Qian Liu
| Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 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 2025-10-18 12:04 -0400 (Sat, 18 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" | 4632 |
| 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. |
| Package: ReUseData |
| Version: 1.9.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.9.0.tar.gz |
| StartedAt: 2025-10-18 03:48:58 -0400 (Sat, 18 Oct 2025) |
| EndedAt: 2025-10-18 03:51:37 -0400 (Sat, 18 Oct 2025) |
| EllapsedTime: 159.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 5.615 0.214 5.831
* 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 re-building of vignette outputs ... OK
* 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/bbs-3.22-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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...
3ca763e4e80ea_GRCh38.primary_assembly.genome.fa.1.bt2 added
3ca764272a270_GRCh38.primary_assembly.genome.fa.2.bt2 added
3ca766413255a_GRCh38.primary_assembly.genome.fa.3.bt2 added
3ca765d268711_GRCh38.primary_assembly.genome.fa.4.bt2 added
3ca764598aace_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3ca765124ab3e_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3ca76d8767e6_outfile.txt added
3ca762759b524_GRCh37_to_GRCh38.chain added
3ca764cdcf45b_GRCh37_to_NCBI34.chain added
3ca762a251619_GRCh37_to_NCBI35.chain added
3ca76435071d0_GRCh37_to_NCBI36.chain added
3ca76bb2cff8_GRCh38_to_GRCh37.chain added
3ca76bd2beb9_GRCh38_to_NCBI34.chain added
3ca763fe932ce_GRCh38_to_NCBI35.chain added
3ca7677300d05_GRCh38_to_NCBI36.chain added
3ca767921a8e5_NCBI34_to_GRCh37.chain added
3ca761151570a_NCBI34_to_GRCh38.chain added
3ca765c8e3dc3_NCBI35_to_GRCh37.chain added
3ca761ba6c19c_NCBI35_to_GRCh38.chain added
3ca766592d894_NCBI36_to_GRCh37.chain added
3ca766d3f077d_NCBI36_to_GRCh38.chain added
3ca76ad58628_GRCm38_to_NCBIM36.chain added
3ca76dee5c1d_GRCm38_to_NCBIM37.chain added
3ca762215e0a2_NCBIM36_to_GRCm38.chain added
3ca767f3732d_NCBIM37_to_GRCm38.chain added
3ca7664d7a057_1000G_omni2.5.b37.vcf.gz added
3ca7613297899_1000G_omni2.5.b37.vcf.gz.tbi added
3ca762d907704_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3ca76694b7052_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3ca76e19b465_1000G_omni2.5.hg38.vcf.gz added
3ca762f302bf0_1000G_omni2.5.hg38.vcf.gz.tbi added
3ca762799f13c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3ca76508c56d5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3ca761343514a_af-only-gnomad.raw.sites.vcf added
3ca764c0784d_af-only-gnomad.raw.sites.vcf.idx added
3ca76162501a3_Mutect2-exome-panel.vcf.idx added
3ca766467fc88_Mutect2-WGS-panel-b37.vcf added
3ca761247e033_Mutect2-WGS-panel-b37.vcf.idx added
3ca763d7eb6c7_small_exac_common_3.vcf added
3ca763144f0e3_small_exac_common_3.vcf.idx added
3ca763c6cf64c_1000g_pon.hg38.vcf.gz added
3ca76cf2898_1000g_pon.hg38.vcf.gz.tbi added
3ca763cf7c0dc_af-only-gnomad.hg38.vcf.gz added
3ca76483fb506_af-only-gnomad.hg38.vcf.gz.tbi added
3ca7640b85b66_small_exac_common_3.hg38.vcf.gz added
3ca763427cde1_small_exac_common_3.hg38.vcf.gz.tbi added
3ca7641615deb_gencode.v41.annotation.gtf added
3ca765209b270_gencode.v42.annotation.gtf added
3ca7610b60ba4_gencode.vM30.annotation.gtf added
3ca765d081f87_gencode.vM31.annotation.gtf added
3ca76379c8b04_gencode.v41.transcripts.fa added
3ca767df51322_gencode.v41.transcripts.fa.fai added
3ca7667dda5af_gencode.v42.transcripts.fa added
3ca76458ae721_gencode.v42.transcripts.fa.fai added
3ca76200af3c4_gencode.vM30.pc_transcripts.fa added
3ca766fd118dc_gencode.vM30.pc_transcripts.fa.fai added
3ca762a628778_gencode.vM31.pc_transcripts.fa added
