Qian Liu
| Snapshot Date: 2025-11-21 13:40 -0500 (Fri, 21 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 Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-22 11:37 -0500 (Sat, 22 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" | 4829 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4603 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4567 |
| 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 1750/2327 | 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 | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
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: 2025-11-22 03:10:36 -0500 (Sat, 22 Nov 2025) |
| EndedAt: 2025-11-22 03:13:20 -0500 (Sat, 22 Nov 2025) |
| EllapsedTime: 164.2 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 5.79 0.359 6.152
* 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...
2181db6e3b183d_GRCh38.primary_assembly.genome.fa.1.bt2 added
2181db4d25e189_GRCh38.primary_assembly.genome.fa.2.bt2 added
2181db337b9e1b_GRCh38.primary_assembly.genome.fa.3.bt2 added
2181db4df3d17d_GRCh38.primary_assembly.genome.fa.4.bt2 added
2181db6217493c_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2181dbc46e57b_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2181db4acd9e72_outfile.txt added
2181db2fc50ae0_GRCh37_to_GRCh38.chain added
2181db16bcdd86_GRCh37_to_NCBI34.chain added
2181db12c2eaab_GRCh37_to_NCBI35.chain added
2181db7a376291_GRCh37_to_NCBI36.chain added
2181db25b77f3_GRCh38_to_GRCh37.chain added
2181db5d8945f7_GRCh38_to_NCBI34.chain added
2181db25921f8c_GRCh38_to_NCBI35.chain added
2181db4f83a1a2_GRCh38_to_NCBI36.chain added
2181db3c9bad34_NCBI34_to_GRCh37.chain added
2181db3a167692_NCBI34_to_GRCh38.chain added
2181dbe02bc6e_NCBI35_to_GRCh37.chain added
2181db76d981d9_NCBI35_to_GRCh38.chain added
2181db68abc68a_NCBI36_to_GRCh37.chain added
2181db6fe483ba_NCBI36_to_GRCh38.chain added
2181db2e617d0a_GRCm38_to_NCBIM36.chain added
2181db469f9b95_GRCm38_to_NCBIM37.chain added
2181db7d03a89a_NCBIM36_to_GRCm38.chain added
2181db2f9db2ad_NCBIM37_to_GRCm38.chain added
2181db2e4cbe79_1000G_omni2.5.b37.vcf.gz added
2181db64160a37_1000G_omni2.5.b37.vcf.gz.tbi added
2181db76c0e357_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2181db5e62b583_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2181db2b4af5ef_1000G_omni2.5.hg38.vcf.gz added
2181db2fa3e069_1000G_omni2.5.hg38.vcf.gz.tbi added
2181db4c9dcdc0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2181db7870d778_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2181db631f7e84_af-only-gnomad.raw.sites.vcf added
2181db1a919f3d_af-only-gnomad.raw.sites.vcf.idx added
2181db5a8820b5_Mutect2-exome-panel.vcf.idx added
2181db6f666400_Mutect2-WGS-panel-b37.vcf added
2181db655f3db0_Mutect2-WGS-panel-b37.vcf.idx added
2181dba4d2b95_small_exac_common_3.vcf added
2181db6234186_small_exac_common_3.vcf.idx added
2181db7822285b_1000g_pon.hg38.vcf.gz added
2181db4848e26_1000g_pon.hg38.vcf.gz.tbi added
2181db87eb97a_af-only-gnomad.hg38.vcf.gz added
2181db55ab6e53_af-only-gnomad.hg38.vcf.gz.tbi added
2181db2a16adb2_small_exac_common_3.hg38.vcf.gz added
2181db58025b1c_small_exac_common_3.hg38.vcf.gz.tbi added
2181db12471b87_gencode.v41.annotation.gtf added
2181db642d2444_gencode.v42.annotation.gtf added
2181db6605178b_gencode.vM30.annotation.gtf added
2181db9209d60_gencode.vM31.annotation.gtf added
2181db4cd8eace_gencode.v41.transcripts.fa added
2181db55e99b45_gencode.v41.transcripts.fa.fai added
2181db37821a6a_gencode.v42.transcripts.fa added
2181db13788663_gencode.v42.transcripts.fa.fai added
2181db52ed43df_gencode.vM30.pc_transcripts.fa added
2181db671fcd17_gencode.vM30.pc_transcripts.fa.fai added
2181db41c544dc_gencode.vM31.pc_transcripts.fa added
