Peng Ni
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/dSimer |
| Branch: RELEASE_3_10 |
| Last Commit: 34f87d4 |
| Last Changed Date: 2019-10-29 13:09:41 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
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 |
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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_1.12.0.tar.gz
###
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* 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 | |