Qian Liu
| Snapshot Date: 2025-12-08 13:45 -0500 (Mon, 08 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_22 |
| git_last_commit: 2d4066b |
| git_last_commit_date: 2025-10-29 11:20:44 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-11 12:06 -0500 (Thu, 11 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4879 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4670 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4604 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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 1773/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.10.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 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: 1.10.0 |
| 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_1.10.0.tar.gz |
| StartedAt: 2025-12-10 19:36:00 -0500 (Wed, 10 Dec 2025) |
| EndedAt: 2025-12-10 19:39:28 -0500 (Wed, 10 Dec 2025) |
| EllapsedTime: 208.1 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.2 Patched (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 ‘1.10.0’
* 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 8.093 0.936 12.820
getCloudData 3.047 0.172 6.433
* 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-arm64/Resources/library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.10.0’ ** 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 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
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...
1843c63b91871_GRCh38.primary_assembly.genome.fa.1.bt2 added
1843ccf3d5dd_GRCh38.primary_assembly.genome.fa.2.bt2 added
1843c5c5da6cf_GRCh38.primary_assembly.genome.fa.3.bt2 added
1843c8728f69_GRCh38.primary_assembly.genome.fa.4.bt2 added
1843c19253ad4_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1843c5b394131_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1843cbe726c1_outfile.txt added
1843c74a14f01_GRCh37_to_GRCh38.chain added
1843ca4a0679_GRCh37_to_NCBI34.chain added
1843c1eef736_GRCh37_to_NCBI35.chain added
1843c6fa7fb37_GRCh37_to_NCBI36.chain added
1843c7d5e1125_GRCh38_to_GRCh37.chain added
1843c2ab7d470_GRCh38_to_NCBI34.chain added
1843cadc1af9_GRCh38_to_NCBI35.chain added
1843c786ed700_GRCh38_to_NCBI36.chain added
1843c34e57ec5_NCBI34_to_GRCh37.chain added
1843c46e5d2a4_NCBI34_to_GRCh38.chain added
1843c1a683159_NCBI35_to_GRCh37.chain added
1843c2e7fd79a_NCBI35_to_GRCh38.chain added
1843c4b23d74f_NCBI36_to_GRCh37.chain added
1843c1e0caa13_NCBI36_to_GRCh38.chain added
1843c5171d4ce_GRCm38_to_NCBIM36.chain added
1843c84a4a28_GRCm38_to_NCBIM37.chain added
1843c454a8c58_NCBIM36_to_GRCm38.chain added
1843c214408f2_NCBIM37_to_GRCm38.chain added
1843c79a758ed_1000G_omni2.5.b37.vcf.gz added
1843c59bf6e00_1000G_omni2.5.b37.vcf.gz.tbi added
1843c26cef008_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1843c5bf0b11f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1843c16fc9961_1000G_omni2.5.hg38.vcf.gz added
1843c21b9bb11_1000G_omni2.5.hg38.vcf.gz.tbi added
1843c28a86a63_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1843c48e09e6f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1843c12c1aeca_af-only-gnomad.raw.sites.vcf added
1843c69ba5964_af-only-gnomad.raw.sites.vcf.idx added
1843c4942ea76_Mutect2-exome-panel.vcf.idx added
1843c482f0e8d_Mutect2-WGS-panel-b37.vcf added
1843c9647001_Mutect2-WGS-panel-b37.vcf.idx added
1843c20f55678_small_exac_common_3.vcf added
1843c4afff12f_small_exac_common_3.vcf.idx added
1843c69336b20_1000g_pon.hg38.vcf.gz added
1843c2ebe37d5_1000g_pon.hg38.vcf.gz.tbi added
1843c4a4398ec_af-only-gnomad.hg38.vcf.gz added
1843c1becd40b_af-only-gnomad.hg38.vcf.gz.tbi added
1843c59552c7f_small_exac_common_3.hg38.vcf.gz added
1843c66dc73aa_small_exac_common_3.hg38.vcf.gz.tbi added
1843c132dd2a8_gencode.v41.annotation.gtf added
1843c25611d6e_gencode.v42.annotation.gtf added
1843cad333ee_gencode.vM30.annotation.gtf added
1843c2ff653cf_gencode.vM31.annotation.gtf added
