Qian Liu
| Snapshot Date: 2025-10-03 13:45 -0400 (Fri, 03 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: c5927b9 |
| git_last_commit_date: 2025-04-15 13:01:44 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-04 12:06 -0400 (Sat, 04 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4853 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
| 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 1757/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.9.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 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: 1.9.0 |
| 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_1.9.0.tar.gz |
| StartedAt: 2025-10-03 21:17:10 -0400 (Fri, 03 Oct 2025) |
| EndedAt: 2025-10-03 21:17:58 -0400 (Fri, 03 Oct 2025) |
| EllapsedTime: 48.5 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_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.9.0’
* 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
* 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 ‘1.9.0’ ** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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...
448e2560774_GRCh38.primary_assembly.genome.fa.1.bt2 added
448e5e0351de_GRCh38.primary_assembly.genome.fa.2.bt2 added
448e2bf3f60a_GRCh38.primary_assembly.genome.fa.3.bt2 added
448e1d9e2111_GRCh38.primary_assembly.genome.fa.4.bt2 added
448e788cf247_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
448e6d765125_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
448e72c98c47_outfile.txt added
448ee18c431_GRCh37_to_GRCh38.chain added
448e7bf87431_GRCh37_to_NCBI34.chain added
448e74947c8c_GRCh37_to_NCBI35.chain added
448e407d071f_GRCh37_to_NCBI36.chain added
448e505ea54c_GRCh38_to_GRCh37.chain added
448e75b649cc_GRCh38_to_NCBI34.chain added
448e12a72c74_GRCh38_to_NCBI35.chain added
448e1d577d3d_GRCh38_to_NCBI36.chain added
448e5adf3ed7_NCBI34_to_GRCh37.chain added
448e7696c3dc_NCBI34_to_GRCh38.chain added
448e2414dd57_NCBI35_to_GRCh37.chain added
448e55cf8d42_NCBI35_to_GRCh38.chain added
448e2d431411_NCBI36_to_GRCh37.chain added
448eeda7f4e_NCBI36_to_GRCh38.chain added
448e2adbe180_GRCm38_to_NCBIM36.chain added
448e49b1b07b_GRCm38_to_NCBIM37.chain added
448e30b98109_NCBIM36_to_GRCm38.chain added
448e62c68edc_NCBIM37_to_GRCm38.chain added
448e59cd402d_1000G_omni2.5.b37.vcf.gz added
448e3230786a_1000G_omni2.5.b37.vcf.gz.tbi added
448ec3190e4_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
448ea1f6efd_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
448e15afa93c_1000G_omni2.5.hg38.vcf.gz added
448e3f8fad43_1000G_omni2.5.hg38.vcf.gz.tbi added
448e71b82a4e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
448e71e1a135_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
448e141ed8fc_af-only-gnomad.raw.sites.vcf added
448e753792b5_af-only-gnomad.raw.sites.vcf.idx added
448e1380e532_Mutect2-exome-panel.vcf.idx added
448e73473f9e_Mutect2-WGS-panel-b37.vcf added
448e4aa1d932_Mutect2-WGS-panel-b37.vcf.idx added
448e47ba87e5_small_exac_common_3.vcf added
448e272ff02d_small_exac_common_3.vcf.idx added
448e3c412e74_1000g_pon.hg38.vcf.gz added
448e5b50e093_1000g_pon.hg38.vcf.gz.tbi added
448e1ac801bb_af-only-gnomad.hg38.vcf.gz added
448e40e9a9b9_af-only-gnomad.hg38.vcf.gz.tbi added
448e2c85d1fa_small_exac_common_3.hg38.vcf.gz added
448e59c8aec_small_exac_common_3.hg38.vcf.gz.tbi added
448e68648ed4_gencode.v41.annotation.gtf added
448e21dd35d7_gencode.v42.annotation.gtf added
448e41f9c79f_gencode.vM30.annotation.gtf added
448e75a0b98f_gencode.vM31.annotation.gtf added
448eaf6979e_gencode.v41.transcripts.fa added
448e435c0bb1_gencode.v41.transcripts.fa.fai added
448e5003b403_gencode.v42.transcripts.fa added
448e231f59ff_gencode.v42.transcripts.fa.fai added
