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 12:07 -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. - 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: 2025-12-09 14:47:09 -0000 (Tue, 09 Dec 2025) |
| EndedAt: 2025-12-09 14:49:54 -0000 (Tue, 09 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 8.977 0.315 9.336
getCloudData 3.519 0.076 6.338
* 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...
25b258736581b1_GRCh38.primary_assembly.genome.fa.1.bt2 added
25b258bd8b04e_GRCh38.primary_assembly.genome.fa.2.bt2 added
25b2589984f8c_GRCh38.primary_assembly.genome.fa.3.bt2 added
25b258e567d2e_GRCh38.primary_assembly.genome.fa.4.bt2 added
25b2584f57ea9f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
25b2587d7830a2_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
25b2588881040_outfile.txt added
25b25846d772f6_GRCh37_to_GRCh38.chain added
25b25811e63c35_GRCh37_to_NCBI34.chain added
25b25823e94fd1_GRCh37_to_NCBI35.chain added
25b258264cab0_GRCh37_to_NCBI36.chain added
25b2583b644d69_GRCh38_to_GRCh37.chain added
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25b2581dc47d3f_GRCh38_to_NCBI36.chain added
25b2581e76ec0b_NCBI34_to_GRCh37.chain added
25b25856f79108_NCBI34_to_GRCh38.chain added
25b2582e2ff0fa_NCBI35_to_GRCh37.chain added
25b2584178fcdc_NCBI35_to_GRCh38.chain added
25b2585b9d3312_NCBI36_to_GRCh37.chain added
25b25829547bc9_NCBI36_to_GRCh38.chain added
25b2581181d6a0_GRCm38_to_NCBIM36.chain added
25b258356908d7_GRCm38_to_NCBIM37.chain added
25b258c7b508f_NCBIM36_to_GRCm38.chain added
25b2581a51c5ea_NCBIM37_to_GRCm38.chain added
25b2586fc44a4c_1000G_omni2.5.b37.vcf.gz added
25b25838f58bb1_1000G_omni2.5.b37.vcf.gz.tbi added
25b25867c45cd8_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
25b25868e1a882_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
25b25877425858_1000G_omni2.5.hg38.vcf.gz added
25b2581aa20e27_1000G_omni2.5.hg38.vcf.gz.tbi added
25b2585c472a33_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
25b25831b08a7_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
25b258243a5db4_af-only-gnomad.raw.sites.vcf added
25b2586a9da762_af-only-gnomad.raw.sites.vcf.idx added
25b2585272f346_Mutect2-exome-panel.vcf.idx added
25b25821b28e56_Mutect2-WGS-panel-b37.vcf added
25b2587325b7a2_Mutect2-WGS-panel-b37.vcf.idx added
25b258194a663c_small_exac_common_3.vcf added
25b2583398ca8b_small_exac_common_3.vcf.idx added
25b258170f0773_1000g_pon.hg38.vcf.gz added
25b2581baf30ec_1000g_pon.hg38.vcf.gz.tbi added
25b2586efd17f5_af-only-gnomad.hg38.vcf.gz added
25b25894c352b_af-only-gnomad.hg38.vcf.gz.tbi added
25b258564cfbe3_small_exac_common_3.hg38.vcf.gz added
25b258cc19534_small_exac_common_3.hg38.vcf.gz.tbi added
25b25827c32136_gencode.v41.annotation.gtf added
25b2582d448ceb_gencode.v42.annotation.gtf added
25b2583af1862e_gencode.vM30.annotation.gtf added
25b258693c1e12_gencode.vM31.annotation.gtf added
25b2588e1bffd_gencode.v41.transcripts.fa added
25b258644601f7_gencode.v41.transcripts.fa.fai added
25b2587abdf4b2_gencode.v42.transcripts.fa added
25b2583e4ac8d5_gencode.v42.transcripts.fa.fai added
25b25870c15287_gencode.vM30.pc_transcripts.fa added
25b258150fba9d_gencode.vM30.pc_transcripts.fa.fai added
25b2582e0f1321_gencode.vM31.pc_transcripts.fa added
25b25829b6de38_gencode.vM31.pc_transcripts.fa.fai added
25b2587cd41775_GRCh38.primary_assembly.genome.fa.1.ht2 added
25b25816f0bba3_GRCh38.primary_assembly.genome.fa.2.ht2 added
