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BioC 3.2: CHECK report for nethet on oaxaca

This page was generated on 2015-08-24 10:58:55 -0700 (Mon, 24 Aug 2015).

Package 681/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nethet 1.1.1
Nicolas Staedler , Frank Dondelinger
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/nethet
Last Changed Rev: 107532 / Revision: 107696
Last Changed Date: 2015-08-18 05:08:01 -0700 (Tue, 18 Aug 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  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: nethet
Version: 1.1.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings nethet_1.1.1.tar.gz
StartedAt: 2015-08-24 02:14:37 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 02:18:23 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 226.1 seconds
RetCode: 0
Status:  OK 
CheckDir: nethet.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 nethet_1.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/nethet.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nethet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nethet’ version ‘1.1.1’
* 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 ‘nethet’ can be installed ... [12s/13s] 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 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 ... [109s/110s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
het_cv_glasso       29.199  0.097  29.408
mixglasso           21.192  0.564  21.892
ggmgsa_multisplit   17.646  0.034  17.902
diffregr_multisplit 13.105  0.092  13.352
diffnet_multisplit   5.799  0.037   5.896
bwprun_mixglasso     4.836  0.081   5.053
* 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

nethet.Rcheck/00install.out:

* installing *source* package ‘nethet’ ...
** 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 betamat_diffnet.c -o betamat_diffnet.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 nethet.so betamat_diffnet.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/nethet.Rcheck/nethet/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (nethet)

nethet.Rcheck/nethet-Ex.timings:

nameusersystemelapsed
aggpval0.0070.0000.008
bwprun_mixglasso4.8360.0815.053
diffnet_multisplit5.7990.0375.896
diffnet_singlesplit2.8020.0092.873
diffregr_multisplit13.105 0.09213.352
diffregr_singlesplit0.7970.0020.840
dot_plot1.0160.0071.110
export_network0.4490.0040.453
generate_2networks0.0730.0010.075
generate_inv_cov0.0700.0690.138
ggmgsa_multisplit17.646 0.03417.902
gsea.iriz0.0140.0000.013
het_cv_glasso29.199 0.09729.408
invcov2parcor0.0010.0000.001
invcov2parcor_array0.0040.0010.004
logratio0.0020.0000.002
mixglasso21.192 0.56421.892
plot_2networks0.0680.0000.069
scatter_plot2.1410.0152.161
screen_aic.glasso0.6910.0020.694
screen_bic.glasso0.6870.0010.691
screen_cv.glasso1.8330.0041.846
screen_cv1se.lasso0.2280.0030.231
screen_cvfix.lasso0.2250.0010.227
screen_cvmin.lasso0.2220.0020.226
screen_cvsqrt.lasso0.2350.0020.237
screen_cvtrunc.lasso0.2370.0000.237
screen_mb0.0110.0000.011
sim_mix0.0040.0020.005
sim_mix_networks0.0090.0000.009