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 12:08 -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 21:13:37 -0400 (Fri, 29 Aug 2025) |
| EndedAt: 2025-08-29 21:14:25 -0400 (Fri, 29 Aug 2025) |
| EllapsedTime: 48.6 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 (2025-06-14 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 13.7.7
* 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...
132cc42ec9326_GRCh38.primary_assembly.genome.fa.1.bt2 added
132cc39b0c61d_GRCh38.primary_assembly.genome.fa.2.bt2 added
132cc49eb782_GRCh38.primary_assembly.genome.fa.3.bt2 added
132cc5021ba2c_GRCh38.primary_assembly.genome.fa.4.bt2 added
132cc5645c7cd_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
132cc7f408ffa_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
132cc67aca75a_outfile.txt added
132cc781f3ae2_GRCh37_to_GRCh38.chain added
132cc4a53090a_GRCh37_to_NCBI34.chain added
132cc117695a5_GRCh37_to_NCBI35.chain added
132cc5a8c98_GRCh37_to_NCBI36.chain added
132cc38c44f56_GRCh38_to_GRCh37.chain added
132cc6034b437_GRCh38_to_NCBI34.chain added
132cc2423b839_GRCh38_to_NCBI35.chain added
132cc2513b8b8_GRCh38_to_NCBI36.chain added
132cc31c44b0c_NCBI34_to_GRCh37.chain added
132cc4e1b1a5a_NCBI34_to_GRCh38.chain added
132cc555f32c5_NCBI35_to_GRCh37.chain added
132cc5cfe4f4c_NCBI35_to_GRCh38.chain added
132cc3c083646_NCBI36_to_GRCh37.chain added
132cc3f234c74_NCBI36_to_GRCh38.chain added
132cc2670740e_GRCm38_to_NCBIM36.chain added
132cc20d356d9_GRCm38_to_NCBIM37.chain added
132cc12ead165_NCBIM36_to_GRCm38.chain added
132cc76594796_NCBIM37_to_GRCm38.chain added
132cc5f6b058d_1000G_omni2.5.b37.vcf.gz added
132cc6b399ceb_1000G_omni2.5.b37.vcf.gz.tbi added
132cc136d3f4c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
132cc6956a08a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
132cc3645fa0d_1000G_omni2.5.hg38.vcf.gz added
132cc2c238751_1000G_omni2.5.hg38.vcf.gz.tbi added
132cc5088ed7a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
132cc4d9f0de4_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
132cc5491b8c_af-only-gnomad.raw.sites.vcf added
132cc2af870a_af-only-gnomad.raw.sites.vcf.idx added
132cc51caa2e6_Mutect2-exome-panel.vcf.idx added
132cc4e8cd3fd_Mutect2-WGS-panel-b37.vcf added
132cc7fb1af54_Mutect2-WGS-panel-b37.vcf.idx added
132cc6a6df54a_small_exac_common_3.vcf added
132cc590303dc_small_exac_common_3.vcf.idx added
132cc54f28e2b_1000g_pon.hg38.vcf.gz added
132cc53d49f_1000g_pon.hg38.vcf.gz.tbi added
132cc7fac12e3_af-only-gnomad.hg38.vcf.gz added
132cc7a0c3690_af-only-gnomad.hg38.vcf.gz.tbi added
132cc37d26689_small_exac_common_3.hg38.vcf.gz added
132cc5649c900_small_exac_common_3.hg38.vcf.gz.tbi added
132cc62b4b42_gencode.v41.annotation.gtf added
132cc459dd38_gencode.v42.annotation.gtf added
132cc27ca89c3_gencode.vM30.annotation.gtf added
132cc621a759d_gencode.vM31.annotation.gtf added
132cc371fc8bc_gencode.v41.transcripts.fa added
132cc7b3caea_gencode.v41.transcripts.fa.fai added
132cc2ccecc99_gencode.v42.transcripts.fa added
132cc3cda67ca_gencode.v42.transcripts.fa.fai added
132cc26d41dfc_gencode.vM30.pc_transcripts.fa added
132cc2ffc9f4e_gencode.vM30.pc_transcripts.fa.fai added
132cc723ed27e_gencode.vM31.pc_transcripts.fa added
132cc7a6d88ca_gencode.vM31.pc_transcripts.fa.fai added
132cc2d2fc491_GRCh38.primary_assembly.genome.fa.1.ht2 added
132cc1b1222c4_GRCh38.primary_assembly.genome.fa.2.ht2 added
132cc43a87fbe_GRCh38.primary_assembly.genome.fa.3.ht2 added
132cc6b5ab5a5_GRCh38.primary_assembly.genome.fa.4.ht2 added
132cc104b9ab3_GRCh38.primary_assembly.genome.fa.5.ht2 added
132cc53996620_GRCh38.primary_assembly.genome.fa.6.ht2 added
132cc7bffe9c0_GRCh38.primary_assembly.genome.fa.7.ht2 added
132cc5e4b7bd9_GRCh38.primary_assembly.genome.fa.8.ht2 added
132cc2db013ec_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
132cc2ec0263_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
132cc5490b314_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
132cc67dd116b_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
132cc62a2bd12_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
132cc2a2b1b55_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
132cc740f7f13_GRCh38_full_analysis_set_plus_decoy_hla.fa added
132cc255ff3ec_GRCh38.primary_assembly.genome.fa.fai added
132cc3e871e1f_GRCh38.primary_assembly.genome.fa.amb added
132cc18caa54b_GRCh38.primary_assembly.genome.fa.ann added
132cc2029eba4_GRCh38.primary_assembly.genome.fa.bwt added
132cc202d6c7b_GRCh38.primary_assembly.genome.fa.pac added
132cc62d0fbe_GRCh38.primary_assembly.genome.fa.sa added
132cc7864861c_GRCh38.primary_assembly.genome.fa added
132ccfa0d604_hs37d5.fa.fai added
132cc842a8a0_hs37d5.fa.amb added
132cc504ca49c_hs37d5.fa.ann added
132cc57cb26f3_hs37d5.fa.bwt added
132cc5a6a488c_hs37d5.fa.pac added
132cc77c10db3_hs37d5.fa.sa added
132cc236aa031_hs37d5.fa added
132cc2d3b0321_complete_ref_lens.bin added
132cc7d4a82b9_ctable.bin added
132cc26cc7ff2_ctg_offsets.bin added
132cc3be3fcc4_duplicate_clusters.tsv added
132cc74e7c693_info.json added
132cc1c9e18db_mphf.bin added
132cc4f71e08a_pos.bin added
132cc3d4cacc5_pre_indexing.log added
132cc74e2d8f3_rank.bin added
132cc59117578_ref_indexing.log added
132cc93746f7_refAccumLengths.bin added
132ccc1406db_reflengths.bin added
132cc76ce1a0e_refseq.bin added
132cc5510ca11_seq.bin added
132cc41424db8_versionInfo.json added
132cc67fc8c80_salmon_index added
132cc756c5cd5_chrLength.txt added
132cc1d42e02d_chrName.txt added
132cc118bb95d_chrNameLength.txt added
132cc6c3691aa_chrStart.txt added
132cc72956766_exonGeTrInfo.tab added
132cc2eb7944f_exonInfo.tab added
132cc1669e67f_geneInfo.tab added
132cc29ba758_Genome added
132cc390783be_genomeParameters.txt added
132cc1c5a4c32_Log.out added
132cc6c407528_SA added
132cc7bcbcc9d_SAindex added
132cce696ea_sjdbInfo.txt added
132cc22bddd1c_sjdbList.fromGTF.out.tab added
132cc5eff6b15_sjdbList.out.tab added
132cc52cf606c_transcriptInfo.tab added
132cc2cc37ced_GRCh38.GENCODE.v42_100 added
132cc563ec290_knownGene_hg38.sql added
132cc3257a82c_knownGene_hg38.txt added
132cc18e1fa86_refGene_hg38.sql added
132cc1c06802d_refGene_hg38.txt added
132cc6ec918ba_knownGene_mm39.sql added
132cc54769428_knownGene_mm39.txt added
132cc34f8f96a_refGene_mm39.sql added
132cc45beb951_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//Rtmpln6FX0/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
6.375 0.706 7.786
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.055 | 0.242 | 2.319 | |
| dataSearch | 0.339 | 0.015 | 0.353 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 0.921 | 0.061 | 2.097 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.044 | 0.005 | 0.049 | |
| recipeLoad | 0.395 | 0.034 | 0.436 | |
| recipeMake | 0.000 | 0.001 | 0.000 | |
| recipeSearch | 0.160 | 0.011 | 0.172 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |