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CHECK report for ArrayExpress on merida1

This page was generated on 2020-04-15 12:35:40 -0400 (Wed, 15 Apr 2020).

Package 77/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayExpress 1.46.0
Suhaib Mohammed
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/ArrayExpress
Branch: RELEASE_3_10
Last Commit: 4eb2ee5
Last Changed Date: 2019-10-29 13:07:58 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ArrayExpress
Version: 1.46.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ArrayExpress.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ArrayExpress_1.46.0.tar.gz
StartedAt: 2020-04-15 00:25:32 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:29:36 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 243.6 seconds
RetCode: 0
Status:  OK 
CheckDir: ArrayExpress.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ArrayExpress.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ArrayExpress_1.46.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/ArrayExpress.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ArrayExpress/DESCRIPTION’ ... OK
* this is package ‘ArrayExpress’ version ‘1.46.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
queryAE      15.124  0.742  20.620
ArrayExpress  5.734  2.740  18.087
getAE         3.780  0.454  12.509
* 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
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/ArrayExpress.Rcheck/00check.log’
for details.



Installation output

ArrayExpress.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ArrayExpress
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ArrayExpress’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘oligo’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘oligo’
** testing if installed package can be loaded from final location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘oligo’
** testing if installed package keeps a record of temporary installation path
* DONE (ArrayExpress)

Tests output


Example timings

ArrayExpress.Rcheck/ArrayExpress-Ex.timings

nameusersystemelapsed
ArrayExpress 5.734 2.74018.087
ae2bioc000
getAE 3.780 0.45412.509
procset000
queryAE15.124 0.74220.620