Qian Liu
| Snapshot Date: 2025-12-15 13:40 -0500 (Mon, 15 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: 4a5d06b |
| git_last_commit_date: 2025-10-29 11:20:44 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-16 11:35 -0500 (Tue, 16 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4875 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4583 |
| 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 1754/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.11.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 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: 1.11.0 |
| 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_1.11.0.tar.gz |
| StartedAt: 2025-12-15 21:45:47 -0500 (Mon, 15 Dec 2025) |
| EndedAt: 2025-12-15 21:46:45 -0500 (Mon, 15 Dec 2025) |
| EllapsedTime: 58.7 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* 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 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.11.0’
* 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-3.23-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/4.6-arm64/Resources/library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.11.0’ ** 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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
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...
669d429ee81_GRCh38.primary_assembly.genome.fa.1.bt2 added
669d5ce95949_GRCh38.primary_assembly.genome.fa.2.bt2 added
669d5be4f746_GRCh38.primary_assembly.genome.fa.3.bt2 added
669d152643cc_GRCh38.primary_assembly.genome.fa.4.bt2 added
669d32d10ed_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
669d3b2393c_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
669d29cb9409_outfile.txt added
669d7463f04e_GRCh37_to_GRCh38.chain added
669d4d35cc94_GRCh37_to_NCBI34.chain added
669d70a3026_GRCh37_to_NCBI35.chain added
669d2ddf1266_GRCh37_to_NCBI36.chain added
669d1030fe11_GRCh38_to_GRCh37.chain added
669d781665_GRCh38_to_NCBI34.chain added
669d4c064120_GRCh38_to_NCBI35.chain added
669d2e9dc2de_GRCh38_to_NCBI36.chain added
669d776494ba_NCBI34_to_GRCh37.chain added
669d6c607c92_NCBI34_to_GRCh38.chain added
669d32928cd4_NCBI35_to_GRCh37.chain added
669d335bcc3c_NCBI35_to_GRCh38.chain added
669d4fbd917b_NCBI36_to_GRCh37.chain added
669d269a4b23_NCBI36_to_GRCh38.chain added
669d5bbafaa1_GRCm38_to_NCBIM36.chain added
669d509c8f13_GRCm38_to_NCBIM37.chain added
669d567551bd_NCBIM36_to_GRCm38.chain added
669d30497ba3_NCBIM37_to_GRCm38.chain added
669d28542319_1000G_omni2.5.b37.vcf.gz added
669d2bcc52fe_1000G_omni2.5.b37.vcf.gz.tbi added
669d735cb828_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
669d4c3e8543_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
669d1c9f18d0_1000G_omni2.5.hg38.vcf.gz added
669d11160e5e_1000G_omni2.5.hg38.vcf.gz.tbi added
669d3f094615_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
669d79d82d07_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
669d5f74650f_af-only-gnomad.raw.sites.vcf added
669d5296ecbe_af-only-gnomad.raw.sites.vcf.idx added
669d3290d84e_Mutect2-exome-panel.vcf.idx added
669d436902d1_Mutect2-WGS-panel-b37.vcf added
669d233809ea_Mutect2-WGS-panel-b37.vcf.idx added
669d3412f3b6_small_exac_common_3.vcf added
669d483e4c6f_small_exac_common_3.vcf.idx added
669d720c3076_1000g_pon.hg38.vcf.gz added
669d7e41cd78_1000g_pon.hg38.vcf.gz.tbi added
669d1218c20a_af-only-gnomad.hg38.vcf.gz added
669d176b27ce_af-only-gnomad.hg38.vcf.gz.tbi added
669d7c025164_small_exac_common_3.hg38.vcf.gz added
669d7c2dbbd6_small_exac_common_3.hg38.vcf.gz.tbi added
669d1e871e4b_gencode.v41.annotation.gtf added
669d38d5dd95_gencode.v42.annotation.gtf added
669d60c67e59_gencode.vM30.annotation.gtf added
669d79136b2_gencode.vM31.annotation.gtf added
669d4e9de3ff_gencode.v41.transcripts.fa added
669d5fe3a2ab_gencode.v41.transcripts.fa.fai added
