BioC 3.6: CHECK report for dSimer on veracruz1

Package: dSimer

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings dSimer_1.3.0.tar.gz

StartedAt: 2017-08-16 02:27:08 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:31:03 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 234.9 seconds

RetCode: 0

Status:  OK

CheckDir: dSimer.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings dSimer_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/dSimer.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.3.0’
* 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 21.209  3.839  25.503
FunSim               12.444  0.717  13.498
plot_net             12.924  0.069  13.365
plot_heatmap         12.537  0.071  12.912
HypergeometricTest   10.001  0.043  10.294
PSB                   9.645  0.301  10.095
x2y_conv2_y2x         6.099  0.049   6.235
* 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-3.6-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)

name	user	system	elapsed
BOG	4.204	0.012	4.313
CosineDFV	0.356	0.011	0.372
FunSim	12.444	0.717	13.498
HumanNet_sample	0.019	0.003	0.021
HypergeometricTest	10.001	0.043	10.294
ICod	1.120	0.019	1.167
InformationContent	0.055	0.001	0.057
LLSn2List	0.087	0.005	0.097
Normalize	0.001	0.000	0.001
PPI_HPRD	0.113	0.002	0.116
PSB	9.645	0.301	10.095
Separation	2.823	0.032	2.932
Separation2Similarity	0.000	0.000	0.001
Sun_annotation	0.047	0.002	0.048
Sun_function	0.002	0.001	0.003
Sun_topology	0.301	0.013	0.348
d2g_fundo_entrezid	0.048	0.001	0.056
d2g_fundo_symbol	0.048	0.001	0.048
d2g_separation	0.028	0.000	0.029
d2go_sample	0.001	0.000	0.001
d2s_hsdn	0.091	0.002	0.093
d2s_hsdn_sample	0.004	0.000	0.004
get_GOterm2GeneAssos	21.209	3.839	25.503
go2g_sample	0.081	0.004	0.090
graphlet_sig_hprd	0.081	0.010	0.091
interactome	0.450	0.003	0.467
jaccardindex	0.002	0.000	0.002
orbit_dependency_count	0.001	0.001	0.003
plot_bipartite	0.310	0.005	0.330
plot_heatmap	12.537	0.071	12.912
plot_net	12.924	0.069	13.365
plot_topo	0.265	0.006	0.289
setWeight	0.002	0.001	0.003
weight	0.001	0.001	0.002
x2y_conv2_y2x	6.099	0.049	6.235
x2y_df2list	0.024	0.001	0.026