Qian Liu
| Snapshot Date: 2026-01-06 13:40 -0500 (Tue, 06 Jan 2026) |
| 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 2026-01-07 11:35 -0500 (Wed, 07 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4815 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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: 2026-01-06 21:58:11 -0500 (Tue, 06 Jan 2026) |
| EndedAt: 2026-01-06 21:59:07 -0500 (Tue, 06 Jan 2026) |
| EllapsedTime: 55.6 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_1.11.0.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...
13b87141aaa9_GRCh38.primary_assembly.genome.fa.1.bt2 added
13b8e2b7756_GRCh38.primary_assembly.genome.fa.2.bt2 added
13b847a7b65e_GRCh38.primary_assembly.genome.fa.3.bt2 added
13b853b5fa12_GRCh38.primary_assembly.genome.fa.4.bt2 added
13b85034dead_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
13b83f0758fe_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
13b87b63ac05_outfile.txt added
13b84cb2bb8c_GRCh37_to_GRCh38.chain added
13b86a370baa_GRCh37_to_NCBI34.chain added
13b843defc60_GRCh37_to_NCBI35.chain added
13b8648b256f_GRCh37_to_NCBI36.chain added
13b86b46cdfa_GRCh38_to_GRCh37.chain added
13b8757d0f1b_GRCh38_to_NCBI34.chain added
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13b8502d9b7d_GRCh38_to_NCBI36.chain added
13b8623b54aa_NCBI34_to_GRCh37.chain added
13b825339748_NCBI34_to_GRCh38.chain added
13b85e110b0c_NCBI35_to_GRCh37.chain added
13b830ec7113_NCBI35_to_GRCh38.chain added
13b872f3af7c_NCBI36_to_GRCh37.chain added
13b85c8630d9_NCBI36_to_GRCh38.chain added
13b86df12603_GRCm38_to_NCBIM36.chain added
13b872f6c758_GRCm38_to_NCBIM37.chain added
13b827999d5f_NCBIM36_to_GRCm38.chain added
13b8562adc48_NCBIM37_to_GRCm38.chain added
13b817e4272a_1000G_omni2.5.b37.vcf.gz added
13b83c742a7_1000G_omni2.5.b37.vcf.gz.tbi added
13b8ee8e3e1_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
13b85bc8d06c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
13b85ceb9187_1000G_omni2.5.hg38.vcf.gz added
13b86d9f65b9_1000G_omni2.5.hg38.vcf.gz.tbi added
13b87bcf8ce8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
13b8772c12d8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
13b86e896007_af-only-gnomad.raw.sites.vcf added
13b87cffa442_af-only-gnomad.raw.sites.vcf.idx added
13b87379292a_Mutect2-exome-panel.vcf.idx added
13b8177dbfa0_Mutect2-WGS-panel-b37.vcf added
13b840afad6c_Mutect2-WGS-panel-b37.vcf.idx added
13b84da2aea1_small_exac_common_3.vcf added
13b87376f3d8_small_exac_common_3.vcf.idx added
13b86832521_1000g_pon.hg38.vcf.gz added
13b8bfa9cde_1000g_pon.hg38.vcf.gz.tbi added
13b87250b8f6_af-only-gnomad.hg38.vcf.gz added
13b8119f591c_af-only-gnomad.hg38.vcf.gz.tbi added
13b87493464d_small_exac_common_3.hg38.vcf.gz added
13b870eca505_small_exac_common_3.hg38.vcf.gz.tbi added
13b84046252e_gencode.v41.annotation.gtf added
13b83d330ff9_gencode.v42.annotation.gtf added
13b8635dc3d2_gencode.vM30.annotation.gtf added
13b820e342f5_gencode.vM31.annotation.gtf added
13b82840f3b1_gencode.v41.transcripts.fa added
13b8403efe1c_gencode.v41.transcripts.fa.fai added
13b8679d0137_gencode.v42.transcripts.fa added
13b874baf705_gencode.v42.transcripts.fa.fai added
13b81eafa522_gencode.vM30.pc_transcripts.fa added
13b81d826aeb_gencode.vM30.pc_transcripts.fa.fai added
13b85d39796f_gencode.vM31.pc_transcripts.fa added
13b868539639_gencode.vM31.pc_transcripts.fa.fai added
13b847abadb1_GRCh38.primary_assembly.genome.fa.1.ht2 added
