Qian Liu
| Snapshot Date: 2025-10-07 13:45 -0400 (Tue, 07 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 2025-10-08 12:54 -0400 (Wed, 08 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" | 4854 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4641 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4586 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4584 |
| 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 1757/2341 | 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: 2025-10-07 11:19:54 -0000 (Tue, 07 Oct 2025) |
| EndedAt: 2025-10-07 11:22:31 -0000 (Tue, 07 Oct 2025) |
| EllapsedTime: 156.2 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 8.562 0.359 8.960
getCloudData 3.542 0.188 6.708
* 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...
1b8b49594b1557_GRCh38.primary_assembly.genome.fa.1.bt2 added
1b8b491937d2d2_GRCh38.primary_assembly.genome.fa.2.bt2 added
1b8b4974e014f3_GRCh38.primary_assembly.genome.fa.3.bt2 added
1b8b492e120b31_GRCh38.primary_assembly.genome.fa.4.bt2 added
1b8b492852d8e3_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1b8b49354d5e74_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1b8b492c8e50d5_outfile.txt added
1b8b4967c6f5c_GRCh37_to_GRCh38.chain added
1b8b4971d49725_GRCh37_to_NCBI34.chain added
1b8b4921419316_GRCh37_to_NCBI35.chain added
1b8b4966a66727_GRCh37_to_NCBI36.chain added
1b8b4933f5072c_GRCh38_to_GRCh37.chain added
1b8b494a0eb368_GRCh38_to_NCBI34.chain added
1b8b4954681ccd_GRCh38_to_NCBI35.chain added
1b8b49718d9c6e_GRCh38_to_NCBI36.chain added
1b8b49673e036_NCBI34_to_GRCh37.chain added
1b8b49743e43f8_NCBI34_to_GRCh38.chain added
1b8b4913042f2b_NCBI35_to_GRCh37.chain added
1b8b494f72e048_NCBI35_to_GRCh38.chain added
1b8b496f8c862d_NCBI36_to_GRCh37.chain added
1b8b497d111e1c_NCBI36_to_GRCh38.chain added
1b8b495b2e9201_GRCm38_to_NCBIM36.chain added
1b8b494f8fd2f2_GRCm38_to_NCBIM37.chain added
1b8b49452acb37_NCBIM36_to_GRCm38.chain added
1b8b494f55722f_NCBIM37_to_GRCm38.chain added
1b8b496d34d025_1000G_omni2.5.b37.vcf.gz added
1b8b4932d1fdcc_1000G_omni2.5.b37.vcf.gz.tbi added
1b8b49578d1825_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1b8b494fb56cd8_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1b8b496f19e3d_1000G_omni2.5.hg38.vcf.gz added
1b8b4952ed0ef_1000G_omni2.5.hg38.vcf.gz.tbi added
1b8b4929008230_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1b8b492029710f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1b8b497a0ee5e2_af-only-gnomad.raw.sites.vcf added
1b8b4957128d61_af-only-gnomad.raw.sites.vcf.idx added
1b8b49487c49f3_Mutect2-exome-panel.vcf.idx added
1b8b492f5c4456_Mutect2-WGS-panel-b37.vcf added
1b8b493a0de36_Mutect2-WGS-panel-b37.vcf.idx added
1b8b494ef8b94f_small_exac_common_3.vcf added
1b8b492130db7b_small_exac_common_3.vcf.idx added
1b8b4924e2714c_1000g_pon.hg38.vcf.gz added
1b8b49359f2076_1000g_pon.hg38.vcf.gz.tbi added
1b8b495525e2a7_af-only-gnomad.hg38.vcf.gz added
1b8b496ef124b5_af-only-gnomad.hg38.vcf.gz.tbi added
1b8b49a073d43_small_exac_common_3.hg38.vcf.gz added
1b8b4946b37f16_small_exac_common_3.hg38.vcf.gz.tbi added
1b8b49756504eb_gencode.v41.annotation.gtf added
1b8b497e45813b_gencode.v42.annotation.gtf added
1b8b4959b7ae41_gencode.vM30.annotation.gtf added
1b8b4944d7e534_gencode.vM31.annotation.gtf added
1b8b496dd20769_gencode.v41.transcripts.fa added
1b8b4956c8cc5d_gencode.v41.transcripts.fa.fai added
1b8b4920067735_gencode.v42.transcripts.fa added
1b8b493d61da5b_gencode.v42.transcripts.fa.fai added
1b8b491bf39794_gencode.vM30.pc_transcripts.fa added
1b8b496f5be965_gencode.vM30.pc_transcripts.fa.fai added
1b8b492a96aa80_gencode.vM31.pc_transcripts.fa added
