Qian Liu
| Snapshot Date: 2025-09-14 13:45 -0400 (Sun, 14 Sep 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 2025-09-15 12:07 -0400 (Mon, 15 Sep 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" | 4719 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4538 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4522 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4543 |
| 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 1747/2327 | 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 12.7.1 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: 2025-09-12 11:03:46 -0000 (Fri, 12 Sep 2025) |
| EndedAt: 2025-09-12 11:06:50 -0000 (Fri, 12 Sep 2025) |
| EllapsedTime: 184.2 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 8.670 0.315 9.537
getCloudData 3.266 0.081 6.736
* 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...
2827611bfe0efc_GRCh38.primary_assembly.genome.fa.1.bt2 added
28276124738497_GRCh38.primary_assembly.genome.fa.2.bt2 added
2827614dffeae6_GRCh38.primary_assembly.genome.fa.3.bt2 added
2827614baa8298_GRCh38.primary_assembly.genome.fa.4.bt2 added
282761311c3412_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2827612468f1da_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2827615a23842c_outfile.txt added
2827617adb6da2_GRCh37_to_GRCh38.chain added
282761246d25a4_GRCh37_to_NCBI34.chain added
28276151a7bb7d_GRCh37_to_NCBI35.chain added
28276158a07a2d_GRCh37_to_NCBI36.chain added
2827611dbc15f3_GRCh38_to_GRCh37.chain added
2827617a160e7f_GRCh38_to_NCBI34.chain added
2827615dc4e03c_GRCh38_to_NCBI35.chain added
2827611aac25c2_GRCh38_to_NCBI36.chain added
28276165e5904c_NCBI34_to_GRCh37.chain added
2827613b5b2a12_NCBI34_to_GRCh38.chain added
282761748de39f_NCBI35_to_GRCh37.chain added
282761342dbc72_NCBI35_to_GRCh38.chain added
28276165b445df_NCBI36_to_GRCh37.chain added
2827617338c89a_NCBI36_to_GRCh38.chain added
28276129c99b1b_GRCm38_to_NCBIM36.chain added
2827615e44a287_GRCm38_to_NCBIM37.chain added
2827614c76ccc6_NCBIM36_to_GRCm38.chain added
28276166f6517e_NCBIM37_to_GRCm38.chain added
28276134a6914c_1000G_omni2.5.b37.vcf.gz added
282761786b770e_1000G_omni2.5.b37.vcf.gz.tbi added
282761311d4255_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
282761710cd19d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
28276152dd4985_1000G_omni2.5.hg38.vcf.gz added
2827616f4eb8d2_1000G_omni2.5.hg38.vcf.gz.tbi added
282761d0ae099_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2827617750ce1d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2827613d4ea3b8_af-only-gnomad.raw.sites.vcf added
28276158b56331_af-only-gnomad.raw.sites.vcf.idx added
282761286d022f_Mutect2-exome-panel.vcf.idx added
28276161b79593_Mutect2-WGS-panel-b37.vcf added
28276132d8e75d_Mutect2-WGS-panel-b37.vcf.idx added
28276123486fd1_small_exac_common_3.vcf added
282761624bb37_small_exac_common_3.vcf.idx added
282761480a2da_1000g_pon.hg38.vcf.gz added
2827617be8e9ff_1000g_pon.hg38.vcf.gz.tbi added
28276123e0d12a_af-only-gnomad.hg38.vcf.gz added
2827617e96b159_af-only-gnomad.hg38.vcf.gz.tbi added
28276159adca3b_small_exac_common_3.hg38.vcf.gz added
2827613e8cf6ed_small_exac_common_3.hg38.vcf.gz.tbi added
282761647c41a5_gencode.v41.annotation.gtf added
2827611508f44d_gencode.v42.annotation.gtf added
282761331ada8c_gencode.vM30.annotation.gtf added
28276118a9fe17_gencode.vM31.annotation.gtf added
2827617abd3a2d_gencode.v41.transcripts.fa added
2827612653a327_gencode.v41.transcripts.fa.fai added
28276142739933_gencode.v42.transcripts.fa added
2827615901dcb4_gencode.v42.transcripts.fa.fai added
28276172ca6fed_gencode.vM30.pc_transcripts.fa added
2827612969eab1_gencode.vM30.pc_transcripts.fa.fai added
