Qian Liu
| Snapshot Date: 2025-12-08 13:45 -0500 (Mon, 08 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_22 |
| git_last_commit: 2d4066b |
| git_last_commit_date: 2025-10-29 11:20:44 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-11 12:05 -0500 (Thu, 11 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4879 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4670 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4604 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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 1773/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.10.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 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: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.10.0.tar.gz |
| StartedAt: 2025-12-09 10:31:19 -0500 (Tue, 09 Dec 2025) |
| EndedAt: 2025-12-09 10:35:50 -0500 (Tue, 09 Dec 2025) |
| EllapsedTime: 271.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.10.0’
* 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 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 12.037 1.227 14.562
getCloudData 4.550 0.201 6.223
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.10.0’ ** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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...
bc411e426bb9_GRCh38.primary_assembly.genome.fa.1.bt2 added
bc411aae4e34_GRCh38.primary_assembly.genome.fa.2.bt2 added
bc412990459b_GRCh38.primary_assembly.genome.fa.3.bt2 added
bc413ec9d86e_GRCh38.primary_assembly.genome.fa.4.bt2 added
bc4135a03df6_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
bc412b43fcfb_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
bc417c95d8ed_outfile.txt added
bc4151d4ef81_GRCh37_to_GRCh38.chain added
bc4172b8281f_GRCh37_to_NCBI34.chain added
bc4118524610_GRCh37_to_NCBI35.chain added
bc414175d0e9_GRCh37_to_NCBI36.chain added
bc411de69292_GRCh38_to_GRCh37.chain added
bc41ca0be94_GRCh38_to_NCBI34.chain added
bc41d3fed06_GRCh38_to_NCBI35.chain added
bc415fe22bb5_GRCh38_to_NCBI36.chain added
bc4179a3a940_NCBI34_to_GRCh37.chain added
bc4167bce723_NCBI34_to_GRCh38.chain added
bc4122eae00a_NCBI35_to_GRCh37.chain added
bc416a1ac26e_NCBI35_to_GRCh38.chain added
bc412d2fa2e_NCBI36_to_GRCh37.chain added
bc416926e374_NCBI36_to_GRCh38.chain added
bc41781f0a9a_GRCm38_to_NCBIM36.chain added
bc413df14212_GRCm38_to_NCBIM37.chain added
bc412a28cb83_NCBIM36_to_GRCm38.chain added
bc415c491b14_NCBIM37_to_GRCm38.chain added
bc414390ed61_1000G_omni2.5.b37.vcf.gz added
bc415fd09dee_1000G_omni2.5.b37.vcf.gz.tbi added
bc417930a566_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
bc4168bb09b2_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
bc414f79bad5_1000G_omni2.5.hg38.vcf.gz added
bc4140d91eb6_1000G_omni2.5.hg38.vcf.gz.tbi added
bc416e6f5ffc_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
bc415206d208_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
bc413dc7354a_af-only-gnomad.raw.sites.vcf added
bc41617bacf5_af-only-gnomad.raw.sites.vcf.idx added
bc417e983ad2_Mutect2-exome-panel.vcf.idx added
bc413c3df1ec_Mutect2-WGS-panel-b37.vcf added
bc416d5dbda_Mutect2-WGS-panel-b37.vcf.idx added
bc414254c8b7_small_exac_common_3.vcf added
bc414c458866_small_exac_common_3.vcf.idx added
bc4168fe07a8_1000g_pon.hg38.vcf.gz added
bc417da8dc71_1000g_pon.hg38.vcf.gz.tbi added
bc415920bf2a_af-only-gnomad.hg38.vcf.gz added
bc4174e68c1c_af-only-gnomad.hg38.vcf.gz.tbi added
bc414bf8be39_small_exac_common_3.hg38.vcf.gz added
bc413790b726_small_exac_common_3.hg38.vcf.gz.tbi added
bc417de83c49_gencode.v41.annotation.gtf added
bc4119ce1d33_gencode.v42.annotation.gtf added
bc412adf0c81_gencode.vM30.annotation.gtf added
bc4119adff24_gencode.vM31.annotation.gtf added
bc416e49a1a7_gencode.v41.transcripts.fa added
bc4124141382_gencode.v41.transcripts.fa.fai added
