Qian Liu
| Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 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 2025-08-09 12:10 -0400 (Sat, 09 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| 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 1739/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.9.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | 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: 2025-08-08 21:11:16 -0400 (Fri, 08 Aug 2025) |
| EndedAt: 2025-08-08 21:12:04 -0400 (Fri, 08 Aug 2025) |
| EllapsedTime: 48.5 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 (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* 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
* 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-arm64/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 (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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...
15dc73d287132_GRCh38.primary_assembly.genome.fa.1.bt2 added
15dc72a1fa8fc_GRCh38.primary_assembly.genome.fa.2.bt2 added
15dc748f4dff_GRCh38.primary_assembly.genome.fa.3.bt2 added
15dc75c49a2af_GRCh38.primary_assembly.genome.fa.4.bt2 added
15dc76657be7e_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
15dc7a9b76b0_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
15dc7648d2240_outfile.txt added
15dc76dc3cb52_GRCh37_to_GRCh38.chain added
15dc75159acca_GRCh37_to_NCBI34.chain added
15dc7565f2b7f_GRCh37_to_NCBI35.chain added
15dc7220cb26_GRCh37_to_NCBI36.chain added
15dc736f92ce1_GRCh38_to_GRCh37.chain added
15dc720f183f9_GRCh38_to_NCBI34.chain added
15dc7500f6154_GRCh38_to_NCBI35.chain added
15dc721befadc_GRCh38_to_NCBI36.chain added
15dc714792d3_NCBI34_to_GRCh37.chain added
15dc71f85b4d_NCBI34_to_GRCh38.chain added
15dc758321d3d_NCBI35_to_GRCh37.chain added
15dc7421dbd07_NCBI35_to_GRCh38.chain added
15dc72e65387a_NCBI36_to_GRCh37.chain added
15dc7775ee961_NCBI36_to_GRCh38.chain added
15dc7782c1c80_GRCm38_to_NCBIM36.chain added
15dc718035523_GRCm38_to_NCBIM37.chain added
15dc72ca7926_NCBIM36_to_GRCm38.chain added
15dc73ad7af38_NCBIM37_to_GRCm38.chain added
15dc72630a3b6_1000G_omni2.5.b37.vcf.gz added
15dc7434c1550_1000G_omni2.5.b37.vcf.gz.tbi added
15dc7380b59b4_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
15dc7712e552a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
15dc718d97273_1000G_omni2.5.hg38.vcf.gz added
15dc76be8e8c3_1000G_omni2.5.hg38.vcf.gz.tbi added
15dc7809918e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
15dc72c3305c1_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
15dc749bed892_af-only-gnomad.raw.sites.vcf added
15dc7107c7f11_af-only-gnomad.raw.sites.vcf.idx added
15dc75d7a3d8b_Mutect2-exome-panel.vcf.idx added
15dc745ea09f_Mutect2-WGS-panel-b37.vcf added
15dc7608328f6_Mutect2-WGS-panel-b37.vcf.idx added
15dc742f65ffa_small_exac_common_3.vcf added
15dc73d17386e_small_exac_common_3.vcf.idx added
15dc73f79dd17_1000g_pon.hg38.vcf.gz added
15dc759a2318f_1000g_pon.hg38.vcf.gz.tbi added
15dc72763d142_af-only-gnomad.hg38.vcf.gz added
15dc7a3f5842_af-only-gnomad.hg38.vcf.gz.tbi added
15dc744bb5a4f_small_exac_common_3.hg38.vcf.gz added
15dc768261bc9_small_exac_common_3.hg38.vcf.gz.tbi added
15dc71dea5e8a_gencode.v41.annotation.gtf added
15dc75e4c55e_gencode.v42.annotation.gtf added
15dc76e59a157_gencode.vM30.annotation.gtf added
15dc73e6f8f5a_gencode.vM31.annotation.gtf added
15dc7e2c7dbc_gencode.v41.transcripts.fa added
15dc7af2c8e9_gencode.v41.transcripts.fa.fai added
15dc749643e9c_gencode.v42.transcripts.fa added
15dc7544a9968_gencode.v42.transcripts.fa.fai added
15dc76d9da613_gencode.vM30.pc_transcripts.fa added
15dc7902619e_gencode.vM30.pc_transcripts.fa.fai added
