Qian Liu
| Snapshot Date: 2026-01-07 13:40 -0500 (Wed, 07 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: 4a5d06b |
| git_last_commit_date: 2025-10-29 11:20:44 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-08 11:35 -0500 (Thu, 08 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4815 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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 1754/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.11.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.11.0 |
| 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_1.11.0.tar.gz |
| StartedAt: 2026-01-07 21:59:55 -0500 (Wed, 07 Jan 2026) |
| EndedAt: 2026-01-07 22:00:55 -0500 (Wed, 07 Jan 2026) |
| EllapsedTime: 59.7 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.11.0’
* 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
* 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-3.23-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/4.6-arm64/Resources/library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.11.0’ ** 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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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...
ea0512a70842_GRCh38.primary_assembly.genome.fa.1.bt2 added
ea05140f2e9f_GRCh38.primary_assembly.genome.fa.2.bt2 added
ea0570bdd302_GRCh38.primary_assembly.genome.fa.3.bt2 added
ea053e686221_GRCh38.primary_assembly.genome.fa.4.bt2 added
ea0537028489_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
ea0564b5a96_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
ea053d283114_outfile.txt added
ea0519ae376a_GRCh37_to_GRCh38.chain added
ea057cb81d51_GRCh37_to_NCBI34.chain added
ea051b8cf0cf_GRCh37_to_NCBI35.chain added
ea054215b42a_GRCh37_to_NCBI36.chain added
ea051ee7534b_GRCh38_to_GRCh37.chain added
ea05650d70c6_GRCh38_to_NCBI34.chain added
ea0555670afe_GRCh38_to_NCBI35.chain added
ea056002d57f_GRCh38_to_NCBI36.chain added
ea055a0eb617_NCBI34_to_GRCh37.chain added
ea057bd4ce31_NCBI34_to_GRCh38.chain added
ea05502d327a_NCBI35_to_GRCh37.chain added
ea05474d10b5_NCBI35_to_GRCh38.chain added
ea051483ffa5_NCBI36_to_GRCh37.chain added
ea056604b428_NCBI36_to_GRCh38.chain added
ea053ecfe26b_GRCm38_to_NCBIM36.chain added
ea054219ff04_GRCm38_to_NCBIM37.chain added
ea0538b58183_NCBIM36_to_GRCm38.chain added
ea051449dc8b_NCBIM37_to_GRCm38.chain added
ea057d2e3414_1000G_omni2.5.b37.vcf.gz added
ea05645d4d40_1000G_omni2.5.b37.vcf.gz.tbi added
ea05297ad83a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
ea054009dd1c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
ea0547937a1c_1000G_omni2.5.hg38.vcf.gz added
ea052335e8fa_1000G_omni2.5.hg38.vcf.gz.tbi added
ea0528528725_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
ea054226a2d1_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
ea05768b6944_af-only-gnomad.raw.sites.vcf added
ea053aac2c29_af-only-gnomad.raw.sites.vcf.idx added
ea057d8755d6_Mutect2-exome-panel.vcf.idx added
ea05401494fc_Mutect2-WGS-panel-b37.vcf added
ea057414d42_Mutect2-WGS-panel-b37.vcf.idx added
ea0550372bc6_small_exac_common_3.vcf added
ea05561afd4e_small_exac_common_3.vcf.idx added
ea055ec380c_1000g_pon.hg38.vcf.gz added
ea0557539edd_1000g_pon.hg38.vcf.gz.tbi added
ea0532e2ebf5_af-only-gnomad.hg38.vcf.gz added
ea054ff13bec_af-only-gnomad.hg38.vcf.gz.tbi added
ea0566952bf4_small_exac_common_3.hg38.vcf.gz added
ea054b78d4c9_small_exac_common_3.hg38.vcf.gz.tbi added
ea0569d9fed4_gencode.v41.annotation.gtf added
ea0566e94696_gencode.v42.annotation.gtf added
ea055d1956a2_gencode.vM30.annotation.gtf added
ea052a86d56e_gencode.vM31.annotation.gtf added
ea057a263e91_gencode.v41.transcripts.fa added
ea0564d5e03d_gencode.v41.transcripts.fa.fai added
ea051574f883_gencode.v42.transcripts.fa added
