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CHECK report for dSimer on merida1

This page was generated on 2019-04-16 11:59:39 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:dSimer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings dSimer_1.8.0.tar.gz
StartedAt: 2019-04-15 23:39:19 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:43:50 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 271.1 seconds
RetCode: 0
Status:  OK 
CheckDir: dSimer.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:dSimer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings dSimer_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/dSimer.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.8.0’
* 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 ... 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 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 45.187  7.770  53.410
FunSim               20.079  1.735  21.956
plot_net             16.749  0.137  17.027
plot_heatmap         16.248  0.153  16.530
PSB                  15.793  0.316  16.237
HypergeometricTest   14.673  0.072  14.872
x2y_conv2_y2x         7.795  0.039   7.903
BOG                   5.272  0.018   5.334
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/dSimer.Rcheck/00check.log’
for details.



Installation output

dSimer.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL dSimer
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘dSimer’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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 /Library/Frameworks/R.framework/Versions/3.5/Resources/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
BOG5.2720.0185.334
CosineDFV0.3180.0510.372
FunSim20.079 1.73521.956
HumanNet_sample0.0250.0030.027
HypergeometricTest14.673 0.07214.872
ICod1.1170.0241.147
InformationContent0.0690.0010.070
LLSn2List0.0920.0070.101
Normalize000
PPI_HPRD0.1590.0020.161
PSB15.793 0.31616.237
Separation3.5620.0423.629
Separation2Similarity0.0000.0000.001
Sun_annotation0.0560.0020.058
Sun_function0.0020.0000.003
Sun_topology0.2150.0160.233
d2g_fundo_entrezid0.0500.0020.051
d2g_fundo_symbol0.0880.0020.091
d2g_separation0.0750.0020.078
d2go_sample0.0020.0010.003
d2s_hsdn0.1360.0050.143
d2s_hsdn_sample0.0050.0010.006
get_GOterm2GeneAssos45.187 7.77053.410
go2g_sample0.1130.0040.118
graphlet_sig_hprd0.1060.0110.120
interactome0.6190.0050.630
jaccardindex0.0020.0000.003
orbit_dependency_count0.0010.0000.001
plot_bipartite0.1950.0020.199
plot_heatmap16.248 0.15316.530
plot_net16.749 0.13717.027
plot_topo0.2830.0100.294
setWeight0.0020.0010.003
weight0.0010.0000.002
x2y_conv2_y2x7.7950.0397.903
x2y_df2list0.0050.0000.004