Peng Ni
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/dSimer |
| Branch: master |
| Last Commit: 97fd519 |
| Last Changed Date: 2018-10-30 11:54:36 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:16:18 -0400 (Tue, 09 Apr 2019).
| Package 459/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| dSimer 1.9.0 Peng Ni
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: dSimer |
| Version: 1.9.0 |
| 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_1.9.0.tar.gz |
| StartedAt: 2019-04-09 01:34:44 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:40:59 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 374.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: dSimer.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.9.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/dSimer.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.9.0’
* 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 64.838 15.803 80.703
FunSim 24.764 3.686 28.451
plot_heatmap 18.249 0.349 18.598
PSB 17.045 1.527 18.572
plot_net 17.632 0.296 17.931
HypergeometricTest 14.491 0.306 14.797
Separation 13.976 0.171 14.146
x2y_conv2_y2x 12.321 0.163 12.486
BOG 4.968 0.037 5.008
* 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-3.9-bioc/meat/dSimer.Rcheck/00check.log’
for details.
dSimer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL dSimer ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘dSimer’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c BOG.cpp -o BOG.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c GO2GeneAssos.cpp -o GO2GeneAssos.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ICod.cpp -o ICod.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c R_dSimer_init.c -o R_dSimer_init.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Sun.cpp -o Sun.o clang++ -std=gnu++11 -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/3.6/Resources/library/00LOCK-dSimer/00new/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 from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (dSimer)
dSimer.Rcheck/dSimer-Ex.timings
| name | user | system | elapsed | |
| BOG | 4.968 | 0.037 | 5.008 | |
| CosineDFV | 0.410 | 0.046 | 0.456 | |
| FunSim | 24.764 | 3.686 | 28.451 | |
| HumanNet_sample | 0.017 | 0.003 | 0.021 | |
| HypergeometricTest | 14.491 | 0.306 | 14.797 | |
| ICod | 1.905 | 0.083 | 1.986 | |
| InformationContent | 0.082 | 0.005 | 0.087 | |
| LLSn2List | 0.138 | 0.013 | 0.151 | |
| Normalize | 0.001 | 0.001 | 0.001 | |
| PPI_HPRD | 0.173 | 0.005 | 0.178 | |
| PSB | 17.045 | 1.527 | 18.572 | |
| Separation | 13.976 | 0.171 | 14.146 | |
| Separation2Similarity | 0.001 | 0.000 | 0.001 | |
| Sun_annotation | 0.083 | 0.005 | 0.089 | |
| Sun_function | 0.005 | 0.002 | 0.007 | |
| Sun_topology | 0.253 | 0.033 | 0.287 | |
| d2g_fundo_entrezid | 0.075 | 0.002 | 0.077 | |
| d2g_fundo_symbol | 0.083 | 0.003 | 0.086 | |
| d2g_separation | 0.075 | 0.002 | 0.077 | |
| d2go_sample | 0.002 | 0.002 | 0.004 | |
| d2s_hsdn | 0.130 | 0.005 | 0.135 | |
| d2s_hsdn_sample | 0.005 | 0.002 | 0.006 | |
| get_GOterm2GeneAssos | 64.838 | 15.803 | 80.703 | |
| go2g_sample | 0.130 | 0.007 | 0.137 | |
| graphlet_sig_hprd | 0.117 | 0.020 | 0.138 | |
| interactome | 0.720 | 0.012 | 0.731 | |
| jaccardindex | 0.003 | 0.002 | 0.006 | |
| orbit_dependency_count | 0.002 | 0.002 | 0.004 | |
| plot_bipartite | 0.317 | 0.003 | 0.320 | |
| plot_heatmap | 18.249 | 0.349 | 18.598 | |
| plot_net | 17.632 | 0.296 | 17.931 | |
| plot_topo | 0.287 | 0.018 | 0.305 | |
| setWeight | 0.002 | 0.002 | 0.003 | |
| weight | 0.002 | 0.001 | 0.004 | |
| x2y_conv2_y2x | 12.321 | 0.163 | 12.486 | |
| x2y_df2list | 0.003 | 0.000 | 0.004 | |