Qian Liu
| Snapshot Date: 2025-12-30 13:40 -0500 (Tue, 30 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 2025-12-31 11:35 -0500 (Wed, 31 Dec 2025).
| 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" | 4808 |
| 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: 2025-12-30 21:55:40 -0500 (Tue, 30 Dec 2025) |
| EndedAt: 2025-12-30 21:56:37 -0500 (Tue, 30 Dec 2025) |
| EllapsedTime: 56.6 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...
e9b3638751ec_GRCh38.primary_assembly.genome.fa.1.bt2 added
e9b349139000_GRCh38.primary_assembly.genome.fa.2.bt2 added
e9b32353157b_GRCh38.primary_assembly.genome.fa.3.bt2 added
e9b323a7505b_GRCh38.primary_assembly.genome.fa.4.bt2 added
e9b33d8c98a6_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
e9b35979d9db_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
e9b34ecde6c1_outfile.txt added
e9b32fe8b152_GRCh37_to_GRCh38.chain added
e9b355d19710_GRCh37_to_NCBI34.chain added
e9b33314c774_GRCh37_to_NCBI35.chain added
e9b31932aadf_GRCh37_to_NCBI36.chain added
e9b34d702365_GRCh38_to_GRCh37.chain added
e9b37d23e39a_GRCh38_to_NCBI34.chain added
e9b33f33d3a5_GRCh38_to_NCBI35.chain added
e9b3638c160d_GRCh38_to_NCBI36.chain added
e9b31fbe28a_NCBI34_to_GRCh37.chain added
e9b33fd5d30a_NCBI34_to_GRCh38.chain added
e9b36f125643_NCBI35_to_GRCh37.chain added
e9b31cdd81ad_NCBI35_to_GRCh38.chain added
e9b3126c93a9_NCBI36_to_GRCh37.chain added
e9b3165245b2_NCBI36_to_GRCh38.chain added
e9b3735db490_GRCm38_to_NCBIM36.chain added
e9b3cf9951c_GRCm38_to_NCBIM37.chain added
e9b355ac67eb_NCBIM36_to_GRCm38.chain added
e9b329daa13e_NCBIM37_to_GRCm38.chain added
e9b3509002e9_1000G_omni2.5.b37.vcf.gz added
e9b31eaf3851_1000G_omni2.5.b37.vcf.gz.tbi added
e9b319a5d94_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
e9b33d75a05e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
e9b375739ad7_1000G_omni2.5.hg38.vcf.gz added
e9b378bad57e_1000G_omni2.5.hg38.vcf.gz.tbi added
e9b33216811e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
e9b36376f242_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
e9b3161afe12_af-only-gnomad.raw.sites.vcf added
e9b3461e5b14_af-only-gnomad.raw.sites.vcf.idx added
e9b372eda202_Mutect2-exome-panel.vcf.idx added
e9b34f276c40_Mutect2-WGS-panel-b37.vcf added
e9b325340659_Mutect2-WGS-panel-b37.vcf.idx added
e9b37a8cd023_small_exac_common_3.vcf added
e9b332b4e8b0_small_exac_common_3.vcf.idx added
e9b331894d2_1000g_pon.hg38.vcf.gz added
e9b342d26894_1000g_pon.hg38.vcf.gz.tbi added
e9b33cfeed2_af-only-gnomad.hg38.vcf.gz added
e9b348481ef2_af-only-gnomad.hg38.vcf.gz.tbi added
e9b376e7c6f0_small_exac_common_3.hg38.vcf.gz added
e9b36ab5f38c_small_exac_common_3.hg38.vcf.gz.tbi added
e9b34f88a30f_gencode.v41.annotation.gtf added
e9b313895694_gencode.v42.annotation.gtf added
e9b31d931891_gencode.vM30.annotation.gtf added
e9b32431e6c2_gencode.vM31.annotation.gtf added
e9b34824dd1e_gencode.v41.transcripts.fa added
e9b36c310192_gencode.v41.transcripts.fa.fai added
e9b355e4fbc_gencode.v42.transcripts.fa added
e9b372c4c264_gencode.v42.transcripts.fa.fai added
e9b353b66e19_gencode.vM30.pc_transcripts.fa added
e9b36df6563e_gencode.vM30.pc_transcripts.fa.fai added
e9b3479838d8_gencode.vM31.pc_transcripts.fa added
e9b35abc11a0_gencode.vM31.pc_transcripts.fa.fai added
e9b371294de9_GRCh38.primary_assembly.genome.fa.1.ht2 added
e9b34eba3609_GRCh38.primary_assembly.genome.fa.2.ht2 added
