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CHECK report for pageRank on tokay1

This page was generated on 2021-05-06 12:32:40 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the pageRank package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1291/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pageRank 1.0.0  (landing page)
Hongxu Ding
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/pageRank
Branch: RELEASE_3_12
Last Commit: 8a30acb
Last Changed Date: 2020-10-27 12:01:15 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: pageRank
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pageRank.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings pageRank_1.0.0.tar.gz
StartedAt: 2021-05-06 05:19:49 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:28:04 -0400 (Thu, 06 May 2021)
EllapsedTime: 495.1 seconds
RetCode: 0
Status:   OK   
CheckDir: pageRank.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pageRank.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings pageRank_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/pageRank.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pageRank/DESCRIPTION' ... OK
* this is package 'pageRank' 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 'pageRank' 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 ... NOTE
accessibility_network : <anonymous>: no visible global function
  definition for 'name'
Undefined global functions or variables:
  name
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
accessibility_network 11.51   0.87   34.73
conformation_network   9.64   0.31    9.95
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
accessibility_network 17.83   0.59   20.15
conformation_network  14.47   0.28   15.45
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/pageRank.Rcheck/00check.log'
for details.



Installation output

pageRank.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/pageRank_1.0.0.tar.gz && rm -rf pageRank.buildbin-libdir && mkdir pageRank.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pageRank.buildbin-libdir pageRank_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL pageRank_1.0.0.zip && rm pageRank_1.0.0.tar.gz pageRank_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     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 14348  100 14348    0     0   652k      0 --:--:-- --:--:-- --:--:--  667k

install for i386

* installing *source* package 'pageRank' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pageRank'
    finding HTML links ... done
    PX                                      html  
    PXPY                                    html  
    PXY                                     html  
    P_dist                                  html  
    P_graph                                 html  
    P_null                                  html  
    accessibility_network                   html  
    adjust_graph                            html  
    aracne_network                          html  
    bubble_plot                             html  
    clean_graph                             html  
    conformation_network                    html  
    diff_graph                              html  
    gene_bin                                html  
    get_color_gradient                      html  
    multiplex_page_rank                     html  
    time_expmat                             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 'pageRank' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pageRank' as pageRank_1.0.0.zip
* DONE (pageRank)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'pageRank' successfully unpacked and MD5 sums checked

Tests output


Example timings

pageRank.Rcheck/examples_i386/pageRank-Ex.timings

nameusersystemelapsed
P_graph2.530.092.62
P_null1.810.051.86
accessibility_network11.51 0.8734.73
adjust_graph0.050.000.04
aracne_network1.780.061.85
bubble_plot0.020.000.01
clean_graph0.010.000.02
conformation_network9.640.319.95
diff_graph0.080.000.07
get_color_gradient000
multiplex_page_rank0.010.000.02
time_expmat000

pageRank.Rcheck/examples_x64/pageRank-Ex.timings

nameusersystemelapsed
P_graph3.310.083.50
P_null1.890.061.95
accessibility_network17.83 0.5920.15
adjust_graph0.030.000.03
aracne_network1.770.071.83
bubble_plot0.010.000.01
clean_graph0.050.000.05
conformation_network14.47 0.2815.45
diff_graph0.150.000.16
get_color_gradient000
multiplex_page_rank0.050.000.04
time_expmat000