Qian Liu
| Snapshot Date: 2025-10-20 13:45 -0400 (Mon, 20 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: c5927b9 |
| git_last_commit_date: 2025-04-15 13:01:44 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-21 12:07 -0400 (Tue, 21 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 1765/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.9.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 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: 1.9.0 |
| 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_1.9.0.tar.gz |
| StartedAt: 2025-10-17 12:44:15 -0000 (Fri, 17 Oct 2025) |
| EndedAt: 2025-10-17 12:46:53 -0000 (Fri, 17 Oct 2025) |
| EllapsedTime: 158.1 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_1.9.0.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 ‘1.9.0’
* 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 9.023 0.383 9.456
getCloudData 3.186 0.076 6.131
* 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 ‘1.9.0’ ** 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...
32da916ca337a8_GRCh38.primary_assembly.genome.fa.1.bt2 added
32da91b34193_GRCh38.primary_assembly.genome.fa.2.bt2 added
32da912e50e774_GRCh38.primary_assembly.genome.fa.3.bt2 added
32da913f60af17_GRCh38.primary_assembly.genome.fa.4.bt2 added
32da91777346f3_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
32da9127ba2ef4_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
32da9157ffd5a1_outfile.txt added
32da915b95ee7a_GRCh37_to_GRCh38.chain added
32da91bb3a827_GRCh37_to_NCBI34.chain added
32da913d15ae7c_GRCh37_to_NCBI35.chain added
32da913dd29059_GRCh37_to_NCBI36.chain added
32da914fd279cd_GRCh38_to_GRCh37.chain added
32da912896ef8f_GRCh38_to_NCBI34.chain added
32da91596368ae_GRCh38_to_NCBI35.chain added
32da91555c5350_GRCh38_to_NCBI36.chain added
32da91769431c8_NCBI34_to_GRCh37.chain added
32da9121be31c8_NCBI34_to_GRCh38.chain added
32da915a1492fc_NCBI35_to_GRCh37.chain added
32da914cb91e9c_NCBI35_to_GRCh38.chain added
32da91255ed534_NCBI36_to_GRCh37.chain added
32da914652eb8f_NCBI36_to_GRCh38.chain added
32da91eb2534f_GRCm38_to_NCBIM36.chain added
32da9140f7749a_GRCm38_to_NCBIM37.chain added
32da917298c00_NCBIM36_to_GRCm38.chain added
32da915059c1ea_NCBIM37_to_GRCm38.chain added
32da914afc046d_1000G_omni2.5.b37.vcf.gz added
32da91275ad0d1_1000G_omni2.5.b37.vcf.gz.tbi added
32da91787d495a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
32da914dc19564_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
32da914c6623a8_1000G_omni2.5.hg38.vcf.gz added
32da91ed3c2e8_1000G_omni2.5.hg38.vcf.gz.tbi added
32da913a64cd0c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
32da914d19653c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
32da913d24aa5c_af-only-gnomad.raw.sites.vcf added
32da9179c57c23_af-only-gnomad.raw.sites.vcf.idx added
32da91448cac2f_Mutect2-exome-panel.vcf.idx added
32da9164ded951_Mutect2-WGS-panel-b37.vcf added
32da9151c551c4_Mutect2-WGS-panel-b37.vcf.idx added
32da9120229aa9_small_exac_common_3.vcf added
32da9170928178_small_exac_common_3.vcf.idx added
32da91edb0041_1000g_pon.hg38.vcf.gz added
32da915df52b03_1000g_pon.hg38.vcf.gz.tbi added
32da914064fb45_af-only-gnomad.hg38.vcf.gz added
32da913771efd0_af-only-gnomad.hg38.vcf.gz.tbi added
32da91375893b1_small_exac_common_3.hg38.vcf.gz added
32da9115c14e95_small_exac_common_3.hg38.vcf.gz.tbi added
32da912e062198_gencode.v41.annotation.gtf added
32da915916c57a_gencode.v42.annotation.gtf added
32da916fd5e192_gencode.vM30.annotation.gtf added
32da917abf4035_gencode.vM31.annotation.gtf added
32da917e759aae_gencode.v41.transcripts.fa added
32da913628cd21_gencode.v41.transcripts.fa.fai added
32da919719384_gencode.v42.transcripts.fa added
32da913f6d0f48_gencode.v42.transcripts.fa.fai added
32da913d525922_gencode.vM30.pc_transcripts.fa added
