BioC 3.6: CHECK report for dSimer on malbec1

Package: dSimer

Version: 1.3.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings dSimer_1.3.0.tar.gz

StartedAt: 2017-08-15 22:45:42 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:49:03 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 200.7 seconds

RetCode: 0

Status:  OK

CheckDir: dSimer.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings dSimer_1.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/dSimer.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.3.0’
* 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 ... 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 18.320  1.192  19.755
plot_heatmap         13.808  0.040  13.853
plot_net             13.704  0.048  13.757
FunSim               11.288  0.008  11.301
HypergeometricTest   10.060  0.032  10.095
PSB                   9.708  0.012   9.725
x2y_conv2_y2x         5.572  0.000   5.575
* 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-3.6-bioc/meat/dSimer.Rcheck/00check.log’
for details.

* installing *source* package ‘dSimer’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c BOG.cpp -o BOG.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c GO2GeneAssos.cpp -o GO2GeneAssos.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ICod.cpp -o ICod.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c PSB.cpp -o PSB.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-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-3.6-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-3.6-bioc/R/lib -lR
installing to /home/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	3.996	0.020	4.017
CosineDFV	0.312	0.008	0.321
FunSim	11.288	0.008	11.301
HumanNet_sample	0.02	0.00	0.02
HypergeometricTest	10.060	0.032	10.095
ICod	1.168	0.048	1.218
InformationContent	0.052	0.012	0.063
LLSn2List	0.064	0.004	0.066
Normalize	0	0	0
PPI_HPRD	0.076	0.000	0.074
PSB	9.708	0.012	9.725
Separation	3.164	0.044	3.209
Separation2Similarity	0	0	0
Sun_annotation	0.036	0.028	0.064
Sun_function	0.004	0.000	0.002
Sun_topology	0.328	0.036	0.365
d2g_fundo_entrezid	0.052	0.016	0.068
d2g_fundo_symbol	0.048	0.016	0.067
d2g_separation	0.044	0.016	0.061
d2go_sample	0.000	0.000	0.002
d2s_hsdn	0.092	0.000	0.092
d2s_hsdn_sample	0.004	0.000	0.004
get_GOterm2GeneAssos	18.320	1.192	19.755
go2g_sample	0.060	0.008	0.070
graphlet_sig_hprd	0.088	0.000	0.087
interactome	0.376	0.036	0.409
jaccardindex	0.004	0.000	0.003
orbit_dependency_count	0.000	0.000	0.001
plot_bipartite	0.304	0.016	0.330
plot_heatmap	13.808	0.040	13.853
plot_net	13.704	0.048	13.757
plot_topo	0.232	0.016	0.251
setWeight	0.000	0.000	0.002
weight	0.004	0.000	0.001
x2y_conv2_y2x	5.572	0.000	5.575
x2y_df2list	0.016	0.000	0.017