Back to Multiple platform build/check report for BioC 3.10 |
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This page was generated on 2020-04-15 12:43:42 -0400 (Wed, 15 Apr 2020).
Package 488/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Peng Ni
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | ERROR | ERROR | skipped | skipped | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK |
Package: dSimer |
Version: 1.12.0 |
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_1.12.0.tar.gz |
StartedAt: 2020-04-15 02:00:39 -0400 (Wed, 15 Apr 2020) |
EndedAt: 2020-04-15 02:05:29 -0400 (Wed, 15 Apr 2020) |
EllapsedTime: 290.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: dSimer.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/dSimer.Rcheck’ * using R version 3.6.3 (2020-02-29) * 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 ‘1.12.0’ * 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 ... WARNING Found the following significant warnings: Warning: Package 'dSimer' is deprecated and will be removed from Bioconductor See ‘/Users/biocbuild/bbs-3.10-bioc/meat/dSimer.Rcheck/00install.out’ for details. * 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 42.943 8.079 52.248 FunSim 20.121 1.435 21.699 plot_heatmap 15.424 0.140 15.687 plot_net 15.253 0.116 15.482 PSB 14.591 0.326 15.059 HypergeometricTest 13.528 0.107 13.721 Separation 13.002 0.091 13.210 x2y_conv2_y2x 8.046 0.071 8.203 BOG 5.143 0.020 5.207 * 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 WARNING, 1 NOTE See ‘/Users/biocbuild/bbs-3.10-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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 Warning: Package 'dSimer' is deprecated and will be removed from Bioconductor version 3.11 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: Package 'dSimer' is deprecated and will be removed from Bioconductor version 3.11 ** testing if installed package keeps a record of temporary installation path * DONE (dSimer)
dSimer.Rcheck/dSimer-Ex.timings
name | user | system | elapsed | |
BOG | 5.143 | 0.020 | 5.207 | |
CosineDFV | 0.284 | 0.016 | 0.301 | |
FunSim | 20.121 | 1.435 | 21.699 | |
HumanNet_sample | 0.022 | 0.004 | 0.027 | |
HypergeometricTest | 13.528 | 0.107 | 13.721 | |
ICod | 1.689 | 0.029 | 1.727 | |
InformationContent | 0.081 | 0.002 | 0.085 | |
LLSn2List | 0.096 | 0.008 | 0.104 | |
Normalize | 0.000 | 0.000 | 0.001 | |
PPI_HPRD | 0.185 | 0.003 | 0.189 | |
PSB | 14.591 | 0.326 | 15.059 | |
Separation | 13.002 | 0.091 | 13.210 | |
Separation2Similarity | 0.000 | 0.001 | 0.000 | |
Sun_annotation | 0.083 | 0.002 | 0.084 | |
Sun_function | 0.003 | 0.002 | 0.005 | |
Sun_topology | 0.233 | 0.021 | 0.263 | |
d2g_fundo_entrezid | 0.053 | 0.001 | 0.055 | |
d2g_fundo_symbol | 0.072 | 0.001 | 0.073 | |
d2g_separation | 0.070 | 0.001 | 0.071 | |
d2go_sample | 0.001 | 0.001 | 0.002 | |
d2s_hsdn | 0.129 | 0.003 | 0.133 | |
d2s_hsdn_sample | 0.008 | 0.001 | 0.009 | |
get_GOterm2GeneAssos | 42.943 | 8.079 | 52.248 | |
go2g_sample | 0.090 | 0.003 | 0.095 | |
graphlet_sig_hprd | 0.109 | 0.011 | 0.119 | |
interactome | 0.642 | 0.006 | 0.657 | |
jaccardindex | 0.002 | 0.001 | 0.003 | |
orbit_dependency_count | 0.002 | 0.001 | 0.003 | |
plot_bipartite | 0.316 | 0.002 | 0.361 | |
plot_heatmap | 15.424 | 0.140 | 15.687 | |
plot_net | 15.253 | 0.116 | 15.482 | |
plot_topo | 0.254 | 0.011 | 0.267 | |
setWeight | 0.002 | 0.001 | 0.003 | |
weight | 0.001 | 0.001 | 0.002 | |
x2y_conv2_y2x | 8.046 | 0.071 | 8.203 | |
x2y_df2list | 0.003 | 0.000 | 0.003 | |