Qian Liu
| Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 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 2025-08-04 12:11 -0400 (Mon, 04 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4536 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
| 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 1737/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.9.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 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: 2025-08-03 21:12:21 -0400 (Sun, 03 Aug 2025) |
| EndedAt: 2025-08-03 21:13:11 -0400 (Sun, 03 Aug 2025) |
| EllapsedTime: 49.6 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 (2025-06-14 r88325)
* 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 13.7.1
* 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 (2025-06-14 r88325) -- "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...
99024148d80c_GRCh38.primary_assembly.genome.fa.1.bt2 added
990215601d50_GRCh38.primary_assembly.genome.fa.2.bt2 added
990259247a26_GRCh38.primary_assembly.genome.fa.3.bt2 added
990269cf8282_GRCh38.primary_assembly.genome.fa.4.bt2 added
990236815b13_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
990266825859_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
990277766fa2_outfile.txt added
99029b31f4_GRCh37_to_GRCh38.chain added
99024cec8a7b_GRCh37_to_NCBI34.chain added
99023d77b8b1_GRCh37_to_NCBI35.chain added
99027efe8bfd_GRCh37_to_NCBI36.chain added
99027998d02d_GRCh38_to_GRCh37.chain added
99021f8b78b9_GRCh38_to_NCBI34.chain added
99027da2c9dc_GRCh38_to_NCBI35.chain added
99024a72caf4_GRCh38_to_NCBI36.chain added
9902366a7f5b_NCBI34_to_GRCh37.chain added
99029cf4b46_NCBI34_to_GRCh38.chain added
9902856e5b2_NCBI35_to_GRCh37.chain added
99021020d65_NCBI35_to_GRCh38.chain added
99022dbd6267_NCBI36_to_GRCh37.chain added
99026c876fa6_NCBI36_to_GRCh38.chain added
99022fb332f4_GRCm38_to_NCBIM36.chain added
99021dd649a3_GRCm38_to_NCBIM37.chain added
99025f7c7ba2_NCBIM36_to_GRCm38.chain added
99026598f9a7_NCBIM37_to_GRCm38.chain added
99021e2e770d_1000G_omni2.5.b37.vcf.gz added
99027c8a05f5_1000G_omni2.5.b37.vcf.gz.tbi added
9902498d57b3_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
99025e78ce7e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
99024d3ce2a6_1000G_omni2.5.hg38.vcf.gz added
9902584427e7_1000G_omni2.5.hg38.vcf.gz.tbi added
99026297dbf6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
99025fea260b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
9902567cd5f_af-only-gnomad.raw.sites.vcf added
990261dc1abe_af-only-gnomad.raw.sites.vcf.idx added
9902395fe223_Mutect2-exome-panel.vcf.idx added
990245f78542_Mutect2-WGS-panel-b37.vcf added
99027d4dd3f0_Mutect2-WGS-panel-b37.vcf.idx added
99029571d5_small_exac_common_3.vcf added
99025364573f_small_exac_common_3.vcf.idx added
9902609c13de_1000g_pon.hg38.vcf.gz added
990226dc855f_1000g_pon.hg38.vcf.gz.tbi added
990257b833e7_af-only-gnomad.hg38.vcf.gz added
99027e57afae_af-only-gnomad.hg38.vcf.gz.tbi added
99022ecf094f_small_exac_common_3.hg38.vcf.gz added
99021a6c398b_small_exac_common_3.hg38.vcf.gz.tbi added
99023735e23a_gencode.v41.annotation.gtf added
990232976a27_gencode.v42.annotation.gtf added
990272ba4063_gencode.vM30.annotation.gtf added
990221d95e6d_gencode.vM31.annotation.gtf added
990245c65777_gencode.v41.transcripts.fa added
99026098696a_gencode.v41.transcripts.fa.fai added
99023630dfb1_gencode.v42.transcripts.fa added
990242adf942_gencode.v42.transcripts.fa.fai added
99022bc77e41_gencode.vM30.pc_transcripts.fa added
99023631f3db_gencode.vM30.pc_transcripts.fa.fai added
