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BioC 3.2: CHECK report for nethet on oaxaca

This page was generated on 2016-04-23 10:28:41 -0700 (Sat, 23 Apr 2016).

Package 703/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nethet 1.2.0
Nicolas Staedler , Frank Dondelinger
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/nethet
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
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: nethet
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings nethet_1.2.0.tar.gz
StartedAt: 2016-04-23 02:38:20 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 02:41:48 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 208.0 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_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/nethet.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 ‘nethet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nethet’ version ‘1.2.0’
* 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 ‘nethet’ can be installed ... [10s/12s] 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 ... [101s/101s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
het_cv_glasso       28.175  0.071  28.268
mixglasso           19.648  0.313  19.978
ggmgsa_multisplit   16.030  0.037  16.077
diffregr_multisplit 11.518  0.083  11.613
diffnet_multisplit   5.139  0.035   5.212
* 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
aggpval0.0060.0010.007
bwprun_mixglasso4.4500.0684.558
diffnet_multisplit5.1390.0355.212
diffnet_singlesplit2.5560.0122.570
diffregr_multisplit11.518 0.08311.613
diffregr_singlesplit0.7130.0030.717
dot_plot1.0480.0041.054
export_network0.4190.0010.422
generate_2networks0.0560.0010.057
generate_inv_cov0.0680.0690.137
ggmgsa_multisplit16.030 0.03716.077
gsea.iriz0.0120.0000.013
het_cv_glasso28.175 0.07128.268
invcov2parcor0.0020.0000.002
invcov2parcor_array0.0050.0000.005
logratio0.0020.0000.002
mixglasso19.648 0.31319.978
plot_2networks0.0620.0010.064
scatter_plot1.8830.0081.893
screen_aic.glasso0.6510.0020.652
screen_bic.glasso0.6640.0010.666
screen_cv.glasso1.7760.0031.780
screen_cv1se.lasso0.2040.0020.205
screen_cvfix.lasso0.2140.0010.214
screen_cvmin.lasso0.1930.0010.194
screen_cvsqrt.lasso0.2000.0020.202
screen_cvtrunc.lasso0.1860.0020.187
screen_mb0.0100.0000.011
sim_mix0.0020.0020.004
sim_mix_networks0.0080.0000.008