Qian Liu
| Snapshot Date: 2025-10-02 13:40 -0400 (Thu, 02 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_21 |
| git_last_commit: 601a107 |
| git_last_commit_date: 2025-04-15 13:01:44 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-06 11:38 -0400 (Mon, 06 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4832 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4613 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4554 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4585 |
| 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 1758/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.8.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | 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: 1.8.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReUseData_1.8.0.tar.gz |
| StartedAt: 2025-10-06 02:43:20 -0400 (Mon, 06 Oct 2025) |
| EndedAt: 2025-10-06 02:46:17 -0400 (Mon, 06 Oct 2025) |
| EllapsedTime: 177.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReUseData_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.8.0’
* 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 6.38 0.653 7.038
* 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-3.21-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.8.0’ ** 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 (2025-06-13) -- "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...
5013752ee123c_GRCh38.primary_assembly.genome.fa.1.bt2 added
501373b4971d1_GRCh38.primary_assembly.genome.fa.2.bt2 added
50137563d5f28_GRCh38.primary_assembly.genome.fa.3.bt2 added
501375b8e5884_GRCh38.primary_assembly.genome.fa.4.bt2 added
5013754886dcc_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
50137680ac981_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
50137143a3d61_outfile.txt added
50137605fbee2_GRCh37_to_GRCh38.chain added
501372646d670_GRCh37_to_NCBI34.chain added
5013731aa2815_GRCh37_to_NCBI35.chain added
50137432f003a_GRCh37_to_NCBI36.chain added
5013769e43fbd_GRCh38_to_GRCh37.chain added
50137351b0ac5_GRCh38_to_NCBI34.chain added
501375e9576fe_GRCh38_to_NCBI35.chain added
501371a9407cd_GRCh38_to_NCBI36.chain added
501371dc15380_NCBI34_to_GRCh37.chain added
501377dc45616_NCBI34_to_GRCh38.chain added
5013777b24f01_NCBI35_to_GRCh37.chain added
501372278c95_NCBI35_to_GRCh38.chain added
50137477a607e_NCBI36_to_GRCh37.chain added
5013727b5f511_NCBI36_to_GRCh38.chain added
501374fbdeab3_GRCm38_to_NCBIM36.chain added
50137a9bfefd_GRCm38_to_NCBIM37.chain added
5013778111389_NCBIM36_to_GRCm38.chain added
501377d5ed906_NCBIM37_to_GRCm38.chain added
501371ed65275_1000G_omni2.5.b37.vcf.gz added
501376a670c8b_1000G_omni2.5.b37.vcf.gz.tbi added
50137747277df_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
5013775b711a6_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
50137708b693e_1000G_omni2.5.hg38.vcf.gz added
501378f954f0_1000G_omni2.5.hg38.vcf.gz.tbi added
5013748a523e2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
501372bd4db0f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
501375f36b418_af-only-gnomad.raw.sites.vcf added
5013724337c66_af-only-gnomad.raw.sites.vcf.idx added
501375d48db_Mutect2-exome-panel.vcf.idx added
5013747417d99_Mutect2-WGS-panel-b37.vcf added
50137386db9c8_Mutect2-WGS-panel-b37.vcf.idx added
5013760bd07bd_small_exac_common_3.vcf added
501376d885409_small_exac_common_3.vcf.idx added
501376a17e1dd_1000g_pon.hg38.vcf.gz added
5013723ec07f7_1000g_pon.hg38.vcf.gz.tbi added
50137576c93c7_af-only-gnomad.hg38.vcf.gz added
501371f32eca3_af-only-gnomad.hg38.vcf.gz.tbi added
501372817ef5_small_exac_common_3.hg38.vcf.gz added
5013772009b94_small_exac_common_3.hg38.vcf.gz.tbi added
501373cf44023_gencode.v41.annotation.gtf added
5013745d50b_gencode.v42.annotation.gtf added
5013769b2ea96_gencode.vM30.annotation.gtf added
501373f1bccb8_gencode.vM31.annotation.gtf added
5013747c0358a_gencode.v41.transcripts.fa added
501371168dfa7_gencode.v41.transcripts.fa.fai added
50137ed9b76b_gencode.v42.transcripts.fa added
50137525c3487_gencode.v42.transcripts.fa.fai added
50137979f331_gencode.vM30.pc_transcripts.fa added
50137c389071_gencode.vM30.pc_transcripts.fa.fai added
50137713286fc_gencode.vM31.pc_transcripts.fa added
5013773e0ffbc_gencode.vM31.pc_transcripts.fa.fai added
50137ab0851_GRCh38.primary_assembly.genome.fa.1.ht2 added
5013766e998a2_GRCh38.primary_assembly.genome.fa.2.ht2 added
50137646c68fa_GRCh38.primary_assembly.genome.fa.3.ht2 added
501379a45d41_GRCh38.primary_assembly.genome.fa.4.ht2 added
501372f8ebc85_GRCh38.primary_assembly.genome.fa.5.ht2 added
5013710414409_GRCh38.primary_assembly.genome.fa.6.ht2 added
5013768db1159_GRCh38.primary_assembly.genome.fa.7.ht2 added
5013753c238eb_GRCh38.primary_assembly.genome.fa.8.ht2 added
50137109e8ce5_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
50137301c8ef2_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
50137c2ff2b3_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
50137715b94a2_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
501371da4e2fc_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
501377647d491_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
5013715479c9a_GRCh38_full_analysis_set_plus_decoy_hla.fa added
50137751176c3_GRCh38.primary_assembly.genome.fa.fai added
50137157ac134_GRCh38.primary_assembly.genome.fa.amb added
5013717c91b8f_GRCh38.primary_assembly.genome.fa.ann added
5013767121257_GRCh38.primary_assembly.genome.fa.bwt added
50137526f0157_GRCh38.primary_assembly.genome.fa.pac added
50137180ef09b_GRCh38.primary_assembly.genome.fa.sa added
5013750c4fced_GRCh38.primary_assembly.genome.fa added
50137118ace0f_hs37d5.fa.fai added
501375fcf2625_hs37d5.fa.amb added
50137622ddc95_hs37d5.fa.ann added
501372064857a_hs37d5.fa.bwt added
50137322b5aac_hs37d5.fa.pac added
501376ba7cfc6_hs37d5.fa.sa added
501372c9d15eb_hs37d5.fa added
50137235de1a9_complete_ref_lens.bin added
501375f88cf82_ctable.bin added
501372d481e3c_ctg_offsets.bin added
50137a477a4b_duplicate_clusters.tsv added
5013743f5387d_info.json added
5013736ec7b7d_mphf.bin added
5013739d636d0_pos.bin added
5013754367c86_pre_indexing.log added
501371fc78cd6_rank.bin added
50137d986fbc_ref_indexing.log added
5013764d5096b_refAccumLengths.bin added
501374fe41bc9_reflengths.bin added
5013719c8626f_refseq.bin added
5013756309e0e_seq.bin added
501376d88fec5_versionInfo.json added
5013710103700_salmon_index added
501376b783aa8_chrLength.txt added
50137629a7588_chrName.txt added
50137258af834_chrNameLength.txt added
501373415637_chrStart.txt added
5013749ac87df_exonGeTrInfo.tab added
5013777f9f98b_exonInfo.tab added
501371b5046d2_geneInfo.tab added
501371a7184cd_Genome added
50137984c79a_genomeParameters.txt added
501377b1f6cf7_Log.out added
501377c9f6162_SA added
5013729e94d14_SAindex added
501372d4ac7a4_sjdbInfo.txt added
5013768473128_sjdbList.fromGTF.out.tab added
5013756866300_sjdbList.out.tab added
5013750a8a94d_transcriptInfo.tab added
5013747d000aa_GRCh38.GENCODE.v42_100 added
501373ce813c_knownGene_hg38.sql added
501375af02398_knownGene_hg38.txt added
50137bc53927_refGene_hg38.sql added
501373abafcba_refGene_hg38.txt added
5013714c65a69_knownGene_mm39.sql added
501375ffbb5ae_knownGene_mm39.txt added
501375a828990_refGene_mm39.sql added
50137225eca25_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/RtmpdiKBuE/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
20.141 1.629 22.208
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.380 | 0.653 | 7.038 | |
| dataSearch | 1.154 | 0.016 | 1.170 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.703 | 0.223 | 4.200 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0.000 | 0.001 | 0.001 | |
| recipeHub-class | 0.124 | 0.003 | 0.128 | |
| recipeLoad | 1.295 | 0.060 | 1.355 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.554 | 0.034 | 0.588 | |
| recipeUpdate | 0 | 0 | 0 | |