Qian Liu
| Snapshot Date: 2025-09-14 13:45 -0400 (Sun, 14 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: c5927b9 |
| git_last_commit_date: 2025-04-15 13:01:44 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-15 12:03 -0400 (Mon, 15 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4719 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4538 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4522 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4543 |
| 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 1747/2327 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.9.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.9.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.9.0.tar.gz |
| StartedAt: 2025-09-15 03:09:16 -0400 (Mon, 15 Sep 2025) |
| EndedAt: 2025-09-15 03:12:01 -0400 (Mon, 15 Sep 2025) |
| EllapsedTime: 165.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘1.9.0’
* 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 5.572 0.221 5.795
* 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-3.22-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.9.0’ ** 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 version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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...
28ce0b2269283_GRCh38.primary_assembly.genome.fa.1.bt2 added
28ce0b44158357_GRCh38.primary_assembly.genome.fa.2.bt2 added
28ce0b7da4389e_GRCh38.primary_assembly.genome.fa.3.bt2 added
28ce0b385a954_GRCh38.primary_assembly.genome.fa.4.bt2 added
28ce0b2d659fab_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
28ce0b55f0284c_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
28ce0be5f4d7a_outfile.txt added
28ce0b5f6d5257_GRCh37_to_GRCh38.chain added
28ce0b3daf03f3_GRCh37_to_NCBI34.chain added
28ce0b8fa2573_GRCh37_to_NCBI35.chain added
28ce0b250a5fd9_GRCh37_to_NCBI36.chain added
28ce0b1244e865_GRCh38_to_GRCh37.chain added
28ce0b1dbba167_GRCh38_to_NCBI34.chain added
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28ce0b794265c1_NCBI34_to_GRCh37.chain added
28ce0b668e36f3_NCBI34_to_GRCh38.chain added
28ce0b348b9994_NCBI35_to_GRCh37.chain added
28ce0b6007fcb1_NCBI35_to_GRCh38.chain added
28ce0b5f083f49_NCBI36_to_GRCh37.chain added
28ce0b3a271fa0_NCBI36_to_GRCh38.chain added
28ce0b16cb849b_GRCm38_to_NCBIM36.chain added
28ce0b7ef46331_GRCm38_to_NCBIM37.chain added
28ce0b3a10ff09_NCBIM36_to_GRCm38.chain added
28ce0b6f614d04_NCBIM37_to_GRCm38.chain added
28ce0b415170d_1000G_omni2.5.b37.vcf.gz added
28ce0b382b40f8_1000G_omni2.5.b37.vcf.gz.tbi added
28ce0b50638630_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
28ce0b22b65b18_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
28ce0bc8b14af_1000G_omni2.5.hg38.vcf.gz added
28ce0b6fcfc6e5_1000G_omni2.5.hg38.vcf.gz.tbi added
28ce0b24dced9b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
28ce0b50a09806_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
28ce0b6d73ff83_af-only-gnomad.raw.sites.vcf added
28ce0b286296ef_af-only-gnomad.raw.sites.vcf.idx added
28ce0b7e0637b1_Mutect2-exome-panel.vcf.idx added
28ce0b436427cf_Mutect2-WGS-panel-b37.vcf added
28ce0b36c1e46a_Mutect2-WGS-panel-b37.vcf.idx added
28ce0b5d738a08_small_exac_common_3.vcf added
28ce0b1132bc2_small_exac_common_3.vcf.idx added
28ce0b3fbc09dd_1000g_pon.hg38.vcf.gz added
28ce0b27de9e2_1000g_pon.hg38.vcf.gz.tbi added
28ce0b13581428_af-only-gnomad.hg38.vcf.gz added
28ce0b5d77ab44_af-only-gnomad.hg38.vcf.gz.tbi added
28ce0b64819a34_small_exac_common_3.hg38.vcf.gz added
28ce0b73eb9f8e_small_exac_common_3.hg38.vcf.gz.tbi added
28ce0b56ba1105_gencode.v41.annotation.gtf added
28ce0b4b0fd127_gencode.v42.annotation.gtf added
28ce0b28773922_gencode.vM30.annotation.gtf added
28ce0b36c20db6_gencode.vM31.annotation.gtf added
28ce0b2a181070_gencode.v41.transcripts.fa added
28ce0b629e58c2_gencode.v41.transcripts.fa.fai added
28ce0b4d8d9251_gencode.v42.transcripts.fa added
28ce0b290c73a2_gencode.v42.transcripts.fa.fai added
28ce0b1caf57cc_gencode.vM30.pc_transcripts.fa added
28ce0b3ceedf56_gencode.vM30.pc_transcripts.fa.fai added
28ce0b2d218aaf_gencode.vM31.pc_transcripts.fa added
28ce0b54da98c4_gencode.vM31.pc_transcripts.fa.fai added
28ce0bd526586_GRCh38.primary_assembly.genome.fa.1.ht2 added
28ce0b4fd7e5c7_GRCh38.primary_assembly.genome.fa.2.ht2 added
28ce0b6165ad73_GRCh38.primary_assembly.genome.fa.3.ht2 added
28ce0b7d222c6c_GRCh38.primary_assembly.genome.fa.4.ht2 added
28ce0b74b4d362_GRCh38.primary_assembly.genome.fa.5.ht2 added
28ce0b32064579_GRCh38.primary_assembly.genome.fa.6.ht2 added
28ce0b6a962bef_GRCh38.primary_assembly.genome.fa.7.ht2 added
28ce0b1d176a52_GRCh38.primary_assembly.genome.fa.8.ht2 added
28ce0b300c7d2b_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
28ce0b2dfa53bf_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
28ce0b53d94ebc_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
28ce0bd800733_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
28ce0b2f0d7f81_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
28ce0b13955899_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
28ce0bffdf115_GRCh38_full_analysis_set_plus_decoy_hla.fa added
28ce0b426593a9_GRCh38.primary_assembly.genome.fa.fai added
28ce0b710d03de_GRCh38.primary_assembly.genome.fa.amb added
28ce0b747f8b49_GRCh38.primary_assembly.genome.fa.ann added
28ce0b36513338_GRCh38.primary_assembly.genome.fa.bwt added
28ce0b47c714e3_GRCh38.primary_assembly.genome.fa.pac added
28ce0b3f8f5c70_GRCh38.primary_assembly.genome.fa.sa added
28ce0b5ec86c5a_GRCh38.primary_assembly.genome.fa added
28ce0b7e89229a_hs37d5.fa.fai added
28ce0b69a76ce1_hs37d5.fa.amb added
28ce0b4166c51d_hs37d5.fa.ann added
28ce0b4c16b4eb_hs37d5.fa.bwt added
28ce0b12b3e083_hs37d5.fa.pac added
28ce0b5e161ce9_hs37d5.fa.sa added
28ce0b9059441_hs37d5.fa added
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28ce0b32f0b5ad_ctable.bin added
28ce0b1657f9c8_ctg_offsets.bin added
28ce0bfad50fa_duplicate_clusters.tsv added
28ce0b14566320_info.json added
28ce0b137a2634_mphf.bin added
28ce0b462245c_pos.bin added
28ce0b465ca899_pre_indexing.log added
28ce0b7e105223_rank.bin added
28ce0b21798eae_ref_indexing.log added
28ce0b766925c4_refAccumLengths.bin added
28ce0b2c0aa5e2_reflengths.bin added
28ce0b7552dd6a_refseq.bin added
28ce0b3e92cf8_seq.bin added
28ce0b5b182564_versionInfo.json added
28ce0b8e83604_salmon_index added
28ce0b13e71e0d_chrLength.txt added
28ce0b1d7db90d_chrName.txt added
28ce0b79f539e2_chrNameLength.txt added
28ce0b866a957_chrStart.txt added
28ce0b53ceec45_exonGeTrInfo.tab added
28ce0b41bc4ec5_exonInfo.tab added
28ce0b47f605c7_geneInfo.tab added
28ce0b329758a0_Genome added
28ce0b4045715f_genomeParameters.txt added
28ce0b319d72a8_Log.out added
28ce0b73fe1dbd_SA added
28ce0bc5c264b_SAindex added
28ce0b4451532b_sjdbInfo.txt added
28ce0b52143aa6_sjdbList.fromGTF.out.tab added
28ce0b1561ba8c_sjdbList.out.tab added
28ce0b426be5e_transcriptInfo.tab added
28ce0b504f053_GRCh38.GENCODE.v42_100 added
28ce0b2bb9b454_knownGene_hg38.sql added
28ce0b13d40f58_knownGene_hg38.txt added
28ce0b195b5373_refGene_hg38.sql added
28ce0b3f33da88_refGene_hg38.txt added
28ce0b183633b4_knownGene_mm39.sql added
28ce0b5fb7fc0c_knownGene_mm39.txt added
28ce0b3d442cac_refGene_mm39.sql added
28ce0b39afc263_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/RtmpgsF3Mg/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
17.459 0.919 18.891
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.572 | 0.221 | 5.795 | |
| dataSearch | 1.060 | 0.007 | 1.066 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.649 | 0.177 | 3.835 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.119 | 0.001 | 0.120 | |
| recipeLoad | 1.258 | 0.042 | 1.301 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.533 | 0.006 | 0.539 | |
| recipeUpdate | 0 | 0 | 0 | |