3ca7633346c5d_gencode.vM31.pc_transcripts.fa.fai added
3ca761d618fe0_GRCh38.primary_assembly.genome.fa.1.ht2 added
3ca7613adf7ca_GRCh38.primary_assembly.genome.fa.2.ht2 added
3ca76414e20c2_GRCh38.primary_assembly.genome.fa.3.ht2 added
3ca764c91bbd0_GRCh38.primary_assembly.genome.fa.4.ht2 added
3ca763b47e906_GRCh38.primary_assembly.genome.fa.5.ht2 added
3ca7611da7798_GRCh38.primary_assembly.genome.fa.6.ht2 added
3ca765fd50d1b_GRCh38.primary_assembly.genome.fa.7.ht2 added
3ca7640086153_GRCh38.primary_assembly.genome.fa.8.ht2 added
3ca7627ff793b_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3ca76443d09a3_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3ca7652504187_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3ca76657e3003_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3ca767581fa87_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3ca76ebd37d3_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3ca76664d589b_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3ca763279bb63_GRCh38.primary_assembly.genome.fa.fai added
3ca7656fcecd9_GRCh38.primary_assembly.genome.fa.amb added
3ca762705b401_GRCh38.primary_assembly.genome.fa.ann added
3ca7666a18944_GRCh38.primary_assembly.genome.fa.bwt added
3ca76185e4ac4_GRCh38.primary_assembly.genome.fa.pac added
3ca76790f6671_GRCh38.primary_assembly.genome.fa.sa added
3ca76775794e8_GRCh38.primary_assembly.genome.fa added
3ca7675666a4b_hs37d5.fa.fai added
3ca7630abf175_hs37d5.fa.amb added
3ca76754ca80a_hs37d5.fa.ann added
3ca765d440ffa_hs37d5.fa.bwt added
3ca767636d896_hs37d5.fa.pac added
3ca7615579bce_hs37d5.fa.sa added
3ca764d1528d6_hs37d5.fa added
3ca762099600e_complete_ref_lens.bin added
3ca76488c082c_ctable.bin added
3ca766a76b8b6_ctg_offsets.bin added
3ca76344757d9_duplicate_clusters.tsv added
3ca769da28ee_info.json added
3ca7637087487_mphf.bin added
3ca766f8f40df_pos.bin added
3ca761bb4a086_pre_indexing.log added
3ca7616dd81a2_rank.bin added
3ca762f97a233_ref_indexing.log added
3ca7643b419c2_refAccumLengths.bin added
3ca765b1a8b45_reflengths.bin added
3ca761e7e3ba_refseq.bin added
3ca76293249c5_seq.bin added
3ca76509c85cc_versionInfo.json added
3ca7610a51b8d_salmon_index added
3ca76f7fa260_chrLength.txt added
3ca76316412f_chrName.txt added
3ca7667a20867_chrNameLength.txt added
3ca7636855661_chrStart.txt added
3ca7669b7ca73_exonGeTrInfo.tab added
3ca76532b_exonInfo.tab added
3ca762f94bcd2_geneInfo.tab added
3ca76610f5f5c_Genome added
3ca767566bd77_genomeParameters.txt added
3ca766040ae47_Log.out added
3ca76565c0766_SA added
3ca7652aacd71_SAindex added
3ca76567786dd_sjdbInfo.txt added
3ca766bb3a335_sjdbList.fromGTF.out.tab added
3ca761fbff648_sjdbList.out.tab added
3ca767710e6eb_transcriptInfo.tab added
3ca76343fab61_GRCh38.GENCODE.v42_100 added
3ca76a36aefe_knownGene_hg38.sql added
3ca762b583ec4_knownGene_hg38.txt added
3ca763e19d44f_refGene_hg38.sql added
3ca76413f2385_refGene_hg38.txt added
3ca761ae77fa4_knownGene_mm39.sql added
3ca7659ce74d6_knownGene_mm39.txt added
3ca76581ca527_refGene_mm39.sql added
3ca764a7f21d7_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:
/tmp/Rtmp6N9D1H/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
17.594 1.018 19.110
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.615 | 0.214 | 5.831 | |
| dataSearch | 1.087 | 0.004 | 1.091 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.706 | 0.123 | 3.977 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.001 | 0.001 | |
| recipeHub-class | 0.119 | 0.004 | 0.123 | |
| recipeLoad | 1.221 | 0.053 | 1.275 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.518 | 0.041 | 0.559 | |
| recipeUpdate | 0 | 0 | 0 | |