ea0532676b76_gencode.v42.transcripts.fa.fai added
ea0523c029d4_gencode.vM30.pc_transcripts.fa added
ea051cfa2fa2_gencode.vM30.pc_transcripts.fa.fai added
ea056d4d438a_gencode.vM31.pc_transcripts.fa added
ea056b8d5115_gencode.vM31.pc_transcripts.fa.fai added
ea05ac670dd_GRCh38.primary_assembly.genome.fa.1.ht2 added
ea056a1bc2b1_GRCh38.primary_assembly.genome.fa.2.ht2 added
ea05448b28e3_GRCh38.primary_assembly.genome.fa.3.ht2 added
ea05c29723d_GRCh38.primary_assembly.genome.fa.4.ht2 added
ea05750b0907_GRCh38.primary_assembly.genome.fa.5.ht2 added
ea05277de699_GRCh38.primary_assembly.genome.fa.6.ht2 added
ea053aae5b10_GRCh38.primary_assembly.genome.fa.7.ht2 added
ea05cdc9589_GRCh38.primary_assembly.genome.fa.8.ht2 added
ea0565dd5bf7_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
ea0527c0e960_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
ea056a19b203_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
ea053cf61960_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
ea0540fc0ce4_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
ea0563b26e10_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
ea0557580f92_GRCh38_full_analysis_set_plus_decoy_hla.fa added
ea055666670a_GRCh38.primary_assembly.genome.fa.fai added
ea055cf6edd6_GRCh38.primary_assembly.genome.fa.amb added
ea055778ac48_GRCh38.primary_assembly.genome.fa.ann added
ea053376d7d5_GRCh38.primary_assembly.genome.fa.bwt added
ea053f53fb58_GRCh38.primary_assembly.genome.fa.pac added
ea05229a6ee3_GRCh38.primary_assembly.genome.fa.sa added
ea0548e60ad4_GRCh38.primary_assembly.genome.fa added
ea0576d109af_hs37d5.fa.fai added
ea0515d2fd1a_hs37d5.fa.amb added
ea054ee6c127_hs37d5.fa.ann added
ea05f930fe9_hs37d5.fa.bwt added
ea057ff991fb_hs37d5.fa.pac added
ea0559df3760_hs37d5.fa.sa added
ea054dacadb8_hs37d5.fa added
ea053c132df_complete_ref_lens.bin added
ea05f2d066_ctable.bin added
ea05454fd906_ctg_offsets.bin added
ea057d313c76_duplicate_clusters.tsv added
ea052b78a730_info.json added
ea057e28569b_mphf.bin added
ea05a4e1ad2_pos.bin added
ea05dc2d647_pre_indexing.log added
ea057281d65f_rank.bin added
ea052a2131b4_ref_indexing.log added
ea0569463607_refAccumLengths.bin added
ea05853b90_reflengths.bin added
ea052b096b34_refseq.bin added
ea05775d38fe_seq.bin added
ea05948e8eb_versionInfo.json added
ea0511b3a110_salmon_index added
ea0528132a84_chrLength.txt added
ea0524c54aa_chrName.txt added
ea05614a6613_chrNameLength.txt added
ea055b739b4b_chrStart.txt added
ea052d887d5_exonGeTrInfo.tab added
ea0555bdb268_exonInfo.tab added
ea05190bf5d2_geneInfo.tab added
ea056037bad6_Genome added
ea056acb68f3_genomeParameters.txt added
ea055057604b_Log.out added
ea0518730522_SA added
ea05275607b8_SAindex added
ea05114d535_sjdbInfo.txt added
ea057eb98b20_sjdbList.fromGTF.out.tab added
ea05475d22df_sjdbList.out.tab added
ea05339c8313_transcriptInfo.tab added
ea0568616edd_GRCh38.GENCODE.v42_100 added
ea0554b5a4b4_knownGene_hg38.sql added
ea05615050de_knownGene_hg38.txt added
ea055fed50bb_refGene_hg38.sql added
ea05554f5630_refGene_hg38.txt added
ea054ba39511_knownGene_mm39.sql added
ea05608fb5e2_knownGene_mm39.txt added
ea057aee39f4_refGene_mm39.sql added
ea052e1f0139_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:
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpD6GAzs/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
7.161 0.874 9.376
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.100 | 0.270 | 2.506 | |
| dataSearch | 0.387 | 0.021 | 0.429 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.933 | 0.062 | 2.004 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.039 | 0.005 | 0.045 | |
| recipeLoad | 0.414 | 0.030 | 0.479 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.176 | 0.013 | 0.193 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |