Nicolas Staedler
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/nethet |
| Branch: RELEASE_3_10 |
| Last Commit: a7e4ace |
| Last Changed Date: 2019-10-29 13:09:07 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:41:11 -0400 (Wed, 15 Apr 2020).
| Package 1145/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| nethet 1.18.0 Nicolas Staedler
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: nethet |
| Version: 1.18.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:nethet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings nethet_1.18.0.tar.gz |
| StartedAt: 2020-04-15 04:13:48 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:17:25 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 217.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: nethet.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:nethet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings nethet_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/nethet.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 ‘nethet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nethet’ version ‘1.18.0’
* 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 ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘mclust::dmvnorm’ by ‘mvtnorm::dmvnorm’ when loading ‘nethet’
Warning: replacing previous import ‘multtest::update’ by ‘stats::update’ when loading ‘nethet’
See ‘/Users/biocbuild/bbs-3.10-bioc/meat/nethet.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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
het_cv_glasso 31.071 0.058 32.923
ggmgsa_multisplit 17.580 0.043 18.047
mixglasso 13.646 0.399 14.153
diffregr_multisplit 10.593 0.118 10.863
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
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: 1 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.10-bioc/meat/nethet.Rcheck/00check.log’
for details.
nethet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL nethet ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘nethet’ ... ** using staged installation ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -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 /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-nethet/00new/nethet/libs ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘mclust::dmvnorm’ by ‘mvtnorm::dmvnorm’ when loading ‘nethet’ Warning: replacing previous import ‘multtest::update’ by ‘stats::update’ when loading ‘nethet’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘mclust::dmvnorm’ by ‘mvtnorm::dmvnorm’ when loading ‘nethet’ Warning: replacing previous import ‘multtest::update’ by ‘stats::update’ when loading ‘nethet’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: replacing previous import ‘mclust::dmvnorm’ by ‘mvtnorm::dmvnorm’ when loading ‘nethet’ Warning: replacing previous import ‘multtest::update’ by ‘stats::update’ when loading ‘nethet’ ** testing if installed package keeps a record of temporary installation path * DONE (nethet)
nethet.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(nethet)
Warning messages:
1: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'nethet'
2: replacing previous import 'multtest::update' by 'stats::update' when loading 'nethet'
>
> test_check("nethet")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 18 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
10.503 0.502 11.043
nethet.Rcheck/nethet-Ex.timings
| name | user | system | elapsed | |
| aggpval | 0.007 | 0.000 | 0.007 | |
| bwprun_mixglasso | 2.523 | 0.129 | 2.672 | |
| diffnet_multisplit | 4.958 | 0.010 | 4.999 | |
| diffnet_singlesplit | 2.503 | 0.007 | 2.526 | |
| diffregr_multisplit | 10.593 | 0.118 | 10.863 | |
| diffregr_singlesplit | 0.635 | 0.009 | 0.646 | |
| dot_plot | 1.160 | 0.013 | 1.186 | |
| export_network | 0.213 | 0.001 | 0.214 | |
| generate_2networks | 0.057 | 0.001 | 0.058 | |
| generate_inv_cov | 0.092 | 0.080 | 0.173 | |
| ggmgsa_multisplit | 17.580 | 0.043 | 18.047 | |
| gsea.iriz | 0.013 | 0.001 | 0.016 | |
| het_cv_glasso | 31.071 | 0.058 | 32.923 | |
| invcov2parcor | 0.001 | 0.000 | 0.001 | |
| invcov2parcor_array | 0.008 | 0.000 | 0.008 | |
| logratio | 0.002 | 0.000 | 0.002 | |
| mixglasso | 13.646 | 0.399 | 14.153 | |
| plot_2networks | 0.061 | 0.001 | 0.062 | |
| scatter_plot | 1.962 | 0.013 | 1.995 | |
| screen_aic.glasso | 0.967 | 0.006 | 0.981 | |
| screen_bic.glasso | 0.946 | 0.002 | 0.959 | |
| screen_cv.glasso | 1.958 | 0.003 | 1.982 | |
| screen_cv1se.lasso | 0.198 | 0.001 | 0.199 | |
| screen_cvfix.lasso | 0.188 | 0.001 | 0.190 | |
| screen_cvmin.lasso | 0.174 | 0.001 | 0.175 | |
| screen_cvsqrt.lasso | 0.183 | 0.000 | 0.184 | |
| screen_cvtrunc.lasso | 0.191 | 0.000 | 0.192 | |
| screen_mb | 0.011 | 0.000 | 0.012 | |
| sim_mix | 0.005 | 0.003 | 0.009 | |
| sim_mix_networks | 0.012 | 0.001 | 0.012 | |