Qian Liu
| Snapshot Date: 2025-08-01 13:25 -0400 (Fri, 01 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: c5927b9 |
| git_last_commit_date: 2025-04-15 13:01:44 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-02 12:09 -0400 (Sat, 02 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4535 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1737/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.9.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the ReUseData package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ReUseData.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: ReUseData |
| Version: 1.9.0 |
| Command: /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_1.9.0.tar.gz |
| StartedAt: 2025-08-01 23:20:05 -0400 (Fri, 01 Aug 2025) |
| EndedAt: 2025-08-01 23:22:31 -0400 (Fri, 01 Aug 2025) |
| EllapsedTime: 145.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /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_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.9.0’
* 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 ... 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 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
dataHub-class 7.7 0.903 8.705
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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 NOTE
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.9.0’ ** 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 (ReUseData)
ReUseData.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(ReUseData)
>
> test_check("ReUseData")
Note: you need to assign a name for the recipe: rcpName <- recipeLoad('xx')
Data recipe loaded!
Use inputs() to check required input parameters before evaluation.
Check here: https://rcwl.org/dataRecipes/echo_out.html
for user instructions (e.g., eligible input values, data source, etc.)
}[1;30mINFO[0m Final process status is success
Updating data record...
outfile.txt added
Updating data record...
4abf3398e7ca_GRCh38.primary_assembly.genome.fa.1.bt2 added
4abf7b99993c_GRCh38.primary_assembly.genome.fa.2.bt2 added
4abf211b7189_GRCh38.primary_assembly.genome.fa.3.bt2 added
4abf10baea5a_GRCh38.primary_assembly.genome.fa.4.bt2 added
4abf5f6fc34a_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
4abf227e6039_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
4abf16df4fe0_outfile.txt added
4abf1ef506db_GRCh37_to_GRCh38.chain added
4abf689523bd_GRCh37_to_NCBI34.chain added
4abf175d82ef_GRCh37_to_NCBI35.chain added
4abf7c3f24e4_GRCh37_to_NCBI36.chain added
4abf158f3476_GRCh38_to_GRCh37.chain added
4abf6cbd3a08_GRCh38_to_NCBI34.chain added
4abf7b2d1afd_GRCh38_to_NCBI35.chain added
4abf4e471738_GRCh38_to_NCBI36.chain added
4abf1d4585ae_NCBI34_to_GRCh37.chain added
4abf3f4b7185_NCBI34_to_GRCh38.chain added
4abf7209f339_NCBI35_to_GRCh37.chain added
4abf6b3f5dac_NCBI35_to_GRCh38.chain added
4abfd1efe36_NCBI36_to_GRCh37.chain added
4abf6dc391f4_NCBI36_to_GRCh38.chain added
4abf42a36278_GRCm38_to_NCBIM36.chain added
4abf7495d675_GRCm38_to_NCBIM37.chain added
4abf1932d71f_NCBIM36_to_GRCm38.chain added
4abf58c94125_NCBIM37_to_GRCm38.chain added
4abf4d411ad_1000G_omni2.5.b37.vcf.gz added
4abf7ed47754_1000G_omni2.5.b37.vcf.gz.tbi added
4abf2ee66cd9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
4abf19f4329d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
4abf6f26eeba_1000G_omni2.5.hg38.vcf.gz added
4abf65032e58_1000G_omni2.5.hg38.vcf.gz.tbi added
4abf33d7c737_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
4abf1b580678_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
4abf3010be4e_af-only-gnomad.raw.sites.vcf added
4abf1b3e0b89_af-only-gnomad.raw.sites.vcf.idx added
4abf6675d58_Mutect2-exome-panel.vcf.idx added
4abf6c213fb0_Mutect2-WGS-panel-b37.vcf added
4abf7adc7345_Mutect2-WGS-panel-b37.vcf.idx added
4abf1f13f607_small_exac_common_3.vcf added
4abf577d5581_small_exac_common_3.vcf.idx added
4abf6578b506_1000g_pon.hg38.vcf.gz added
4abf57b4d0f5_1000g_pon.hg38.vcf.gz.tbi added
4abf2002b1cf_af-only-gnomad.hg38.vcf.gz added
4abf10e79d74_af-only-gnomad.hg38.vcf.gz.tbi added
4abf56123357_small_exac_common_3.hg38.vcf.gz added
4abf44e8c0e6_small_exac_common_3.hg38.vcf.gz.tbi added
4abfcd05f62_gencode.v41.annotation.gtf added
4abf44262180_gencode.v42.annotation.gtf added
4abf23617d74_gencode.vM30.annotation.gtf added
4abf55735cd1_gencode.vM31.annotation.gtf added
4abf8d2c92b_gencode.v41.transcripts.fa added
4abf46952a93_gencode.v41.transcripts.fa.fai added
4abf6b1e3d18_gencode.v42.transcripts.fa added
4abfe3d2999_gencode.v42.transcripts.fa.fai added
4abf5176031c_gencode.vM30.pc_transcripts.fa added
4abf1ac64d0c_gencode.vM30.pc_transcripts.fa.fai added
4abf50ec5c8f_gencode.vM31.pc_transcripts.fa added
4abf4db0d9ca_gencode.vM31.pc_transcripts.fa.fai added
4abf15aa849f_GRCh38.primary_assembly.genome.fa.1.ht2 added
4abf6de8edd5_GRCh38.primary_assembly.genome.fa.2.ht2 added
4abf57567352_GRCh38.primary_assembly.genome.fa.3.ht2 added