282761da86e00_gencode.vM31.pc_transcripts.fa added
2827616b35e6fc_gencode.vM31.pc_transcripts.fa.fai added
2827615a872d06_GRCh38.primary_assembly.genome.fa.1.ht2 added
2827617eb53f9d_GRCh38.primary_assembly.genome.fa.2.ht2 added
2827613e133081_GRCh38.primary_assembly.genome.fa.3.ht2 added
28276149d5e5d8_GRCh38.primary_assembly.genome.fa.4.ht2 added
282761bc02036_GRCh38.primary_assembly.genome.fa.5.ht2 added
2827613563fe9e_GRCh38.primary_assembly.genome.fa.6.ht2 added
2827617248990_GRCh38.primary_assembly.genome.fa.7.ht2 added
28276164758367_GRCh38.primary_assembly.genome.fa.8.ht2 added
2827615dd100cd_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
28276168dc1f23_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
282761174e6ac4_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
282761119709f_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2827616f00da5b_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2827611bcf0d9e_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2827617d025a9e_GRCh38_full_analysis_set_plus_decoy_hla.fa added
28276112e1ab85_GRCh38.primary_assembly.genome.fa.fai added
2827611a65bef8_GRCh38.primary_assembly.genome.fa.amb added
28276156b024d9_GRCh38.primary_assembly.genome.fa.ann added
282761516ea272_GRCh38.primary_assembly.genome.fa.bwt added
2827617ee2009d_GRCh38.primary_assembly.genome.fa.pac added
2827616bb91927_GRCh38.primary_assembly.genome.fa.sa added
2827614897cff_GRCh38.primary_assembly.genome.fa added
282761178bfeb5_hs37d5.fa.fai added
28276166765354_hs37d5.fa.amb added
2827612add2026_hs37d5.fa.ann added
28276159ff97e8_hs37d5.fa.bwt added
2827613f783008_hs37d5.fa.pac added
2827611da79013_hs37d5.fa.sa added
2827613698299_hs37d5.fa added
2827614d209e08_complete_ref_lens.bin added
2827618dd770f_ctable.bin added
2827615df0af9f_ctg_offsets.bin added
2827614bd5dda6_duplicate_clusters.tsv added
28276146f0a791_info.json added
28276127c69577_mphf.bin added
2827615795fddc_pos.bin added
2827617c54a62f_pre_indexing.log added
2827612eeb1f07_rank.bin added
2827613c0b8144_ref_indexing.log added
2827615a25a6fd_refAccumLengths.bin added
28276117c73e2b_reflengths.bin added
2827615359ec08_refseq.bin added
2827615b3f179c_seq.bin added
2827616c81886_versionInfo.json added
2827616f28f9a7_salmon_index added
2827615841723a_chrLength.txt added
28276119a9c40b_chrName.txt added
28276198eb89f_chrNameLength.txt added
2827612ef19713_chrStart.txt added
2827616b18667e_exonGeTrInfo.tab added
282761870b93c_exonInfo.tab added
2827611aaab03a_geneInfo.tab added
2827616fa1e37d_Genome added
2827611ffcb7f1_genomeParameters.txt added
282761121038e_Log.out added
2827611a7f03a3_SA added
28276179fc4fd9_SAindex added
28276140993396_sjdbInfo.txt added
282761382693b6_sjdbList.fromGTF.out.tab added
2827617d65d272_sjdbList.out.tab added
282761db9d19f_transcriptInfo.tab added
28276141040ac6_GRCh38.GENCODE.v42_100 added
2827615b568211_knownGene_hg38.sql added
282761598faf45_knownGene_hg38.txt added
2827617f4b257_refGene_hg38.sql added
28276131d1788_refGene_hg38.txt added
2827613125ad21_knownGene_mm39.sql added
2827614495886_knownGene_mm39.txt added
28276132083690_refGene_mm39.sql added
2827616d312e65_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/Rtmp6RRcus/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
24.989 1.126 32.540
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 8.670 | 0.315 | 9.537 | |
| dataSearch | 1.578 | 0.023 | 1.696 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 3.266 | 0.081 | 6.736 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.165 | 0.008 | 0.182 | |
| recipeLoad | 1.892 | 0.055 | 2.191 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.789 | 0.004 | 0.799 | |
| recipeUpdate | 0 | 0 | 0 | |