Qian Liu
| Snapshot Date: 2025-12-03 13:40 -0500 (Wed, 03 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 2025-12-04 11:35 -0500 (Thu, 04 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" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4576 |
| 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 1753/2331 | 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: 2025-12-04 05:15:18 -0500 (Thu, 04 Dec 2025) |
| EndedAt: 2025-12-04 05:18:05 -0500 (Thu, 04 Dec 2025) |
| EllapsedTime: 167.3 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 5.862 0.362 6.225
* 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...
3b27b4387cb88f_GRCh38.primary_assembly.genome.fa.1.bt2 added
3b27b42e663c80_GRCh38.primary_assembly.genome.fa.2.bt2 added
3b27b46dfd3dde_GRCh38.primary_assembly.genome.fa.3.bt2 added
3b27b4e8fa658_GRCh38.primary_assembly.genome.fa.4.bt2 added
3b27b4387d64de_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3b27b444ad3a07_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3b27b45dd01547_outfile.txt added
3b27b411b0ccb7_GRCh37_to_GRCh38.chain added
3b27b424685267_GRCh37_to_NCBI34.chain added
3b27b479180d29_GRCh37_to_NCBI35.chain added
3b27b47bf272e1_GRCh37_to_NCBI36.chain added
3b27b4304fc275_GRCh38_to_GRCh37.chain added
3b27b46208ac47_GRCh38_to_NCBI34.chain added
3b27b44ab66a63_GRCh38_to_NCBI35.chain added
3b27b455cd01a0_GRCh38_to_NCBI36.chain added
3b27b467f8dfed_NCBI34_to_GRCh37.chain added
3b27b429987c7c_NCBI34_to_GRCh38.chain added
3b27b471b9f43a_NCBI35_to_GRCh37.chain added
3b27b46be0266f_NCBI35_to_GRCh38.chain added
3b27b4371efe29_NCBI36_to_GRCh37.chain added
3b27b42b256525_NCBI36_to_GRCh38.chain added
3b27b461e977cd_GRCm38_to_NCBIM36.chain added
3b27b422f712ed_GRCm38_to_NCBIM37.chain added
3b27b4c3a77f7_NCBIM36_to_GRCm38.chain added
3b27b4ffb3b2d_NCBIM37_to_GRCm38.chain added
3b27b421c3e053_1000G_omni2.5.b37.vcf.gz added
3b27b478f6603_1000G_omni2.5.b37.vcf.gz.tbi added
3b27b4688fb04c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3b27b44cfd3ffc_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3b27b44214551_1000G_omni2.5.hg38.vcf.gz added
3b27b46090088_1000G_omni2.5.hg38.vcf.gz.tbi added
3b27b4579f88b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3b27b4328781d1_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3b27b474063e66_af-only-gnomad.raw.sites.vcf added
3b27b414099ee3_af-only-gnomad.raw.sites.vcf.idx added
3b27b46b04e6af_Mutect2-exome-panel.vcf.idx added
3b27b438b3786d_Mutect2-WGS-panel-b37.vcf added
3b27b471d9b42a_Mutect2-WGS-panel-b37.vcf.idx added
3b27b47cb5b366_small_exac_common_3.vcf added
3b27b45d1bcad4_small_exac_common_3.vcf.idx added
3b27b46af1c153_1000g_pon.hg38.vcf.gz added
3b27b478a82648_1000g_pon.hg38.vcf.gz.tbi added
3b27b4d6b8d49_af-only-gnomad.hg38.vcf.gz added
3b27b44cfa6d9a_af-only-gnomad.hg38.vcf.gz.tbi added
3b27b4435e90ab_small_exac_common_3.hg38.vcf.gz added
3b27b463388ee9_small_exac_common_3.hg38.vcf.gz.tbi added
3b27b434f34d87_gencode.v41.annotation.gtf added
3b27b46cf70d28_gencode.v42.annotation.gtf added
3b27b454f28323_gencode.vM30.annotation.gtf added
3b27b420d373f6_gencode.vM31.annotation.gtf added
3b27b424160b51_gencode.v41.transcripts.fa added
3b27b417e848_gencode.v41.transcripts.fa.fai added
3b27b42bcebc3_gencode.v42.transcripts.fa added
3b27b4470d1e3f_gencode.v42.transcripts.fa.fai added
3b27b4c52603f_gencode.vM30.pc_transcripts.fa added
3b27b412b826f0_gencode.vM30.pc_transcripts.fa.fai added
3b27b468d0fe92_gencode.vM31.pc_transcripts.fa added
3b27b413e1c642_gencode.vM31.pc_transcripts.fa.fai added
3b27b47b47d73c_GRCh38.primary_assembly.genome.fa.1.ht2 added
3b27b435ce3e8e_GRCh38.primary_assembly.genome.fa.2.ht2 added
3b27b418030b93_GRCh38.primary_assembly.genome.fa.3.ht2 added
3b27b4150d7c4_GRCh38.primary_assembly.genome.fa.4.ht2 added
3b27b43b483719_GRCh38.primary_assembly.genome.fa.5.ht2 added
3b27b44a8a8d64_GRCh38.primary_assembly.genome.fa.6.ht2 added
3b27b47557162a_GRCh38.primary_assembly.genome.fa.7.ht2 added
3b27b44f51d5fc_GRCh38.primary_assembly.genome.fa.8.ht2 added
3b27b4358f7413_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3b27b42e0a8e97_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3b27b4412b8a26_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3b27b43245277a_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3b27b4b26596b_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3b27b42c1d4b79_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3b27b42aed4dc2_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3b27b41891e6b4_GRCh38.primary_assembly.genome.fa.fai added
3b27b47917b913_GRCh38.primary_assembly.genome.fa.amb added
3b27b46e4bde6d_GRCh38.primary_assembly.genome.fa.ann added
3b27b47bca759e_GRCh38.primary_assembly.genome.fa.bwt added
3b27b42e0b069a_GRCh38.primary_assembly.genome.fa.pac added
3b27b45b42eb95_GRCh38.primary_assembly.genome.fa.sa added
3b27b450bcf8c1_GRCh38.primary_assembly.genome.fa added
3b27b44ede7a90_hs37d5.fa.fai added
3b27b47f58f6e7_hs37d5.fa.amb added
3b27b450d4e10a_hs37d5.fa.ann added
3b27b4519b6654_hs37d5.fa.bwt added
3b27b446661526_hs37d5.fa.pac added
3b27b45d274149_hs37d5.fa.sa added
3b27b464538d44_hs37d5.fa added
3b27b42f3713b8_complete_ref_lens.bin added
3b27b47109078c_ctable.bin added
3b27b45f9b6481_ctg_offsets.bin added
3b27b465055246_duplicate_clusters.tsv added
3b27b490c131f_info.json added
3b27b460ec3c45_mphf.bin added
3b27b4204d895f_pos.bin added
3b27b45396a084_pre_indexing.log added
3b27b456435270_rank.bin added
3b27b46f9f5f5b_ref_indexing.log added
3b27b49261497_refAccumLengths.bin added
3b27b444de107_reflengths.bin added
3b27b430cae981_refseq.bin added
3b27b43b6b3c11_seq.bin added
3b27b4f743a73_versionInfo.json added
3b27b45ce834fa_salmon_index added
3b27b4665889d3_chrLength.txt added
3b27b428062127_chrName.txt added
3b27b455ffee0d_chrNameLength.txt added
3b27b454a46841_chrStart.txt added
3b27b423d096c5_exonGeTrInfo.tab added
3b27b440af4a7_exonInfo.tab added
3b27b42fe753d6_geneInfo.tab added
3b27b4748d8f87_Genome added
3b27b452e96f37_genomeParameters.txt added
3b27b42f404abd_Log.out added
3b27b445627091_SA added
3b27b42484d58b_SAindex added
3b27b475a65fe3_sjdbInfo.txt added
3b27b42289b1da_sjdbList.fromGTF.out.tab added
3b27b48d862d0_sjdbList.out.tab added
3b27b424dd739b_transcriptInfo.tab added
3b27b41392b966_GRCh38.GENCODE.v42_100 added
3b27b46873c751_knownGene_hg38.sql added
3b27b49e2c5e1_knownGene_hg38.txt added
3b27b41c9ecc86_refGene_hg38.sql added
3b27b449600396_refGene_hg38.txt added
3b27b42a304f40_knownGene_mm39.sql added
3b27b470356d0a_knownGene_mm39.txt added
3b27b41fa35606_refGene_mm39.sql added
3b27b419cfae9b_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/RtmpIIn47k/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
18.346 1.260 20.182
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.862 | 0.362 | 6.225 | |
| dataSearch | 1.082 | 0.031 | 1.115 | |
| dataUpdate | 0.001 | 0.001 | 0.001 | |
| getCloudData | 2.568 | 0.141 | 3.859 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.001 | 0.001 | |
| recipeHub-class | 0.123 | 0.006 | 0.129 | |
| recipeLoad | 1.275 | 0.086 | 1.361 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.524 | 0.009 | 0.533 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |