Qian Liu
| Snapshot Date: 2025-11-07 13:40 -0500 (Fri, 07 Nov 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 Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-08 11:32 -0500 (Sat, 08 Nov 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" | 4821 |
| 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 1746/2323 | 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 | | ||||||||
|
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: 2025-11-08 03:08:26 -0500 (Sat, 08 Nov 2025) |
| EndedAt: 2025-11-08 03:11:12 -0500 (Sat, 08 Nov 2025) |
| EllapsedTime: 166.2 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 6.441 0.347 6.796
* 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...
2ecf836b0ecdfe_GRCh38.primary_assembly.genome.fa.1.bt2 added
2ecf83790bbfb0_GRCh38.primary_assembly.genome.fa.2.bt2 added
2ecf8337d4d4f_GRCh38.primary_assembly.genome.fa.3.bt2 added
2ecf8322b2f7f5_GRCh38.primary_assembly.genome.fa.4.bt2 added
2ecf837568187d_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2ecf83535bf094_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2ecf835372bc77_outfile.txt added
2ecf83495c1d18_GRCh37_to_GRCh38.chain added
2ecf832549fd2c_GRCh37_to_NCBI34.chain added
2ecf8343ee59b5_GRCh37_to_NCBI35.chain added
2ecf835001edf6_GRCh37_to_NCBI36.chain added
2ecf8345958da7_GRCh38_to_GRCh37.chain added
2ecf8322d829a0_GRCh38_to_NCBI34.chain added
2ecf837c78262d_GRCh38_to_NCBI35.chain added
2ecf83542f1e81_GRCh38_to_NCBI36.chain added
2ecf83618314c8_NCBI34_to_GRCh37.chain added
2ecf834a8e6bb5_NCBI34_to_GRCh38.chain added
2ecf8325dbc8b4_NCBI35_to_GRCh37.chain added
2ecf836cafef07_NCBI35_to_GRCh38.chain added
2ecf836a9012aa_NCBI36_to_GRCh37.chain added
2ecf8350c467b4_NCBI36_to_GRCh38.chain added
2ecf836c0c69ed_GRCm38_to_NCBIM36.chain added
2ecf8362e260e0_GRCm38_to_NCBIM37.chain added
2ecf837ea14e3c_NCBIM36_to_GRCm38.chain added
2ecf8321c400e3_NCBIM37_to_GRCm38.chain added
2ecf831bd3fdec_1000G_omni2.5.b37.vcf.gz added
2ecf8327d4268_1000G_omni2.5.b37.vcf.gz.tbi added
2ecf835dfc856_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2ecf832b634257_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2ecf833dfc3906_1000G_omni2.5.hg38.vcf.gz added
2ecf8376417eee_1000G_omni2.5.hg38.vcf.gz.tbi added
2ecf8316721055_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2ecf833707f8b6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2ecf8379becc3d_af-only-gnomad.raw.sites.vcf added
2ecf833925084a_af-only-gnomad.raw.sites.vcf.idx added
2ecf832c701133_Mutect2-exome-panel.vcf.idx added
2ecf834d1abcd1_Mutect2-WGS-panel-b37.vcf added
2ecf83c97c4c1_Mutect2-WGS-panel-b37.vcf.idx added
2ecf8375cc2e4b_small_exac_common_3.vcf added
2ecf837264b9fd_small_exac_common_3.vcf.idx added
2ecf8350861e76_1000g_pon.hg38.vcf.gz added
2ecf8345ce1c41_1000g_pon.hg38.vcf.gz.tbi added
2ecf8337fa47a5_af-only-gnomad.hg38.vcf.gz added
2ecf83735e4816_af-only-gnomad.hg38.vcf.gz.tbi added
2ecf834246426e_small_exac_common_3.hg38.vcf.gz added
2ecf83c296626_small_exac_common_3.hg38.vcf.gz.tbi added
2ecf8354e15cde_gencode.v41.annotation.gtf added
2ecf83cd4ae23_gencode.v42.annotation.gtf added
2ecf8332052eda_gencode.vM30.annotation.gtf added
2ecf8341914be6_gencode.vM31.annotation.gtf added
2ecf837764c0cd_gencode.v41.transcripts.fa added
2ecf832c9968e_gencode.v41.transcripts.fa.fai added
2ecf832d9db5d3_gencode.v42.transcripts.fa added
2ecf835a4721ad_gencode.v42.transcripts.fa.fai added
2ecf8316ae4ca_gencode.vM30.pc_transcripts.fa added
2ecf834f61b6b7_gencode.vM30.pc_transcripts.fa.fai added
2ecf83761b1f9a_gencode.vM31.pc_transcripts.fa added
2ecf833e82732_gencode.vM31.pc_transcripts.fa.fai added
