BioC 3.5: CHECK report for dSimer on veracruz2

Package: dSimer

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings dSimer_1.2.0.tar.gz

StartedAt: 2017-10-18 02:58:15 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 03:02:37 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 262.1 seconds

RetCode: 0

Status:  OK

CheckDir: dSimer.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings dSimer_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/dSimer.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.2.0’
* 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 ... 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
* 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 22.499  4.222  27.537
FunSim               15.260  0.280  16.025
plot_net             15.045  0.140  15.743
plot_heatmap         14.472  0.130  15.188
PSB                  11.681  0.167  12.229
HypergeometricTest   10.976  0.077  11.453
x2y_conv2_y2x         7.064  0.057   7.360
* 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: OK

* 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-3.5-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)

name	user	system	elapsed
BOG	4.560	0.024	4.697
CosineDFV	0.385	0.012	0.405
FunSim	15.260	0.280	16.025
HumanNet_sample	0.019	0.003	0.022
HypergeometricTest	10.976	0.077	11.453
ICod	1.337	0.021	1.393
InformationContent	0.070	0.002	0.076
LLSn2List	0.093	0.007	0.104
Normalize	0.000	0.001	0.005
PPI_HPRD	0.137	0.002	0.147
PSB	11.681	0.167	12.229
Separation	2.630	0.029	2.725
Separation2Similarity	0.000	0.000	0.001
Sun_annotation	0.050	0.001	0.053
Sun_function	0.003	0.000	0.004
Sun_topology	0.162	0.013	0.179
d2g_fundo_entrezid	0.040	0.000	0.042
d2g_fundo_symbol	0.065	0.006	0.072
d2g_separation	0.041	0.001	0.042
d2go_sample	0.001	0.000	0.001
d2s_hsdn	0.089	0.003	0.095
d2s_hsdn_sample	0.005	0.000	0.005
get_GOterm2GeneAssos	22.499	4.222	27.537
go2g_sample	0.077	0.004	0.084
graphlet_sig_hprd	0.098	0.013	0.114
interactome	0.593	0.006	0.616
jaccardindex	0.003	0.000	0.003
orbit_dependency_count	0.002	0.000	0.003
plot_bipartite	0.479	0.007	0.506
plot_heatmap	14.472	0.130	15.188
plot_net	15.045	0.140	15.743
plot_topo	0.268	0.007	0.290
setWeight	0.002	0.001	0.003
weight	0.002	0.000	0.002
x2y_conv2_y2x	7.064	0.057	7.360
x2y_df2list	0.023	0.000	0.024