Qian Liu
| Snapshot Date: 2025-12-31 13:40 -0500 (Wed, 31 Dec 2025) |
| 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 2026-01-01 11:35 -0500 (Thu, 01 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" | 4808 |
| 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: 2025-12-31 21:58:28 -0500 (Wed, 31 Dec 2025) |
| EndedAt: 2025-12-31 21:59:25 -0500 (Wed, 31 Dec 2025) |
| EllapsedTime: 56.7 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...
4b7d5fffde20_GRCh38.primary_assembly.genome.fa.1.bt2 added
4b7d1750381d_GRCh38.primary_assembly.genome.fa.2.bt2 added
4b7d139403e0_GRCh38.primary_assembly.genome.fa.3.bt2 added
4b7d5a8a712a_GRCh38.primary_assembly.genome.fa.4.bt2 added
4b7d370baad6_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
4b7d5efce3d5_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
4b7d2cd1e5ab_outfile.txt added
4b7d83d548a_GRCh37_to_GRCh38.chain added
4b7d7279343f_GRCh37_to_NCBI34.chain added
4b7d73554ecf_GRCh37_to_NCBI35.chain added
4b7d65a93330_GRCh37_to_NCBI36.chain added
4b7d475fc874_GRCh38_to_GRCh37.chain added
4b7d61615c47_GRCh38_to_NCBI34.chain added
4b7d3ef16b43_GRCh38_to_NCBI35.chain added
4b7d5bb91bfd_GRCh38_to_NCBI36.chain added
4b7d55dcae16_NCBI34_to_GRCh37.chain added
4b7db295264_NCBI34_to_GRCh38.chain added
4b7d45e028f5_NCBI35_to_GRCh37.chain added
4b7d7fa110a9_NCBI35_to_GRCh38.chain added
4b7d274d08b5_NCBI36_to_GRCh37.chain added
4b7d3276b73b_NCBI36_to_GRCh38.chain added
4b7dff79c5f_GRCm38_to_NCBIM36.chain added
4b7d493b2929_GRCm38_to_NCBIM37.chain added
4b7d4b0b684e_NCBIM36_to_GRCm38.chain added
4b7d59ecff5f_NCBIM37_to_GRCm38.chain added
4b7d5671e418_1000G_omni2.5.b37.vcf.gz added
4b7d4f360ffe_1000G_omni2.5.b37.vcf.gz.tbi added
4b7d66541552_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
4b7d1a43eefa_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
4b7d61fe6c8e_1000G_omni2.5.hg38.vcf.gz added
4b7d68910e5_1000G_omni2.5.hg38.vcf.gz.tbi added
4b7d10b42dbd_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
4b7d2526dbdc_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
4b7d1a2c5b92_af-only-gnomad.raw.sites.vcf added
4b7d562fdbaa_af-only-gnomad.raw.sites.vcf.idx added
4b7d5ffea21a_Mutect2-exome-panel.vcf.idx added
4b7d46448a32_Mutect2-WGS-panel-b37.vcf added
4b7d3dccfca8_Mutect2-WGS-panel-b37.vcf.idx added
4b7d5cdf994a_small_exac_common_3.vcf added
4b7d5bc8f8e8_small_exac_common_3.vcf.idx added
4b7d674d766b_1000g_pon.hg38.vcf.gz added
4b7de999fc9_1000g_pon.hg38.vcf.gz.tbi added
4b7d7c94c9c_af-only-gnomad.hg38.vcf.gz added
4b7d30c499c2_af-only-gnomad.hg38.vcf.gz.tbi added
4b7d3b4aa891_small_exac_common_3.hg38.vcf.gz added
4b7d2280e600_small_exac_common_3.hg38.vcf.gz.tbi added
4b7d3c7c1bb2_gencode.v41.annotation.gtf added
4b7d77fe6223_gencode.v42.annotation.gtf added
4b7d5ddd2560_gencode.vM30.annotation.gtf added
4b7d61c0f1c4_gencode.vM31.annotation.gtf added
4b7d4240acff_gencode.v41.transcripts.fa added
4b7d241dbb54_gencode.v41.transcripts.fa.fai added
4b7d1bf59a52_gencode.v42.transcripts.fa added
4b7d19668bd5_gencode.v42.transcripts.fa.fai added
4b7d1b6659fa_gencode.vM30.pc_transcripts.fa added
4b7d5c9d3a23_gencode.vM30.pc_transcripts.fa.fai added
4b7d5653ff55_gencode.vM31.pc_transcripts.fa added
4b7d24a051ba_gencode.vM31.pc_transcripts.fa.fai added
4b7d19559d1f_GRCh38.primary_assembly.genome.fa.1.ht2 added
4b7d43be6b37_GRCh38.primary_assembly.genome.fa.2.ht2 added
