Qian Liu
| Snapshot Date: 2025-10-10 13:45 -0400 (Fri, 10 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 2025-10-11 12:05 -0400 (Sat, 11 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" | 4864 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
| 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 1762/2346 | 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. |
| Package: ReUseData |
| Version: 1.9.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.9.0.tar.gz |
| StartedAt: 2025-10-11 00:29:57 -0400 (Sat, 11 Oct 2025) |
| EndedAt: 2025-10-11 00:32:30 -0400 (Sat, 11 Oct 2025) |
| EllapsedTime: 153.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 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 7.62 0.959 8.804
* 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
‘/Users/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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...
2abc4800f3be_GRCh38.primary_assembly.genome.fa.1.bt2 added
2abc368263e0_GRCh38.primary_assembly.genome.fa.2.bt2 added
2abc2a6b2315_GRCh38.primary_assembly.genome.fa.3.bt2 added
2abc5fcc4d74_GRCh38.primary_assembly.genome.fa.4.bt2 added
2abc5df12bce_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2abc4731191_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2abc1e8648df_outfile.txt added
2abc21a3821_GRCh37_to_GRCh38.chain added
2abc75aff9b_GRCh37_to_NCBI34.chain added
2abc67431ce2_GRCh37_to_NCBI35.chain added
2abc671d6e64_GRCh37_to_NCBI36.chain added
2abc3d3a9c1f_GRCh38_to_GRCh37.chain added
2abc52dfd6a0_GRCh38_to_NCBI34.chain added
2abc6583cce1_GRCh38_to_NCBI35.chain added
2abc2ffffbd8_GRCh38_to_NCBI36.chain added
2abc4eef3a86_NCBI34_to_GRCh37.chain added
2abc3beb5be6_NCBI34_to_GRCh38.chain added
2abc58de77c5_NCBI35_to_GRCh37.chain added
2abc75895417_NCBI35_to_GRCh38.chain added
2abcaefee4a_NCBI36_to_GRCh37.chain added
2abce0541e2_NCBI36_to_GRCh38.chain added
2abc7b28639e_GRCm38_to_NCBIM36.chain added
2abc18a4593d_GRCm38_to_NCBIM37.chain added
2abc4ddec06e_NCBIM36_to_GRCm38.chain added
2abc5b2b9db2_NCBIM37_to_GRCm38.chain added
2abcc7e3fe1_1000G_omni2.5.b37.vcf.gz added
2abc3493d32f_1000G_omni2.5.b37.vcf.gz.tbi added
2abc550dcda0_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2abc7d36eeff_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2abc2184e792_1000G_omni2.5.hg38.vcf.gz added
2abc1c7f336f_1000G_omni2.5.hg38.vcf.gz.tbi added
2abc6309cb06_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2abc17f029b6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2abc18427801_af-only-gnomad.raw.sites.vcf added
2abc33d49618_af-only-gnomad.raw.sites.vcf.idx added
2abc49ca1c3d_Mutect2-exome-panel.vcf.idx added
2abc74040ea3_Mutect2-WGS-panel-b37.vcf added
2abc365d2ad6_Mutect2-WGS-panel-b37.vcf.idx added
2abc1ea7637c_small_exac_common_3.vcf added
2abc7f74719c_small_exac_common_3.vcf.idx added
2abc35cefa23_1000g_pon.hg38.vcf.gz added
2abc27882b6e_1000g_pon.hg38.vcf.gz.tbi added
2abc5cdb5708_af-only-gnomad.hg38.vcf.gz added
2abc442efdd8_af-only-gnomad.hg38.vcf.gz.tbi added
2abc691b92e0_small_exac_common_3.hg38.vcf.gz added
2abc1147e609_small_exac_common_3.hg38.vcf.gz.tbi added
2abc74f61bc_gencode.v41.annotation.gtf added
2abc6c998163_gencode.v42.annotation.gtf added
2abc51fdc248_gencode.vM30.annotation.gtf added
2abc6ade2f05_gencode.vM31.annotation.gtf added
2abc20e12813_gencode.v41.transcripts.fa added
2abc1e0e0842_gencode.v41.transcripts.fa.fai added
2abc2b403478_gencode.v42.transcripts.fa added
2abc434c877_gencode.v42.transcripts.fa.fai added
2abc2554fec9_gencode.vM30.pc_transcripts.fa added
2abc6f235144_gencode.vM30.pc_transcripts.fa.fai added
