Multiple platform build/check report for BioC 3.13 - CHECK results for PFP on tokay2

Package: PFP

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PFP.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings PFP_1.0.0.tar.gz

StartedAt: 2021-10-15 03:18:43 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 03:23:57 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 314.2 seconds

RetCode: 0

Status: OK

CheckDir: PFP.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PFP.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings PFP_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/PFP.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.0.0'
* 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 11.41   0.51   11.92
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
calc_PFP_score 12.36   0.11   12.47
* 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://155.52.207.165/BBS/3.13/bioc/src/contrib/PFP_1.0.0.tar.gz && rm -rf PFP.buildbin-libdir && mkdir PFP.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PFP.buildbin-libdir PFP_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL PFP_1.0.0.zip && rm PFP_1.0.0.tar.gz PFP_1.0.0.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
  0 1191k    0  9235    0     0   109k      0  0:00:10 --:--:--  0:00:10  108k
 70 1191k   70  841k    0     0   771k      0  0:00:01  0:00:01 --:--:--  771k
100 1191k  100 1191k    0     0   922k      0  0:00:01  0:00:01 --:--:--  922k

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_1.0.0.zip
* DONE (PFP)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'PFP' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 
   8.75    0.78    9.50


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 
   8.73    0.43    9.15

name	user	system	elapsed
PFP-class	0.16	0.00	0.16
PFPRefnet-class	0.59	0.09	0.68
PFPRefnet_hsa	0.32	0.03	0.35
PFPRefnet_mmu	1.03	0.02	1.05
PFP_score-methods	0	0	0
PFP_test1	0.01	0.00	0.02
PFP_test2	0	0	0
calc_PFP_score	11.41	0.51	11.92
data_std	0.01	0.00	0.01
gene_list_hsa	0	0	0
genes_score-methods	0.02	0.00	0.02
get_PFPRefnet	0	0	0
get_asso_net	1.94	0.00	1.94
get_bg_related_kegg	2.53	0.00	2.58
get_exp_cor_edges	0.19	0.02	0.20
get_pathway_info	0.20	0.01	1.48
group-methods	0.42	0.00	0.42
kegg_download	0	0	0
net_info-methods	0.56	0.00	0.57
net_names-methods	0.35	0.00	0.34
network-methods	0.33	0.00	0.33
pathway_info	0	0	0
pathway_info_hsa	0.01	0.00	0.01
pathways_score-methods	0	0	0
plot_PFP-methods	0.25	0.00	0.25
plot_PFPlist	0.17	0.00	0.18
rank_PFP-methods	0.14	0.02	0.15
refnet_info-methods	0	0	0
refnet_names-methods	0.02	0.00	0.02
result_PFP-methods	0	0	0
show_PFP-methods	0.01	0.00	0.01
show_net-methods	0.41	0.00	0.41
stats_test-methods	0.00	0.01	0.02
sub_PFP-methods	0.14	0.00	0.14
subnet-methods	0.39	0.00	0.39
trans_edges_id	2.00	0.03	2.03
trans_graph2PFPRefnet	0.5	0.0	0.5
trans_xml2graph	0	0	0

name	user	system	elapsed
PFP-class	0.11	0.04	0.15
PFPRefnet-class	0.52	0.00	0.52
PFPRefnet_hsa	0.24	0.02	0.25
PFPRefnet_mmu	0.34	0.02	0.35
PFP_score-methods	0	0	0
PFP_test1	0.00	0.01	0.02
PFP_test2	0	0	0
calc_PFP_score	12.36	0.11	12.47
data_std	0.01	0.00	0.01
gene_list_hsa	0	0	0
genes_score-methods	0.02	0.00	0.02
get_PFPRefnet	0	0	0
get_asso_net	1.89	0.00	1.89
get_bg_related_kegg	2.14	0.00	2.14
get_exp_cor_edges	0.14	0.00	0.14
get_pathway_info	0.17	0.03	1.15
group-methods	0.39	0.00	0.39
kegg_download	0	0	0
net_info-methods	0.28	0.02	0.30
net_names-methods	0.29	0.00	0.29
network-methods	0.29	0.01	0.30
pathway_info	0	0	0
pathway_info_hsa	0	0	0
pathways_score-methods	0.00	0.02	0.02
plot_PFP-methods	0.28	0.00	0.28
plot_PFPlist	0.22	0.00	0.22
rank_PFP-methods	0.14	0.00	0.14
refnet_info-methods	0.00	0.01	0.01
refnet_names-methods	0	0	0
result_PFP-methods	0	0	0
show_PFP-methods	0.00	0.02	0.02
show_net-methods	0.26	0.00	0.26
stats_test-methods	0	0	0
sub_PFP-methods	0.16	0.00	0.16
subnet-methods	0.26	0.00	0.27
trans_edges_id	1.52	0.02	1.53
trans_graph2PFPRefnet	0.45	0.00	0.45
trans_xml2graph	0	0	0

CHECK results for PFP on tokay2

Summary

Command output

Installation output

Tests output

Example timings