1b8b494ec59560_gencode.vM31.pc_transcripts.fa.fai added
1b8b4946e9018a_GRCh38.primary_assembly.genome.fa.1.ht2 added
1b8b497a4c1758_GRCh38.primary_assembly.genome.fa.2.ht2 added
1b8b4955b7339d_GRCh38.primary_assembly.genome.fa.3.ht2 added
1b8b494c17d279_GRCh38.primary_assembly.genome.fa.4.ht2 added
1b8b49234c9988_GRCh38.primary_assembly.genome.fa.5.ht2 added
1b8b4975e0a4ad_GRCh38.primary_assembly.genome.fa.6.ht2 added
1b8b494626b85c_GRCh38.primary_assembly.genome.fa.7.ht2 added
1b8b497a5f26e9_GRCh38.primary_assembly.genome.fa.8.ht2 added
1b8b493e5ceea0_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1b8b497582fcb2_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1b8b497e000520_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1b8b49d55a7ef_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1b8b4916b3d82e_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1b8b4922e2766c_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1b8b4942f4c865_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1b8b496bd9bad5_GRCh38.primary_assembly.genome.fa.fai added
1b8b4911d39b21_GRCh38.primary_assembly.genome.fa.amb added
1b8b494cfc05a8_GRCh38.primary_assembly.genome.fa.ann added
1b8b49328d39eb_GRCh38.primary_assembly.genome.fa.bwt added
1b8b49738a00d_GRCh38.primary_assembly.genome.fa.pac added
1b8b494b4186e3_GRCh38.primary_assembly.genome.fa.sa added
1b8b49c44e82d_GRCh38.primary_assembly.genome.fa added
1b8b494c108541_hs37d5.fa.fai added
1b8b4939138e4c_hs37d5.fa.amb added
1b8b49630db48a_hs37d5.fa.ann added
1b8b496c16fc76_hs37d5.fa.bwt added
1b8b49767568a7_hs37d5.fa.pac added
1b8b497f014c1f_hs37d5.fa.sa added
1b8b495b72e5db_hs37d5.fa added
1b8b49210c1327_complete_ref_lens.bin added
1b8b494dc6e17f_ctable.bin added
1b8b49225be766_ctg_offsets.bin added
1b8b491b582a80_duplicate_clusters.tsv added
1b8b49237e151d_info.json added
1b8b496e73b9df_mphf.bin added
1b8b493ea4c408_pos.bin added
1b8b49195eb9ca_pre_indexing.log added
1b8b49349a723b_rank.bin added
1b8b493903eaf2_ref_indexing.log added
1b8b4957bba86a_refAccumLengths.bin added
1b8b492a1d6eee_reflengths.bin added
1b8b493703f012_refseq.bin added
1b8b4965115059_seq.bin added
1b8b4940d1471c_versionInfo.json added
1b8b4959e6667e_salmon_index added
1b8b49280618be_chrLength.txt added
1b8b492cab01f1_chrName.txt added
1b8b496bba01a0_chrNameLength.txt added
1b8b4975021e66_chrStart.txt added
1b8b495f383bdd_exonGeTrInfo.tab added
1b8b4972f2a1ad_exonInfo.tab added
1b8b494043a549_geneInfo.tab added
1b8b496b7d240a_Genome added
1b8b493f0326ee_genomeParameters.txt added
1b8b4979573396_Log.out added
1b8b494e8ad894_SA added
1b8b492b1a2364_SAindex added
1b8b496fcc9c3d_sjdbInfo.txt added
1b8b494d8c24b3_sjdbList.fromGTF.out.tab added
1b8b4968d0940_sjdbList.out.tab added
1b8b4910d8af65_transcriptInfo.tab added
1b8b491b530633_GRCh38.GENCODE.v42_100 added
1b8b4928e8f0a6_knownGene_hg38.sql added
1b8b492c30d9e5_knownGene_hg38.txt added
1b8b493ed11b50_refGene_hg38.sql added
1b8b49175caa85_refGene_hg38.txt added
1b8b496ad59ded_knownGene_mm39.sql added
1b8b49582fd51a_knownGene_mm39.txt added
1b8b494bf71cc1_refGene_mm39.sql added
1b8b4923d988df_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/Rtmpdyaros/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
24.736 1.439 28.852
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 8.562 | 0.359 | 8.960 | |
| dataSearch | 1.634 | 0.016 | 1.655 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 3.542 | 0.188 | 6.708 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.200 | 0.012 | 0.215 | |
| recipeLoad | 1.953 | 0.104 | 2.068 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.915 | 0.056 | 0.974 | |
| recipeUpdate | 0 | 0 | 0 | |