Qian Liu
| Snapshot Date: 2025-09-25 13:45 -0400 (Thu, 25 Sep 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 2025-09-26 12:06 -0400 (Fri, 26 Sep 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" | 4831 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4619 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4563 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
| 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 1752/2334 | 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: 2025-09-25 21:14:34 -0400 (Thu, 25 Sep 2025) |
| EndedAt: 2025-09-25 21:15:22 -0400 (Thu, 25 Sep 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...
113394a644adc_GRCh38.primary_assembly.genome.fa.1.bt2 added
113397e6ed7ab_GRCh38.primary_assembly.genome.fa.2.bt2 added
113391f115c66_GRCh38.primary_assembly.genome.fa.3.bt2 added
113392cc93c79_GRCh38.primary_assembly.genome.fa.4.bt2 added
113394fa142e7_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
11339642f7488_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
11339678bc01a_outfile.txt added
113397f12012_GRCh37_to_GRCh38.chain added
11339677081d0_GRCh37_to_NCBI34.chain added
11339b5ab3be_GRCh37_to_NCBI35.chain added
113396fce84c4_GRCh37_to_NCBI36.chain added
113395f6e9934_GRCh38_to_GRCh37.chain added
11339560c55de_GRCh38_to_NCBI34.chain added
1133943d98df4_GRCh38_to_NCBI35.chain added
113397ff6b0f8_GRCh38_to_NCBI36.chain added
113391cdcab6a_NCBI34_to_GRCh37.chain added
113395b79caf3_NCBI34_to_GRCh38.chain added
1133918fb4670_NCBI35_to_GRCh37.chain added
1133918cd6fe0_NCBI35_to_GRCh38.chain added
11339576be7d8_NCBI36_to_GRCh37.chain added
113396d4242be_NCBI36_to_GRCh38.chain added
11339192bfffc_GRCm38_to_NCBIM36.chain added
1133917b3064d_GRCm38_to_NCBIM37.chain added
113396a62b562_NCBIM36_to_GRCm38.chain added
1133976726b7e_NCBIM37_to_GRCm38.chain added
1133951ef59f2_1000G_omni2.5.b37.vcf.gz added
1133938fa48e4_1000G_omni2.5.b37.vcf.gz.tbi added
1133937c78df5_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
11339e38ec6f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
113393b2a72b4_1000G_omni2.5.hg38.vcf.gz added
113395fd0a5c4_1000G_omni2.5.hg38.vcf.gz.tbi added
113397b331800_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
11339576ce730_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
113392ebe2d27_af-only-gnomad.raw.sites.vcf added
113394786736a_af-only-gnomad.raw.sites.vcf.idx added
113394c0358d5_Mutect2-exome-panel.vcf.idx added
113396fbd2eef_Mutect2-WGS-panel-b37.vcf added
113396d548638_Mutect2-WGS-panel-b37.vcf.idx added
113394837fe9b_small_exac_common_3.vcf added
11339542c9727_small_exac_common_3.vcf.idx added
113393b77ac9d_1000g_pon.hg38.vcf.gz added
113392de595eb_1000g_pon.hg38.vcf.gz.tbi added
113393bd58ed7_af-only-gnomad.hg38.vcf.gz added
113394194e3f1_af-only-gnomad.hg38.vcf.gz.tbi added
11339160104da_small_exac_common_3.hg38.vcf.gz added
113391ce58f7f_small_exac_common_3.hg38.vcf.gz.tbi added
11339232fe9ab_gencode.v41.annotation.gtf added
113391e95eb99_gencode.v42.annotation.gtf added
1133949e997f_gencode.vM30.annotation.gtf added
11339486f6337_gencode.vM31.annotation.gtf added
113398dad508_gencode.v41.transcripts.fa added
1133956d804c2_gencode.v41.transcripts.fa.fai added
11339208919_gencode.v42.transcripts.fa added
113395808c85f_gencode.v42.transcripts.fa.fai added
11339289b0220_gencode.vM30.pc_transcripts.fa added
1133958a897b3_gencode.vM30.pc_transcripts.fa.fai added
11339247f963e_gencode.vM31.pc_transcripts.fa added
