##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:getDEE2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings getDEE2_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/getDEE2.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘getDEE2/DESCRIPTION’ ... OK
* this is package ‘getDEE2’ version ‘1.15.0’
* package encoding: UTF-8
* 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 ‘getDEE2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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
srx_agg: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
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 ‘getDEE2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: loadTxInfo
> ### Title: Load Transcript Info
> ### Aliases: loadTxInfo
> ### Keywords: Load Transcript
> 
> ### ** Examples
> 
> x <- getDEE2("ecoli",c("SRR1613487","SRR1613488"),outfile="mydata.zip")
trying URL 'http://dee2.io/metadata/ecoli_metadata.tsv.cut'
Content type 'text/tab-separated-values' length 2078161 bytes (2.0 MB)
==============================================
downloaded 1.8 MB

Warning in FUN(URL, ...) :
  downloaded length 1933312 != reported length 2078161
Warning in FUN(URL, ...) :
  URL 'https://dee2.io/metadata/ecoli_metadata.tsv.cut': Timeout of 600 seconds was reached
Error in getURL(URL = metadataURL, FUN = download.file, N.TRIES = 1L,  : 
  'getURL()' failed:
  URL: http://dee2.io/metadata/ecoli_metadata.tsv.cut
  error: download from 'http://dee2.io/metadata/ecoli_metadata.tsv.cut' failed
Calls: getDEE2 -> queryDEE2 -> getDEE2Metadata -> getURL
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-getDEE2.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/getDEE2.Rcheck/00check.log’
for details.