Nicolas Staedler
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/nethet |
| git_branch: RELEASE_3_17 |
| git_last_commit: 707c60a |
| git_last_commit_date: 2023-04-25 10:36:49 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:07 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1375/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| nethet 1.32.0 (landing page) Nicolas Staedler
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the nethet package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: nethet |
| Version: 1.32.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nethet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nethet_1.32.0.tar.gz |
| StartedAt: 2023-10-18 11:15:51 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 11:20:56 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 305.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: nethet.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nethet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nethet_1.32.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/nethet.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nethet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nethet’ version ‘1.32.0’
* 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-3.17-bioc-mac-arm64/meat/nethet.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... NOTE
screen_shrink: no visible global function definition for
‘performance.pcor’
Undefined global functions or variables:
performance.pcor
* 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 28.157 0.198 40.617
ggmgsa_multisplit 16.870 0.117 26.047
mixglasso 15.600 0.310 23.308
diffregr_multisplit 8.004 0.154 12.544
diffnet_multisplit 4.926 0.037 7.608
* 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, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/nethet.Rcheck/00check.log’
for details.
nethet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL nethet ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘nethet’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c betamat_diffnet.c -o betamat_diffnet.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.3-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
>
> proc.time()
user system elapsed
7.954 0.389 12.647
nethet.Rcheck/nethet-Ex.timings
| name | user | system | elapsed | |
| aggpval | 0.006 | 0.000 | 0.010 | |
| bwprun_mixglasso | 2.210 | 0.072 | 3.496 | |
| diffnet_multisplit | 4.926 | 0.037 | 7.608 | |
| diffnet_singlesplit | 2.471 | 0.018 | 3.761 | |
| diffregr_multisplit | 8.004 | 0.154 | 12.544 | |
| diffregr_singlesplit | 0.607 | 0.010 | 0.934 | |
| dot_plot | 0.836 | 0.018 | 1.310 | |
| export_network | 0.161 | 0.004 | 0.252 | |
| generate_2networks | 0.039 | 0.003 | 0.065 | |
| generate_inv_cov | 0.060 | 0.120 | 0.279 | |
| ggmgsa_multisplit | 16.870 | 0.117 | 26.047 | |
| gsea.iriz | 0.008 | 0.000 | 0.011 | |
| het_cv_glasso | 28.157 | 0.198 | 40.617 | |
| invcov2parcor | 0.001 | 0.000 | 0.001 | |
| invcov2parcor_array | 0.005 | 0.000 | 0.010 | |
| logratio | 0.001 | 0.000 | 0.001 | |
| mixglasso | 15.600 | 0.310 | 23.308 | |
| plot_2networks | 0.052 | 0.004 | 0.086 | |
| scatter_plot | 1.538 | 0.034 | 2.390 | |
| screen_aic.glasso | 0.963 | 0.009 | 1.492 | |
| screen_bic.glasso | 0.959 | 0.007 | 1.471 | |
| screen_cv.glasso | 1.917 | 0.013 | 2.930 | |
| screen_cv1se.lasso | 0.146 | 0.004 | 0.228 | |
| screen_cvfix.lasso | 0.146 | 0.003 | 0.232 | |
| screen_cvmin.lasso | 0.161 | 0.005 | 0.252 | |
| screen_cvsqrt.lasso | 0.147 | 0.003 | 0.234 | |
| screen_cvtrunc.lasso | 0.159 | 0.005 | 0.247 | |
| sim_mix | 0.003 | 0.006 | 0.014 | |
| sim_mix_networks | 0.009 | 0.001 | 0.018 | |