e9b32331b140_GRCh38.primary_assembly.genome.fa.3.ht2 added
e9b3136bf2cd_GRCh38.primary_assembly.genome.fa.4.ht2 added
e9b314117ab1_GRCh38.primary_assembly.genome.fa.5.ht2 added
e9b378e04c2_GRCh38.primary_assembly.genome.fa.6.ht2 added
e9b37cda606d_GRCh38.primary_assembly.genome.fa.7.ht2 added
e9b364f0d424_GRCh38.primary_assembly.genome.fa.8.ht2 added
e9b37ef7bb41_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
e9b33a26e986_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
e9b350ad7a3d_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
e9b32d34642c_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
e9b34a9c9be3_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
e9b36fbe7a59_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
e9b34252a25f_GRCh38_full_analysis_set_plus_decoy_hla.fa added
e9b33f222cfd_GRCh38.primary_assembly.genome.fa.fai added
e9b35cb7b66c_GRCh38.primary_assembly.genome.fa.amb added
e9b321299c02_GRCh38.primary_assembly.genome.fa.ann added
e9b332c15850_GRCh38.primary_assembly.genome.fa.bwt added
e9b3338d0638_GRCh38.primary_assembly.genome.fa.pac added
e9b36f9360f8_GRCh38.primary_assembly.genome.fa.sa added
e9b334c37302_GRCh38.primary_assembly.genome.fa added
e9b3bb3a35e_hs37d5.fa.fai added
e9b33eaa7652_hs37d5.fa.amb added
e9b3293e21a2_hs37d5.fa.ann added
e9b32e1227d5_hs37d5.fa.bwt added
e9b329f52894_hs37d5.fa.pac added
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e9b33c399998_hs37d5.fa added
e9b36992e90b_complete_ref_lens.bin added
e9b32c020753_ctable.bin added
e9b3392ef0b7_ctg_offsets.bin added
e9b338bd9bb5_duplicate_clusters.tsv added
e9b32839a52d_info.json added
e9b3608b41fc_mphf.bin added
e9b3569938e8_pos.bin added
e9b3656733c2_pre_indexing.log added
e9b35a773990_rank.bin added
e9b349644b56_ref_indexing.log added
e9b3578e20be_refAccumLengths.bin added
e9b33407c6da_reflengths.bin added
e9b36a902ce5_refseq.bin added
e9b31f73a50b_seq.bin added
e9b36158854e_versionInfo.json added
e9b37a97f5cf_salmon_index added
e9b3e8b27ea_chrLength.txt added
e9b351e97b1b_chrName.txt added
e9b3379153a0_chrNameLength.txt added
e9b3260949e0_chrStart.txt added
e9b32bd124a2_exonGeTrInfo.tab added
e9b32fbc1e27_exonInfo.tab added
e9b3675faaec_geneInfo.tab added
e9b339cea0f9_Genome added
e9b32caa5915_genomeParameters.txt added
e9b363be889b_Log.out added
e9b371faab45_SA added
e9b327979_SAindex added
e9b32274f6f0_sjdbInfo.txt added
e9b32d00183c_sjdbList.fromGTF.out.tab added
e9b361372238_sjdbList.out.tab added
e9b36aa7bc64_transcriptInfo.tab added
e9b32a417ff0_GRCh38.GENCODE.v42_100 added
e9b332367b3c_knownGene_hg38.sql added
e9b316d4b9e5_knownGene_hg38.txt added
e9b367f87518_refGene_hg38.sql added
e9b368cfaffb_refGene_hg38.txt added
e9b31b2abd7f_knownGene_mm39.sql added
e9b312feeac8_knownGene_mm39.txt added
e9b31de7fa36_refGene_mm39.sql added
e9b368dbfe90_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//RtmpUsMAiV/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
6.995 0.828 8.559
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.051 | 0.259 | 2.423 | |
| dataSearch | 0.357 | 0.018 | 0.384 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.911 | 0.057 | 2.204 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.042 | 0.005 | 0.051 | |
| recipeLoad | 0.420 | 0.029 | 0.466 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.184 | 0.013 | 0.210 | |
| recipeUpdate | 0 | 0 | 0 | |