Nicolas Staedler
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/nethet |
| Branch: master |
| Last Commit: e3c39ab |
| Last Changed Date: 2019-10-29 13:38:41 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:41:00 -0500 (Thu, 16 Jan 2020).
| Package 1143/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| nethet 1.19.0 Nicolas Staedler
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: nethet |
| Version: 1.19.0 |
| 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_1.19.0.tar.gz |
| StartedAt: 2020-01-16 06:57:53 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 07:02:47 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 294.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: nethet.Rcheck |
| Warnings: 1 |
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### Running command:
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### /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_1.19.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/nethet.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.19.0’
* 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-3.11-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 (user + system) or elapsed time > 5s
user system elapsed
het_cv_glasso 37.486 0.096 42.741
ggmgsa_multisplit 22.657 0.092 25.805
mixglasso 16.134 1.362 17.499
diffregr_multisplit 12.536 0.505 13.042
diffnet_multisplit 6.600 0.027 6.631
* 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-3.11-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/4.0/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/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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")
-mixglasso: comp too small; min(n_k)= 4.928062
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 18 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
12.210 1.095 13.257
nethet.Rcheck/nethet-Ex.timings
| name | user | system | elapsed | |
| aggpval | 0.008 | 0.000 | 0.008 | |
| bwprun_mixglasso | 3.874 | 0.260 | 4.612 | |
| diffnet_multisplit | 6.600 | 0.027 | 6.631 | |
| diffnet_singlesplit | 3.261 | 0.006 | 3.269 | |
| diffregr_multisplit | 12.536 | 0.505 | 13.042 | |
| diffregr_singlesplit | 0.927 | 0.026 | 0.952 | |
| dot_plot | 1.656 | 0.035 | 1.692 | |
| export_network | 0.274 | 0.016 | 0.290 | |
| generate_2networks | 0.089 | 0.014 | 0.104 | |
| generate_inv_cov | 0.184 | 0.232 | 0.415 | |
| ggmgsa_multisplit | 22.657 | 0.092 | 25.805 | |
| gsea.iriz | 0.013 | 0.001 | 0.014 | |
| het_cv_glasso | 37.486 | 0.096 | 42.741 | |
| invcov2parcor | 0.002 | 0.000 | 0.001 | |
| invcov2parcor_array | 0.009 | 0.000 | 0.010 | |
| logratio | 0.002 | 0.000 | 0.003 | |
| mixglasso | 16.134 | 1.362 | 17.499 | |
| plot_2networks | 0.070 | 0.002 | 0.072 | |
| scatter_plot | 2.298 | 0.043 | 2.343 | |
| screen_aic.glasso | 1.286 | 0.016 | 1.303 | |
| screen_bic.glasso | 1.224 | 0.001 | 1.225 | |
| screen_cv.glasso | 2.552 | 0.003 | 2.555 | |
| screen_cv1se.lasso | 0.247 | 0.000 | 0.247 | |
| screen_cvfix.lasso | 0.252 | 0.004 | 0.256 | |
| screen_cvmin.lasso | 0.267 | 0.014 | 0.282 | |
| screen_cvsqrt.lasso | 0.222 | 0.003 | 0.226 | |
| screen_cvtrunc.lasso | 0.265 | 0.003 | 0.269 | |
| screen_mb | 0.016 | 0.001 | 0.017 | |
| sim_mix | 0.008 | 0.005 | 0.013 | |
| sim_mix_networks | 0.032 | 0.006 | 0.037 | |