13b858186439_GRCh38.primary_assembly.genome.fa.2.ht2 added
13b8295c075e_GRCh38.primary_assembly.genome.fa.3.ht2 added
13b858e7c188_GRCh38.primary_assembly.genome.fa.4.ht2 added
13b85752f551_GRCh38.primary_assembly.genome.fa.5.ht2 added
13b8767c5a1_GRCh38.primary_assembly.genome.fa.6.ht2 added
13b82ddfd0d3_GRCh38.primary_assembly.genome.fa.7.ht2 added
13b84106e42c_GRCh38.primary_assembly.genome.fa.8.ht2 added
13b82b6e260e_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
13b84c847768_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
13b8cbb7417_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
13b866c29888_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
13b871ac3d6c_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
13b862f4b7c1_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
13b8304c12a8_GRCh38_full_analysis_set_plus_decoy_hla.fa added
13b8525cec5d_GRCh38.primary_assembly.genome.fa.fai added
13b852a1f7e9_GRCh38.primary_assembly.genome.fa.amb added
13b879b0c61_GRCh38.primary_assembly.genome.fa.ann added
13b85449b82d_GRCh38.primary_assembly.genome.fa.bwt added
13b833dabd96_GRCh38.primary_assembly.genome.fa.pac added
13b85dd4dd72_GRCh38.primary_assembly.genome.fa.sa added
13b84216977e_GRCh38.primary_assembly.genome.fa added
13b85933f317_hs37d5.fa.fai added
13b8619c98c1_hs37d5.fa.amb added
13b86ff0d8f7_hs37d5.fa.ann added
13b82d34798b_hs37d5.fa.bwt added
13b85017abdc_hs37d5.fa.pac added
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13b837a9a40c_hs37d5.fa added
13b862512c60_complete_ref_lens.bin added
13b83f38850d_ctable.bin added
13b817a738e8_ctg_offsets.bin added
13b863891379_duplicate_clusters.tsv added
13b83c5d9ffc_info.json added
13b826b2785a_mphf.bin added
13b8efb708f_pos.bin added
13b81d9ac3f8_pre_indexing.log added
13b81bb7ddf7_rank.bin added
13b8444d9158_ref_indexing.log added
13b840814b70_refAccumLengths.bin added
13b8687fc725_reflengths.bin added
13b81ceb83bc_refseq.bin added
13b82a15ba79_seq.bin added
13b878857384_versionInfo.json added
13b81631ced_salmon_index added
13b812000c51_chrLength.txt added
13b84128a312_chrName.txt added
13b852ea1429_chrNameLength.txt added
13b85d1ba46_chrStart.txt added
13b8c1c4ca6_exonGeTrInfo.tab added
13b815ec2c80_exonInfo.tab added
13b8445d92be_geneInfo.tab added
13b85b4d1b02_Genome added
13b823284f22_genomeParameters.txt added
13b82b635336_Log.out added
13b85ec147b_SA added
13b84e349a46_SAindex added
13b85f7c91c6_sjdbInfo.txt added
13b86b468f23_sjdbList.fromGTF.out.tab added
13b8655f79da_sjdbList.out.tab added
13b85f390b34_transcriptInfo.tab added
13b81a0eb3c3_GRCh38.GENCODE.v42_100 added
13b83b3bd492_knownGene_hg38.sql added
13b85500db9f_knownGene_hg38.txt added
13b82b52cf52_refGene_hg38.sql added
13b849a926b6_refGene_hg38.txt added
13b82c9c82_knownGene_mm39.sql added
13b870d71ae4_knownGene_mm39.txt added
13b83a26a89c_refGene_mm39.sql added
13b84007b797_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//Rtmp6OBGyz/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
7.031 0.822 8.774
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.049 | 0.259 | 2.377 | |
| dataSearch | 0.352 | 0.018 | 0.380 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.911 | 0.058 | 2.023 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.041 | 0.005 | 0.047 | |
| recipeLoad | 0.429 | 0.030 | 0.465 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.169 | 0.012 | 0.186 | |
| recipeUpdate | 0 | 0 | 0 | |