Qian Liu
| Snapshot Date: 2025-12-11 13:45 -0500 (Thu, 11 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 2025-12-15 12:09 -0500 (Mon, 15 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" | 4882 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: ReUseData |
| Version: 1.10.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReUseData_1.10.0.tar.gz |
| StartedAt: 2025-12-12 14:20:49 -0000 (Fri, 12 Dec 2025) |
| EndedAt: 2025-12-12 14:23:34 -0000 (Fri, 12 Dec 2025) |
| EllapsedTime: 165.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReUseData_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 loading without being on the library search path ... 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 8.726 0.287 9.061
getCloudData 3.216 0.075 7.642
* 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
‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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...
3d995170af47c5_GRCh38.primary_assembly.genome.fa.1.bt2 added
3d995176e29cdf_GRCh38.primary_assembly.genome.fa.2.bt2 added
3d9951f1607cc_GRCh38.primary_assembly.genome.fa.3.bt2 added
3d995171c0b67d_GRCh38.primary_assembly.genome.fa.4.bt2 added
3d995128514b7f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3d99515b9268dc_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3d99514e6b653_outfile.txt added
3d99513bb5f3d4_GRCh37_to_GRCh38.chain added
3d995172f935b1_GRCh37_to_NCBI34.chain added
3d9951622edaa_GRCh37_to_NCBI35.chain added
3d99511a3e29e8_GRCh37_to_NCBI36.chain added
3d9951388f0945_GRCh38_to_GRCh37.chain added
3d995126598440_GRCh38_to_NCBI34.chain added
3d9951195eb9ad_GRCh38_to_NCBI35.chain added
3d99512a927bb7_GRCh38_to_NCBI36.chain added
3d99515ce36ad2_NCBI34_to_GRCh37.chain added
3d995115dea3d3_NCBI34_to_GRCh38.chain added
3d995134e09aaa_NCBI35_to_GRCh37.chain added
3d99516388ea89_NCBI35_to_GRCh38.chain added
3d995126e2d414_NCBI36_to_GRCh37.chain added
3d99511a1927bc_NCBI36_to_GRCh38.chain added
3d995177d2c755_GRCm38_to_NCBIM36.chain added
3d9951c9b0037_GRCm38_to_NCBIM37.chain added
3d9951dced3cd_NCBIM36_to_GRCm38.chain added
3d9951510a07d3_NCBIM37_to_GRCm38.chain added
3d99515ca72480_1000G_omni2.5.b37.vcf.gz added
3d99513869c386_1000G_omni2.5.b37.vcf.gz.tbi added
3d995142e5c1e6_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3d995179d5b761_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3d995137067ef9_1000G_omni2.5.hg38.vcf.gz added
3d9951421b70e6_1000G_omni2.5.hg38.vcf.gz.tbi added
3d99516a84ff26_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3d99512de91bd8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3d9951513178b2_af-only-gnomad.raw.sites.vcf added
3d99515c45b5a4_af-only-gnomad.raw.sites.vcf.idx added
3d9951563a6757_Mutect2-exome-panel.vcf.idx added
3d99512cc3e18e_Mutect2-WGS-panel-b37.vcf added
3d9951612c6bf7_Mutect2-WGS-panel-b37.vcf.idx added
3d995111f05b2c_small_exac_common_3.vcf added
3d99511fbd173f_small_exac_common_3.vcf.idx added
3d9951674f59a1_1000g_pon.hg38.vcf.gz added
3d99512c2e8514_1000g_pon.hg38.vcf.gz.tbi added
3d9951584c2085_af-only-gnomad.hg38.vcf.gz added
3d9951da8dde1_af-only-gnomad.hg38.vcf.gz.tbi added
3d9951458d3ec2_small_exac_common_3.hg38.vcf.gz added
3d99512de9c3c_small_exac_common_3.hg38.vcf.gz.tbi added
3d99516a8c48b3_gencode.v41.annotation.gtf added
3d99515b6be295_gencode.v42.annotation.gtf added
3d995137bf36e6_gencode.vM30.annotation.gtf added
3d99514e15333d_gencode.vM31.annotation.gtf added
3d995124eb6a9_gencode.v41.transcripts.fa added
3d995151d85ea2_gencode.v41.transcripts.fa.fai added
3d995145e7fa92_gencode.v42.transcripts.fa added
3d9951ee9b6e0_gencode.v42.transcripts.fa.fai added
3d99515fa7326f_gencode.vM30.pc_transcripts.fa added
3d995116f20265_gencode.vM30.pc_transcripts.fa.fai added
