Qian Liu
| Snapshot Date: 2025-12-14 13:40 -0500 (Sun, 14 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 2025-12-15 11:35 -0500 (Mon, 15 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: /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: 2025-12-15 03:35:36 -0500 (Mon, 15 Dec 2025) |
| EndedAt: 2025-12-15 03:38:24 -0500 (Mon, 15 Dec 2025) |
| EllapsedTime: 168.4 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 5.786 0.331 6.119
* 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...
7c35f12fde531_GRCh38.primary_assembly.genome.fa.1.bt2 added
7c35f5aa09bee_GRCh38.primary_assembly.genome.fa.2.bt2 added
7c35f315a044c_GRCh38.primary_assembly.genome.fa.3.bt2 added
7c35f5808091_GRCh38.primary_assembly.genome.fa.4.bt2 added
7c35f52ebaa72_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
7c35f5085a5c0_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
7c35f5af8a1b5_outfile.txt added
7c35f57668f00_GRCh37_to_GRCh38.chain added
7c35f1e425203_GRCh37_to_NCBI34.chain added
7c35f240624d6_GRCh37_to_NCBI35.chain added
7c35fee7dadf_GRCh37_to_NCBI36.chain added
7c35f3113b471_GRCh38_to_GRCh37.chain added
7c35f2bf60082_GRCh38_to_NCBI34.chain added
7c35f37474c6f_GRCh38_to_NCBI35.chain added
7c35f7ae71f60_GRCh38_to_NCBI36.chain added
7c35f2178f35c_NCBI34_to_GRCh37.chain added
7c35f3ace23a_NCBI34_to_GRCh38.chain added
7c35f26787790_NCBI35_to_GRCh37.chain added
7c35f44d0b90e_NCBI35_to_GRCh38.chain added
7c35f8635f88_NCBI36_to_GRCh37.chain added
7c35f4e94d486_NCBI36_to_GRCh38.chain added
7c35f107a8127_GRCm38_to_NCBIM36.chain added
7c35f2619c475_GRCm38_to_NCBIM37.chain added
7c35f4fde63b2_NCBIM36_to_GRCm38.chain added
7c35f5ee7e1d5_NCBIM37_to_GRCm38.chain added
7c35f1277d05b_1000G_omni2.5.b37.vcf.gz added
7c35f1c1de1a5_1000G_omni2.5.b37.vcf.gz.tbi added
7c35ffef2b12_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
7c35f4e0119f0_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
7c35f6d4614e6_1000G_omni2.5.hg38.vcf.gz added
7c35f620d4b61_1000G_omni2.5.hg38.vcf.gz.tbi added
7c35f60feff21_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
7c35f47e6b0d4_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
7c35f13674fad_af-only-gnomad.raw.sites.vcf added
7c35f667f7fb2_af-only-gnomad.raw.sites.vcf.idx added
7c35f1ad25b46_Mutect2-exome-panel.vcf.idx added
7c35f63ecf56e_Mutect2-WGS-panel-b37.vcf added
7c35f41782167_Mutect2-WGS-panel-b37.vcf.idx added
7c35f7238ea47_small_exac_common_3.vcf added
7c35f22f4771_small_exac_common_3.vcf.idx added
7c35f657e463e_1000g_pon.hg38.vcf.gz added
7c35f120c526_1000g_pon.hg38.vcf.gz.tbi added
7c35f3342fbe2_af-only-gnomad.hg38.vcf.gz added
7c35f117446c0_af-only-gnomad.hg38.vcf.gz.tbi added
7c35f38681195_small_exac_common_3.hg38.vcf.gz added
7c35f2e2a1b42_small_exac_common_3.hg38.vcf.gz.tbi added
7c35f32ed3a1c_gencode.v41.annotation.gtf added
7c35f3c14f3cf_gencode.v42.annotation.gtf added
7c35f54a292d3_gencode.vM30.annotation.gtf added
7c35f77bdf32b_gencode.vM31.annotation.gtf added
7c35f44785358_gencode.v41.transcripts.fa added
7c35f23376759_gencode.v41.transcripts.fa.fai added
7c35f8387452_gencode.v42.transcripts.fa added
7c35f6a9217cd_gencode.v42.transcripts.fa.fai added
7c35f7315cb0b_gencode.vM30.pc_transcripts.fa added
7c35f67205627_gencode.vM30.pc_transcripts.fa.fai added
7c35f7d09e828_gencode.vM31.pc_transcripts.fa added
7c35ff33acb0_gencode.vM31.pc_transcripts.fa.fai added
7c35f770f8139_GRCh38.primary_assembly.genome.fa.1.ht2 added
