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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:ArrayExpress.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings ArrayExpress_1.56.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/ArrayExpress.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.56.0’
* 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 ... ERROR
Running examples in ‘ArrayExpress-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ArrayExpress
> ### Title: R objects from ArrayExpress database
> ### Aliases: ArrayExpress
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ETABM25.affybatch = ArrayExpress("E-TABM-25")
trying URL 'https://www.ebi.ac.uk/arrayexpress/files/A-AFFY-1/A-AFFY-1.adf.txt'
Content type 'text/plain' length 1431292 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://www.ebi.ac.uk/arrayexpress/files/E-TABM-25/E-TABM-25.sdrf.txt'
Content type 'text/plain' length 9769 bytes
==================================================
downloaded 9769 bytes

trying URL 'https://www.ebi.ac.uk/arrayexpress/files/E-TABM-25/E-TABM-25.idf.txt'
Content type 'text/plain' length 2965 bytes
==================================================
downloaded 2965 bytes

Copying raw data files

trying URL 'https://www.ebi.ac.uk/arrayexpress/files/E-TABM-25/E-TABM-25.raw.1.zip'
Content type 'application/zip' length 48026722 bytes (45.8 MB)
=============================================
downloaded 41.9 MB

Warning in download.file(url, filedest, mode = "wb") :
  downloaded length 43922100 != reported length 48026722
Warning in download.file(url, filedest, mode = "wb") :
  URL 'https://www.ebi.ac.uk/arrayexpress/files/E-TABM-25/E-TABM-25.raw.1.zip': Timeout of 300 seconds was reached
Error in download.file(url, filedest, mode = "wb") : 
  download from 'https://www.ebi.ac.uk/arrayexpress/files/E-TABM-25/E-TABM-25.raw.1.zip' failed
Warning in FUN(X[[i]], ...) :
  https://www.ebi.ac.uk/arrayexpress/files/E-TABM-25/E-TABM-25.raw.1.zip  does not exist or is empty. 

Unpacking data files
Error in extract.zip(file = paste(path, zipfile, sep = "/")) : 
  /tmp/RtmpwdaCgM/E-TABM-25.raw.1.zip  does not exist or is empty. 
 does not exist
Calls: ArrayExpress -> getAE -> lapply -> FUN -> extract.zip
Execution halted
* 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: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/ArrayExpress.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL ArrayExpress
###
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* installing to library ‘/home/biocbuild/bbs-3.15-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)