BioC 3.5: CHECK report for dSimer on toluca2

Package: dSimer

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings dSimer_1.1.0.tar.gz

StartedAt: 2017-04-23 03:12:38 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 03:17:06 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 267.3 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_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/dSimer.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.1.0’
* 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 33.464  5.252  38.982
FunSim               16.036  0.988  17.559
plot_heatmap         15.431  0.127  15.751
plot_net             13.768  0.089  13.877
PSB                  12.645  0.339  12.999
HypergeometricTest   12.879  0.057  13.049
x2y_conv2_y2x         8.581  0.107   8.745
BOG                   5.271  0.014   5.325
* 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 -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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 -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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 -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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 -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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 -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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 -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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 -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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	5.271	0.014	5.325
CosineDFV	0.423	0.014	0.438
FunSim	16.036	0.988	17.559
HumanNet_sample	0.021	0.005	0.029
HypergeometricTest	12.879	0.057	13.049
ICod	1.243	0.016	1.259
InformationContent	0.048	0.001	0.049
LLSn2List	0.103	0.006	0.108
Normalize	0.000	0.000	0.001
PPI_HPRD	0.130	0.001	0.131
PSB	12.645	0.339	12.999
Separation	2.843	0.022	2.865
Separation2Similarity	0.001	0.000	0.000
Sun_annotation	0.047	0.002	0.049
Sun_function	0.002	0.001	0.003
Sun_topology	0.206	0.011	0.217
d2g_fundo_entrezid	0.056	0.000	0.057
d2g_fundo_symbol	0.074	0.001	0.075
d2g_separation	0.060	0.000	0.061
d2go_sample	0.001	0.001	0.001
d2s_hsdn	0.284	0.005	0.290
d2s_hsdn_sample	0.004	0.000	0.004
get_GOterm2GeneAssos	33.464	5.252	38.982
go2g_sample	0.102	0.005	0.107
graphlet_sig_hprd	0.112	0.015	0.131
interactome	0.599	0.004	0.607
jaccardindex	0.002	0.001	0.003
orbit_dependency_count	0.002	0.000	0.002
plot_bipartite	0.493	0.002	0.497
plot_heatmap	15.431	0.127	15.751
plot_net	13.768	0.089	13.877
plot_topo	0.265	0.008	0.276
setWeight	0.002	0.001	0.003
weight	0.002	0.001	0.002
x2y_conv2_y2x	8.581	0.107	8.745
x2y_df2list	0.028	0.000	0.029