XC Zhang
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/PFP |
| git_branch: master |
| git_last_commit: db0fc63 |
| git_last_commit_date: 2021-10-26 13:06:03 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:17 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PFP.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1409/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PFP 1.3.0 (landing page) XC Zhang
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: PFP |
| Version: 1.3.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PFP.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings PFP_1.3.0.tar.gz |
| StartedAt: 2022-03-17 19:51:09 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:54:32 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 203.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PFP.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PFP.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings PFP_1.3.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/PFP.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PFP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PFP' version '1.3.0'
* 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 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
calc_PFP_score 7.45 0.23 7.69
* 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
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL PFP
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'PFP' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'PFP'
finding HTML links ... done
PFP-class html
PFP html
PFPRefnet-class html
PFPRefnet_hsa html
PFPRefnet_mmu html
PFP_score-methods html
PFP_test1 html
PFP_test2 html
calc_PFP_score html
data_std html
gene_list_hsa html
genes_score-methods html
get_PFPRefnet html
get_asso_net html
get_bg_related_kegg html
get_exp_cor_edges html
get_pathway_info html
group-methods html
kegg_download html
net_info-methods html
net_names-methods html
network-methods html
pathway_info html
pathway_info_hsa html
pathways_score-methods html
plot_PFP-methods html
plot_PFPlist html
rank_PFP-methods html
refnet_info-methods html
refnet_names-methods html
result_PFP-methods html
show_PFP-methods html
show_net-methods html
stats_test-methods html
sub_PFP-methods html
subnet-methods html
trans_edges_id html
trans_graph2PFPRefnet html
finding level-2 HTML links ... done
trans_xml2graph html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'methylCC' is missing or broken
done
PFP.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
5.92 0.60 6.51
PFP.Rcheck/PFP-Ex.timings
| name | user | system | elapsed | |
| PFP-class | 0.13 | 0.03 | 0.16 | |
| PFPRefnet-class | 0.31 | 0.02 | 0.32 | |
| PFPRefnet_hsa | 0.18 | 0.01 | 0.19 | |
| PFPRefnet_mmu | 0.25 | 0.02 | 0.26 | |
| PFP_score-methods | 0 | 0 | 0 | |
| PFP_test1 | 0.01 | 0.00 | 0.02 | |
| PFP_test2 | 0 | 0 | 0 | |
| calc_PFP_score | 7.45 | 0.23 | 7.69 | |
| data_std | 0.00 | 0.02 | 0.01 | |
| gene_list_hsa | 0 | 0 | 0 | |
| genes_score-methods | 0 | 0 | 0 | |
| get_PFPRefnet | 0 | 0 | 0 | |
| get_asso_net | 1.33 | 0.00 | 1.33 | |
| get_bg_related_kegg | 1.51 | 0.01 | 1.53 | |
| get_exp_cor_edges | 0.11 | 0.00 | 0.11 | |
| get_pathway_info | 0.05 | 0.00 | 1.39 | |
| group-methods | 0.17 | 0.00 | 0.17 | |
| kegg_download | 0.00 | 0.02 | 0.01 | |
| net_info-methods | 0.17 | 0.00 | 0.18 | |
| net_names-methods | 0.19 | 0.00 | 0.18 | |
| network-methods | 0.17 | 0.00 | 0.18 | |
| pathway_info | 0 | 0 | 0 | |
| pathway_info_hsa | 0.00 | 0.02 | 0.01 | |
| pathways_score-methods | 0 | 0 | 0 | |
| plot_PFP-methods | 0.21 | 0.01 | 0.22 | |
| plot_PFPlist | 0.15 | 0.00 | 0.16 | |
| rank_PFP-methods | 0.10 | 0.02 | 0.11 | |
| refnet_info-methods | 0 | 0 | 0 | |
| refnet_names-methods | 0 | 0 | 0 | |
| result_PFP-methods | 0.01 | 0.00 | 0.01 | |
| show_PFP-methods | 0 | 0 | 0 | |
| show_net-methods | 0.17 | 0.01 | 0.19 | |
| stats_test-methods | 0.02 | 0.00 | 0.01 | |
| sub_PFP-methods | 0.06 | 0.05 | 0.11 | |
| subnet-methods | 0.17 | 0.00 | 0.18 | |
| trans_edges_id | 1.01 | 0.00 | 1.02 | |
| trans_graph2PFPRefnet | 0.32 | 0.00 | 0.31 | |
| trans_xml2graph | 0 | 0 | 0 | |