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This page was generated on 2021-06-17 12:05:35 -0400 (Thu, 17 Jun 2021).

CHECK results for keggorthology on riesling1

To the developers/maintainers of the keggorthology package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/keggorthology.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 942/1993HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
keggorthology 2.45.0  (landing page)
VJ Carey
Snapshot Date: 2021-06-16 14:50:06 -0400 (Wed, 16 Jun 2021)
URL: https://git.bioconductor.org/packages/keggorthology
Branch: master
Last Commit: c0972aa
Last Changed Date: 2021-05-19 11:39:23 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: keggorthology
Version: 2.45.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:keggorthology.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings keggorthology_2.45.0.tar.gz
StartedAt: 2021-06-17 00:35:50 -0400 (Thu, 17 Jun 2021)
EndedAt: 2021-06-17 00:37:37 -0400 (Thu, 17 Jun 2021)
EllapsedTime: 107.1 seconds
RetCode: 0
Status:   OK  
CheckDir: keggorthology.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:keggorthology.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings keggorthology_2.45.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/keggorthology.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'keggorthology/DESCRIPTION' ... OK
* this is package 'keggorthology' version '2.45.0'
* 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 'keggorthology' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'graph' 'stats'
A package should be listed in only one of these fields.
* 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 ... NOTE
Namespace in Imports field not imported from: 'DBI'
  All declared Imports should be used.
Package in Depends field not imported from: 'hgu95av2.db'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getKOprobes: no visible binding for global variable 'KOgraph'
getKOtags: no visible binding for global variable 'KOgraph'
Undefined global functions or variables:
  KOgraph
* 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
** running examples for arch 'x64' ... 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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.14-bioc/meat/keggorthology.Rcheck/00check.log'
for details.



Installation output

keggorthology.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/keggorthology_2.45.0.tar.gz && rm -rf keggorthology.buildbin-libdir && mkdir keggorthology.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=keggorthology.buildbin-libdir keggorthology_2.45.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL keggorthology_2.45.0.zip && rm keggorthology_2.45.0.tar.gz keggorthology_2.45.0.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  591k  100  591k    0     0  3459k      0 --:--:-- --:--:-- --:--:-- 3459k

install for i386

* installing *source* package 'keggorthology' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'keggorthology'
    finding HTML links ... done
    getKOprobes                             html  
    indRender                               html  
    keggDF2graph                            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 'keggorthology' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'keggorthology' as keggorthology_2.45.0.zip
* DONE (keggorthology)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'keggorthology' successfully unpacked and MD5 sums checked

Tests output


Example timings

keggorthology.Rcheck/examples_i386/keggorthology-Ex.timings

nameusersystemelapsed
getKOprobes0.140.080.22
indRender0.030.000.03
keggDF2graph0.000.020.02

keggorthology.Rcheck/examples_x64/keggorthology-Ex.timings

nameusersystemelapsed
getKOprobes0.170.050.22
indRender0.030.000.03
keggDF2graph000