Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-26 13:06:16 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 BioPlex on tokay2


To the developers/maintainers of the BioPlex package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioPlex.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 190/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioPlex 1.0.1  (landing page)
Ludwig Geistlinger
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/BioPlex
git_branch: RELEASE_3_14
git_last_commit: 68b42b2
git_last_commit_date: 2021-10-29 12:05:32 -0500 (Fri, 29 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: BioPlex
Version: 1.0.1
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioPlex.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BioPlex_1.0.1.tar.gz
StartedAt: 2022-01-25 16:28:39 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 16:35:43 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 423.1 seconds
RetCode: 0
Status:   OK  
CheckDir: BioPlex.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioPlex.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BioPlex_1.0.1.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/BioPlex.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 'BioPlex/DESCRIPTION' ... OK
* this is package 'BioPlex' version '1.0.1'
* 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 'BioPlex' 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
getCorum: no visible binding for global variable 'Organism'
Undefined global functions or variables:
  Organism
* 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
ccleProteome2SummarizedExperiment 55.05   2.45   60.74
annotatePFAM                      21.60   3.16   28.62
mapSummarizedExperimentOntoGraph   6.94   0.64    7.68
bioplex2graph                      7.42   0.11    7.63
corum2graphlist                    5.17   0.81    8.12
hasSubunit                         4.93   0.56    5.59
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
ccleProteome2SummarizedExperiment 49.55   1.43   52.02
annotatePFAM                      23.21   0.76   25.25
mapSummarizedExperimentOntoGraph   9.81   0.37   10.31
bioplex2graph                      7.58   0.10    7.73
hasSubunit                         6.22   0.05    6.38
corum2graphlist                    5.72   0.16    6.16
* 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-3.14-bioc/meat/BioPlex.Rcheck/00check.log'
for details.



Installation output

BioPlex.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BioPlex_1.0.1.tar.gz && rm -rf BioPlex.buildbin-libdir && mkdir BioPlex.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioPlex.buildbin-libdir BioPlex_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BioPlex_1.0.1.zip && rm BioPlex_1.0.1.tar.gz BioPlex_1.0.1.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 20106  100 20106    0     0   171k      0 --:--:-- --:--:-- --:--:--  172k

install for i386

* installing *source* package 'BioPlex' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BioPlex'
    finding HTML links ... done
    annotatePFAM                            html  
    finding level-2 HTML links ... done

    bioplex2graph                           html  
    ccleProteome2SummarizedExperiment       html  
    corum2graphlist                         html  
    corum2list                              html  
    getBioPlex                              html  
    getBioplexProteome                      html  
    getCorum                                html  
    getGSE122425                            html  
    hasSubunit                              html  
    mapSummarizedExperimentOntoGraph        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 'BioPlex' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioPlex' as BioPlex_1.0.1.zip
* DONE (BioPlex)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'BioPlex' successfully unpacked and MD5 sums checked

Tests output


Example timings

BioPlex.Rcheck/examples_i386/BioPlex-Ex.timings

nameusersystemelapsed
annotatePFAM21.60 3.1628.62
bioplex2graph7.420.117.63
ccleProteome2SummarizedExperiment55.05 2.4560.74
corum2graphlist5.170.818.12
corum2list1.030.021.28
getBioPlex3.690.084.89
getBioplexProteome1.260.011.47
getCorum1.330.081.64
getGSE1224251.450.021.66
hasSubunit4.930.565.59
mapSummarizedExperimentOntoGraph6.940.647.68

BioPlex.Rcheck/examples_x64/BioPlex-Ex.timings

nameusersystemelapsed
annotatePFAM23.21 0.7625.25
bioplex2graph7.580.107.73
ccleProteome2SummarizedExperiment49.55 1.4352.02
corum2graphlist5.720.166.16
corum2list1.120.031.37
getBioPlex3.650.133.93
getBioplexProteome1.180.031.26
getCorum1.270.011.52
getGSE1224251.090.001.10
hasSubunit6.220.056.38
mapSummarizedExperimentOntoGraph 9.81 0.3710.31