Qian Liu
| Snapshot Date: 2025-11-14 13:40 -0500 (Fri, 14 Nov 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 2025-11-15 11:34 -0500 (Sat, 15 Nov 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" | 4826 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4561 |
| 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 1748/2325 | 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 | ERROR | skipped | skipped | |||||||||
|
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: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.11.0.tar.gz |
| StartedAt: 2025-11-15 03:17:38 -0500 (Sat, 15 Nov 2025) |
| EndedAt: 2025-11-15 03:20:24 -0500 (Sat, 15 Nov 2025) |
| EllapsedTime: 166.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataHub-class 5.853 0.338 6.193
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-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) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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...
2239d925c02733_GRCh38.primary_assembly.genome.fa.1.bt2 added
2239d91f6d5dac_GRCh38.primary_assembly.genome.fa.2.bt2 added
2239d910abdd81_GRCh38.primary_assembly.genome.fa.3.bt2 added
2239d911d3af17_GRCh38.primary_assembly.genome.fa.4.bt2 added
2239d93389672f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2239d944494856_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2239d97e59a514_outfile.txt added
2239d95760b4cd_GRCh37_to_GRCh38.chain added
2239d946ae6f36_GRCh37_to_NCBI34.chain added
2239d911cffd64_GRCh37_to_NCBI35.chain added
2239d928e7cdad_GRCh37_to_NCBI36.chain added
2239d92ed4a956_GRCh38_to_GRCh37.chain added
2239d9100c33cb_GRCh38_to_NCBI34.chain added
2239d94def343b_GRCh38_to_NCBI35.chain added
2239d97ef11919_GRCh38_to_NCBI36.chain added
2239d9103c20e4_NCBI34_to_GRCh37.chain added
2239d97c70c5ae_NCBI34_to_GRCh38.chain added
2239d92400763f_NCBI35_to_GRCh37.chain added
2239d927ab28f5_NCBI35_to_GRCh38.chain added
2239d9366cad43_NCBI36_to_GRCh37.chain added
2239d936484afc_NCBI36_to_GRCh38.chain added
2239d91b8d3a7b_GRCm38_to_NCBIM36.chain added
2239d92b55222d_GRCm38_to_NCBIM37.chain added
2239d91b24a249_NCBIM36_to_GRCm38.chain added
2239d94f6da1c8_NCBIM37_to_GRCm38.chain added
2239d9423480d6_1000G_omni2.5.b37.vcf.gz added
2239d9230350bb_1000G_omni2.5.b37.vcf.gz.tbi added
2239d9420afa70_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2239d96eb2ca18_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2239d910142ef0_1000G_omni2.5.hg38.vcf.gz added
2239d9140c7aee_1000G_omni2.5.hg38.vcf.gz.tbi added
2239d91472f14b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2239d92f818c9d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2239d924b8586f_af-only-gnomad.raw.sites.vcf added
2239d92646a063_af-only-gnomad.raw.sites.vcf.idx added
2239d9630af3cc_Mutect2-exome-panel.vcf.idx added
2239d96901a0c5_Mutect2-WGS-panel-b37.vcf added
2239d924a04577_Mutect2-WGS-panel-b37.vcf.idx added
2239d93a6ba89a_small_exac_common_3.vcf added
2239d92fb00ffb_small_exac_common_3.vcf.idx added
2239d9367042db_1000g_pon.hg38.vcf.gz added
2239d963537647_1000g_pon.hg38.vcf.gz.tbi added
2239d95e84b951_af-only-gnomad.hg38.vcf.gz added
2239d9467c76a6_af-only-gnomad.hg38.vcf.gz.tbi added
2239d93142aa82_small_exac_common_3.hg38.vcf.gz added
2239d95d75d26b_small_exac_common_3.hg38.vcf.gz.tbi added
2239d956b8978a_gencode.v41.annotation.gtf added
2239d92db37031_gencode.v42.annotation.gtf added
2239d917648aa_gencode.vM30.annotation.gtf added
2239d97e63c07f_gencode.vM31.annotation.gtf added
2239d964201d74_gencode.v41.transcripts.fa added
2239d937be93a6_gencode.v41.transcripts.fa.fai added
2239d919f0fafa_gencode.v42.transcripts.fa added
2239d9f753fa1_gencode.v42.transcripts.fa.fai added
2239d952e335ef_gencode.vM30.pc_transcripts.fa added