25b25820f93690_GRCh38.primary_assembly.genome.fa.3.ht2 added
25b2581776259d_GRCh38.primary_assembly.genome.fa.4.ht2 added
25b2587337e5d6_GRCh38.primary_assembly.genome.fa.5.ht2 added
25b25824143f37_GRCh38.primary_assembly.genome.fa.6.ht2 added
25b2583bb08351_GRCh38.primary_assembly.genome.fa.7.ht2 added
25b2585dd58d38_GRCh38.primary_assembly.genome.fa.8.ht2 added
25b2587687327d_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
25b2585d6311a7_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
25b25850fb44da_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
25b258fd198b9_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
25b25810fbdc33_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
25b258680a4c4d_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
25b2582b80c9a6_GRCh38_full_analysis_set_plus_decoy_hla.fa added
25b2587ff8f428_GRCh38.primary_assembly.genome.fa.fai added
25b25871568179_GRCh38.primary_assembly.genome.fa.amb added
25b2581cdc589_GRCh38.primary_assembly.genome.fa.ann added
25b258cba895c_GRCh38.primary_assembly.genome.fa.bwt added
25b2581919a2af_GRCh38.primary_assembly.genome.fa.pac added
25b2582f125274_GRCh38.primary_assembly.genome.fa.sa added
25b25847ac0f8a_GRCh38.primary_assembly.genome.fa added
25b258255c0c2_hs37d5.fa.fai added
25b25837f41271_hs37d5.fa.amb added
25b2582bf21181_hs37d5.fa.ann added
25b2587d13b574_hs37d5.fa.bwt added
25b258763edb46_hs37d5.fa.pac added
25b2581cb36408_hs37d5.fa.sa added
25b25812237011_hs37d5.fa added
25b258244dee67_complete_ref_lens.bin added
25b258466a4240_ctable.bin added
25b258ef78787_ctg_offsets.bin added
25b2583b3eaa0a_duplicate_clusters.tsv added
25b258676378d1_info.json added
25b258266dad24_mphf.bin added
25b2582e768fe1_pos.bin added
25b258b77b808_pre_indexing.log added
25b258621e3075_rank.bin added
25b258c4c1d19_ref_indexing.log added
25b2581feea86_refAccumLengths.bin added
25b2583f81421c_reflengths.bin added
25b2585d4761f4_refseq.bin added
25b25811d0833f_seq.bin added
25b258507d1e4f_versionInfo.json added
25b2584551ae41_salmon_index added
25b2583d514ce5_chrLength.txt added
25b25850761277_chrName.txt added
25b25836a82fba_chrNameLength.txt added
25b2583f1f126e_chrStart.txt added
25b2585d309bd3_exonGeTrInfo.tab added
25b2584fc1d26a_exonInfo.tab added
25b2586e3164e2_geneInfo.tab added
25b25824dcab5d_Genome added
25b2585217932c_genomeParameters.txt added
25b25826257754_Log.out added
25b25850cebcdf_SA added
25b2584f2b48a0_SAindex added
25b2581c64529a_sjdbInfo.txt added
25b2586d8220e7_sjdbList.fromGTF.out.tab added
25b258614eb8b2_sjdbList.out.tab added
25b25840b24102_transcriptInfo.tab added
25b25833ec6328_GRCh38.GENCODE.v42_100 added
25b25870464039_knownGene_hg38.sql added
25b2587bf0eb0c_knownGene_hg38.txt added
25b2581b4fdbf9_refGene_hg38.sql added
25b25816b3ed5d_refGene_hg38.txt added
25b2582a677aed_knownGene_mm39.sql added
25b25826c79401_knownGene_mm39.txt added
25b25878d21dd2_refGene_mm39.sql added
25b25836b39807_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/RtmpPEa01A/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
25.283 2.097 29.238
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 8.977 | 0.315 | 9.336 | |
| dataSearch | 1.814 | 0.036 | 1.856 | |
| dataUpdate | 0.001 | 0.000 | 0.000 | |
| getCloudData | 3.519 | 0.076 | 6.338 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.202 | 0.004 | 0.210 | |
| recipeLoad | 2.100 | 0.040 | 2.153 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.886 | 0.004 | 0.894 | |
| recipeUpdate | 0 | 0 | 0 | |