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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/ReUseData.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    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 ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.2.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ReUseData’ 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 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 ... 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 ... ERROR
Running examples in ‘ReUseData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getCloudData
> ### Title: getCloudData Download the pregenerated curated data sets from
> ###   ReUseData cloud bucket
> ### Aliases: getCloudData
> 
> ### ** Examples
> 
> outdir <- file.path(tempdir(), "gcpData")
> dataUpdate(outdir, cloud=TRUE)

Updating data record...
c7055ef38bb2_GRCh38.primary_assembly.genome.fa.1.bt2 added
c705475883d1_GRCh38.primary_assembly.genome.fa.2.bt2 added
c70543632ef_GRCh38.primary_assembly.genome.fa.3.bt2 added
c705249eb12_GRCh38.primary_assembly.genome.fa.4.bt2 added
c70542e7ebea_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
c70583171f7_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
c70566311354_outfile.txt added
c7051fec2436_GRCh37_to_GRCh38.chain added
c705483d6599_GRCh37_to_NCBI34.chain added
c70536d944dc_GRCh37_to_NCBI35.chain added
c7057237e3a5_GRCh37_to_NCBI36.chain added
c7053342a038_GRCh38_to_GRCh37.chain added
c7055b24d6d2_GRCh38_to_NCBI34.chain added
c7054f93a3bd_GRCh38_to_NCBI35.chain added
c70565e2f61b_GRCh38_to_NCBI36.chain added
c705178b9adf_NCBI34_to_GRCh37.chain added
c7054e64b28c_NCBI34_to_GRCh38.chain added
c70535062d89_NCBI35_to_GRCh37.chain added
c70528979891_NCBI35_to_GRCh38.chain added
c70578a16c68_NCBI36_to_GRCh37.chain added
c7052dd45db7_NCBI36_to_GRCh38.chain added
c7055154b0e2_GRCm38_to_NCBIM36.chain added
c705f28ef25_GRCm38_to_NCBIM37.chain added
c705486c6de9_NCBIM36_to_GRCm38.chain added
c70546a40124_NCBIM37_to_GRCm38.chain added
c705394706b7_1000G_omni2.5.b37.vcf.gz added
c7056609f5c1_1000G_omni2.5.b37.vcf.gz.tbi added
c70517e5863d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
c7055dd01b0c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
c70599fe0f2_1000G_omni2.5.hg38.vcf.gz added
c7055f6934cd_1000G_omni2.5.hg38.vcf.gz.tbi added
c7057409afaa_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
c70527ebfd6a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
c705764a4e9f_af-only-gnomad.raw.sites.vcf added
c70586fe565_af-only-gnomad.raw.sites.vcf.idx added
c7056a3d4e36_Mutect2-exome-panel.vcf.idx added
c7055ed9f1b7_Mutect2-WGS-panel-b37.vcf added
c705368c5607_Mutect2-WGS-panel-b37.vcf.idx added
c7053764018b_small_exac_common_3.vcf added
c7056a16916_small_exac_common_3.vcf.idx added
c7054efa26c0_1000g_pon.hg38.vcf.gz added
c7059062fc2_1000g_pon.hg38.vcf.gz.tbi added
c70575296e2e_af-only-gnomad.hg38.vcf.gz added
c7057300ca19_af-only-gnomad.hg38.vcf.gz.tbi added
c70538d46a4b_small_exac_common_3.hg38.vcf.gz added
c70518e7f13_small_exac_common_3.hg38.vcf.gz.tbi added
c7053238b931_gencode.v41.annotation.gtf added
c7052a0659b9_gencode.v42.annotation.gtf added
c7056ec963d_gencode.vM30.annotation.gtf added
c705167b8258_gencode.vM31.annotation.gtf added
c7056aa6af0_gencode.v41.transcripts.fa added
c7051e52b5fb_gencode.v41.transcripts.fa.fai added
c7054829814a_gencode.v42.transcripts.fa added
c7051ce74649_gencode.v42.transcripts.fa.fai added
c70513b77172_gencode.vM30.pc_transcripts.fa added
c7057078fd7a_gencode.vM30.pc_transcripts.fa.fai added
c70517498e46_gencode.vM31.pc_transcripts.fa added
c7055e1ba19b_gencode.vM31.pc_transcripts.fa.fai added
c705680ef761_GRCh38.primary_assembly.genome.fa.1.ht2 added
c7052e9336a6_GRCh38.primary_assembly.genome.fa.2.ht2 added
c70542e8e42d_GRCh38.primary_assembly.genome.fa.3.ht2 added
c70547dc68ac_GRCh38.primary_assembly.genome.fa.4.ht2 added
c705575c190f_GRCh38.primary_assembly.genome.fa.5.ht2 added
c7055f715497_GRCh38.primary_assembly.genome.fa.6.ht2 added
c705968b675_GRCh38.primary_assembly.genome.fa.7.ht2 added
c70539a2c026_GRCh38.primary_assembly.genome.fa.8.ht2 added
c7056bf51c59_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
c70529184e6e_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
c7057ac52cd5_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
