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BioC 3.2: CHECK report for nethet on perceval

This page was generated on 2015-11-10 14:49:24 -0800 (Tue, 10 Nov 2015).

Package 703/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nethet 1.2.0
Nicolas Staedler , Frank Dondelinger
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/nethet
Last Changed Rev: 109589 / Revision: 110496
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
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: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings nethet_1.2.0.tar.gz
StartedAt: 2015-11-10 07:35:56 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 07:39:43 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 226.7 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
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/nethet.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [11s/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 ... [118s/118s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
het_cv_glasso       33.444  0.027  33.472
mixglasso           24.421  0.053  24.475
ggmgsa_multisplit   19.687  0.020  19.708
diffregr_multisplit 11.929  0.047  12.000
diffnet_multisplit   6.260  0.027   6.321
* 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
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c betamat_diffnet.c -o betamat_diffnet.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 -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
aggpval0.0060.0000.006
bwprun_mixglasso4.8220.0254.908
diffnet_multisplit6.2600.0276.321
diffnet_singlesplit3.1550.0043.160
diffregr_multisplit11.929 0.04712.000
diffregr_singlesplit0.7190.0030.721
dot_plot1.0430.0061.051
export_network0.4530.0020.455
generate_2networks0.0710.0020.072
generate_inv_cov0.0820.0830.165
ggmgsa_multisplit19.687 0.02019.708
gsea.iriz0.0120.0000.013
het_cv_glasso33.444 0.02733.472
invcov2parcor0.0020.0000.001
invcov2parcor_array0.0040.0000.004
logratio0.0010.0000.001
mixglasso24.421 0.05324.475
plot_2networks0.0760.0010.077
scatter_plot1.9680.0071.976
screen_aic.glasso0.8630.0000.864
screen_bic.glasso0.8580.0010.858
screen_cv.glasso2.1270.0012.127
screen_cv1se.lasso0.2130.0010.213
screen_cvfix.lasso0.2170.0000.218
screen_cvmin.lasso0.2150.0010.216
screen_cvsqrt.lasso0.2130.0010.214
screen_cvtrunc.lasso0.2110.0000.212
screen_mb0.0100.0010.011
sim_mix0.0040.0020.006
sim_mix_networks0.0110.0000.011