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BioC 3.4: CHECK report for dSimer on malbec1

This page was generated on 2017-04-15 16:13:50 -0400 (Sat, 15 Apr 2017).

Package 347/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dSimer 1.0.0
Peng Ni
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/dSimer
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: dSimer
Version: 1.0.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings dSimer_1.0.0.tar.gz
StartedAt: 2017-04-14 22:12:03 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:15:28 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 205.0 seconds
RetCode: 0
Status:  OK 
CheckDir: dSimer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings dSimer_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/dSimer.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.0.0’
* 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  6.3Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.6Mb
* 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 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 18.608  0.892  19.511
plot_heatmap         16.032  0.044  16.084
plot_net             15.608  0.068  15.686
HypergeometricTest   10.812  0.040  10.860
FunSim               10.584  0.020  10.613
PSB                  10.432  0.008  10.451
x2y_conv2_y2x         6.640  0.004   6.647
* 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-3.4-bioc/meat/dSimer.Rcheck/00check.log’
for details.


dSimer.Rcheck/00install.out:

* installing *source* package ‘dSimer’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c BOG.cpp -o BOG.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c GO2GeneAssos.cpp -o GO2GeneAssos.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c ICod.cpp -o ICod.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c PSB.cpp -o PSB.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c R_dSimer_init.c -o R_dSimer_init.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c Sun.cpp -o Sun.o
g++ -shared -L/home/biocbuild/bbs-3.4-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-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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)

dSimer.Rcheck/dSimer-Ex.timings:

nameusersystemelapsed
BOG4.2560.0124.270
CosineDFV0.2880.0000.290
FunSim10.584 0.02010.613
HumanNet_sample0.0240.0000.023
HypergeometricTest10.812 0.04010.860
ICod1.3280.0521.377
InformationContent0.0520.0240.075
LLSn2List0.0520.0040.058
Normalize0.0000.0000.001
PPI_HPRD0.1120.0000.111
PSB10.432 0.00810.451
Separation3.1840.0443.229
Separation2Similarity0.0000.0000.001
Sun_annotation0.0480.0120.059
Sun_function0.0040.0000.002
Sun_topology0.1760.0200.195
d2g_fundo_entrezid0.0520.0200.072
d2g_fundo_symbol0.0600.0160.075
d2g_separation0.0520.0200.071
d2go_sample0.0040.0000.002
d2s_hsdn0.2360.0040.242
d2s_hsdn_sample0.0080.0000.005
get_GOterm2GeneAssos18.608 0.89219.511
go2g_sample0.0720.0040.076
graphlet_sig_hprd0.1120.0000.111
interactome0.4800.0320.514
jaccardindex0.0040.0000.002
orbit_dependency_count0.0000.0000.001
plot_bipartite0.1600.0160.176
plot_heatmap16.032 0.04416.084
plot_net15.608 0.06815.686
plot_topo0.2080.0200.231
setWeight0.0040.0000.002
weight0.0000.0000.001
x2y_conv2_y2x6.6400.0046.647
x2y_df2list0.0000.0040.003