| Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-03-16 11:02:07 -0400 (Thu, 16 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" | 4115 |
| 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 | ||||
|
To the developers/maintainers of the PFP package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1475/2189 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PFP 1.7.0 (landing page) XC Zhang
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | ||||||||
| Package: PFP |
| Version: 1.7.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PFP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PFP_1.7.0.tar.gz |
| StartedAt: 2023-03-14 09:35:35 -0400 (Tue, 14 Mar 2023) |
| EndedAt: 2023-03-14 09:37:13 -0400 (Tue, 14 Mar 2023) |
| EllapsedTime: 97.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PFP.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PFP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PFP_1.7.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/PFP.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 13.0.0 (clang-1300.0.29.3)
GNU Fortran (GCC) 12.0.1 20220312 (experimental)
* running under: macOS Monterey 12.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PFP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PFP’ version ‘1.7.0’
* package encoding: UTF-8
* 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 ‘PFP’ can be installed ... 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: OK
PFP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PFP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘PFP’ ... ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (PFP)
PFP.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
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(PFP)
> test_check('PFP')
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 31 ]
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 31 ]
>
> proc.time()
user system elapsed
3.794 0.152 3.941
PFP.Rcheck/PFP-Ex.timings
| name | user | system | elapsed | |
| PFP-class | 0.039 | 0.014 | 0.053 | |
| PFPRefnet-class | 0.256 | 0.018 | 0.274 | |
| PFPRefnet_hsa | 0.172 | 0.003 | 0.175 | |
| PFPRefnet_mmu | 0.265 | 0.002 | 0.267 | |
| PFP_score-methods | 0.003 | 0.001 | 0.003 | |
| PFP_test1 | 0.002 | 0.000 | 0.003 | |
| PFP_test2 | 0.002 | 0.001 | 0.002 | |
| calc_PFP_score | 4.124 | 0.052 | 4.177 | |
| data_std | 0.005 | 0.000 | 0.007 | |
| gene_list_hsa | 0.001 | 0.001 | 0.001 | |
| genes_score-methods | 0.002 | 0.000 | 0.003 | |
| get_PFPRefnet | 0 | 0 | 0 | |
| get_asso_net | 1.093 | 0.023 | 1.117 | |
| get_bg_related_kegg | 0.592 | 0.019 | 0.610 | |
| get_exp_cor_edges | 0.068 | 0.004 | 0.072 | |
| get_pathway_info | 0.044 | 0.002 | 1.434 | |
| group-methods | 0.194 | 0.000 | 0.195 | |
| kegg_download | 0 | 0 | 0 | |
| net_info-methods | 0.177 | 0.000 | 0.178 | |
| net_names-methods | 0.174 | 0.001 | 0.175 | |
| network-methods | 0.174 | 0.002 | 0.176 | |
| pathway_info | 0.001 | 0.000 | 0.002 | |
| pathway_info_hsa | 0.001 | 0.000 | 0.001 | |
| pathways_score-methods | 0.002 | 0.000 | 0.002 | |
| plot_PFP-methods | 0.113 | 0.003 | 0.115 | |
| plot_PFPlist | 0.073 | 0.001 | 0.074 | |
| rank_PFP-methods | 0.039 | 0.013 | 0.053 | |
| refnet_info-methods | 0.003 | 0.001 | 0.003 | |
| refnet_names-methods | 0.002 | 0.000 | 0.003 | |
| result_PFP-methods | 0.002 | 0.000 | 0.003 | |
| show_PFP-methods | 0.003 | 0.002 | 0.004 | |
| show_net-methods | 0.181 | 0.001 | 0.182 | |
| stats_test-methods | 0.002 | 0.000 | 0.003 | |
| sub_PFP-methods | 0.037 | 0.013 | 0.051 | |
| subnet-methods | 0.180 | 0.000 | 0.181 | |
| trans_edges_id | 0.670 | 0.009 | 0.679 | |
| trans_graph2PFPRefnet | 0.250 | 0.017 | 0.267 | |
| trans_xml2graph | 0.001 | 0.000 | 0.000 | |