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CHECK report for ArrayExpress on malbec1

This page was generated on 2021-05-06 12:26:53 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the ArrayExpress package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 81/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayExpress 1.50.0  (landing page)
Suhaib Mohammed
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/ArrayExpress
Branch: RELEASE_3_12
Last Commit: 3a8e996
Last Changed Date: 2020-10-27 10:34:31 -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: ArrayExpress
Version: 1.50.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ArrayExpress.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ArrayExpress_1.50.0.tar.gz
StartedAt: 2021-05-05 23:03:27 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 23:07:28 -0400 (Wed, 05 May 2021)
EllapsedTime: 241.0 seconds
RetCode: 0
Status:   OK  
CheckDir: ArrayExpress.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ArrayExpress.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ArrayExpress_1.50.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/ArrayExpress.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ArrayExpress/DESCRIPTION’ ... OK
* this is package ‘ArrayExpress’ version ‘1.50.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ArrayExpress’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
ae2bioc: no visible global function definition for ‘new’
extract.zip : <anonymous>: no visible global function definition for
  ‘unzip’
getAE : <anonymous>: no visible global function definition for
  ‘download.file’
getAE: no visible global function definition for ‘download.file’
getDataColsForAE1: no visible global function definition for
  ‘read.table’
preparePhenoDataFor2channel: no visible global function definition for
  ‘new’
queryAE: no visible global function definition for ‘download.file’
readDerivedDataFiles: no visible global function definition for
  ‘read.table’
readDerivedDataFiles: no visible global function definition for ‘new’
readDerivedDataMatrixFile: no visible global function definition for
  ‘read.table’
readDerivedDataMatrixFile: no visible global function definition for
  ‘new’
readExperimentData: no visible global function definition for ‘new’
readFeatures: no visible global function definition for ‘read.table’
readFeatures: no visible global function definition for ‘new’
readPhenoData: no visible global function definition for ‘new’
Undefined global functions or variables:
  download.file new read.table unzip
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "download.file", "read.table", "unzip")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
ArrayExpress 7.824  0.556  21.669
queryAE      5.356  0.464  11.057
getAE        3.540  0.252  14.244
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/ArrayExpress.Rcheck/00check.log’
for details.



Installation output

ArrayExpress.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL ArrayExpress
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘ArrayExpress’ ...
** 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
* DONE (ArrayExpress)

Tests output


Example timings

ArrayExpress.Rcheck/ArrayExpress-Ex.timings

nameusersystemelapsed
ArrayExpress 7.824 0.55621.669
ae2bioc000
getAE 3.540 0.25214.244
procset000
queryAE 5.356 0.46411.057