Qian Liu
| Snapshot Date: 2026-05-18 13:45 -0400 (Mon, 18 May 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: caf380d |
| git_last_commit_date: 2026-04-28 08:59:39 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-19 12:55 -0400 (Tue, 19 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4898 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There" | 4617 |
| 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 1786/2377 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.13.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | | |||||||||
| See other builds for ReUseData in R Universe. | ||||||||||||||
|
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: 1.13.0 |
| 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_1.13.0.tar.gz |
| StartedAt: 2026-05-18 23:27:44 -0400 (Mon, 18 May 2026) |
| EndedAt: 2026-05-18 23:28:36 -0400 (Mon, 18 May 2026) |
| EllapsedTime: 51.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/ReUseData.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-19 03:27:44 UTC
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.13.0’
* 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-3.24-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/Resources/library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.13.0’ ** 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 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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...
120e41c9fef63_GRCh38.primary_assembly.genome.fa.1.bt2 added
120e4481d5b43_GRCh38.primary_assembly.genome.fa.2.bt2 added
120e47f52b0b1_GRCh38.primary_assembly.genome.fa.3.bt2 added
120e4dce75c5_GRCh38.primary_assembly.genome.fa.4.bt2 added
120e46d95df97_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
120e4a8a6ab6_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
120e4563d822_outfile.txt added
120e45e02a2f1_GRCh37_to_GRCh38.chain added
120e47f17ac6e_GRCh37_to_NCBI34.chain added
120e46b39aaf1_GRCh37_to_NCBI35.chain added
120e41705eb36_GRCh37_to_NCBI36.chain added
120e45953209_GRCh38_to_GRCh37.chain added
120e4607efbc_GRCh38_to_NCBI34.chain added
120e4730c22bb_GRCh38_to_NCBI35.chain added
120e421bc5dff_GRCh38_to_NCBI36.chain added
120e455bf21a6_NCBI34_to_GRCh37.chain added
120e4773a4544_NCBI34_to_GRCh38.chain added
120e41299b083_NCBI35_to_GRCh37.chain added
120e4281371ff_NCBI35_to_GRCh38.chain added
120e414a130e7_NCBI36_to_GRCh37.chain added
120e462919845_NCBI36_to_GRCh38.chain added
120e444a40c91_GRCm38_to_NCBIM36.chain added
120e46e3526cb_GRCm38_to_NCBIM37.chain added
120e4638611f3_NCBIM36_to_GRCm38.chain added
120e477049b90_NCBIM37_to_GRCm38.chain added
120e44f8147fb_1000G_omni2.5.b37.vcf.gz added
120e4309cd884_1000G_omni2.5.b37.vcf.gz.tbi added
120e494adb0b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
120e41172b3f1_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
120e41839c2a_1000G_omni2.5.hg38.vcf.gz added
120e467818a2c_1000G_omni2.5.hg38.vcf.gz.tbi added
120e4699683ca_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
120e418a678ee_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
120e4594d5de6_af-only-gnomad.raw.sites.vcf added
120e4664fd4d7_af-only-gnomad.raw.sites.vcf.idx added
120e431ea3bb_Mutect2-exome-panel.vcf.idx added
120e4508f4b96_Mutect2-WGS-panel-b37.vcf added
120e46fab8e2b_Mutect2-WGS-panel-b37.vcf.idx added
120e46802e253_small_exac_common_3.vcf added
120e41558ec7e_small_exac_common_3.vcf.idx added
120e410e4f25_1000g_pon.hg38.vcf.gz added
120e4526e06ad_1000g_pon.hg38.vcf.gz.tbi added
120e435787222_af-only-gnomad.hg38.vcf.gz added
120e4768d319a_af-only-gnomad.hg38.vcf.gz.tbi added
120e42fb3b244_small_exac_common_3.hg38.vcf.gz added
120e43e7ca6d3_small_exac_common_3.hg38.vcf.gz.tbi added
120e469ac86b1_gencode.v41.annotation.gtf added
120e43dbf04aa_gencode.v42.annotation.gtf added
120e447cb5491_gencode.vM30.annotation.gtf added
120e4761d2069_gencode.vM31.annotation.gtf added
120e4723b0a13_gencode.v41.transcripts.fa added