c705270292eb_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
c70519fb964f_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
c705544929dc_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
c705f5b55bf_GRCh38_full_analysis_set_plus_decoy_hla.fa added
c705355a7679_GRCh38.primary_assembly.genome.fa.fai added
c70546181d4c_GRCh38.primary_assembly.genome.fa.amb added
c705592b8c87_GRCh38.primary_assembly.genome.fa.ann added
c7053a1720cd_GRCh38.primary_assembly.genome.fa.bwt added
c705446a9086_GRCh38.primary_assembly.genome.fa.pac added
c70530367081_GRCh38.primary_assembly.genome.fa.sa added
c70546143de1_GRCh38.primary_assembly.genome.fa added
c7055aeaa2b8_hs37d5.fa.fai added
c70562610ca9_hs37d5.fa.amb added
c70551865db4_hs37d5.fa.ann added
c7054c71fe3c_hs37d5.fa.bwt added
c7054fea3c59_hs37d5.fa.pac added
c7051b20200c_hs37d5.fa.sa added
c7055a1801bd_hs37d5.fa added
c7055e1a4d80_complete_ref_lens.bin added
c70510d63ec4_ctable.bin added
c70561b2be7e_ctg_offsets.bin added
c7051df8744e_duplicate_clusters.tsv added
c705229bbc41_info.json added
c7051e646127_mphf.bin added
c70550265707_pos.bin added
c70551bb5ad_pre_indexing.log added
c7055e347379_rank.bin added
c70545893d40_ref_indexing.log added
c7053514586a_refAccumLengths.bin added
c7054ab8b25f_reflengths.bin added
c70523c6a14c_refseq.bin added
c705458796ed_seq.bin added
c70548c5c544_versionInfo.json added
c705301a18af_salmon_index added
c70514aa1d5_chrLength.txt added
c7054ac6a79c_chrName.txt added
c7053826191e_chrNameLength.txt added
c7054d3b1d5e_chrStart.txt added
c70564052dee_exonGeTrInfo.tab added
c705100a978f_exonInfo.tab added
c70527643583_geneInfo.tab added
c70523f53fa9_Genome added
c7053a2682b0_genomeParameters.txt added
c705364e0ea3_Log.out added
c7053ea30b2f_SA added
c70542335ac9_SAindex added
c705398d6413_sjdbInfo.txt added
c70571a538e9_sjdbList.fromGTF.out.tab added
c705163b8349_sjdbList.out.tab added
c7051d283906_transcriptInfo.tab added
c7053bb7c7de_GRCh38.GENCODE.v42_100 added
c7051ea2de73_knownGene_hg38.sql added
c70556ba5fbb_knownGene_hg38.txt added
c70565e31a78_refGene_hg38.sql added
c70520def08a_refGene_hg38.txt added
c705c8204e2_knownGene_mm39.sql added
c7052c0e97d8_knownGene_mm39.txt added
c7057212fc80_refGene_mm39.sql added
c7053c7f7202_refGene_mm39.txt added
dataHub with 152 records
cache path:  /Users/biocbuild/Library/Caches/org.R-project.R/R/ReUseData 
# dataUpdate() to update the local data cache
# dataSearch() to query a specific dataset
# Additional information can be retrieved using: 
# dataNames(), dataParams(), dataNotes(), dataPaths(), dataTag() or mcols()

              name                  
  BFC115764 | outfile.txt           
  BFC116021 | GRCh37_to_GRCh38.chain
  BFC116022 | outfile.txt           
  BFC116280 | outfile.txt           
  BFC116537 | outfile.txt           
  ...         ...                   
  BFC121682 | refGene_hg38.txt      
  BFC121683 | knownGene_mm39.sql    
  BFC121684 | knownGene_mm39.txt    
  BFC121685 | refGene_mm39.sql      
  BFC121686 | refGene_mm39.txt      
            Path                                                               
  BFC115764 /tmp/RtmpcS9XlD/SharedData/outfile.txt                             
  BFC116021 /tmp/RtmpcS9XlD/gcpData/GRCh37_to_GRCh38.chain                     
  BFC116022 /tmp/Rtmpac1QuT/test_SharedData/outfile.txt                        
  BFC116280 /tmp/RtmpGSLB4k/SharedData/outfile.txt                             
  BFC116537 /tmp/RtmpgiyQTL/test_SharedData/outfile.txt                        
  ...       ...                                                                
  BFC121682 https://storage.googleapis.com/reusedata/ucsc_database/refGene_h...
  BFC121683 https://storage.googleapis.com/reusedata/ucsc_database/knownGene...
  BFC121684 https://storage.googleapis.com/reusedata/ucsc_database/knownGene...
  BFC121685 https://storage.googleapis.com/reusedata/ucsc_database/refGene_m...
  BFC121686 https://storage.googleapis.com/reusedata/ucsc_database/refGene_m...
> dh <- dataSearch(c("ensembl", "GRCh38"))
> 
> ## download data from google bucket
> getCloudData(dh[1], outdir = outdir)
Error in getCloudData(dh[1], outdir = outdir) : 
  The 'data' is not a cloud object. Please double check the data name(s).
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/ReUseData.Rcheck/00check.log’
for details.