Qian Liu
| Snapshot Date: 2025-12-18 13:45 -0500 (Thu, 18 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 2025-12-22 12:06 -0500 (Mon, 22 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" | 4883 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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: 2025-12-20 19:09:49 -0500 (Sat, 20 Dec 2025) |
| EndedAt: 2025-12-20 19:13:21 -0500 (Sat, 20 Dec 2025) |
| EllapsedTime: 211.4 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 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* 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 8.029 0.921 12.227
getCloudData 3.111 0.181 6.430
* 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-arm64/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 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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...
10485683e3488_GRCh38.primary_assembly.genome.fa.1.bt2 added
104854beb022f_GRCh38.primary_assembly.genome.fa.2.bt2 added
1048531dc8299_GRCh38.primary_assembly.genome.fa.3.bt2 added
104854022462_GRCh38.primary_assembly.genome.fa.4.bt2 added
1048528a29ffc_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
104854cb56e3b_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
104851b580ad5_outfile.txt added
10485312f33f9_GRCh37_to_GRCh38.chain added
1048511fd39a9_GRCh37_to_NCBI34.chain added
104857d48f79_GRCh37_to_NCBI35.chain added
10485141754f3_GRCh37_to_NCBI36.chain added
104857ca27d3_GRCh38_to_GRCh37.chain added
1048568fc91a3_GRCh38_to_NCBI34.chain added
104851dbd9a2e_GRCh38_to_NCBI35.chain added
10485ad55143_GRCh38_to_NCBI36.chain added
104853aca0b43_NCBI34_to_GRCh37.chain added
1048526a979dc_NCBI34_to_GRCh38.chain added
10485407f6e58_NCBI35_to_GRCh37.chain added
104856e25747c_NCBI35_to_GRCh38.chain added
104855d02b162_NCBI36_to_GRCh37.chain added
104855bcbc8a2_NCBI36_to_GRCh38.chain added
104851fe132c3_GRCm38_to_NCBIM36.chain added
1048579cbb08e_GRCm38_to_NCBIM37.chain added
104852bb4791a_NCBIM36_to_GRCm38.chain added
10485557ab060_NCBIM37_to_GRCm38.chain added
1048569d19a77_1000G_omni2.5.b37.vcf.gz added
104853ff430e7_1000G_omni2.5.b37.vcf.gz.tbi added
1048538b6ae7e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
104856179ef48_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
10485c4c91f7_1000G_omni2.5.hg38.vcf.gz added
104857702f56f_1000G_omni2.5.hg38.vcf.gz.tbi added
10485633f8773_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
104855fd5c1ec_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
104854aae9e1b_af-only-gnomad.raw.sites.vcf added
10485e0e24eb_af-only-gnomad.raw.sites.vcf.idx added
104854299c782_Mutect2-exome-panel.vcf.idx added
104857df949f6_Mutect2-WGS-panel-b37.vcf added
104857966f616_Mutect2-WGS-panel-b37.vcf.idx added
1048556a65c9e_small_exac_common_3.vcf added
10485440ab583_small_exac_common_3.vcf.idx added
104851b12ce5b_1000g_pon.hg38.vcf.gz added
104856fa9c63f_1000g_pon.hg38.vcf.gz.tbi added
1048573168b5e_af-only-gnomad.hg38.vcf.gz added
104854d180359_af-only-gnomad.hg38.vcf.gz.tbi added
104856383ef99_small_exac_common_3.hg38.vcf.gz added
104856ae758d9_small_exac_common_3.hg38.vcf.gz.tbi added
104857a7a4563_gencode.v41.annotation.gtf added
104857161a566_gencode.v42.annotation.gtf added
1048541b205b1_gencode.vM30.annotation.gtf added
10485e93c929_gencode.vM31.annotation.gtf added
1048587baa39_gencode.v41.transcripts.fa added
104856ee48888_gencode.v41.transcripts.fa.fai added
104855dbfd198_gencode.v42.transcripts.fa added
104855c59823d_gencode.v42.transcripts.fa.fai added
104857875a228_gencode.vM30.pc_transcripts.fa added
1048572e92de0_gencode.vM30.pc_transcripts.fa.fai added
104852ac30810_gencode.vM31.pc_transcripts.fa added
104856a46685e_gencode.vM31.pc_transcripts.fa.fai added
10485346e29d4_GRCh38.primary_assembly.genome.fa.1.ht2 added
104852c7c3830_GRCh38.primary_assembly.genome.fa.2.ht2 added
10485f4cee21_GRCh38.primary_assembly.genome.fa.3.ht2 added
104853a5c060_GRCh38.primary_assembly.genome.fa.4.ht2 added
1048576f8e07e_GRCh38.primary_assembly.genome.fa.5.ht2 added
104854d5aad37_GRCh38.primary_assembly.genome.fa.6.ht2 added
104857c221d8d_GRCh38.primary_assembly.genome.fa.7.ht2 added
1048523c253a6_GRCh38.primary_assembly.genome.fa.8.ht2 added
104852b01c9a1_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1048525c7f16_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1048569b7e90_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
104854a922353_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
10485404d4464_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1048510c52237_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
104857e49517a_GRCh38_full_analysis_set_plus_decoy_hla.fa added
104857f84615b_GRCh38.primary_assembly.genome.fa.fai added
104854c13dec4_GRCh38.primary_assembly.genome.fa.amb added
104852c863ce1_GRCh38.primary_assembly.genome.fa.ann added
104852106ee9d_GRCh38.primary_assembly.genome.fa.bwt added
104854e1b965b_GRCh38.primary_assembly.genome.fa.pac added
10485752c586c_GRCh38.primary_assembly.genome.fa.sa added
104853261568d_GRCh38.primary_assembly.genome.fa added
1048514795cd2_hs37d5.fa.fai added
104852bbce97e_hs37d5.fa.amb added
104857f8565a0_hs37d5.fa.ann added
10485ed32cc8_hs37d5.fa.bwt added
104854a210612_hs37d5.fa.pac added
104853e15adc3_hs37d5.fa.sa added
10485142fd0d_hs37d5.fa added
1048554f36120_complete_ref_lens.bin added
10485366da772_ctable.bin added
10485590c4948_ctg_offsets.bin added
10485359f43a4_duplicate_clusters.tsv added
104856b11df7c_info.json added
1048562677cce_mphf.bin added
104857832eada_pos.bin added
1048556d8cbdc_pre_indexing.log added
104853330050f_rank.bin added
10485159c360a_ref_indexing.log added
10485429fd59b_refAccumLengths.bin added
10485b80d549_reflengths.bin added
104853732b185_refseq.bin added
104856124af12_seq.bin added
104852f61f891_versionInfo.json added
1048549060fe4_salmon_index added
104852cfd6730_chrLength.txt added
1048530819763_chrName.txt added
10485bf9fd76_chrNameLength.txt added
10485496f541e_chrStart.txt added
104852bfba33c_exonGeTrInfo.tab added
104851599ceb3_exonInfo.tab added
1048524d154d9_geneInfo.tab added
104852b198571_Genome added
104851887d3d2_genomeParameters.txt added
104857d638c92_Log.out added
1048512a2058e_SA added
104854b1ab730_SAindex added
1048546f0d6d5_sjdbInfo.txt added
104856da85e55_sjdbList.fromGTF.out.tab added
1048548c956b1_sjdbList.out.tab added
104851a5aa3cc_transcriptInfo.tab added
1048534b7b398_GRCh38.GENCODE.v42_100 added
1048586fdb32_knownGene_hg38.sql added
10485679fb3f1_knownGene_hg38.txt added
1048525dec85d_refGene_hg38.sql added
1048545346517_refGene_hg38.txt added
1048572d8ec7f_knownGene_mm39.sql added
104857f8ec0c0_knownGene_mm39.txt added
104857510beac_refGene_mm39.sql added
104851e564a3f_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/Rtmp3GrOLH/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
25.158 2.552 39.544
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 8.029 | 0.921 | 12.227 | |
| dataSearch | 1.335 | 0.063 | 1.988 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 3.111 | 0.181 | 6.430 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.003 | |
| recipeHub-class | 0.169 | 0.017 | 0.275 | |
| recipeLoad | 1.602 | 0.105 | 2.570 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.710 | 0.047 | 0.997 | |
| recipeUpdate | 0 | 0 | 0 | |