15dc77b56d0b0_gencode.vM31.pc_transcripts.fa added
15dc79f1213_gencode.vM31.pc_transcripts.fa.fai added
15dc74b5b9db6_GRCh38.primary_assembly.genome.fa.1.ht2 added
15dc76bcf3e60_GRCh38.primary_assembly.genome.fa.2.ht2 added
15dc7730847eb_GRCh38.primary_assembly.genome.fa.3.ht2 added
15dc724a9d04d_GRCh38.primary_assembly.genome.fa.4.ht2 added
15dc78aa8209_GRCh38.primary_assembly.genome.fa.5.ht2 added
15dc7723f2150_GRCh38.primary_assembly.genome.fa.6.ht2 added
15dc7ea445c9_GRCh38.primary_assembly.genome.fa.7.ht2 added
15dc742e196a1_GRCh38.primary_assembly.genome.fa.8.ht2 added
15dc768684654_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
15dc715e16a59_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
15dc720d0448_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
15dc724941405_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
15dc775ae6705_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
15dc7cedb59f_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
15dc74a2ee05a_GRCh38_full_analysis_set_plus_decoy_hla.fa added
15dc74b8b5ac2_GRCh38.primary_assembly.genome.fa.fai added
15dc729f39d4d_GRCh38.primary_assembly.genome.fa.amb added
15dc738dc3fbf_GRCh38.primary_assembly.genome.fa.ann added
15dc73dd31c3_GRCh38.primary_assembly.genome.fa.bwt added
15dc72eedfb30_GRCh38.primary_assembly.genome.fa.pac added
15dc7a062462_GRCh38.primary_assembly.genome.fa.sa added
15dc7193ea312_GRCh38.primary_assembly.genome.fa added
15dc75f43ffb0_hs37d5.fa.fai added
15dc76947acac_hs37d5.fa.amb added
15dc760998633_hs37d5.fa.ann added
15dc77f39afd0_hs37d5.fa.bwt added
15dc72445c1f1_hs37d5.fa.pac added
15dc75fbfc7d1_hs37d5.fa.sa added
15dc727d79b73_hs37d5.fa added
15dc73c1eaf74_complete_ref_lens.bin added
15dc72910782_ctable.bin added
15dc77f83e91e_ctg_offsets.bin added
15dc72d3df1f9_duplicate_clusters.tsv added
15dc73dd929a3_info.json added
15dc77c3cac0d_mphf.bin added
15dc77343c933_pos.bin added
15dc7674e6e63_pre_indexing.log added
15dc74e315a91_rank.bin added
15dc7a310db2_ref_indexing.log added
15dc71a7a2658_refAccumLengths.bin added
15dc7496b68fc_reflengths.bin added
15dc72ab99e0c_refseq.bin added
15dc7373bbe_seq.bin added
15dc72a33370e_versionInfo.json added
15dc78638dc7_salmon_index added
15dc73ff1081e_chrLength.txt added
15dc7694c0a5d_chrName.txt added
15dc77f3c95ac_chrNameLength.txt added
15dc762869076_chrStart.txt added
15dc770766582_exonGeTrInfo.tab added
15dc76d02737c_exonInfo.tab added
15dc73bec09cd_geneInfo.tab added
15dc75779077_Genome added
15dc76cad776e_genomeParameters.txt added
15dc7707c0e7f_Log.out added
15dc7609bed8a_SA added
15dc71d083093_SAindex added
15dc74ad11c9_sjdbInfo.txt added
15dc77e6aa584_sjdbList.fromGTF.out.tab added
15dc7b98bdf3_sjdbList.out.tab added
15dc758dea277_transcriptInfo.tab added
15dc77c6036_GRCh38.GENCODE.v42_100 added
15dc765907979_knownGene_hg38.sql added
15dc770172b06_knownGene_hg38.txt added
15dc7109d068_refGene_hg38.sql added
15dc72b515c60_refGene_hg38.txt added
15dc76a87b8d7_knownGene_mm39.sql added
15dc7747861e4_knownGene_mm39.txt added
15dc7b62fb79_refGene_mm39.sql added
15dc7f6bcac6_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:
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpSOc5cy/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
6.398 0.719 7.760
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.013 | 0.244 | 2.264 | |
| dataSearch | 0.353 | 0.015 | 0.369 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.859 | 0.055 | 2.034 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.039 | 0.004 | 0.043 | |
| recipeLoad | 0.394 | 0.028 | 0.435 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.15 | 0.01 | 0.16 | |
| recipeUpdate | 0 | 0 | 0 | |