bc41220cce4f_gencode.v42.transcripts.fa added
bc4176bcb5ff_gencode.v42.transcripts.fa.fai added
bc415f50b53f_gencode.vM30.pc_transcripts.fa added
bc412bab6bfc_gencode.vM30.pc_transcripts.fa.fai added
bc4133e83ca_gencode.vM31.pc_transcripts.fa added
bc417d3e446f_gencode.vM31.pc_transcripts.fa.fai added
bc412ff13a6_GRCh38.primary_assembly.genome.fa.1.ht2 added
bc413862f8d3_GRCh38.primary_assembly.genome.fa.2.ht2 added
bc4169be0190_GRCh38.primary_assembly.genome.fa.3.ht2 added
bc413958cb2c_GRCh38.primary_assembly.genome.fa.4.ht2 added
bc417482d31d_GRCh38.primary_assembly.genome.fa.5.ht2 added
bc4138f250ad_GRCh38.primary_assembly.genome.fa.6.ht2 added
bc412c8eab10_GRCh38.primary_assembly.genome.fa.7.ht2 added
bc414a80be4a_GRCh38.primary_assembly.genome.fa.8.ht2 added
bc414a4d127c_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
bc419f8b100_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
bc41262c7c1d_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
bc413288677f_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
bc411942dcc4_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
bc4174abd4d0_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
bc413d20df87_GRCh38_full_analysis_set_plus_decoy_hla.fa added
bc413933376b_GRCh38.primary_assembly.genome.fa.fai added
bc41517b6f23_GRCh38.primary_assembly.genome.fa.amb added
bc417ebd8c9f_GRCh38.primary_assembly.genome.fa.ann added
bc414e5b5bba_GRCh38.primary_assembly.genome.fa.bwt added
bc414fe33886_GRCh38.primary_assembly.genome.fa.pac added
bc414e940e63_GRCh38.primary_assembly.genome.fa.sa added
bc415a3cade2_GRCh38.primary_assembly.genome.fa added
bc4145bbfeb6_hs37d5.fa.fai added
bc41394f827e_hs37d5.fa.amb added
bc4113003b97_hs37d5.fa.ann added
bc417448403f_hs37d5.fa.bwt added
bc41337223bd_hs37d5.fa.pac added
bc41a8867ae_hs37d5.fa.sa added
bc4114ed5e9_hs37d5.fa added
bc415ebdb4aa_complete_ref_lens.bin added
bc4178a0357d_ctable.bin added
bc415e17df69_ctg_offsets.bin added
bc41714c96c1_duplicate_clusters.tsv added
bc415b3d9303_info.json added
bc41277ed8c1_mphf.bin added
bc4178c87b28_pos.bin added
bc41320dbd0b_pre_indexing.log added
bc4123f636d9_rank.bin added
bc41798af300_ref_indexing.log added
bc411157c357_refAccumLengths.bin added
bc4118d98da6_reflengths.bin added
bc4172e29a08_refseq.bin added
bc417aeebe24_seq.bin added
bc4150056c89_versionInfo.json added
bc411418bf6a_salmon_index added
bc4164bed274_chrLength.txt added
bc412beaf158_chrName.txt added
bc414d8adeee_chrNameLength.txt added
bc4158320307_chrStart.txt added
bc413b64edcd_exonGeTrInfo.tab added
bc415f384c31_exonInfo.tab added
bc41691255cd_geneInfo.tab added
bc4132bf3b9f_Genome added
bc4128e35dc0_genomeParameters.txt added
bc41671ffd38_Log.out added
bc4165299c6c_SA added
bc41edcaa57_SAindex added
bc4139333d60_sjdbInfo.txt added
bc41530286f6_sjdbList.fromGTF.out.tab added
bc414aeaab0d_sjdbList.out.tab added
bc41748408e7_transcriptInfo.tab added
bc41864b174_GRCh38.GENCODE.v42_100 added
bc41abe3afa_knownGene_hg38.sql added
bc414f11f898_knownGene_hg38.txt added
bc4124d7ebb6_refGene_hg38.sql added
bc415bb40c9f_refGene_hg38.txt added
bc419a8c9c2_knownGene_mm39.sql added
bc412855e482_knownGene_mm39.txt added
bc411f0d277e_refGene_mm39.sql added
bc41189bd11f_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/Rtmp205RD1/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
38.353 3.630 51.945
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 12.037 | 1.227 | 14.562 | |
| dataSearch | 2.425 | 0.073 | 2.713 | |
| dataUpdate | 0.001 | 0.001 | 0.001 | |
| getCloudData | 4.550 | 0.201 | 6.223 | |
| getData | 0.000 | 0.001 | 0.002 | |
| meta_data | 0.001 | 0.001 | 0.002 | |
| recipeHub-class | 0.266 | 0.017 | 0.316 | |
| recipeLoad | 2.843 | 0.138 | 3.377 | |
| recipeMake | 0.001 | 0.002 | 0.002 | |
| recipeSearch | 1.138 | 0.056 | 1.300 | |
| recipeUpdate | 0.001 | 0.000 | 0.001 | |