4abf6cad3949_GRCh38.primary_assembly.genome.fa.4.ht2 added
4abf608c1f5c_GRCh38.primary_assembly.genome.fa.5.ht2 added
4abff5f0289_GRCh38.primary_assembly.genome.fa.6.ht2 added
4abf269f7841_GRCh38.primary_assembly.genome.fa.7.ht2 added
4abf2f900736_GRCh38.primary_assembly.genome.fa.8.ht2 added
4abf18c9829f_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
4abf559ea16f_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
4abf2178aa53_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
4abf78f6404f_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
4abf6ef84093_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
4abf6c57abcf_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
4abf6fd0da9a_GRCh38_full_analysis_set_plus_decoy_hla.fa added
4abf78bfedcf_GRCh38.primary_assembly.genome.fa.fai added
4abf95eef8_GRCh38.primary_assembly.genome.fa.amb added
4abf737bdc14_GRCh38.primary_assembly.genome.fa.ann added
4abf48ade047_GRCh38.primary_assembly.genome.fa.bwt added
4abff5f7a98_GRCh38.primary_assembly.genome.fa.pac added
4abf4569990a_GRCh38.primary_assembly.genome.fa.sa added
4abf17be8320_GRCh38.primary_assembly.genome.fa added
4abf5c92b60d_hs37d5.fa.fai added
4abf23ee3ef6_hs37d5.fa.amb added
4abf6e679ae7_hs37d5.fa.ann added
4abf53eaec51_hs37d5.fa.bwt added
4abf6440e4e1_hs37d5.fa.pac added
4abf6072a332_hs37d5.fa.sa added
4abf6385916_hs37d5.fa added
4abf5d60b68a_complete_ref_lens.bin added
4abf78704dea_ctable.bin added
4abf150b7b6c_ctg_offsets.bin added
4abf24d3fa3f_duplicate_clusters.tsv added
4abf58d250fc_info.json added
4abf57c2fdf2_mphf.bin added
4abf42ae47e1_pos.bin added
4abf3ff126fa_pre_indexing.log added
4abf713607e1_rank.bin added
4abf123f7ed8_ref_indexing.log added
4abf6a0a044_refAccumLengths.bin added
4abf1b79d3c2_reflengths.bin added
4abf5b3d73a5_refseq.bin added
4abf1f73846f_seq.bin added
4abf58fba38a_versionInfo.json added
4abf70ade6a9_salmon_index added
4abf29029b0a_chrLength.txt added
4abf6a10c28e_chrName.txt added
4abf72552f08_chrNameLength.txt added
4abf3682f0dc_chrStart.txt added
4abf4e931779_exonGeTrInfo.tab added
4abf1aea313c_exonInfo.tab added
4abf54667f2_geneInfo.tab added
4abf51524392_Genome added
4abf6fd24ff3_genomeParameters.txt added
4abf587f13df_Log.out added
4abf7ef1c2dc_SA added
4abf32303aa0_SAindex added
4abf7c58f81d_sjdbInfo.txt added
4abf350977b2_sjdbList.fromGTF.out.tab added
4abf916252_sjdbList.out.tab added
4abf48cdf5c8_transcriptInfo.tab added
4abf49c342cf_GRCh38.GENCODE.v42_100 added
4abf325749de_knownGene_hg38.sql added
4abfb2a7a4_knownGene_hg38.txt added
4abf511c0057_refGene_hg38.sql added
4abf55a795b_refGene_hg38.txt added
4abf76d5481b_knownGene_mm39.sql added
4abf2c712190_knownGene_mm39.txt added
4abf37528bbb_refGene_mm39.sql added
4abfc53be5d_refGene_mm39.txt added
trying URL 'https://storage.googleapis.com/reusedata/echo/outfile.txt'
Content type 'text/plain' length 30 bytes
==================================================
downloaded 30 bytes
trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.yml'
Content type 'application/x-yaml' length 151 bytes
==================================================
downloaded 151 bytes
trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.cwl'
Content type 'application/octet-stream' length 1152 bytes
==================================================
downloaded 1152 bytes
trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.md5'
Content type 'application/octet-stream' length 45 bytes
==================================================
downloaded 45 bytes
trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.sh'
Content type 'application/x-shellscript' length 68 bytes
==================================================
downloaded 68 bytes
Data is downloaded:
/tmp/RtmpI1PtGh/test_gcpData/outfile.txt
}[1;30mINFO[0m Final process status is success
NOTE: existing caches will be removed and regenerated!
Updating recipes...
STAR_index.R added
bowtie2_index.R added
echo_out.R added
ensembl_liftover.R added
gcp_broad_gatk_hg19.R added
gcp_broad_gatk_hg38.R added
gcp_gatk_mutect2_b37.R added
gcp_gatk_mutect2_hg38.R added
gencode_annotation.R added
gencode_genome_grch38.R added
gencode_transcripts.R added
hisat2_index.R added
reference_genome.R added
salmon_index.R added
ucsc_database.R added
Data recipe loaded!
Use inputs(ensembl_liftover) to check required input parameters before evaluation.
Check here: https://rcwl.org/dataRecipes/ensembl_liftover.html
for user instructions (e.g., eligible input values, data source, etc.)
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
>
>
>
> proc.time()
user system elapsed
22.275 2.492 25.749
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.700 | 0.903 | 8.705 | |
| dataSearch | 1.439 | 0.064 | 1.513 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.952 | 0.173 | 4.402 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.153 | 0.013 | 0.167 | |
| recipeLoad | 1.587 | 0.098 | 1.697 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.630 | 0.040 | 0.671 | |
| recipeUpdate | 0 | 0 | 0 | |