9902980caa9_gencode.vM31.pc_transcripts.fa added
99026679221e_gencode.vM31.pc_transcripts.fa.fai added
99021aaf1421_GRCh38.primary_assembly.genome.fa.1.ht2 added
99025c529036_GRCh38.primary_assembly.genome.fa.2.ht2 added
99023079f894_GRCh38.primary_assembly.genome.fa.3.ht2 added
990217aed569_GRCh38.primary_assembly.genome.fa.4.ht2 added
9902573ceca4_GRCh38.primary_assembly.genome.fa.5.ht2 added
990260d42fba_GRCh38.primary_assembly.genome.fa.6.ht2 added
9902a898e00_GRCh38.primary_assembly.genome.fa.7.ht2 added
99024cc9a767_GRCh38.primary_assembly.genome.fa.8.ht2 added
99024b0d8293_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
990263f7a763_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
9902180e87db_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
990261f94733_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
990234b19785_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
99027752b7c9_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
990257a02a52_GRCh38_full_analysis_set_plus_decoy_hla.fa added
9902543a9a6f_GRCh38.primary_assembly.genome.fa.fai added
99025371189c_GRCh38.primary_assembly.genome.fa.amb added
99022606d490_GRCh38.primary_assembly.genome.fa.ann added
9902a6d4d71_GRCh38.primary_assembly.genome.fa.bwt added
9902df73b10_GRCh38.primary_assembly.genome.fa.pac added
990262469e99_GRCh38.primary_assembly.genome.fa.sa added
9902a568137_GRCh38.primary_assembly.genome.fa added
9902353d472e_hs37d5.fa.fai added
99024a0c3850_hs37d5.fa.amb added
99026845322a_hs37d5.fa.ann added
990216e098e1_hs37d5.fa.bwt added
99027354e782_hs37d5.fa.pac added
99024b2b42f5_hs37d5.fa.sa added
99025390961_hs37d5.fa added
99026396c1f4_complete_ref_lens.bin added
99023e97ad40_ctable.bin added
990257ef64da_ctg_offsets.bin added
990225c65150_duplicate_clusters.tsv added
99027f046e8f_info.json added
99027bf6af6e_mphf.bin added
9902779e57_pos.bin added
99022d3c61fe_pre_indexing.log added
9902574581e5_rank.bin added
990214530e26_ref_indexing.log added
990258c5eb36_refAccumLengths.bin added
990229d553c2_reflengths.bin added
9902746dfb02_refseq.bin added
9902607a7c05_seq.bin added
99029645dbf_versionInfo.json added
99021c46ab6a_salmon_index added
9902639fcaa6_chrLength.txt added
9902fb18b63_chrName.txt added
9902513618a1_chrNameLength.txt added
9902368b1bae_chrStart.txt added
990266c6587b_exonGeTrInfo.tab added
990267db27f3_exonInfo.tab added
9902651bf7c9_geneInfo.tab added
9902f28e0fb_Genome added
990244ca8683_genomeParameters.txt added
99024c4525bd_Log.out added
99024fb0c269_SA added
99025daba45e_SAindex added
99022fb4475d_sjdbInfo.txt added
990264b94322_sjdbList.fromGTF.out.tab added
99023ee6a0d7_sjdbList.out.tab added
99021749a384_transcriptInfo.tab added
9902638e3b0d_GRCh38.GENCODE.v42_100 added
9902ec7058b_knownGene_hg38.sql added
99022c3cf041_knownGene_hg38.txt added
990254c15217_refGene_hg38.sql added
99025ff48f79_refGene_hg38.txt added
990230f78226_knownGene_mm39.sql added
99024981a5e7_knownGene_mm39.txt added
99025eb30664_refGene_mm39.sql added
99023b68bfce_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//Rtmp25NhNn/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
6.340 0.714 7.835
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.992 | 0.246 | 2.246 | |
| dataSearch | 0.349 | 0.018 | 0.369 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.917 | 0.062 | 1.961 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.038 | 0.005 | 0.043 | |
| recipeLoad | 0.399 | 0.028 | 0.430 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.167 | 0.012 | 0.178 | |
| recipeUpdate | 0 | 0 | 0 | |