Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:06:57 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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

CHECK results for PFP on palomino4


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? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1425/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PFP 1.5.0  (landing page)
XC Zhang
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/PFP
git_branch: master
git_last_commit: ff627a7
git_last_commit_date: 2022-04-26 12:11:55 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PFP
Version: 1.5.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PFP.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings PFP_1.5.0.tar.gz
StartedAt: 2022-06-24 04:22:26 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 04:26:11 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 225.5 seconds
RetCode: 0
Status:   OK  
CheckDir: PFP.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PFP.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings PFP_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/PFP.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'PFP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PFP' version '1.5.0'
* 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 10.98   0.19   11.17
* 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


Installation output

PFP.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/PFP_1.5.0.tar.gz && rm -rf PFP.buildbin-libdir && mkdir PFP.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PFP.buildbin-libdir PFP_1.5.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL PFP_1.5.0.zip && rm PFP_1.5.0.tar.gz PFP_1.5.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1193k  100 1193k    0     0  9098k      0 --:--:-- --:--:-- --:--:-- 9179k
only one architecture so ignoring '--merge-multiarch'
* 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
* MD5 sums
packaged installation of 'PFP' as PFP_1.5.0.zip
* DONE (PFP)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'PFP' successfully unpacked and MD5 sums checked

Tests output

PFP.Rcheck/tests/testthat.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 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 
   8.51    0.53    9.04 

Example timings

PFP.Rcheck/PFP-Ex.timings

nameusersystemelapsed
PFP-class0.120.040.15
PFPRefnet-class0.440.030.47
PFPRefnet_hsa0.220.000.22
PFPRefnet_mmu0.360.030.39
PFP_score-methods0.010.000.01
PFP_test1000
PFP_test20.020.000.02
calc_PFP_score10.98 0.1911.17
data_std0.090.000.10
gene_list_hsa000
genes_score-methods0.000.010.01
get_PFPRefnet000
get_asso_net2.350.002.34
get_bg_related_kegg1.390.041.44
get_exp_cor_edges0.120.000.12
get_pathway_info0.140.001.52
group-methods0.400.000.39
kegg_download000
net_info-methods0.400.000.41
net_names-methods0.370.000.37
network-methods0.240.000.24
pathway_info0.010.000.01
pathway_info_hsa000
pathways_score-methods000
plot_PFP-methods0.30.00.3
plot_PFPlist0.160.030.19
rank_PFP-methods0.170.020.18
refnet_info-methods0.010.000.02
refnet_names-methods000
result_PFP-methods0.000.010.01
show_PFP-methods0.020.000.02
show_net-methods0.230.000.23
stats_test-methods0.020.000.02
sub_PFP-methods0.120.020.14
subnet-methods0.250.010.27
trans_edges_id1.500.021.51
trans_graph2PFPRefnet0.440.010.46
trans_xml2graph000