BioC 3.5: CHECK report for dSimer on malbec2

Package: dSimer

Version: 1.2.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings dSimer_1.2.0.tar.gz

StartedAt: 2017-10-17 22:49:22 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 22:52:59 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 216.6 seconds

RetCode: 0

Status:  OK

CheckDir: dSimer.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings dSimer_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/dSimer.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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 ... NOTE
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   3.5Mb
* 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 20.064  1.036  21.734
plot_heatmap         14.180  0.052  14.240
plot_net             13.488  0.044  13.536
FunSim               12.016  0.032  12.055
PSB                  10.840  0.016  10.882
HypergeometricTest   10.432  0.028  10.466
x2y_conv2_y2x         6.400  0.004   6.409
* 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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/dSimer.Rcheck/00check.log’
for details.

* installing *source* package ‘dSimer’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c BOG.cpp -o BOG.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c GO2GeneAssos.cpp -o GO2GeneAssos.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ICod.cpp -o ICod.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c PSB.cpp -o PSB.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c R_dSimer_init.c -o R_dSimer_init.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Sun.cpp -o Sun.o
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o dSimer.so BOG.o GO2GeneAssos.o ICod.o PSB.o R_dSimer_init.o RcppExports.o Sun.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/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	4.420	0.012	4.437
CosineDFV	0.324	0.000	0.326
FunSim	12.016	0.032	12.055
HumanNet_sample	0.016	0.004	0.020
HypergeometricTest	10.432	0.028	10.466
ICod	1.408	0.020	1.677
InformationContent	0.056	0.032	0.090
LLSn2List	0.096	0.008	0.107
Normalize	0.000	0.000	0.001
PPI_HPRD	0.140	0.000	0.139
PSB	10.840	0.016	10.882
Separation	3.684	0.052	3.741
Separation2Similarity	0.000	0.000	0.001
Sun_annotation	0.060	0.008	0.069
Sun_function	0.004	0.000	0.003
Sun_topology	0.172	0.032	0.202
d2g_fundo_entrezid	0.076	0.016	0.092
d2g_fundo_symbol	0.044	0.024	0.067
d2g_separation	0.048	0.012	0.062
d2go_sample	0.004	0.000	0.001
d2s_hsdn	0.096	0.000	0.098
d2s_hsdn_sample	0.004	0.000	0.004
get_GOterm2GeneAssos	20.064	1.036	21.734
go2g_sample	0.072	0.000	0.071
graphlet_sig_hprd	0.088	0.008	0.095
interactome	0.440	0.024	0.467
jaccardindex	0.000	0.000	0.002
orbit_dependency_count	0.004	0.000	0.001
plot_bipartite	0.316	0.020	0.359
plot_heatmap	14.180	0.052	14.240
plot_net	13.488	0.044	13.536
plot_topo	0.192	0.024	0.216
setWeight	0.000	0.000	0.002
weight	0.000	0.000	0.001
x2y_conv2_y2x	6.400	0.004	6.409
x2y_df2list	0.016	0.000	0.019