7c35f4b0b0219_GRCh38.primary_assembly.genome.fa.2.ht2 added
7c35f7c79c196_GRCh38.primary_assembly.genome.fa.3.ht2 added
7c35f591ccc9a_GRCh38.primary_assembly.genome.fa.4.ht2 added
7c35f2c0a013a_GRCh38.primary_assembly.genome.fa.5.ht2 added
7c35f4460726a_GRCh38.primary_assembly.genome.fa.6.ht2 added
7c35f6c841c47_GRCh38.primary_assembly.genome.fa.7.ht2 added
7c35f128980ed_GRCh38.primary_assembly.genome.fa.8.ht2 added
7c35f5f32cdb1_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
7c35f507111b5_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
7c35f5401a254_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
7c35f516bb7f8_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
7c35f52a05927_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
7c35f397fe892_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
7c35f528c7d1e_GRCh38_full_analysis_set_plus_decoy_hla.fa added
7c35f5e35509_GRCh38.primary_assembly.genome.fa.fai added
7c35f4af42f53_GRCh38.primary_assembly.genome.fa.amb added
7c35faf48eb3_GRCh38.primary_assembly.genome.fa.ann added
7c35f340d704c_GRCh38.primary_assembly.genome.fa.bwt added
7c35f7de1696f_GRCh38.primary_assembly.genome.fa.pac added
7c35f47098283_GRCh38.primary_assembly.genome.fa.sa added
7c35f8b0031f_GRCh38.primary_assembly.genome.fa added
7c35f759f5c9a_hs37d5.fa.fai added
7c35fb81d5db_hs37d5.fa.amb added
7c35f2be76a78_hs37d5.fa.ann added
7c35f7dd7d0ec_hs37d5.fa.bwt added
7c35f7613eda8_hs37d5.fa.pac added
7c35f1efd3584_hs37d5.fa.sa added
7c35f64f82713_hs37d5.fa added
7c35f731dd5d1_complete_ref_lens.bin added
7c35f2e30e234_ctable.bin added
7c35f5c07a84c_ctg_offsets.bin added
7c35f3e28d7ea_duplicate_clusters.tsv added
7c35f2aaaa3cb_info.json added
7c35f352474e6_mphf.bin added
7c35f6a32d924_pos.bin added
7c35f6f0b1635_pre_indexing.log added
7c35f21a8912e_rank.bin added
7c35f7cbc5a11_ref_indexing.log added
7c35f4e3de3e6_refAccumLengths.bin added
7c35f7219a2e3_reflengths.bin added
7c35f50bdfc66_refseq.bin added
7c35f1fa99bde_seq.bin added
7c35f44b9fc0a_versionInfo.json added
7c35fa3de4f8_salmon_index added
7c35f723618fc_chrLength.txt added
7c35f4a9d5114_chrName.txt added
7c35f5532144b_chrNameLength.txt added
7c35f7d2aa7b0_chrStart.txt added
7c35f7eaac160_exonGeTrInfo.tab added
7c35f53137dbb_exonInfo.tab added
7c35f44342a33_geneInfo.tab added
7c35f75ac47f_Genome added
7c35f48b2da55_genomeParameters.txt added
7c35f4fb6000e_Log.out added
7c35f33422ef7_SA added
7c35f468aab42_SAindex added
7c35f45c9edb6_sjdbInfo.txt added
7c35f523f647b_sjdbList.fromGTF.out.tab added
7c35f2b82d255_sjdbList.out.tab added
7c35f38e7c387_transcriptInfo.tab added
7c35f7046b0_GRCh38.GENCODE.v42_100 added
7c35f78a7aa2_knownGene_hg38.sql added
7c35f77109b71_knownGene_hg38.txt added
7c35f2b1aea7b_refGene_hg38.sql added
7c35f3caeef88_refGene_hg38.txt added
7c35f61437496_knownGene_mm39.sql added
7c35f1a2600b0_knownGene_mm39.txt added
7c35f5e5780b6_refGene_mm39.sql added
7c35f5dffcea7_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/RtmpUgRaf4/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
18.478 1.595 20.955
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.786 | 0.331 | 6.119 | |
| dataSearch | 1.078 | 0.018 | 1.096 | |
| dataUpdate | 0.000 | 0.001 | 0.000 | |
| getCloudData | 2.623 | 0.101 | 3.966 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.121 | 0.000 | 0.122 | |
| recipeLoad | 1.261 | 0.019 | 1.282 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.524 | 0.009 | 0.533 | |
| recipeUpdate | 0 | 0 | 0 | |