669d59ccb9bb_gencode.v42.transcripts.fa added
669dfb5d20c_gencode.v42.transcripts.fa.fai added
669d69f119e2_gencode.vM30.pc_transcripts.fa added
669d53da7ac4_gencode.vM30.pc_transcripts.fa.fai added
669d2cb204de_gencode.vM31.pc_transcripts.fa added
669d5b5da1be_gencode.vM31.pc_transcripts.fa.fai added
669d6025efce_GRCh38.primary_assembly.genome.fa.1.ht2 added
669d5aa2eeb2_GRCh38.primary_assembly.genome.fa.2.ht2 added
669d7ee5169a_GRCh38.primary_assembly.genome.fa.3.ht2 added
669d722f198b_GRCh38.primary_assembly.genome.fa.4.ht2 added
669d72362f3d_GRCh38.primary_assembly.genome.fa.5.ht2 added
669d4357885f_GRCh38.primary_assembly.genome.fa.6.ht2 added
669d27ba3783_GRCh38.primary_assembly.genome.fa.7.ht2 added
669d32928dd5_GRCh38.primary_assembly.genome.fa.8.ht2 added
669d339db4e3_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
669d36cebd8e_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
669d3efed1be_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
669d4b7c3141_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
669d4685c91e_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
669d7956f4bd_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
669d3bdde287_GRCh38_full_analysis_set_plus_decoy_hla.fa added
669d64432bc5_GRCh38.primary_assembly.genome.fa.fai added
669d75eec5ef_GRCh38.primary_assembly.genome.fa.amb added
669df050a66_GRCh38.primary_assembly.genome.fa.ann added
669d13edb63e_GRCh38.primary_assembly.genome.fa.bwt added
669d5b57aaaa_GRCh38.primary_assembly.genome.fa.pac added
669d5885adbf_GRCh38.primary_assembly.genome.fa.sa added
669d30520400_GRCh38.primary_assembly.genome.fa added
669d5884b4c8_hs37d5.fa.fai added
669d7078e3de_hs37d5.fa.amb added
669d10b83d82_hs37d5.fa.ann added
669d2fce2a61_hs37d5.fa.bwt added
669d8405ecc_hs37d5.fa.pac added
669d3a0fa74f_hs37d5.fa.sa added
669d59b15150_hs37d5.fa added
669d8518931_complete_ref_lens.bin added
669d2105f43b_ctable.bin added
669dde55e6d_ctg_offsets.bin added
669d4d9a4d3b_duplicate_clusters.tsv added
669d4d44844a_info.json added
669d4d493de7_mphf.bin added
669d37f3055_pos.bin added
669d133e1e3e_pre_indexing.log added
669d53338250_rank.bin added
669d5ab07cdc_ref_indexing.log added
669d78d57e07_refAccumLengths.bin added
669d8453b8b_reflengths.bin added
669d794826ea_refseq.bin added
669d6ff30ada_seq.bin added
669d3d4da7a1_versionInfo.json added
669d35385a78_salmon_index added
669d6bb9794_chrLength.txt added
669d5dc7900_chrName.txt added
669d4d8bf201_chrNameLength.txt added
669d1ebd476d_chrStart.txt added
669d1c9c54df_exonGeTrInfo.tab added
669d5b880b25_exonInfo.tab added
669d4093d915_geneInfo.tab added
669d2a9112d2_Genome added
669d1a6aaed3_genomeParameters.txt added
669d51fbac31_Log.out added
669d61e5ef03_SA added
669d3eaee02b_SAindex added
669d4aff4733_sjdbInfo.txt added
669d3d9b8bbc_sjdbList.fromGTF.out.tab added
669d2ef3033d_sjdbList.out.tab added
669d5459b1df_transcriptInfo.tab added
669d4cacd2bc_GRCh38.GENCODE.v42_100 added
669d663f5bf7_knownGene_hg38.sql added
669d49aee992_knownGene_hg38.txt added
669d7a689608_refGene_hg38.sql added
669d68522600_refGene_hg38.txt added
669d693cff81_knownGene_mm39.sql added
669d23aaa421_knownGene_mm39.txt added
669d17fd84d2_refGene_mm39.sql added
669d51b034c_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//RtmpC5XqKS/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
6.924 0.832 8.632
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.074 | 0.267 | 2.451 | |
| dataSearch | 0.368 | 0.018 | 0.390 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 0.905 | 0.061 | 2.261 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.001 | 0.000 | |
| recipeHub-class | 0.037 | 0.004 | 0.040 | |
| recipeLoad | 0.420 | 0.030 | 0.478 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.162 | 0.013 | 0.177 | |
| recipeUpdate | 0 | 0 | 0 | |