Qian Liu
| Snapshot Date: 2025-12-04 13:45 -0500 (Thu, 04 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 2025-12-08 12:02 -0500 (Mon, 08 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" | 4668 |
| 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 | | ||||||||
| 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: 2025-12-05 10:45:11 -0500 (Fri, 05 Dec 2025) |
| EndedAt: 2025-12-05 10:50:38 -0500 (Fri, 05 Dec 2025) |
| EllapsedTime: 326.9 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 12.326 1.304 18.198
getCloudData 4.546 0.201 6.586
* 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...
115212dd019b6_GRCh38.primary_assembly.genome.fa.1.bt2 added
1152139481339_GRCh38.primary_assembly.genome.fa.2.bt2 added
115212ae62090_GRCh38.primary_assembly.genome.fa.3.bt2 added
115216a63e3f0_GRCh38.primary_assembly.genome.fa.4.bt2 added
115214409d821_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
11521624c816c_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
11521cc50bdf_outfile.txt added
115215c8e6405_GRCh37_to_GRCh38.chain added
11521848b3bc_GRCh37_to_NCBI34.chain added
115215d0fffe3_GRCh37_to_NCBI35.chain added
115214568bfd0_GRCh37_to_NCBI36.chain added
1152160091449_GRCh38_to_GRCh37.chain added
115217412f5e0_GRCh38_to_NCBI34.chain added
115218cc80a9_GRCh38_to_NCBI35.chain added
115212a12dbc2_GRCh38_to_NCBI36.chain added
115213c19b322_NCBI34_to_GRCh37.chain added
115213b3f9c01_NCBI34_to_GRCh38.chain added
115214d1b240a_NCBI35_to_GRCh37.chain added
1152130db3412_NCBI35_to_GRCh38.chain added
11521737a2cd_NCBI36_to_GRCh37.chain added
1152155a1446e_NCBI36_to_GRCh38.chain added
115214e93bdad_GRCm38_to_NCBIM36.chain added
115214589d128_GRCm38_to_NCBIM37.chain added
115215b02bcc2_NCBIM36_to_GRCm38.chain added
1152110b6933c_NCBIM37_to_GRCm38.chain added
11521427c50b6_1000G_omni2.5.b37.vcf.gz added
115216f96fed3_1000G_omni2.5.b37.vcf.gz.tbi added
11521223407e1_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
115215f15652_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
11521275a248a_1000G_omni2.5.hg38.vcf.gz added
11521f14f435_1000G_omni2.5.hg38.vcf.gz.tbi added
1152128accb4f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
115216857c465_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
115215a1ef867_af-only-gnomad.raw.sites.vcf added
115212746606a_af-only-gnomad.raw.sites.vcf.idx added
115217d63e34a_Mutect2-exome-panel.vcf.idx added
1152128df4f96_Mutect2-WGS-panel-b37.vcf added
115215ce215d0_Mutect2-WGS-panel-b37.vcf.idx added
115217f063a53_small_exac_common_3.vcf added
1152171df604b_small_exac_common_3.vcf.idx added
115212b1655_1000g_pon.hg38.vcf.gz added
11521cc72689_1000g_pon.hg38.vcf.gz.tbi added
1152166b2f2ec_af-only-gnomad.hg38.vcf.gz added
115216e6a98a0_af-only-gnomad.hg38.vcf.gz.tbi added
11521184a6902_small_exac_common_3.hg38.vcf.gz added
115213d340ec3_small_exac_common_3.hg38.vcf.gz.tbi added
1152124b54399_gencode.v41.annotation.gtf added
11521786904a2_gencode.v42.annotation.gtf added
1152136af6570_gencode.vM30.annotation.gtf added
11521352cb81c_gencode.vM31.annotation.gtf added
11521aeb518a_gencode.v41.transcripts.fa added
115215f36409f_gencode.v41.transcripts.fa.fai added
1152162ccb78e_gencode.v42.transcripts.fa added
115216e26fe4e_gencode.v42.transcripts.fa.fai added
115214201eb61_gencode.vM30.pc_transcripts.fa added
11521c044f22_gencode.vM30.pc_transcripts.fa.fai added
115216ee74757_gencode.vM31.pc_transcripts.fa added
1152111fcd9a3_gencode.vM31.pc_transcripts.fa.fai added
115216f34658e_GRCh38.primary_assembly.genome.fa.1.ht2 added
