Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-07-30 15:06:04 -0400 (Fri, 30 Jul 2021).

CHECK results for pkgDepTools on tokay2

To the developers/maintainers of the pkgDepTools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pkgDepTools.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 1398/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pkgDepTools 1.58.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-07-29 04:50:02 -0400 (Thu, 29 Jul 2021)
URL: https://git.bioconductor.org/packages/pkgDepTools
Branch: RELEASE_3_13
Last Commit: 706a7e5
Last Changed Date: 2021-05-19 11:38:05 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: pkgDepTools
Version: 1.58.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pkgDepTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings pkgDepTools_1.58.0.tar.gz
StartedAt: 2021-07-30 03:49:06 -0400 (Fri, 30 Jul 2021)
EndedAt: 2021-07-30 03:49:56 -0400 (Fri, 30 Jul 2021)
EllapsedTime: 49.5 seconds
RetCode: 0
Status:   OK  
CheckDir: pkgDepTools.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pkgDepTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings pkgDepTools_1.58.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/pkgDepTools.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 'pkgDepTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pkgDepTools' version '1.58.0'
* 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 'pkgDepTools' 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' 'RBGL'
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
'library' or 'require' call to 'RCurl' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'tools:::.split_dependencies'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'pkgDepTools/R/zzz.R':
  .First.lib calls:
    require("RCurl", quietly = TRUE)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

getInstallOrder: no visible global function definition for
  'installed.packages'
makeDepGraph : <anonymous>: no visible global function definition for
  'available.packages'
makeDepGraph : <anonymous>: no visible global function definition for
  'contrib.url'
makeDepGraph: no visible global function definition for
  'installed.packages'
Undefined global functions or variables:
  available.packages contrib.url installed.packages
Consider adding
  importFrom("utils", "available.packages", "contrib.url",
             "installed.packages")
to your NAMESPACE file.
* 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
** 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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/pkgDepTools.Rcheck/00check.log'
for details.



Installation output

pkgDepTools.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/pkgDepTools_1.58.0.tar.gz && rm -rf pkgDepTools.buildbin-libdir && mkdir pkgDepTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pkgDepTools.buildbin-libdir pkgDepTools_1.58.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL pkgDepTools_1.58.0.zip && rm pkgDepTools_1.58.0.tar.gz pkgDepTools_1.58.0.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  7599  100  7599    0     0   135k      0 --:--:-- --:--:-- --:--:--  137k

install for i386

* installing *source* package 'pkgDepTools' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pkgDepTools'
    finding HTML links ... done
    basicInstallOrder                       html  
    cleanPkgField                           html  
    getDownloadSize                         html  
    getInstallOrder                         html  
    makeDepGraph                            html  
    makePkgUrl                              html  
    parseContentLength                      html  
    pkgDepTools-package                     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 'pkgDepTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pkgDepTools' as pkgDepTools_1.58.0.zip
* DONE (pkgDepTools)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'pkgDepTools' successfully unpacked and MD5 sums checked

Tests output


Example timings

pkgDepTools.Rcheck/examples_i386/pkgDepTools-Ex.timings

nameusersystemelapsed
makeDepGraph000

pkgDepTools.Rcheck/examples_x64/pkgDepTools-Ex.timings

nameusersystemelapsed
makeDepGraph000