32da9159cb556e_gencode.vM30.pc_transcripts.fa.fai added
32da91a6913b6_gencode.vM31.pc_transcripts.fa added
32da9164ad29f3_gencode.vM31.pc_transcripts.fa.fai added
32da9152489ec9_GRCh38.primary_assembly.genome.fa.1.ht2 added
32da91582aa91a_GRCh38.primary_assembly.genome.fa.2.ht2 added
32da9131134d9c_GRCh38.primary_assembly.genome.fa.3.ht2 added
32da91611c61b1_GRCh38.primary_assembly.genome.fa.4.ht2 added
32da91128f7626_GRCh38.primary_assembly.genome.fa.5.ht2 added
32da917e2cb2d8_GRCh38.primary_assembly.genome.fa.6.ht2 added
32da911e410c0e_GRCh38.primary_assembly.genome.fa.7.ht2 added
32da91c54f249_GRCh38.primary_assembly.genome.fa.8.ht2 added
32da9142b95f07_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
32da9131fe55f_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
32da915e1a440e_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
32da9162dbf9b1_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
32da9173b266d7_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
32da916cf5444f_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
32da9140d124b4_GRCh38_full_analysis_set_plus_decoy_hla.fa added
32da913417621c_GRCh38.primary_assembly.genome.fa.fai added
32da912467341f_GRCh38.primary_assembly.genome.fa.amb added
32da917829b865_GRCh38.primary_assembly.genome.fa.ann added
32da9149d8b0b1_GRCh38.primary_assembly.genome.fa.bwt added
32da91526d55b7_GRCh38.primary_assembly.genome.fa.pac added
32da9151407ddf_GRCh38.primary_assembly.genome.fa.sa added
32da9139ae9243_GRCh38.primary_assembly.genome.fa added
32da914d2c95ec_hs37d5.fa.fai added
32da914fb6188d_hs37d5.fa.amb added
32da916fd75f65_hs37d5.fa.ann added
32da91569e2971_hs37d5.fa.bwt added
32da91f2327d6_hs37d5.fa.pac added
32da912d29b887_hs37d5.fa.sa added
32da9130697edf_hs37d5.fa added
32da91198c3b8c_complete_ref_lens.bin added
32da9111d6e27a_ctable.bin added
32da912b21da8_ctg_offsets.bin added
32da9171b6e4a6_duplicate_clusters.tsv added
32da9142ea3016_info.json added
32da9163ce7f5a_mphf.bin added
32da914465acc_pos.bin added
32da914116e2ee_pre_indexing.log added
32da9120f8b68_rank.bin added
32da91109b4d15_ref_indexing.log added
32da913d041f6_refAccumLengths.bin added
32da9152f70c7_reflengths.bin added
32da916eb59123_refseq.bin added
32da9166ac3ba7_seq.bin added
32da9178e1d79e_versionInfo.json added
32da915baad572_salmon_index added
32da91277d605b_chrLength.txt added
32da912cf939ba_chrName.txt added
32da91120991_chrNameLength.txt added
32da911fa718c0_chrStart.txt added
32da9176d1ea6b_exonGeTrInfo.tab added
32da91527f5f49_exonInfo.tab added
32da9170e796a0_geneInfo.tab added
32da9130807caf_Genome added
32da911fabf535_genomeParameters.txt added
32da91409daf2d_Log.out added
32da912057dc14_SA added
32da91764a1ea6_SAindex added
32da914fc0d703_sjdbInfo.txt added
32da914d81949b_sjdbList.fromGTF.out.tab added
32da9126b39d86_sjdbList.out.tab added
32da91694d128f_transcriptInfo.tab added
32da915f587715_GRCh38.GENCODE.v42_100 added
32da912965bb2e_knownGene_hg38.sql added
32da915b03f735_knownGene_hg38.txt added
32da912242a72c_refGene_hg38.sql added
32da91d343a88_refGene_hg38.txt added
32da915f4a5201_knownGene_mm39.sql added
32da9163598a1a_knownGene_mm39.txt added
32da91f43c5f0_refGene_mm39.sql added
32da916fe59f17_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/RtmpVlApWt/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
24.935 1.568 29.270
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 9.023 | 0.383 | 9.456 | |
| dataSearch | 1.769 | 0.040 | 1.815 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 3.186 | 0.076 | 6.131 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.170 | 0.000 | 0.173 | |
| recipeLoad | 1.814 | 0.076 | 1.897 | |
| recipeMake | 0.001 | 0.000 | 0.000 | |
| recipeSearch | 0.761 | 0.008 | 0.770 | |
| recipeUpdate | 0 | 0 | 0 | |