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CHECK report for dSimer on malbec1

This page was generated on 2019-04-16 11:52:07 -0400 (Tue, 16 Apr 2019).

Package 438/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dSimer 1.8.0
Peng Ni
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/dSimer
Branch: RELEASE_3_8
Last Commit: 78df868
Last Changed Date: 2018-10-30 11:42:01 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: dSimer
Version: 1.8.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:dSimer.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings dSimer_1.8.0.tar.gz
StartedAt: 2019-04-15 23:38:59 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:42:53 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 234.0 seconds
RetCode: 0
Status:  OK 
CheckDir: dSimer.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:dSimer.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings dSimer_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/dSimer.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.8.0’
* 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  6.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   3.6Mb
* 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 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
get_GOterm2GeneAssos 35.076  1.716  36.849
FunSim               19.120  0.024  19.171
plot_heatmap         18.744  0.124  18.886
plot_net             18.432  0.104  18.555
PSB                  13.040  0.004  13.057
HypergeometricTest   12.824  0.040  12.874
x2y_conv2_y2x         6.776  0.004   6.783
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/dSimer.Rcheck/00check.log’
for details.



Installation output

dSimer.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL dSimer
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘dSimer’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c BOG.cpp -o BOG.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c GO2GeneAssos.cpp -o GO2GeneAssos.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ICod.cpp -o ICod.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c PSB.cpp -o PSB.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-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-3.8-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-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/dSimer/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (dSimer)

Tests output


Example timings

dSimer.Rcheck/dSimer-Ex.timings

nameusersystemelapsed
BOG4.9360.0484.993
CosineDFV0.2200.0040.222
FunSim19.120 0.02419.171
HumanNet_sample0.0240.0040.029
HypergeometricTest12.824 0.04012.874
ICod1.1560.0521.212
InformationContent0.1080.0440.155
LLSn2List0.1000.0040.103
Normalize000
PPI_HPRD0.1560.0080.162
PSB13.040 0.00413.057
Separation4.7080.1324.846
Separation2Similarity0.0000.0000.001
Sun_annotation0.1000.0040.105
Sun_function0.0040.0000.002
Sun_topology0.2520.0400.295
d2g_fundo_entrezid0.0800.0400.124
d2g_fundo_symbol0.0760.0640.143
d2g_separation0.0680.0440.112
d2go_sample0.0040.0000.001
d2s_hsdn0.1160.0000.115
d2s_hsdn_sample0.0040.0000.006
get_GOterm2GeneAssos35.076 1.71636.849
go2g_sample0.0680.0040.071
graphlet_sig_hprd0.0920.0040.098
interactome0.6720.0800.750
jaccardindex0.0040.0000.002
orbit_dependency_count0.0000.0000.002
plot_bipartite0.2400.0520.290
plot_heatmap18.744 0.12418.886
plot_net18.432 0.10418.555
plot_topo0.4920.0520.544
setWeight0.0000.0000.001
weight000
x2y_conv2_y2x6.7760.0046.783
x2y_df2list0.0040.0000.004