildbin-libdir dSimer_0.99.3.tar.gz >dSimer.Rcheck\00install.out 2>&1 && cp dSimer.Rcheck\00install.out dSimer-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=dSimer.buildbin-libdir --install="check:dSimer-install.out" --force-multiarch --no-vignettes --timings dSimer_0.99.3.tar.gz
StartedAt: 2016-09-20 07:28:46 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 07:36:11 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 445.1 seconds
RetCode: 0
Status:  OK  
CheckDir: dSimer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf dSimer.buildbin-libdir dSimer.Rcheck && mkdir dSimer.buildbin-libdir dSimer.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=dSimer.buildbin-libdir dSimer_0.99.3.tar.gz >dSimer.Rcheck\00install.out 2>&1 && cp dSimer.Rcheck\00install.out dSimer-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=dSimer.buildbin-libdir --install="check:dSimer-install.out" --force-multiarch --no-vignettes --timings dSimer_0.99.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/dSimer.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '0.99.3'
* 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 'dSimer' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 'D:/biocbld/bbs-3.4-bioc/meat/dSimer.buildbin-libdir/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 the system RNG.
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
get_GOterm2GeneAssos 28.23   1.99   35.29
plot_heatmap         16.55   0.14   16.69
plot_net             16.10   0.20   16.31
FunSim               13.92   0.06   13.98
PSB                  12.34   0.00   12.34
HypergeometricTest   12.03   0.06   12.09
x2y_conv2_y2x         6.25   0.00    6.26
BOG                   6.03   0.05    6.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
get_GOterm2GeneAssos 25.94   1.48   27.69
FunSim               18.31   0.06   18.37
PSB                  16.41   0.01   16.43
HypergeometricTest   15.46   0.10   15.56
plot_heatmap         14.69   0.19   15.49
plot_net             14.52   0.19   14.71
x2y_conv2_y2x         7.76   0.00    7.76
* 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 NOTE
See
  'D:/biocbld/bbs-3.4-bioc/meat/dSimer.Rcheck/00check.log'
for details.

dSimer.Rcheck/00install.out:


install for i386

* installing *source* package 'dSimer' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c BOG.cpp -o BOG.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c GO2GeneAssos.cpp -o GO2GeneAssos.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c ICod.cpp -o ICod.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c PSB.cpp -o PSB.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_dSimer_init.c -o R_dSimer_init.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/dSimer.buildbin-libdir/dSimer/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'dSimer' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c BOG.cpp -o BOG.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c GO2GeneAssos.cpp -o GO2GeneAssos.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c ICod.cpp -o ICod.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c PSB.cpp -o PSB.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_dSimer_init.c -o R_dSimer_init.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/dSimer.buildbin-libdir/dSimer/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dSimer' as dSimer_0.99.3.zip
* DONE (dSimer)

dSimer.Rcheck/examples_i386/dSimer-Ex.timings:

nameusersystemelapsed
BOG6.030.056.08
FunSim13.92 0.0613.98
HumanNet_sample0.030.000.03
HypergeometricTest12.03 0.0612.09
ICod1.540.041.58
InformationContent0.160.010.17
LLSn2List0.080.020.09
Normalize000
PPI_HPRD0.180.000.19
PSB12.34 0.0012.34
Separation3.570.143.71
Separation2Similarity000
Sun_annotation0.050.110.16
Sun_function000
Sun_topology0.260.060.32
d2g_fundo_entrezid0.070.060.13
d2g_fundo_symbol0.070.060.14
d2g_separation0.100.040.12
d2go_sample000
get_GOterm2GeneAssos28.23 1.9935.29
go2g_sample0.100.000.09
graphlet_sig_hprd0.120.000.13
interactome0.560.020.58
jaccardindex000
orbit_dependency_count000
plot_heatmap16.55 0.1416.69
plot_net16.10 0.2016.31
setWeight000
weight000
x2y_conv2_y2x6.250.006.26
x2y_df2list000

dSimer.Rcheck/examples_x64/dSimer-Ex.timings:

nameusersystemelapsed
BOG4.850.114.96
FunSim18.31 0.0618.37
HumanNet_sample0.030.000.03
HypergeometricTest15.46 0.1015.56
ICod1.560.061.67
InformationContent0.100.060.18
LLSn2List0.140.000.19
Normalize000
PPI_HPRD0.170.020.19
PSB16.41 0.0116.43
Separation3.340.143.47
Separation2Similarity000
Sun_annotation0.070.030.09
Sun_function000
Sun_topology0.200.080.28
d2g_fundo_entrezid0.080.030.11
d2g_fundo_symbol0.040.060.11
d2g_separation0.050.050.10
d2go_sample000
get_GOterm2GeneAssos25.94 1.4827.69
go2g_sample0.080.000.07
graphlet_sig_hprd0.100.000.09
interactome0.370.060.44
jaccardindex0.020.000.02
orbit_dependency_count000
plot_heatmap14.69 0.1915.49
plot_net14.52 0.1914.71
setWeight000
weight0.000.010.01
x2y_conv2_y2x7.760.007.76
x2y_df2list000