4b7da710aa0_GRCh38.primary_assembly.genome.fa.3.ht2 added
4b7d37093bb_GRCh38.primary_assembly.genome.fa.4.ht2 added
4b7d53f2dbc0_GRCh38.primary_assembly.genome.fa.5.ht2 added
4b7d6d39454e_GRCh38.primary_assembly.genome.fa.6.ht2 added
4b7d4af53be7_GRCh38.primary_assembly.genome.fa.7.ht2 added
4b7d2a2fe123_GRCh38.primary_assembly.genome.fa.8.ht2 added
4b7d2d65d678_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
4b7d78e37790_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
4b7d1dbeccf1_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
4b7d5980f178_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
4b7d206d2b30_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
4b7d5f2e6cf1_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
4b7d60f27308_GRCh38_full_analysis_set_plus_decoy_hla.fa added
4b7d4d5e43f1_GRCh38.primary_assembly.genome.fa.fai added
4b7d67beaae5_GRCh38.primary_assembly.genome.fa.amb added
4b7d16c5d599_GRCh38.primary_assembly.genome.fa.ann added
4b7d164a3b7d_GRCh38.primary_assembly.genome.fa.bwt added
4b7d638796f9_GRCh38.primary_assembly.genome.fa.pac added
4b7d5ac8e87b_GRCh38.primary_assembly.genome.fa.sa added
4b7d3c1711cd_GRCh38.primary_assembly.genome.fa added
4b7de91c88d_hs37d5.fa.fai added
4b7d505a874_hs37d5.fa.amb added
4b7d36765a3f_hs37d5.fa.ann added
4b7d141efa08_hs37d5.fa.bwt added
4b7d7db12d89_hs37d5.fa.pac added
4b7d7b24bdd6_hs37d5.fa.sa added
4b7d292b6bc3_hs37d5.fa added
4b7d61afe452_complete_ref_lens.bin added
4b7d62b6f598_ctable.bin added
4b7d59b600c9_ctg_offsets.bin added
4b7d3bedba22_duplicate_clusters.tsv added
4b7d74572cea_info.json added
4b7d745f252_mphf.bin added
4b7d127e939_pos.bin added
4b7d63409dc6_pre_indexing.log added
4b7d27366512_rank.bin added
4b7d642594da_ref_indexing.log added
4b7d5f4fa793_refAccumLengths.bin added
4b7d6682d4c7_reflengths.bin added
4b7d175f8965_refseq.bin added
4b7d13551e0_seq.bin added
4b7d539249be_versionInfo.json added
4b7d292783cf_salmon_index added
4b7d613ea024_chrLength.txt added
4b7d5683cd5c_chrName.txt added
4b7d671f7f63_chrNameLength.txt added
4b7d44e47179_chrStart.txt added
4b7d71d5e244_exonGeTrInfo.tab added
4b7d10fa18bf_exonInfo.tab added
4b7d136eac4e_geneInfo.tab added
4b7d46f23ed9_Genome added
4b7d49fc3cf2_genomeParameters.txt added
4b7d4f0559d0_Log.out added
4b7d684b8f37_SA added
4b7d38a7995f_SAindex added
4b7d3464908_sjdbInfo.txt added
4b7d7b64ade5_sjdbList.fromGTF.out.tab added
4b7ded4d4ad_sjdbList.out.tab added
4b7d36d6b176_transcriptInfo.tab added
4b7d491cd61a_GRCh38.GENCODE.v42_100 added
4b7d42c6a76_knownGene_hg38.sql added
4b7d16b1e_knownGene_hg38.txt added
4b7d5d1f7e92_refGene_hg38.sql added
4b7d3eaed301_refGene_hg38.txt added
4b7d479f06cd_knownGene_mm39.sql added
4b7d1977a177_knownGene_mm39.txt added
4b7d7d0998b0_refGene_mm39.sql added
4b7d1078af2_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//RtmpSpmAKH/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
7.062 0.838 8.594
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.028 | 0.240 | 2.406 | |
| dataSearch | 0.354 | 0.019 | 0.403 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.915 | 0.065 | 2.036 | |
| getData | 0.000 | 0.001 | 0.001 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.040 | 0.008 | 0.047 | |
| recipeLoad | 0.433 | 0.035 | 0.485 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.162 | 0.012 | 0.175 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |