Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-08-06 11:06:29 -0400 (Sat, 06 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4371
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4155
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4155
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 KEGGREST on palomino4


To the developers/maintainers of the KEGGREST package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/KEGGREST.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1006/2137HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KEGGREST 1.37.3  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-08-05 14:00:05 -0400 (Fri, 05 Aug 2022)
git_url: https://git.bioconductor.org/packages/KEGGREST
git_branch: master
git_last_commit: 8f21a71
git_last_commit_date: 2022-07-08 11:20:48 -0400 (Fri, 08 Jul 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: KEGGREST
Version: 1.37.3
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KEGGREST.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings KEGGREST_1.37.3.tar.gz
StartedAt: 2022-08-06 02:55:56 -0400 (Sat, 06 Aug 2022)
EndedAt: 2022-08-06 02:58:57 -0400 (Sat, 06 Aug 2022)
EllapsedTime: 180.5 seconds
RetCode: 0
Status:   OK  
CheckDir: KEGGREST.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KEGGREST.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings KEGGREST_1.37.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/KEGGREST.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'KEGGREST/DESCRIPTION' ... OK
* this is package 'KEGGREST' version '1.37.3'
* 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 'KEGGREST' 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
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
listDatabases 0.70   0.00   11.14
keggLink      0.54   0.00    6.20
keggList      0.47   0.03   12.38
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'KEGGREST_unit_tests.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

KEGGREST.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/KEGGREST_1.37.3.tar.gz && rm -rf KEGGREST.buildbin-libdir && mkdir KEGGREST.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=KEGGREST.buildbin-libdir KEGGREST_1.37.3.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL KEGGREST_1.37.3.zip && rm KEGGREST_1.37.3.tar.gz KEGGREST_1.37.3.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
100 14960  100 14960    0     0   321k      0 --:--:-- --:--:-- --:--:--  332k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'KEGGREST' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* MD5 sums
packaged installation of 'KEGGREST' as KEGGREST_1.37.3.zip
* DONE (KEGGREST)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'KEGGREST' successfully unpacked and MD5 sums checked

Tests output

KEGGREST.Rcheck/tests/KEGGREST_unit_tests.Rout


R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
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.

> BiocGenerics:::testPackage("KEGGREST")
No encoding supplied: defaulting to UTF-8.


RUNIT TEST PROTOCOL -- Sat Aug  6 02:58:48 2022 
*********************************************** 
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
KEGGREST RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  13.76    0.57   63.29 

Example timings

KEGGREST.Rcheck/KEGGREST-Ex.timings

nameusersystemelapsed
keggConv0.120.073.12
keggFind0.020.002.39
keggGet1.460.062.98
keggInfo0.000.001.47
keggLink0.540.006.20
keggList 0.47 0.0312.38
listDatabases 0.70 0.0011.14
mark.pathway.by.objects0.270.032.66