1843c54f853a2_gencode.v41.transcripts.fa added
1843c7b3adc42_gencode.v41.transcripts.fa.fai added
1843c5552b042_gencode.v42.transcripts.fa added
1843c27b1e8d1_gencode.v42.transcripts.fa.fai added
1843c112c05b3_gencode.vM30.pc_transcripts.fa added
1843c612a3393_gencode.vM30.pc_transcripts.fa.fai added
1843c19a029bb_gencode.vM31.pc_transcripts.fa added
1843c6213c121_gencode.vM31.pc_transcripts.fa.fai added
1843c7eec8fd4_GRCh38.primary_assembly.genome.fa.1.ht2 added
1843c5cd6e865_GRCh38.primary_assembly.genome.fa.2.ht2 added
1843c21336e81_GRCh38.primary_assembly.genome.fa.3.ht2 added
1843c379be82e_GRCh38.primary_assembly.genome.fa.4.ht2 added
1843c5ca84087_GRCh38.primary_assembly.genome.fa.5.ht2 added
1843c2a248e97_GRCh38.primary_assembly.genome.fa.6.ht2 added
1843c460d711e_GRCh38.primary_assembly.genome.fa.7.ht2 added
1843c1c7d8c80_GRCh38.primary_assembly.genome.fa.8.ht2 added
1843c7693361c_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1843c3ac5a515_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1843c5d923d8_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1843c72c03ce7_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1843c2ade9c8c_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1843c7cf7c150_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1843c6db4ab48_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1843c70593c3c_GRCh38.primary_assembly.genome.fa.fai added
1843c7281c0c3_GRCh38.primary_assembly.genome.fa.amb added
1843c24967cf0_GRCh38.primary_assembly.genome.fa.ann added
1843c13e48354_GRCh38.primary_assembly.genome.fa.bwt added
1843c7f6a09ff_GRCh38.primary_assembly.genome.fa.pac added
1843cab685b3_GRCh38.primary_assembly.genome.fa.sa added
1843c5503b043_GRCh38.primary_assembly.genome.fa added
1843c65292a4f_hs37d5.fa.fai added
1843c7198dc6b_hs37d5.fa.amb added
1843c6aaf2f10_hs37d5.fa.ann added
1843c133afa28_hs37d5.fa.bwt added
1843c4fd61f5_hs37d5.fa.pac added
1843c172a1e62_hs37d5.fa.sa added
1843c4e30bfcf_hs37d5.fa added
1843c6280d723_complete_ref_lens.bin added
1843c78ac6d5a_ctable.bin added
1843c3f6d9b_ctg_offsets.bin added
1843c4434db3d_duplicate_clusters.tsv added
1843c6a25a4c6_info.json added
1843c4d64f99b_mphf.bin added
1843c203f56cf_pos.bin added
1843c1e5c4093_pre_indexing.log added
1843c3a938277_rank.bin added
1843c2a5a70ac_ref_indexing.log added
1843c179b41ed_refAccumLengths.bin added
1843c52053ab6_reflengths.bin added
1843c5551accb_refseq.bin added
1843c65276f2f_seq.bin added
1843c7ff4aa8a_versionInfo.json added
1843c17e88ba7_salmon_index added
1843c24288d34_chrLength.txt added
1843c624e6377_chrName.txt added
1843c8644c0d_chrNameLength.txt added
1843c70bcedc8_chrStart.txt added
1843c39f1f4b_exonGeTrInfo.tab added
1843c43bf76c8_exonInfo.tab added
1843c4f0f6737_geneInfo.tab added
1843c7c41746d_Genome added
1843c2d42dfd6_genomeParameters.txt added
1843c17571d1_Log.out added
1843c45835116_SA added
1843c30409f01_SAindex added
1843c62871366_sjdbInfo.txt added
1843c120ac013_sjdbList.fromGTF.out.tab added
1843c7fc828a5_sjdbList.out.tab added
1843c2de4aa2d_transcriptInfo.tab added
1843c7f6087e4_GRCh38.GENCODE.v42_100 added
1843c1a79cb11_knownGene_hg38.sql added
1843c3202d6ab_knownGene_hg38.txt added
1843c585b8e33_refGene_hg38.sql added
1843c62d4e396_refGene_hg38.txt added
1843c6a9bf8b_knownGene_mm39.sql added
1843c725e4217_knownGene_mm39.txt added
1843ca452eaa_refGene_mm39.sql added
1843c43faa02a_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/RtmpL4j2F2/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
24.921 2.548 38.712
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 8.093 | 0.936 | 12.820 | |
| dataSearch | 1.373 | 0.064 | 2.139 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 3.047 | 0.172 | 6.433 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.153 | 0.015 | 0.196 | |
| recipeLoad | 1.687 | 0.114 | 2.698 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.697 | 0.046 | 0.950 | |
| recipeUpdate | 0 | 0 | 0 | |