Qian Liu
| Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 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 2025-08-30 12:06 -0400 (Sat, 30 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| 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 1742/2320 | 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: 2025-08-29 23:15:33 -0400 (Fri, 29 Aug 2025) |
| EndedAt: 2025-08-29 23:17:57 -0400 (Fri, 29 Aug 2025) |
| EllapsedTime: 144.4 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 (2025-06-13)
* 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 7.655 0.9 8.668
* 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 (2025-06-13) -- "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...
1817e62e62ac5_GRCh38.primary_assembly.genome.fa.1.bt2 added
1817e75021e3c_GRCh38.primary_assembly.genome.fa.2.bt2 added
1817e5e0f3127_GRCh38.primary_assembly.genome.fa.3.bt2 added
1817e376427af_GRCh38.primary_assembly.genome.fa.4.bt2 added
1817e10696e92_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1817e79da3ba8_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1817e6682d117_outfile.txt added
1817e166d7195_GRCh37_to_GRCh38.chain added
1817e6b3bf8b3_GRCh37_to_NCBI34.chain added
1817e2e44e6c5_GRCh37_to_NCBI35.chain added
1817e2d8aa73e_GRCh37_to_NCBI36.chain added
1817e69e9eecd_GRCh38_to_GRCh37.chain added
1817e7d3d0b0d_GRCh38_to_NCBI34.chain added
1817e32a0c2b7_GRCh38_to_NCBI35.chain added
1817e584f9658_GRCh38_to_NCBI36.chain added
1817e511798b3_NCBI34_to_GRCh37.chain added
1817e642a395c_NCBI34_to_GRCh38.chain added
1817e101bfa64_NCBI35_to_GRCh37.chain added
1817e1cd3c37f_NCBI35_to_GRCh38.chain added
1817e12c7d5a2_NCBI36_to_GRCh37.chain added
1817e7d9a884f_NCBI36_to_GRCh38.chain added
1817e2c6b3af5_GRCm38_to_NCBIM36.chain added
1817e33ebc19b_GRCm38_to_NCBIM37.chain added
1817e3af3c1be_NCBIM36_to_GRCm38.chain added
1817e5934bf2e_NCBIM37_to_GRCm38.chain added
1817e15f392c3_1000G_omni2.5.b37.vcf.gz added
1817e2a284b77_1000G_omni2.5.b37.vcf.gz.tbi added
1817e3b728740_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1817e5c0d993d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1817ec7a302_1000G_omni2.5.hg38.vcf.gz added
1817e329ed8b4_1000G_omni2.5.hg38.vcf.gz.tbi added
1817e5aa52b62_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1817e11c35d6c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1817e312a6690_af-only-gnomad.raw.sites.vcf added
1817e56b39127_af-only-gnomad.raw.sites.vcf.idx added
1817e26fec3e9_Mutect2-exome-panel.vcf.idx added
1817e1ff009ff_Mutect2-WGS-panel-b37.vcf added
1817e482054ba_Mutect2-WGS-panel-b37.vcf.idx added
1817e429aa454_small_exac_common_3.vcf added
1817e369aa8f5_small_exac_common_3.vcf.idx added
1817e63ca88d4_1000g_pon.hg38.vcf.gz added
1817e5dd497b_1000g_pon.hg38.vcf.gz.tbi added
1817e3032d3f_af-only-gnomad.hg38.vcf.gz added
1817e458f84a4_af-only-gnomad.hg38.vcf.gz.tbi added
1817e514d4ea9_small_exac_common_3.hg38.vcf.gz added
1817e2a6762f2_small_exac_common_3.hg38.vcf.gz.tbi added
1817e6991139d_gencode.v41.annotation.gtf added
1817e339ede90_gencode.v42.annotation.gtf added
1817e325da6a_gencode.vM30.annotation.gtf added
1817e2a2666c3_gencode.vM31.annotation.gtf added
1817e3f24a1d3_gencode.v41.transcripts.fa added
1817e7dfc4407_gencode.v41.transcripts.fa.fai added
1817e3cd6682f_gencode.v42.transcripts.fa added
1817e205204dd_gencode.v42.transcripts.fa.fai added
1817e68bd59be_gencode.vM30.pc_transcripts.fa added
1817e674efeaa_gencode.vM30.pc_transcripts.fa.fai added
1817e73317fe2_gencode.vM31.pc_transcripts.fa added
1817e36c30983_gencode.vM31.pc_transcripts.fa.fai added
1817e3ea5938b_GRCh38.primary_assembly.genome.fa.1.ht2 added
1817e6879aace_GRCh38.primary_assembly.genome.fa.2.ht2 added
1817ebbceff8_GRCh38.primary_assembly.genome.fa.3.ht2 added
1817e212e88cd_GRCh38.primary_assembly.genome.fa.4.ht2 added
1817e76175bbf_GRCh38.primary_assembly.genome.fa.5.ht2 added
1817e7788952a_GRCh38.primary_assembly.genome.fa.6.ht2 added
1817e27f935b5_GRCh38.primary_assembly.genome.fa.7.ht2 added
1817e5a351293_GRCh38.primary_assembly.genome.fa.8.ht2 added
1817e52569f29_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1817e34eb66fa_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1817e4ab5c23a_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1817e62e29427_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1817e96cbf29_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1817e427a2194_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1817e60329da4_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1817e1b0bab53_GRCh38.primary_assembly.genome.fa.fai added
1817e1b1ce404_GRCh38.primary_assembly.genome.fa.amb added
1817e5bdd084_GRCh38.primary_assembly.genome.fa.ann added
1817e70c48d0d_GRCh38.primary_assembly.genome.fa.bwt added
1817e78088a51_GRCh38.primary_assembly.genome.fa.pac added
1817e78b10967_GRCh38.primary_assembly.genome.fa.sa added
1817e2ee08718_GRCh38.primary_assembly.genome.fa added
1817e16c550b3_hs37d5.fa.fai added
1817e74352372_hs37d5.fa.amb added
1817e4caa4cf8_hs37d5.fa.ann added
1817e40a3551a_hs37d5.fa.bwt added
1817e23283f1d_hs37d5.fa.pac added
1817e27479af3_hs37d5.fa.sa added
1817e4e0ddbaa_hs37d5.fa added
1817e6fd09dee_complete_ref_lens.bin added
1817e6930ad9b_ctable.bin added
1817e7ad5d110_ctg_offsets.bin added
1817e6b90b070_duplicate_clusters.tsv added
1817e682fc03b_info.json added
1817e16f596ed_mphf.bin added
1817e5587ad61_pos.bin added
1817e3e87e725_pre_indexing.log added
1817e4c584e35_rank.bin added
1817e3976a0bb_ref_indexing.log added
1817e1b327276_refAccumLengths.bin added
1817ecf8aeed_reflengths.bin added
1817e1aa45042_refseq.bin added
1817e19912ab8_seq.bin added
1817e98ba325_versionInfo.json added
1817e2e83d708_salmon_index added
1817e519a6613_chrLength.txt added
1817e6fa3933f_chrName.txt added
1817e5c18465b_chrNameLength.txt added
1817e3db32f99_chrStart.txt added
1817e3efa0574_exonGeTrInfo.tab added
1817e107c22f9_exonInfo.tab added
1817e45dc11e3_geneInfo.tab added
1817e731a71e9_Genome added
1817e4d2cb308_genomeParameters.txt added
1817e319df9cd_Log.out added
1817e7a7b1b2d_SA added
1817e2835662d_SAindex added
1817e49c728fa_sjdbInfo.txt added
1817e32535aed_sjdbList.fromGTF.out.tab added
1817e7e76976a_sjdbList.out.tab added
1817e1bcef103_transcriptInfo.tab added
1817e2f310a38_GRCh38.GENCODE.v42_100 added
1817e3c95fabc_knownGene_hg38.sql added
1817e1a806bb7_knownGene_hg38.txt added
1817e651fc8f8_refGene_hg38.sql added
1817e9c345a6_refGene_hg38.txt added
1817e73119a4b_knownGene_mm39.sql added
1817e8a8ecf2_knownGene_mm39.txt added
1817ea5c084f_refGene_mm39.sql added
1817e20257fd9_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/RtmpyBwti7/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
21.592 2.387 25.066
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.655 | 0.900 | 8.668 | |
| dataSearch | 1.406 | 0.061 | 1.478 | |
| dataUpdate | 0.001 | 0.000 | 0.001 | |
| getCloudData | 2.930 | 0.167 | 4.473 | |
| getData | 0.000 | 0.001 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.152 | 0.012 | 0.167 | |
| recipeLoad | 1.554 | 0.099 | 1.667 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.644 | 0.042 | 0.690 | |
| recipeUpdate | 0 | 0 | 0 | |