2239d9695e9cc3_gencode.vM30.pc_transcripts.fa.fai added
2239d951a9c077_gencode.vM31.pc_transcripts.fa added
2239d975e686aa_gencode.vM31.pc_transcripts.fa.fai added
2239d92b699733_GRCh38.primary_assembly.genome.fa.1.ht2 added
2239d9405c8a8f_GRCh38.primary_assembly.genome.fa.2.ht2 added
2239d95fab59b_GRCh38.primary_assembly.genome.fa.3.ht2 added
2239d93f761221_GRCh38.primary_assembly.genome.fa.4.ht2 added
2239d954cf7bda_GRCh38.primary_assembly.genome.fa.5.ht2 added
2239d9357c4238_GRCh38.primary_assembly.genome.fa.6.ht2 added
2239d9642e6a90_GRCh38.primary_assembly.genome.fa.7.ht2 added
2239d97b161c3d_GRCh38.primary_assembly.genome.fa.8.ht2 added
2239d918873604_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2239d94d300b55_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2239d91fb661b4_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2239d952f2de9e_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2239d97ce01b50_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2239d95626a48f_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2239d9364654e5_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2239d95b64d4a2_GRCh38.primary_assembly.genome.fa.fai added
2239d91ca31b36_GRCh38.primary_assembly.genome.fa.amb added
2239d96788ff68_GRCh38.primary_assembly.genome.fa.ann added
2239d938daa70d_GRCh38.primary_assembly.genome.fa.bwt added
2239d9735bb2c0_GRCh38.primary_assembly.genome.fa.pac added
2239d9153c6f99_GRCh38.primary_assembly.genome.fa.sa added
2239d93a50efb7_GRCh38.primary_assembly.genome.fa added
2239d971bf7340_hs37d5.fa.fai added
2239d9795c8d0d_hs37d5.fa.amb added
2239d9720f835d_hs37d5.fa.ann added
2239d9bb06e3a_hs37d5.fa.bwt added
2239d98d1ccae_hs37d5.fa.pac added
2239d944f2b94d_hs37d5.fa.sa added
2239d9750f0afd_hs37d5.fa added
2239d95a7b8d25_complete_ref_lens.bin added
2239d93ad93ff7_ctable.bin added
2239d92078a231_ctg_offsets.bin added
2239d91ad817b4_duplicate_clusters.tsv added
2239d940d3f592_info.json added
2239d95feeb452_mphf.bin added
2239d96fa7938e_pos.bin added
2239d9765037ca_pre_indexing.log added
2239d9441d1ee3_rank.bin added
2239d96abdafcc_ref_indexing.log added
2239d9ed76dcf_refAccumLengths.bin added
2239d9114d2a38_reflengths.bin added
2239d9a741180_refseq.bin added
2239d961ca4c6d_seq.bin added
2239d9e2d4589_versionInfo.json added
2239d9609ab610_salmon_index added
2239d91810a153_chrLength.txt added
2239d969921a2b_chrName.txt added
2239d97d3dd146_chrNameLength.txt added
2239d97f99a0bb_chrStart.txt added
2239d9226cc138_exonGeTrInfo.tab added
2239d970998406_exonInfo.tab added
2239d914d61054_geneInfo.tab added
2239d95cbdb0ef_Genome added
2239d96258f746_genomeParameters.txt added
2239d9e329d61_Log.out added
2239d94ecd344c_SA added
2239d96e096581_SAindex added
2239d917046a0f_sjdbInfo.txt added
2239d913bfed99_sjdbList.fromGTF.out.tab added
2239d96318707e_sjdbList.out.tab added
2239d9717ff734_transcriptInfo.tab added
2239d94e992d91_GRCh38.GENCODE.v42_100 added
2239d939112af_knownGene_hg38.sql added
2239d9c580ee8_knownGene_hg38.txt added
2239d9f6d2323_refGene_hg38.sql added
2239d9637fc702_refGene_hg38.txt added
2239d97bffa276_knownGene_mm39.sql added
2239d95bd5aee_knownGene_mm39.txt added
2239d9279ce5e5_refGene_mm39.sql added
2239d966bd5242_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:
/tmp/RtmpVCF3Xb/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
18.404 1.197 20.148
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.853 | 0.338 | 6.193 | |
| dataSearch | 1.101 | 0.031 | 1.132 | |
| dataUpdate | 0.001 | 0.000 | 0.000 | |
| getCloudData | 2.579 | 0.139 | 3.927 | |
| getData | 0.001 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.126 | 0.001 | 0.127 | |
| recipeLoad | 1.270 | 0.073 | 1.345 | |
| recipeMake | 0.000 | 0.001 | 0.000 | |
| recipeSearch | 0.542 | 0.011 | 0.552 | |
| recipeUpdate | 0 | 0 | 0 | |