2abc77ac805c_gencode.vM31.pc_transcripts.fa added
2abc5e1f5565_gencode.vM31.pc_transcripts.fa.fai added
2abc5b1f8a29_GRCh38.primary_assembly.genome.fa.1.ht2 added
2abc73a7b87b_GRCh38.primary_assembly.genome.fa.2.ht2 added
2abc840ce8f_GRCh38.primary_assembly.genome.fa.3.ht2 added
2abc56b91284_GRCh38.primary_assembly.genome.fa.4.ht2 added
2abc106ec497_GRCh38.primary_assembly.genome.fa.5.ht2 added
2abc582c9dee_GRCh38.primary_assembly.genome.fa.6.ht2 added
2abc5934a17b_GRCh38.primary_assembly.genome.fa.7.ht2 added
2abce55bffe_GRCh38.primary_assembly.genome.fa.8.ht2 added
2abc1fafc40c_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2abc4c700014_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2abc4d154840_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2abc303a8949_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2abc530b305b_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2abc393d0f5_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2abc5d7b86a8_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2abc58c5af8a_GRCh38.primary_assembly.genome.fa.fai added
2abc1a87ba8e_GRCh38.primary_assembly.genome.fa.amb added
2abc44e8ce3d_GRCh38.primary_assembly.genome.fa.ann added
2abc103c2a23_GRCh38.primary_assembly.genome.fa.bwt added
2abc5df26828_GRCh38.primary_assembly.genome.fa.pac added
2abc55944a47_GRCh38.primary_assembly.genome.fa.sa added
2abc7a98a735_GRCh38.primary_assembly.genome.fa added
2abc3c09c774_hs37d5.fa.fai added
2abc2605af77_hs37d5.fa.amb added
2abc3f42c121_hs37d5.fa.ann added
2abc37957df9_hs37d5.fa.bwt added
2abc378182f1_hs37d5.fa.pac added
2abc17bbb8af_hs37d5.fa.sa added
2abc2559f555_hs37d5.fa added
2abc34f9b29b_complete_ref_lens.bin added
2abc753cf948_ctable.bin added
2abc76122219_ctg_offsets.bin added
2abc207cd3de_duplicate_clusters.tsv added
2abc6339a47b_info.json added
2abc5d5dba21_mphf.bin added
2abc3466fc6a_pos.bin added
2abc5545ae06_pre_indexing.log added
2abc51a437a6_rank.bin added
2abc74419d29_ref_indexing.log added
2abc7fb52a5f_refAccumLengths.bin added
2abc4ef10479_reflengths.bin added
2abc315ccc6c_refseq.bin added
2abc4370dfc5_seq.bin added
2abc2773211a_versionInfo.json added
2abc77824631_salmon_index added
2abc9ce7843_chrLength.txt added
2abc52397bbc_chrName.txt added
2abc3bea9dd0_chrNameLength.txt added
2abc281ee16b_chrStart.txt added
2abc3614c61_exonGeTrInfo.tab added
2abc68dd7602_exonInfo.tab added
2abc236eb317_geneInfo.tab added
2abc38afbd2d_Genome added
2abc19acf26e_genomeParameters.txt added
2abc296020ed_Log.out added
2abc6611bcd3_SA added
2abc1683f4ff_SAindex added
2abc31499ce5_sjdbInfo.txt added
2abc57db97aa_sjdbList.fromGTF.out.tab added
2abc11c246f6_sjdbList.out.tab added
2abc69c0c995_transcriptInfo.tab added
2abc6ff28b70_GRCh38.GENCODE.v42_100 added
2abc1ca09f7b_knownGene_hg38.sql added
2abc754652eb_knownGene_hg38.txt added
2abc5bedfe73_refGene_hg38.sql added
2abc65dc5f2b_refGene_hg38.txt added
2abc66ec344b_knownGene_mm39.sql added
2abc1d5d5cb7_knownGene_mm39.txt added
2abc5c720170_refGene_mm39.sql added
2abc40bc8f7a_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/RtmpIs9hpA/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
22.197 2.511 25.785
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.620 | 0.959 | 8.804 | |
| dataSearch | 1.327 | 0.063 | 1.405 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.765 | 0.180 | 4.113 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.151 | 0.016 | 0.171 | |
| recipeLoad | 1.510 | 0.097 | 1.623 | |
| recipeMake | 0.001 | 0.001 | 0.001 | |
| recipeSearch | 0.634 | 0.042 | 0.679 | |
| recipeUpdate | 0 | 0 | 0 | |