2ecf8355417f0d_GRCh38.primary_assembly.genome.fa.1.ht2 added
2ecf83217e61f1_GRCh38.primary_assembly.genome.fa.2.ht2 added
2ecf8341e46038_GRCh38.primary_assembly.genome.fa.3.ht2 added
2ecf834b82fdfb_GRCh38.primary_assembly.genome.fa.4.ht2 added
2ecf8337f07246_GRCh38.primary_assembly.genome.fa.5.ht2 added
2ecf8378ec58ee_GRCh38.primary_assembly.genome.fa.6.ht2 added
2ecf834541ca38_GRCh38.primary_assembly.genome.fa.7.ht2 added
2ecf8371157a90_GRCh38.primary_assembly.genome.fa.8.ht2 added
2ecf83255c6a22_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2ecf83125c8709_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2ecf837dad3f51_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2ecf831b28986d_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2ecf834c14106_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2ecf834e335dc8_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2ecf8360f6b4af_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2ecf833cbb88ab_GRCh38.primary_assembly.genome.fa.fai added
2ecf834191a5de_GRCh38.primary_assembly.genome.fa.amb added
2ecf83233cf71d_GRCh38.primary_assembly.genome.fa.ann added
2ecf8348e4eed1_GRCh38.primary_assembly.genome.fa.bwt added
2ecf83167302bd_GRCh38.primary_assembly.genome.fa.pac added
2ecf833011a541_GRCh38.primary_assembly.genome.fa.sa added
2ecf837aea1dab_GRCh38.primary_assembly.genome.fa added
2ecf8358044ea3_hs37d5.fa.fai added
2ecf832776660e_hs37d5.fa.amb added
2ecf837db3b43a_hs37d5.fa.ann added
2ecf835a20476_hs37d5.fa.bwt added
2ecf831bd87bc_hs37d5.fa.pac added
2ecf837f1e9904_hs37d5.fa.sa added
2ecf835503bb2d_hs37d5.fa added
2ecf8377d8a756_complete_ref_lens.bin added
2ecf83306c037_ctable.bin added
2ecf832a453a3a_ctg_offsets.bin added
2ecf8319570947_duplicate_clusters.tsv added
2ecf8344eb206f_info.json added
2ecf8375c83835_mphf.bin added
2ecf8351477b8d_pos.bin added
2ecf833dd7795e_pre_indexing.log added
2ecf833b0a026d_rank.bin added
2ecf83425cf61d_ref_indexing.log added
2ecf836333e380_refAccumLengths.bin added
2ecf834d668976_reflengths.bin added
2ecf83400a356e_refseq.bin added
2ecf837e5c7bed_seq.bin added
2ecf835227ca7d_versionInfo.json added
2ecf83e3d9336_salmon_index added
2ecf835f53309c_chrLength.txt added
2ecf83ee35328_chrName.txt added
2ecf834fcf3915_chrNameLength.txt added
2ecf8329027ba_chrStart.txt added
2ecf8357c841fa_exonGeTrInfo.tab added
2ecf8366423bd2_exonInfo.tab added
2ecf8332a1ccfb_geneInfo.tab added
2ecf8352b25fa5_Genome added
2ecf833e468a75_genomeParameters.txt added
2ecf835a183309_Log.out added
2ecf83506613df_SA added
2ecf8343e88eeb_SAindex added
2ecf835bd5bac5_sjdbInfo.txt added
2ecf834f84ace4_sjdbList.fromGTF.out.tab added
2ecf8318ec4a19_sjdbList.out.tab added
2ecf8353ae621b_transcriptInfo.tab added
2ecf83528b6d1b_GRCh38.GENCODE.v42_100 added
2ecf8343318453_knownGene_hg38.sql added
2ecf836d056b62_knownGene_hg38.txt added
2ecf8317768d8a_refGene_hg38.sql added
2ecf8338f9bc89_refGene_hg38.txt added
2ecf833e4ce6ef_knownGene_mm39.sql added
2ecf83554e06e8_knownGene_mm39.txt added
2ecf837403bef6_refGene_mm39.sql added
2ecf83a9dd0c_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/Rtmpu34eR0/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
18.167 1.151 20.215
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.441 | 0.347 | 6.796 | |
| dataSearch | 1.160 | 0.059 | 1.219 | |
| dataUpdate | 0.001 | 0.000 | 0.000 | |
| getCloudData | 2.602 | 0.126 | 3.652 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.121 | 0.002 | 0.123 | |
| recipeLoad | 1.261 | 0.020 | 1.281 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.521 | 0.009 | 0.530 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |