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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GEOfastq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GEOfastq_1.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GEOfastq.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 ‘GEOfastq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GEOfastq’ version ‘1.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.19/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.19/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.19/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.19/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.19/data/experiment/src/contrib/PACKAGES'
 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 ‘GEOfastq’ 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 ... OK
* 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
crawl_gsms   0.217  0.019 317.636
get_fastqs   0.039  0.004 105.881
crawl_gse    0.013  0.012 135.895
extract_gsms 0.010  0.009 135.845
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On Bioconductor (1): 'test-srp_utils.R:18:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-srp_utils.R:12:5'): crawl_gsms gets GSM metadata ─────────────
  nrow(srp_meta) not equal to 1.
  target is NULL, current is numeric
  ── Failure ('test-srp_utils.R:14:5'): crawl_gsms gets GSM metadata ─────────────
  srp_meta$ebi_dir not equal to "SRR964/004/SRR9640294".
  target is NULL, current is character
  
  [ FAIL 2 | WARN 3 | SKIP 1 | PASS 2 ]
  Error: Test failures
  Execution halted
* 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
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/GEOfastq.Rcheck/00check.log’
for details.