Qian Liu
| Snapshot Date: 2025-11-20 13:40 -0500 (Thu, 20 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 2025-11-21 11:38 -0500 (Fri, 21 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" | 4829 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4602 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4566 |
| 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 1750/2327 | 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 | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| 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: 2025-11-21 03:10:24 -0500 (Fri, 21 Nov 2025) |
| EndedAt: 2025-11-21 03:13:09 -0500 (Fri, 21 Nov 2025) |
| EllapsedTime: 164.3 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 6.087 0.371 6.459
* 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...
1ba24e6432ac41_GRCh38.primary_assembly.genome.fa.1.bt2 added
1ba24e179335f6_GRCh38.primary_assembly.genome.fa.2.bt2 added
1ba24e30b5c3a4_GRCh38.primary_assembly.genome.fa.3.bt2 added
1ba24e67cd82f4_GRCh38.primary_assembly.genome.fa.4.bt2 added
1ba24e6e715691_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1ba24e7e50a1e1_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1ba24e3c1e4cee_outfile.txt added
1ba24e7b63b415_GRCh37_to_GRCh38.chain added
1ba24e25d0d17e_GRCh37_to_NCBI34.chain added
1ba24e1bc4b30c_GRCh37_to_NCBI35.chain added
1ba24e354437b3_GRCh37_to_NCBI36.chain added
1ba24e39e4cd54_GRCh38_to_GRCh37.chain added
1ba24e2a24e5bd_GRCh38_to_NCBI34.chain added
1ba24e37823f7e_GRCh38_to_NCBI35.chain added
1ba24e19a06495_GRCh38_to_NCBI36.chain added
1ba24e7059d767_NCBI34_to_GRCh37.chain added
1ba24ea79ce95_NCBI34_to_GRCh38.chain added
1ba24e66be5d69_NCBI35_to_GRCh37.chain added
1ba24e18a8316d_NCBI35_to_GRCh38.chain added
1ba24e732c08f9_NCBI36_to_GRCh37.chain added
1ba24e119714e1_NCBI36_to_GRCh38.chain added
1ba24e4397d7d6_GRCm38_to_NCBIM36.chain added
1ba24e7033a71_GRCm38_to_NCBIM37.chain added
1ba24e43b797_NCBIM36_to_GRCm38.chain added
1ba24e34f73c81_NCBIM37_to_GRCm38.chain added
1ba24e5463c3ce_1000G_omni2.5.b37.vcf.gz added
1ba24e159eebb0_1000G_omni2.5.b37.vcf.gz.tbi added
1ba24e462c326_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1ba24eef5ce18_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1ba24e30da23cc_1000G_omni2.5.hg38.vcf.gz added
1ba24e73f3afbb_1000G_omni2.5.hg38.vcf.gz.tbi added
1ba24e73287a59_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1ba24e486d59c2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1ba24e24a9735f_af-only-gnomad.raw.sites.vcf added
1ba24e5af5fd4d_af-only-gnomad.raw.sites.vcf.idx added
1ba24e36deb054_Mutect2-exome-panel.vcf.idx added
1ba24e22fa1540_Mutect2-WGS-panel-b37.vcf added
1ba24e17144a3c_Mutect2-WGS-panel-b37.vcf.idx added
1ba24e32426469_small_exac_common_3.vcf added
1ba24e48cae6be_small_exac_common_3.vcf.idx added
1ba24e32d8fd48_1000g_pon.hg38.vcf.gz added
1ba24e67869c1d_1000g_pon.hg38.vcf.gz.tbi added
1ba24e2afb412_af-only-gnomad.hg38.vcf.gz added
1ba24e5cfde305_af-only-gnomad.hg38.vcf.gz.tbi added
1ba24e1f08db9b_small_exac_common_3.hg38.vcf.gz added
1ba24e1c5018a7_small_exac_common_3.hg38.vcf.gz.tbi added
1ba24e4d57ba6c_gencode.v41.annotation.gtf added
1ba24e2982aa30_gencode.v42.annotation.gtf added
1ba24e30e7610_gencode.vM30.annotation.gtf added
1ba24e65ffebda_gencode.vM31.annotation.gtf added
1ba24e1caeb329_gencode.v41.transcripts.fa added
1ba24e14a58af2_gencode.v41.transcripts.fa.fai added
1ba24e2997c3b0_gencode.v42.transcripts.fa added
1ba24e23b1ed9a_gencode.v42.transcripts.fa.fai added
1ba24e14e94289_gencode.vM30.pc_transcripts.fa added
1ba24e5e8f0031_gencode.vM30.pc_transcripts.fa.fai added
1ba24e7815b168_gencode.vM31.pc_transcripts.fa added