3d99516b90db61_gencode.vM31.pc_transcripts.fa added
3d99511810f5f5_gencode.vM31.pc_transcripts.fa.fai added
3d995159d7c44c_GRCh38.primary_assembly.genome.fa.1.ht2 added
3d9951656692c2_GRCh38.primary_assembly.genome.fa.2.ht2 added
3d99514f1774ee_GRCh38.primary_assembly.genome.fa.3.ht2 added
3d99511bf33532_GRCh38.primary_assembly.genome.fa.4.ht2 added
3d99514feb91e8_GRCh38.primary_assembly.genome.fa.5.ht2 added
3d99517d0090c6_GRCh38.primary_assembly.genome.fa.6.ht2 added
3d99516d24ade4_GRCh38.primary_assembly.genome.fa.7.ht2 added
3d99512c31478c_GRCh38.primary_assembly.genome.fa.8.ht2 added
3d9951533af81e_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3d995119e88f72_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3d9951d5db383_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3d9951652b534a_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3d995139a5a6b2_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3d995174ad0d25_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3d99511159d85e_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3d995111f1c737_GRCh38.primary_assembly.genome.fa.fai added
3d9951255eb06_GRCh38.primary_assembly.genome.fa.amb added
3d995156e71720_GRCh38.primary_assembly.genome.fa.ann added
3d995114d06373_GRCh38.primary_assembly.genome.fa.bwt added
3d99516ce233ba_GRCh38.primary_assembly.genome.fa.pac added
3d99513252f9b6_GRCh38.primary_assembly.genome.fa.sa added
3d99514c8f9a59_GRCh38.primary_assembly.genome.fa added
3d99513af766f7_hs37d5.fa.fai added
3d995134a1b05f_hs37d5.fa.amb added
3d99511e67f8fb_hs37d5.fa.ann added
3d9951df6189_hs37d5.fa.bwt added
3d9951438b6740_hs37d5.fa.pac added
3d99517e0f2b6a_hs37d5.fa.sa added
3d995117d163ef_hs37d5.fa added
3d99512f1c42a1_complete_ref_lens.bin added
3d99511620215f_ctable.bin added
3d995171a9283b_ctg_offsets.bin added
3d99511482d563_duplicate_clusters.tsv added
3d99516537964e_info.json added
3d9951d9c5d6d_mphf.bin added
3d9951646e674b_pos.bin added
3d995162382714_pre_indexing.log added
3d99517ac10b51_rank.bin added
3d9951109faed8_ref_indexing.log added
3d995135731f32_refAccumLengths.bin added
3d995114a99ac3_reflengths.bin added
3d99511dfd625b_refseq.bin added
3d99511a9e727c_seq.bin added
3d99514e4f4175_versionInfo.json added
3d995112aa6f80_salmon_index added
3d99512bf84adb_chrLength.txt added
3d9951604108ac_chrName.txt added
3d995115005a87_chrNameLength.txt added
3d99512df61fb_chrStart.txt added
3d995175116c1f_exonGeTrInfo.tab added
3d99511e28e41_exonInfo.tab added
3d995135325bb1_geneInfo.tab added
3d995141a10678_Genome added
3d99513cd9f538_genomeParameters.txt added
3d995169d40c11_Log.out added
3d99516008ff73_SA added
3d99513db956c1_SAindex added
3d99512d5f7351_sjdbInfo.txt added
3d99515e182add_sjdbList.fromGTF.out.tab added
3d9951558abab0_sjdbList.out.tab added
3d99515c7bb5f2_transcriptInfo.tab added
3d995174384c3d_GRCh38.GENCODE.v42_100 added
3d99514733e2eb_knownGene_hg38.sql added
3d995170fe8b55_knownGene_hg38.txt added
3d9951596fe28b_refGene_hg38.sql added
3d995154d04058_refGene_hg38.txt added
3d9951556cf2a0_knownGene_mm39.sql added
3d99513ba8099f_knownGene_mm39.txt added
3d99514f914ba9_refGene_mm39.sql added
3d9951660ca178_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:
/home/biocbuild/tmp/RtmpZE6AFB/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
24.434 1.077 29.070
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 8.726 | 0.287 | 9.061 | |
| dataSearch | 1.639 | 0.048 | 1.693 | |
| dataUpdate | 0.001 | 0.000 | 0.000 | |
| getCloudData | 3.216 | 0.075 | 7.642 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.175 | 0.000 | 0.179 | |
| recipeLoad | 1.960 | 0.060 | 2.033 | |
| recipeMake | 0.001 | 0.000 | 0.000 | |
| recipeSearch | 0.763 | 0.020 | 0.785 | |
| recipeUpdate | 0 | 0 | 0 | |