Qian Liu
| Snapshot Date: 2025-08-20 13:45 -0400 (Wed, 20 Aug 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 2025-08-21 12:04 -0400 (Thu, 21 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4819 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4597 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4539 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4536 |
| 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 1740/2318 | 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: 2025-08-21 02:04:01 -0400 (Thu, 21 Aug 2025) |
| EndedAt: 2025-08-21 02:06:46 -0400 (Thu, 21 Aug 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 (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 ‘1.9.0’
* 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 6.385 0.495 6.882
* 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 (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...
2ec9725b16d72c_GRCh38.primary_assembly.genome.fa.1.bt2 added
2ec97239d4602c_GRCh38.primary_assembly.genome.fa.2.bt2 added
2ec9726013c0fd_GRCh38.primary_assembly.genome.fa.3.bt2 added
2ec97218875334_GRCh38.primary_assembly.genome.fa.4.bt2 added
2ec97272bd96d4_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2ec97253ebac4b_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2ec9725593e7cd_outfile.txt added
2ec97273abc52a_GRCh37_to_GRCh38.chain added
2ec972f97cb02_GRCh37_to_NCBI34.chain added
2ec9727b2a87d3_GRCh37_to_NCBI35.chain added
2ec9726f05a6a5_GRCh37_to_NCBI36.chain added
2ec9723e06e84c_GRCh38_to_GRCh37.chain added
2ec9725cab99e6_GRCh38_to_NCBI34.chain added
2ec97241e67470_GRCh38_to_NCBI35.chain added
2ec9727876b55c_GRCh38_to_NCBI36.chain added
2ec9726995fc29_NCBI34_to_GRCh37.chain added
2ec9727eb0e82c_NCBI34_to_GRCh38.chain added
2ec9727b2aded3_NCBI35_to_GRCh37.chain added
2ec9726b5d3f0f_NCBI35_to_GRCh38.chain added
2ec97236b5e141_NCBI36_to_GRCh37.chain added
2ec9721ff66391_NCBI36_to_GRCh38.chain added
2ec972ce39b7f_GRCm38_to_NCBIM36.chain added
2ec9723a172632_GRCm38_to_NCBIM37.chain added
2ec972554838cd_NCBIM36_to_GRCm38.chain added
2ec9725518e412_NCBIM37_to_GRCm38.chain added
2ec97269bdeb7d_1000G_omni2.5.b37.vcf.gz added
2ec972494aa4af_1000G_omni2.5.b37.vcf.gz.tbi added
2ec97236045cdb_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2ec9727485bbf4_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2ec97226fa5cb_1000G_omni2.5.hg38.vcf.gz added
2ec972374327a5_1000G_omni2.5.hg38.vcf.gz.tbi added
2ec9724f9c9320_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2ec9723c4405f8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2ec9721756e8a3_af-only-gnomad.raw.sites.vcf added
2ec9726823e654_af-only-gnomad.raw.sites.vcf.idx added
2ec9722f019ccc_Mutect2-exome-panel.vcf.idx added
2ec9726b4294ee_Mutect2-WGS-panel-b37.vcf added
2ec9723db7ce21_Mutect2-WGS-panel-b37.vcf.idx added
2ec97222ad61f6_small_exac_common_3.vcf added
2ec9727ada5ff0_small_exac_common_3.vcf.idx added
2ec97238e255f5_1000g_pon.hg38.vcf.gz added
2ec97211b3089b_1000g_pon.hg38.vcf.gz.tbi added
2ec97238e1483c_af-only-gnomad.hg38.vcf.gz added
2ec972158defdb_af-only-gnomad.hg38.vcf.gz.tbi added
2ec97253997d0b_small_exac_common_3.hg38.vcf.gz added
2ec9723157fd98_small_exac_common_3.hg38.vcf.gz.tbi added
2ec9727f23ec04_gencode.v41.annotation.gtf added
2ec972524a6537_gencode.v42.annotation.gtf added
2ec9722c82dc6b_gencode.vM30.annotation.gtf added
2ec9726a812b13_gencode.vM31.annotation.gtf added
2ec9729004679_gencode.v41.transcripts.fa added
2ec9724c793ffc_gencode.v41.transcripts.fa.fai added
2ec9727764c693_gencode.v42.transcripts.fa added
2ec97243176cab_gencode.v42.transcripts.fa.fai added
2ec97221c178c9_gencode.vM30.pc_transcripts.fa added
2ec9724c7daaa5_gencode.vM30.pc_transcripts.fa.fai added