1ba24e2a882e3a_gencode.vM31.pc_transcripts.fa.fai added
1ba24e62f1c357_GRCh38.primary_assembly.genome.fa.1.ht2 added
1ba24e70b7f80_GRCh38.primary_assembly.genome.fa.2.ht2 added
1ba24e5b625206_GRCh38.primary_assembly.genome.fa.3.ht2 added
1ba24e56e57312_GRCh38.primary_assembly.genome.fa.4.ht2 added
1ba24e7a33f9da_GRCh38.primary_assembly.genome.fa.5.ht2 added
1ba24e23cfabc9_GRCh38.primary_assembly.genome.fa.6.ht2 added
1ba24e7b8ee672_GRCh38.primary_assembly.genome.fa.7.ht2 added
1ba24e5529f727_GRCh38.primary_assembly.genome.fa.8.ht2 added
1ba24e5aae5c1d_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1ba24e1e88fbb2_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1ba24e6c3e4163_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1ba24ecf0c086_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1ba24e6753e271_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1ba24e1f173eab_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1ba24e74775ca3_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1ba24e6a039683_GRCh38.primary_assembly.genome.fa.fai added
1ba24e7c1521b0_GRCh38.primary_assembly.genome.fa.amb added
1ba24e1380383e_GRCh38.primary_assembly.genome.fa.ann added
1ba24e653af2b_GRCh38.primary_assembly.genome.fa.bwt added
1ba24e496cdc1d_GRCh38.primary_assembly.genome.fa.pac added
1ba24e3d02e26e_GRCh38.primary_assembly.genome.fa.sa added
1ba24e962253b_GRCh38.primary_assembly.genome.fa added
1ba24e2f6cc7f7_hs37d5.fa.fai added
1ba24e59b19597_hs37d5.fa.amb added
1ba24e1e07b02d_hs37d5.fa.ann added
1ba24e59048ba7_hs37d5.fa.bwt added
1ba24e7d638331_hs37d5.fa.pac added
1ba24e32f0f2b7_hs37d5.fa.sa added
1ba24e37938bd9_hs37d5.fa added
1ba24e75793499_complete_ref_lens.bin added
1ba24e5d7920f1_ctable.bin added
1ba24e1a854f30_ctg_offsets.bin added
1ba24e7c84b41a_duplicate_clusters.tsv added
1ba24e38db72f7_info.json added
1ba24e716ac243_mphf.bin added
1ba24e76b8adf4_pos.bin added
1ba24e5cab1ec0_pre_indexing.log added
1ba24e6cf9a8b5_rank.bin added
1ba24e4be2a51b_ref_indexing.log added
1ba24e37597add_refAccumLengths.bin added
1ba24eb82a467_reflengths.bin added
1ba24e3820e67f_refseq.bin added
1ba24e444a3b64_seq.bin added
1ba24e72d686d8_versionInfo.json added
1ba24e5738252a_salmon_index added
1ba24e38c19807_chrLength.txt added
1ba24e5cda1d5c_chrName.txt added
1ba24e534d46db_chrNameLength.txt added
1ba24e4c41d046_chrStart.txt added
1ba24e632dcc87_exonGeTrInfo.tab added
1ba24e1cba22f8_exonInfo.tab added
1ba24e944b2b4_geneInfo.tab added
1ba24e6c8ff1c2_Genome added
1ba24e4c26eaef_genomeParameters.txt added
1ba24e62f6484c_Log.out added
1ba24ea97a1f0_SA added
1ba24e252b7696_SAindex added
1ba24e6059cb7d_sjdbInfo.txt added
1ba24e3d8894a7_sjdbList.fromGTF.out.tab added
1ba24e5cbf026f_sjdbList.out.tab added
1ba24e55d30017_transcriptInfo.tab added
1ba24e1b01b598_GRCh38.GENCODE.v42_100 added
1ba24e774451a0_knownGene_hg38.sql added
1ba24e5257b431_knownGene_hg38.txt added
1ba24e53dd288f_refGene_hg38.sql added
1ba24e68af13e3_refGene_hg38.txt added
1ba24e49106225_knownGene_mm39.sql added
1ba24e30884750_knownGene_mm39.txt added
1ba24e55a8bc98_refGene_mm39.sql added
1ba24e14f30740_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/RtmpXulkNU/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
17.756 1.113 19.573
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.087 | 0.371 | 6.459 | |
| dataSearch | 1.130 | 0.052 | 1.182 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.524 | 0.146 | 3.776 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.120 | 0.005 | 0.126 | |
| recipeLoad | 1.304 | 0.069 | 1.375 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.536 | 0.024 | 0.560 | |
| recipeUpdate | 0 | 0 | 0 | |