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BioC 3.2: CHECK report for BiRewire on oaxaca

This page was generated on 2016-04-23 10:27:05 -0700 (Sat, 23 Apr 2016).

Package 112/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiRewire 3.0.1
Andrea Gobbi
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/BiRewire
Last Changed Rev: 115795 / Revision: 116712
Last Changed Date: 2016-04-05 01:14:34 -0700 (Tue, 05 Apr 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BiRewire
Version: 3.0.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiRewire_3.0.1.tar.gz
StartedAt: 2016-04-22 22:12:52 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 22:16:16 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 203.9 seconds
RetCode: 0
Status:  OK 
CheckDir: BiRewire.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiRewire_3.0.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/BiRewire.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiRewire/DESCRIPTION’ ... OK
* this is package ‘BiRewire’ version ‘3.0.1’
* 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 ‘BiRewire’ can be installed ... [6s/7s] 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [120s/120s] OK
Examples with CPU or elapsed time > 5s
                                        user system elapsed
birewire.visual.monitoring.dsg        47.957  0.423  48.421
birewire.analysis.undirected          43.040  0.103  43.244
birewire.visual.monitoring.undirected 15.621  0.959  16.596
birewire.visual.monitoring.bipartite   7.168  0.077   7.250
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [23s/23s]
 [24s/24s] OK
* 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: OK

BiRewire.Rcheck/00install.out:

* installing *source* package ‘BiRewire’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c BiRewire.c -o BiRewire.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c interface.c -o interface.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 BiRewire.so BiRewire.o interface.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/BiRewire.Rcheck/BiRewire/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 (BiRewire)

BiRewire.Rcheck/BiRewire-Ex.timings:

nameusersystemelapsed
birewire.analysis.bipartite0.0940.1120.207
birewire.analysis.dsg0.0560.0050.061
birewire.analysis.undirected43.040 0.10343.244
birewire.bipartite.from.incidence0.0090.0110.020
birewire.build.dsg0.0160.0020.018
birewire.induced.bipartite0.0050.0010.005
birewire.rewire.bipartite0.0090.0100.019
birewire.rewire.bipartite.and.projections0.2590.0270.286
birewire.rewire.dsg0.0050.0010.006
birewire.rewire.undirected1.4270.0451.473
birewire.similarity0.0140.0010.014
birewire.similarity.dsg0.0480.0010.050
birewire.visual.monitoring.bipartite7.1680.0777.250
birewire.visual.monitoring.dsg47.957 0.42348.421
birewire.visual.monitoring.undirected15.621 0.95916.596