1152158f786ab_GRCh38.primary_assembly.genome.fa.2.ht2 added
1152162aa722e_GRCh38.primary_assembly.genome.fa.3.ht2 added
11521242e5c9d_GRCh38.primary_assembly.genome.fa.4.ht2 added
115215fc259f9_GRCh38.primary_assembly.genome.fa.5.ht2 added
1152150a11b8c_GRCh38.primary_assembly.genome.fa.6.ht2 added
11521117adaf_GRCh38.primary_assembly.genome.fa.7.ht2 added
11521398bbcb8_GRCh38.primary_assembly.genome.fa.8.ht2 added
11521512f18c_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
115211eb020ee_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
115213d41f8ff_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1152136424cc4_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
115213abdf3b0_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
11521cc9c5f1_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1152112e257c6_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1152149f091d9_GRCh38.primary_assembly.genome.fa.fai added
1152150f7637b_GRCh38.primary_assembly.genome.fa.amb added
1152121a449c4_GRCh38.primary_assembly.genome.fa.ann added
1152128e6f41d_GRCh38.primary_assembly.genome.fa.bwt added
1152152a4b0e5_GRCh38.primary_assembly.genome.fa.pac added
115213a59b4c6_GRCh38.primary_assembly.genome.fa.sa added
11521576b5117_GRCh38.primary_assembly.genome.fa added
115214698e9d7_hs37d5.fa.fai added
1152161204676_hs37d5.fa.amb added
11521df21ecb_hs37d5.fa.ann added
1152112c3a894_hs37d5.fa.bwt added
115216b70962b_hs37d5.fa.pac added
115212c931828_hs37d5.fa.sa added
115216d1700f4_hs37d5.fa added
1152113fcb20_complete_ref_lens.bin added
11521330a284_ctable.bin added
115216dfd89be_ctg_offsets.bin added
11521205e515c_duplicate_clusters.tsv added
11521102f7f9e_info.json added
115211e63665f_mphf.bin added
11521fd5f68f_pos.bin added
11521282e2e68_pre_indexing.log added
115216fe8c273_rank.bin added
115211a36456b_ref_indexing.log added
115216107813e_refAccumLengths.bin added
1152133b63f36_reflengths.bin added
115211f00cc0_refseq.bin added
1152136d5123e_seq.bin added
115215ea0c091_versionInfo.json added
11521bc2a020_salmon_index added
11521169e9ae8_chrLength.txt added
115216cc00f2_chrName.txt added
115213b52135a_chrNameLength.txt added
115219749823_chrStart.txt added
1152145b026ae_exonGeTrInfo.tab added
115212fbb8d40_exonInfo.tab added
1152142367d3b_geneInfo.tab added
11521757ce73_Genome added
1152115b2e3c9_genomeParameters.txt added
115211388ac40_Log.out added
1152171e4a7c4_SA added
115215ac26f46_SAindex added
1152113178b37_sjdbInfo.txt added
115216eb4d1ab_sjdbList.fromGTF.out.tab added
1152121316a55_sjdbList.out.tab added
11521333c0379_transcriptInfo.tab added
1152129081736_GRCh38.GENCODE.v42_100 added
11521522bef45_knownGene_hg38.sql added
115214269c528_knownGene_hg38.txt added
115212e0ee728_refGene_hg38.sql added
11521546a0ab7_refGene_hg38.txt added
115217de59fac_knownGene_mm39.sql added
115216e5615c6_knownGene_mm39.txt added
1152155afb2c1_refGene_mm39.sql added
11521200c8da_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/RtmpK5n3y2/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
39.027 3.941 62.047
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 12.326 | 1.304 | 18.198 | |
| dataSearch | 2.402 | 0.073 | 3.149 | |
| dataUpdate | 0.000 | 0.001 | 0.002 | |
| getCloudData | 4.546 | 0.201 | 6.586 | |
| getData | 0.000 | 0.000 | 0.002 | |
| meta_data | 0.001 | 0.001 | 0.003 | |
| recipeHub-class | 0.265 | 0.018 | 0.365 | |
| recipeLoad | 2.878 | 0.141 | 3.943 | |
| recipeMake | 0.001 | 0.002 | 0.002 | |
| recipeSearch | 1.166 | 0.059 | 1.586 | |
| recipeUpdate | 0.000 | 0.001 | 0.000 | |