2ec9722cd55828_gencode.vM31.pc_transcripts.fa added
2ec9726b0c1d79_gencode.vM31.pc_transcripts.fa.fai added
2ec9722820780_GRCh38.primary_assembly.genome.fa.1.ht2 added
2ec972215b141c_GRCh38.primary_assembly.genome.fa.2.ht2 added
2ec9726d7bc344_GRCh38.primary_assembly.genome.fa.3.ht2 added
2ec97239c52f26_GRCh38.primary_assembly.genome.fa.4.ht2 added
2ec97270f7a73d_GRCh38.primary_assembly.genome.fa.5.ht2 added
2ec97229bfc93c_GRCh38.primary_assembly.genome.fa.6.ht2 added
2ec972511c17c9_GRCh38.primary_assembly.genome.fa.7.ht2 added
2ec972591b8d91_GRCh38.primary_assembly.genome.fa.8.ht2 added
2ec97258c16608_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2ec9723c5eacb7_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2ec97216d35bb3_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2ec9727b6ec7ff_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2ec97237390ca7_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2ec9724fb5b1a8_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2ec972d21d09a_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2ec972701a54e3_GRCh38.primary_assembly.genome.fa.fai added
2ec9726543a183_GRCh38.primary_assembly.genome.fa.amb added
2ec97260bb4da6_GRCh38.primary_assembly.genome.fa.ann added
2ec9722172527b_GRCh38.primary_assembly.genome.fa.bwt added
2ec97264678d87_GRCh38.primary_assembly.genome.fa.pac added
2ec9723305b2dd_GRCh38.primary_assembly.genome.fa.sa added
2ec9724df52ee6_GRCh38.primary_assembly.genome.fa added
2ec9724ee8b89b_hs37d5.fa.fai added
2ec9723c05f956_hs37d5.fa.amb added
2ec9721a6e6ee2_hs37d5.fa.ann added
2ec972464d7f2e_hs37d5.fa.bwt added
2ec9727f1d6601_hs37d5.fa.pac added
2ec9723c2fe7ac_hs37d5.fa.sa added
2ec97212cb29d3_hs37d5.fa added
2ec9722bf2be2a_complete_ref_lens.bin added
2ec972273c0525_ctable.bin added
2ec972154d3154_ctg_offsets.bin added
2ec9724d4dd246_duplicate_clusters.tsv added
2ec97214b7c869_info.json added
2ec9724f12607a_mphf.bin added
2ec9723e457983_pos.bin added
2ec9723e7791a6_pre_indexing.log added
2ec972202e7843_rank.bin added
2ec97217610715_ref_indexing.log added
2ec9721738f7ae_refAccumLengths.bin added
2ec9725c8d24fa_reflengths.bin added
2ec9722e3462c8_refseq.bin added
2ec97212a7bfad_seq.bin added
2ec97213c631a1_versionInfo.json added
2ec9727dea1470_salmon_index added
2ec9721fc99048_chrLength.txt added
2ec9723e08684_chrName.txt added
2ec972632db5f3_chrNameLength.txt added
2ec97284ddee_chrStart.txt added
2ec9722552d8ff_exonGeTrInfo.tab added
2ec9724795437a_exonInfo.tab added
2ec972338a90cb_geneInfo.tab added
2ec972734807e5_Genome added
2ec972167dfc15_genomeParameters.txt added
2ec9726f908a22_Log.out added
2ec972db676c7_SA added
2ec9725ccb7b43_SAindex added
2ec9726eadf023_sjdbInfo.txt added
2ec97249e65e73_sjdbList.fromGTF.out.tab added
2ec9726f96a517_sjdbList.out.tab added
2ec9721aa0ae4d_transcriptInfo.tab added
2ec97271226398_GRCh38.GENCODE.v42_100 added
2ec9724e3d66b_knownGene_hg38.sql added
2ec97267ee8094_knownGene_hg38.txt added
2ec9725da2c02_refGene_hg38.sql added
2ec97253f636e5_refGene_hg38.txt added
2ec9722633fa17_knownGene_mm39.sql added
2ec9724451bda8_knownGene_mm39.txt added
2ec9727424af28_refGene_mm39.sql added
2ec9723d95012c_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/RtmpHu7t6s/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
18.110 1.289 19.676
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.385 | 0.495 | 6.882 | |
| dataSearch | 1.104 | 0.024 | 1.129 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.580 | 0.123 | 3.624 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.127 | 0.002 | 0.128 | |
| recipeLoad | 1.225 | 0.016 | 1.243 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.517 | 0.043 | 0.559 | |
| recipeUpdate | 0 | 0 | 0 | |