448e5f4d865c_gencode.vM30.pc_transcripts.fa added
448e5ab032e5_gencode.vM30.pc_transcripts.fa.fai added
448e65dd86e6_gencode.vM31.pc_transcripts.fa added
448e32c39a49_gencode.vM31.pc_transcripts.fa.fai added
448e47c648a8_GRCh38.primary_assembly.genome.fa.1.ht2 added
448e2acc3268_GRCh38.primary_assembly.genome.fa.2.ht2 added
448e44015fcb_GRCh38.primary_assembly.genome.fa.3.ht2 added
448e36382b4e_GRCh38.primary_assembly.genome.fa.4.ht2 added
448e21a329b1_GRCh38.primary_assembly.genome.fa.5.ht2 added
448e5f0634b7_GRCh38.primary_assembly.genome.fa.6.ht2 added
448e106f0b1e_GRCh38.primary_assembly.genome.fa.7.ht2 added
448e6a42e6ff_GRCh38.primary_assembly.genome.fa.8.ht2 added
448e4e4ba5d9_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
448e487571b7_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
448e167cca8b_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
448e5ad57735_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
448e74856729_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
448e6237f082_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
448e468f192e_GRCh38_full_analysis_set_plus_decoy_hla.fa added
448e5cbe3f32_GRCh38.primary_assembly.genome.fa.fai added
448e4e271b2f_GRCh38.primary_assembly.genome.fa.amb added
448e6969d2be_GRCh38.primary_assembly.genome.fa.ann added
448e228aee03_GRCh38.primary_assembly.genome.fa.bwt added
448e4f1018ac_GRCh38.primary_assembly.genome.fa.pac added
448e29c3ecc1_GRCh38.primary_assembly.genome.fa.sa added
448e7dec8852_GRCh38.primary_assembly.genome.fa added
448e33ea0014_hs37d5.fa.fai added
448e47ab3bac_hs37d5.fa.amb added
448e3adabdf6_hs37d5.fa.ann added
448e6eed7fa9_hs37d5.fa.bwt added
448e2a586924_hs37d5.fa.pac added
448e125ed034_hs37d5.fa.sa added
448eeb70f58_hs37d5.fa added
448e145061f4_complete_ref_lens.bin added
448e294ee497_ctable.bin added
448e7a818ab0_ctg_offsets.bin added
448e4eb867a5_duplicate_clusters.tsv added
448e2c9caa03_info.json added
448e615dc1d6_mphf.bin added
448e5260fa8a_pos.bin added
448e5ce0a446_pre_indexing.log added
448e20411f4d_rank.bin added
448e136e08c6_ref_indexing.log added
448e1d020921_refAccumLengths.bin added
448e70a56467_reflengths.bin added
448e7a62dff7_refseq.bin added
448e715e0fe6_seq.bin added
448e5665ff2f_versionInfo.json added
448e425492f9_salmon_index added
448e3e7d3b74_chrLength.txt added
448efca5cb9_chrName.txt added
448e2e8d7dc8_chrNameLength.txt added
448e4b3ced58_chrStart.txt added
448ed0252ff_exonGeTrInfo.tab added
448e1396ea05_exonInfo.tab added
448e18ddf84f_geneInfo.tab added
448e14d9174a_Genome added
448e388805f7_genomeParameters.txt added
448e6a3fb81f_Log.out added
448e7d5131b7_SA added
448e5d9725a7_SAindex added
448e6e2926f1_sjdbInfo.txt added
448e4fbbd0b7_sjdbList.fromGTF.out.tab added
448e3383c746_sjdbList.out.tab added
448e108fdf16_transcriptInfo.tab added
448e557f25d8_GRCh38.GENCODE.v42_100 added
448ee8db3c2_knownGene_hg38.sql added
448e79148d04_knownGene_hg38.txt added
448e34363fb6_refGene_hg38.sql added
448e5590e081_refGene_hg38.txt added
448e1a83610a_knownGene_mm39.sql added
448e2757e51f_knownGene_mm39.txt added
448e7b836a66_refGene_mm39.sql added
448e70be8de3_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:
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoO8kaf/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
6.328 0.655 7.693
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.927 | 0.213 | 2.144 | |
| dataSearch | 0.321 | 0.013 | 0.334 | |
| dataUpdate | 0.000 | 0.001 | 0.000 | |
| getCloudData | 0.895 | 0.053 | 2.009 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.037 | 0.005 | 0.042 | |
| recipeLoad | 0.392 | 0.026 | 0.419 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.173 | 0.011 | 0.189 | |
| recipeUpdate | 0 | 0 | 0 | |