Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-11-29 15:05:33 -0500 (Mon, 29 Nov 2021).

CHECK results for PFP on tokay2

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.

raw results

Package 1401/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PFP 1.2.0  (landing page)
XC Zhang
Snapshot Date: 2021-11-28 04:15:06 -0500 (Sun, 28 Nov 2021)
git_url: https://git.bioconductor.org/packages/PFP
git_branch: RELEASE_3_14
git_last_commit: 0d1251a
git_last_commit_date: 2021-10-26 13:06:03 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PFP
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PFP.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings PFP_1.2.0.tar.gz
StartedAt: 2021-11-29 02:42:59 -0500 (Mon, 29 Nov 2021)
EndedAt: 2021-11-29 02:48:11 -0500 (Mon, 29 Nov 2021)
EllapsedTime: 312.6 seconds
RetCode: 0
Status:   OK  
CheckDir: PFP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PFP.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings PFP_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/PFP.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.2.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
calc_PFP_score 12.6      0   12.59
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
calc_PFP_score 11.99   0.06   12.05
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/PFP_1.2.0.tar.gz && rm -rf PFP.buildbin-libdir && mkdir PFP.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PFP.buildbin-libdir PFP_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL PFP_1.2.0.zip && rm PFP_1.2.0.tar.gz PFP_1.2.0.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
 37 1193k   37  442k    0     0  1491k      0 --:--:-- --:--:-- --:--:-- 1490k
100 1193k  100 1193k    0     0  3219k      0 --:--:-- --:--:-- --:--:-- 3216k

install for i386

* 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

install for x64

* installing *source* package 'PFP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PFP' as PFP_1.2.0.zip
* DONE (PFP)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'PFP' successfully unpacked and MD5 sums checked

Tests output

PFP.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 ]
> 
> proc.time()
   user  system elapsed 
   7.87    0.87    8.75 

PFP.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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 ]
> 
> proc.time()
   user  system elapsed 
   8.62    0.48    9.07 

Example timings

PFP.Rcheck/examples_i386/PFP-Ex.timings

nameusersystemelapsed
PFP-class0.140.020.15
PFPRefnet-class0.610.030.64
PFPRefnet_hsa0.440.030.47
PFPRefnet_mmu0.470.090.56
PFP_score-methods0.020.000.02
PFP_test1000
PFP_test20.010.000.02
calc_PFP_score12.60 0.0012.59
data_std0.010.000.01
gene_list_hsa000
genes_score-methods000
get_PFPRefnet0.020.000.02
get_asso_net3.110.493.59
get_bg_related_kegg1.840.262.11
get_exp_cor_edges0.170.050.22
get_pathway_info0.170.061.66
group-methods0.580.000.58
kegg_download000
net_info-methods0.410.020.42
net_names-methods0.530.000.53
network-methods0.450.000.45
pathway_info000
pathway_info_hsa0.020.000.02
pathways_score-methods000
plot_PFP-methods0.370.060.44
plot_PFPlist0.300.060.36
rank_PFP-methods0.160.000.15
refnet_info-methods000
refnet_names-methods0.010.000.02
result_PFP-methods000
show_PFP-methods0.020.000.01
show_net-methods0.340.000.35
stats_test-methods000
sub_PFP-methods0.110.050.15
subnet-methods0.340.000.35
trans_edges_id2.460.112.56
trans_graph2PFPRefnet0.610.030.65
trans_xml2graph000

PFP.Rcheck/examples_x64/PFP-Ex.timings

nameusersystemelapsed
PFP-class0.140.030.17
PFPRefnet-class0.530.020.55
PFPRefnet_hsa0.250.010.26
PFPRefnet_mmu0.310.020.33
PFP_score-methods0.020.000.02
PFP_test1000
PFP_test20.010.000.01
calc_PFP_score11.99 0.0612.05
data_std0.000.020.01
gene_list_hsa000
genes_score-methods000
get_PFPRefnet000
get_asso_net1.760.001.77
get_bg_related_kegg2.070.002.06
get_exp_cor_edges0.230.000.24
get_pathway_info0.210.001.41
group-methods0.430.000.42
kegg_download000
net_info-methods0.480.000.48
net_names-methods0.360.000.36
network-methods0.30.00.3
pathway_info000
pathway_info_hsa000
pathways_score-methods0.000.010.02
plot_PFP-methods0.280.000.28
plot_PFPlist0.20.00.2
rank_PFP-methods0.160.000.16
refnet_info-methods0.000.020.01
refnet_names-methods000
result_PFP-methods0.010.000.02
show_PFP-methods000
show_net-methods0.280.010.30
stats_test-methods000
sub_PFP-methods0.140.000.14
subnet-methods0.270.000.26
trans_edges_id1.510.001.51
trans_graph2PFPRefnet0.440.000.44
trans_xml2graph000