Multiple platform build/check report for BioC 3.14 - CHECK results for PFP on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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: 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: 2022-04-13 00:25:38 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 00:31:03 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 324.5 seconds

RetCode: 0

Status: OK

CheckDir: PFP.Rcheck

Warnings: 0

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###
### 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
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/PFP.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 11.37      0   11.38
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
calc_PFP_score 13.03   0.06   13.09
* 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

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

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 24 1193k   24  287k    0     0   763k      0  0:00:01 --:--:--  0:00:01  763k
100 1193k  100 1193k    0     0  1186k      0  0:00:01  0:00:01 --:--:-- 1187k

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


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 31 ]
> 
> proc.time()
   user  system elapsed 
   8.57    0.65    9.20


R version 4.1.3 (2022-03-10) -- "One Push-Up"
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 
   8.06    0.46    8.60

name	user	system	elapsed
PFP-class	0.18	0.02	0.20
PFPRefnet-class	0.61	0.04	0.66
PFPRefnet_hsa	0.31	0.03	0.35
PFPRefnet_mmu	0.58	0.11	0.68
PFP_score-methods	0.50	0.02	0.52
PFP_test1	0	0	0
PFP_test2	0.02	0.00	0.01
calc_PFP_score	11.37	0.00	11.38
data_std	0.02	0.00	0.02
gene_list_hsa	0	0	0
genes_score-methods	0.01	0.00	0.01
get_PFPRefnet	0	0	0
get_asso_net	2.19	0.37	2.56
get_bg_related_kegg	1.42	0.15	1.57
get_exp_cor_edges	0.16	0.06	0.21
get_pathway_info	0.20	0.04	1.83
group-methods	0.52	0.00	0.53
kegg_download	0	0	0
net_info-methods	0.36	0.02	0.38
net_names-methods	0.5	0.0	0.5
network-methods	0.42	0.00	0.43
pathway_info	0	0	0
pathway_info_hsa	0	0	0
pathways_score-methods	0.00	0.02	0.01
plot_PFP-methods	0.25	0.01	0.27
plot_PFPlist	0.21	0.03	0.23
rank_PFP-methods	0.15	0.00	0.16
refnet_info-methods	0	0	0
refnet_names-methods	0.02	0.00	0.01
result_PFP-methods	0	0	0
show_PFP-methods	0.01	0.00	0.02
show_net-methods	0.35	0.00	0.34
stats_test-methods	0	0	0
sub_PFP-methods	0.14	0.00	0.14
subnet-methods	0.34	0.00	0.35
trans_edges_id	1.64	0.05	1.69
trans_graph2PFPRefnet	0.49	0.00	0.48
trans_xml2graph	0	0	0

name	user	system	elapsed
PFP-class	0.17	0.01	0.19
PFPRefnet-class	0.63	0.04	0.66
PFPRefnet_hsa	0.29	0.00	0.30
PFPRefnet_mmu	0.41	0.00	0.40
PFP_score-methods	0.01	0.00	0.02
PFP_test1	0	0	0
PFP_test2	0.02	0.00	0.02
calc_PFP_score	13.03	0.06	13.09
data_std	0.02	0.00	0.01
gene_list_hsa	0	0	0
genes_score-methods	0	0	0
get_PFPRefnet	0	0	0
get_asso_net	2.03	0.00	2.04
get_bg_related_kegg	2.31	0.00	2.31
get_exp_cor_edges	0.13	0.00	0.12
get_pathway_info	0.28	0.01	1.57
group-methods	0.64	0.00	0.64
kegg_download	0	0	0
net_info-methods	0.37	0.00	0.37
net_names-methods	0.31	0.00	0.31
network-methods	0.29	0.02	0.30
pathway_info	0	0	0
pathway_info_hsa	0.00	0.02	0.02
pathways_score-methods	0	0	0
plot_PFP-methods	0.29	0.00	0.29
plot_PFPlist	0.21	0.01	0.22
rank_PFP-methods	0.12	0.03	0.16
refnet_info-methods	0	0	0
refnet_names-methods	0.02	0.00	0.01
result_PFP-methods	0	0	0
show_PFP-methods	0.01	0.00	0.02
show_net-methods	0.28	0.00	0.28
stats_test-methods	0	0	0
sub_PFP-methods	0.14	0.02	0.16
subnet-methods	0.30	0.00	0.29
trans_edges_id	1.80	0.01	1.82
trans_graph2PFPRefnet	0.61	0.05	0.65
trans_xml2graph	0.01	0.00	0.02

CHECK results for PFP on tokay2

Summary

Command output

Installation output

Tests output

Example timings