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CHECK report for dSimer on veracruz1

This page was generated on 2018-04-12 13:42:59 -0400 (Thu, 12 Apr 2018).

Package 390/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dSimer 1.4.0
Peng Ni
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/dSimer
Branch: RELEASE_3_6
Last Commit: e900703
Last Changed Date: 2017-10-30 12:41:17 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: dSimer
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings dSimer_1.4.0.tar.gz
StartedAt: 2018-04-12 03:05:30 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 03:09:49 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 259.4 seconds
RetCode: 0
Status:  OK 
CheckDir: dSimer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings dSimer_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/dSimer.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dSimer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dSimer’ version ‘1.4.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘dSimer’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.6Mb
* 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
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
get_GOterm2GeneAssos 28.773  4.837  34.137
FunSim               13.954  0.559  14.777
plot_heatmap         13.624  0.094  13.893
plot_net             12.797  0.082  13.060
PSB                  11.306  0.276  11.728
HypergeometricTest   10.484  0.073  10.761
x2y_conv2_y2x         7.038  0.025   7.128
* 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
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/dSimer.Rcheck/00check.log’
for details.



Installation output

dSimer.Rcheck/00install.out

* installing *source* package ‘dSimer’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c BOG.cpp -o BOG.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c GO2GeneAssos.cpp -o GO2GeneAssos.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c ICod.cpp -o ICod.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c PSB.cpp -o PSB.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_dSimer_init.c -o R_dSimer_init.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Sun.cpp -o Sun.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o dSimer.so BOG.o GO2GeneAssos.o ICod.o PSB.o R_dSimer_init.o RcppExports.o Sun.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/dSimer.Rcheck/dSimer/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (dSimer)

Tests output


Example timings

dSimer.Rcheck/dSimer-Ex.timings

nameusersystemelapsed
BOG4.5860.0144.662
CosineDFV0.4090.0120.427
FunSim13.954 0.55914.777
HumanNet_sample0.0190.0030.021
HypergeometricTest10.484 0.07310.761
ICod1.1230.0171.159
InformationContent0.0540.0010.055
LLSn2List0.0830.0050.089
Normalize0.0000.0000.001
PPI_HPRD0.1130.0020.116
PSB11.306 0.27611.728
Separation3.4180.0633.528
Separation2Similarity0.0010.0000.000
Sun_annotation0.0610.0020.067
Sun_function0.0030.0010.003
Sun_topology0.1660.0120.183
d2g_fundo_entrezid0.0460.0010.047
d2g_fundo_symbol0.0460.0010.052
d2g_separation0.0410.0000.045
d2go_sample0.0020.0010.002
d2s_hsdn0.1020.0020.106
d2s_hsdn_sample0.0050.0000.005
get_GOterm2GeneAssos28.773 4.83734.137
go2g_sample0.0770.0050.081
graphlet_sig_hprd0.0830.0120.095
interactome0.4400.0050.446
jaccardindex0.0020.0010.003
orbit_dependency_count0.0010.0010.002
plot_bipartite0.3310.0040.337
plot_heatmap13.624 0.09413.893
plot_net12.797 0.08213.060
plot_topo0.2520.0070.263
setWeight0.0020.0000.003
weight0.0020.0000.003
x2y_conv2_y2x7.0380.0257.128
x2y_df2list0.0210.0000.024