120e42129ffc_gencode.v41.transcripts.fa.fai added
120e414c55a74_gencode.v42.transcripts.fa added
120e428b58053_gencode.v42.transcripts.fa.fai added
120e423fbde06_gencode.vM30.pc_transcripts.fa added
120e46cad6e5e_gencode.vM30.pc_transcripts.fa.fai added
120e46e29150f_gencode.vM31.pc_transcripts.fa added
120e44b25c449_gencode.vM31.pc_transcripts.fa.fai added
120e41c79bb2a_GRCh38.primary_assembly.genome.fa.1.ht2 added
120e47beed100_GRCh38.primary_assembly.genome.fa.2.ht2 added
120e47bdb9690_GRCh38.primary_assembly.genome.fa.3.ht2 added
120e4d7a0777_GRCh38.primary_assembly.genome.fa.4.ht2 added
120e446801c8a_GRCh38.primary_assembly.genome.fa.5.ht2 added
120e44d1cc2f_GRCh38.primary_assembly.genome.fa.6.ht2 added
120e469b42421_GRCh38.primary_assembly.genome.fa.7.ht2 added
120e431b028be_GRCh38.primary_assembly.genome.fa.8.ht2 added
120e42442eb6e_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
120e4256e955b_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
120e47f0f9c8f_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
120e459efb174_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
120e476b64cd_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
120e41ba6d289_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
120e465482e8d_GRCh38_full_analysis_set_plus_decoy_hla.fa added
120e465e85eed_GRCh38.primary_assembly.genome.fa.fai added
120e47ab04ddf_GRCh38.primary_assembly.genome.fa.amb added
120e44cc8aa66_GRCh38.primary_assembly.genome.fa.ann added
120e4a2b35ec_GRCh38.primary_assembly.genome.fa.bwt added
120e41ae11e2b_GRCh38.primary_assembly.genome.fa.pac added
120e43183a6d6_GRCh38.primary_assembly.genome.fa.sa added
120e43a3e44ff_GRCh38.primary_assembly.genome.fa added
120e44e23df38_hs37d5.fa.fai added
120e41513fd9c_hs37d5.fa.amb added
120e4536f1793_hs37d5.fa.ann added
120e42274deb0_hs37d5.fa.bwt added
120e426c8067c_hs37d5.fa.pac added
120e41621cac8_hs37d5.fa.sa added
120e44881bd2_hs37d5.fa added
120e43da7a51_complete_ref_lens.bin added
120e47c945dd0_ctable.bin added
120e4709b4295_ctg_offsets.bin added
120e461307df4_duplicate_clusters.tsv added
120e4369d5005_info.json added
120e411f09446_mphf.bin added
120e4499688dd_pos.bin added
120e439f38ae9_pre_indexing.log added
120e42424e4b8_rank.bin added
120e47223fe91_ref_indexing.log added
120e4191e1c22_refAccumLengths.bin added
120e47c90910_reflengths.bin added
120e41f71fd6e_refseq.bin added
120e474b550e2_seq.bin added
120e42bd1614a_versionInfo.json added
120e43f4a57bf_salmon_index added
120e429c6dd0f_chrLength.txt added
120e43edb1936_chrName.txt added
120e422544877_chrNameLength.txt added
120e44b618e3c_chrStart.txt added
120e471c12bcd_exonGeTrInfo.tab added
120e44122da13_exonInfo.tab added
120e4571b36cd_geneInfo.tab added
120e43baaf968_Genome added
120e455dc3972_genomeParameters.txt added
120e46d3f9767_Log.out added
120e469ed2339_SA added
120e44fa3a983_SAindex added
120e41ce004e_sjdbInfo.txt added
120e47b7601ce_sjdbList.fromGTF.out.tab added
120e470bab5_sjdbList.out.tab added
120e468f1c14c_transcriptInfo.tab added
120e457c99a67_GRCh38.GENCODE.v42_100 added
120e474b80d37_knownGene_hg38.sql added
120e45f6bd1be_knownGene_hg38.txt added
120e41f9741e3_refGene_hg38.sql added
120e4366ae49_refGene_hg38.txt added
120e44a3c3c5d_knownGene_mm39.sql added
120e4389f23be_knownGene_mm39.txt added
120e457e3abfc_refGene_mm39.sql added
120e424305a78_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//Rtmpcz2sh2/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 1 | SKIP 0 | PASS 44 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
>
>
>
> proc.time()
user system elapsed
6.697 0.833 8.368
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.895 | 0.255 | 2.154 | |
| dataSearch | 0.352 | 0.017 | 0.367 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 0.850 | 0.050 | 1.655 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.043 | 0.004 | 0.047 | |
| recipeLoad | 0.616 | 0.082 | 0.699 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.157 | 0.013 | 0.169 | |
| recipeUpdate | 0 | 0 | 0 | |