2181db37034e16_gencode.vM31.pc_transcripts.fa.fai added
2181db5de0b06e_GRCh38.primary_assembly.genome.fa.1.ht2 added
2181db2027fa5f_GRCh38.primary_assembly.genome.fa.2.ht2 added
2181db624e4406_GRCh38.primary_assembly.genome.fa.3.ht2 added
2181dbd8490d7_GRCh38.primary_assembly.genome.fa.4.ht2 added
2181db6cc5c820_GRCh38.primary_assembly.genome.fa.5.ht2 added
2181db5abf1b7e_GRCh38.primary_assembly.genome.fa.6.ht2 added
2181db70a40f5c_GRCh38.primary_assembly.genome.fa.7.ht2 added
2181db757675d_GRCh38.primary_assembly.genome.fa.8.ht2 added
2181db35473c33_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2181db600a735c_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2181db6cb6a50d_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2181db3f9467c8_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2181db662db4e2_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2181db64d8cd69_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2181db4418f5ee_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2181db6eac6e5c_GRCh38.primary_assembly.genome.fa.fai added
2181db3a843bbc_GRCh38.primary_assembly.genome.fa.amb added
2181db6e2fa3a1_GRCh38.primary_assembly.genome.fa.ann added
2181db46aec979_GRCh38.primary_assembly.genome.fa.bwt added
2181db4ccb5743_GRCh38.primary_assembly.genome.fa.pac added
2181db525cc7e5_GRCh38.primary_assembly.genome.fa.sa added
2181db2cb3e104_GRCh38.primary_assembly.genome.fa added
2181db55ebf4a3_hs37d5.fa.fai added
2181db1f35b2b4_hs37d5.fa.amb added
2181db29d7c49_hs37d5.fa.ann added
2181dbd6e0f0d_hs37d5.fa.bwt added
2181db32ae3917_hs37d5.fa.pac added
2181db558ac028_hs37d5.fa.sa added
2181db748ddc25_hs37d5.fa added
2181db74737df4_complete_ref_lens.bin added
2181dbc8e0e3e_ctable.bin added
2181db526e8c93_ctg_offsets.bin added
2181db149b7853_duplicate_clusters.tsv added
2181db6edc5244_info.json added
2181db5ff31d6b_mphf.bin added
2181db1614073_pos.bin added
2181db499b6dc3_pre_indexing.log added
2181db50972cc7_rank.bin added
2181db8b8a7d1_ref_indexing.log added
2181db7ee2a9f6_refAccumLengths.bin added
2181db30a1a023_reflengths.bin added
2181db756f4cde_refseq.bin added
2181db3e7711bf_seq.bin added
2181db16cf5505_versionInfo.json added
2181db5a481a47_salmon_index added
2181db29007ad_chrLength.txt added
2181db57bc362_chrName.txt added
2181db14cc5603_chrNameLength.txt added
2181db70bfab4e_chrStart.txt added
2181db4c2a8cdb_exonGeTrInfo.tab added
2181db6197ad46_exonInfo.tab added
2181db431c7334_geneInfo.tab added
2181db78de6ddf_Genome added
2181db3783a1e9_genomeParameters.txt added
2181db625225e8_Log.out added
2181db7b7bea28_SA added
2181db44f1b0f7_SAindex added
2181db15005eff_sjdbInfo.txt added
2181db5106aa50_sjdbList.fromGTF.out.tab added
2181db397f8d1c_sjdbList.out.tab added
2181db973dcf3_transcriptInfo.tab added
2181db5d94b88e_GRCh38.GENCODE.v42_100 added
2181dbbee19af_knownGene_hg38.sql added
2181db1e0f5547_knownGene_hg38.txt added
2181db4c710ad3_refGene_hg38.sql added
2181db6be1371a_refGene_hg38.txt added
2181db1f7095ba_knownGene_mm39.sql added
2181db160c7896_knownGene_mm39.txt added
2181db3c7863e1_refGene_mm39.sql added
2181db28293d8b_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/RtmpJ9ucov/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
17.937 1.077 19.743
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.790 | 0.359 | 6.152 | |
| dataSearch | 1.173 | 0.032 | 1.208 | |
| dataUpdate | 0.000 | 0.001 | 0.000 | |
| getCloudData | 2.649 | 0.097 | 3.963 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.128 | 0.009 | 0.138 | |
| recipeLoad | 1.264 | 0.043 | 1.309 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.534 | 0.006 | 0.541 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |