Back to Multiple platform build/check report for BioC 3.9
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for ArrayExpress on malbec2

This page was generated on 2019-08-23 11:52:53 -0400 (Fri, 23 Aug 2019).

Package 74/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayExpress 1.44.0
Suhaib Mohammed
Snapshot Date: 2019-08-22 17:01:39 -0400 (Thu, 22 Aug 2019)
URL: https://git.bioconductor.org/packages/ArrayExpress
Branch: RELEASE_3_9
Last Commit: afd988a
Last Changed Date: 2019-05-02 11:53:11 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ArrayExpress
Version: 1.44.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ArrayExpress.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ArrayExpress_1.44.0.tar.gz
StartedAt: 2019-08-22 23:49:12 -0400 (Thu, 22 Aug 2019)
EndedAt: 2019-08-23 00:05:54 -0400 (Fri, 23 Aug 2019)
EllapsedTime: 1002.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ArrayExpress.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ArrayExpress.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ArrayExpress_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ArrayExpress.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.44.0’
* 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 or elapsed time > 5s
               user system elapsed
queryAE      14.459  0.565 219.403
ArrayExpress  6.859  0.737 400.067
getAE         3.959  0.311 217.002
* 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-3.9-bioc/meat/ArrayExpress.Rcheck/00check.log’
for details.



Installation output

ArrayExpress.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ArrayExpress
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-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 6.859 0.737400.067
ae2bioc000
getAE 3.959 0.311217.002
procset000
queryAE 14.459 0.565219.403