113393460d32a_gencode.vM31.pc_transcripts.fa.fai added
1133940c78543_GRCh38.primary_assembly.genome.fa.1.ht2 added
113396afe12ee_GRCh38.primary_assembly.genome.fa.2.ht2 added
113394e8cfe22_GRCh38.primary_assembly.genome.fa.3.ht2 added
11339a809278_GRCh38.primary_assembly.genome.fa.4.ht2 added
113397f1009aa_GRCh38.primary_assembly.genome.fa.5.ht2 added
1133975eab911_GRCh38.primary_assembly.genome.fa.6.ht2 added
1133951c4792_GRCh38.primary_assembly.genome.fa.7.ht2 added
1133939ec4dd_GRCh38.primary_assembly.genome.fa.8.ht2 added
113392c8e8b06_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1133942494dc4_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
113395a90a0db_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
113394d30b850_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
113393994b3c7_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1133951a6eb59_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1133925a549f0_GRCh38_full_analysis_set_plus_decoy_hla.fa added
113396993edf_GRCh38.primary_assembly.genome.fa.fai added
1133936eea5db_GRCh38.primary_assembly.genome.fa.amb added
113396dcae909_GRCh38.primary_assembly.genome.fa.ann added
113392489862f_GRCh38.primary_assembly.genome.fa.bwt added
1133940c88a66_GRCh38.primary_assembly.genome.fa.pac added
113392df64fc4_GRCh38.primary_assembly.genome.fa.sa added
113395eee46f_GRCh38.primary_assembly.genome.fa added
113396d73674_hs37d5.fa.fai added
113391b37fd2e_hs37d5.fa.amb added
1133978cee4f7_hs37d5.fa.ann added
11339571a5217_hs37d5.fa.bwt added
1133910390ae_hs37d5.fa.pac added
11339110f9007_hs37d5.fa.sa added
1133914b8c451_hs37d5.fa added
113396e60ac77_complete_ref_lens.bin added
11339cdaf13e_ctable.bin added
113397a142409_ctg_offsets.bin added
11339404a097c_duplicate_clusters.tsv added
113393cb4ccdd_info.json added
113391f5e04e_mphf.bin added
11339355921e3_pos.bin added
113396ebfd971_pre_indexing.log added
11339755cc284_rank.bin added
113391ce6a44e_ref_indexing.log added
113396a2d0bb4_refAccumLengths.bin added
11339335b8ce1_reflengths.bin added
113393f7e221e_refseq.bin added
1133971f20022_seq.bin added
1133946e6f29f_versionInfo.json added
113396442c916_salmon_index added
113395c9ff6c6_chrLength.txt added
11339a0270ac_chrName.txt added
1133926333156_chrNameLength.txt added
113396aec18b1_chrStart.txt added
113393249434e_exonGeTrInfo.tab added
1133967e1cfac_exonInfo.tab added
113391a095a7c_geneInfo.tab added
113395c13903e_Genome added
1133986305ac_genomeParameters.txt added
113391d096381_Log.out added
113395363b90b_SA added
113393809abf2_SAindex added
113392f7b99c_sjdbInfo.txt added
1133955bab249_sjdbList.fromGTF.out.tab added
11339540f0297_sjdbList.out.tab added
113392573329e_transcriptInfo.tab added
113392e003647_GRCh38.GENCODE.v42_100 added
11339feb86e9_knownGene_hg38.sql added
113392fe63329_knownGene_hg38.txt added
113393228e150_refGene_hg38.sql added
1133919e064ea_refGene_hg38.txt added
113395b014beb_knownGene_mm39.sql added
11339321f5ffa_knownGene_mm39.txt added
1133929d62fcb_refGene_mm39.sql added
113392cdbcde2_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//RtmpTBiMh7/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
6.261 0.666 7.652
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.900 | 0.212 | 2.123 | |
| dataSearch | 0.325 | 0.014 | 0.340 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.851 | 0.053 | 2.250 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.037 | 0.005 | 0.043 | |
| recipeLoad | 0.389 | 0.028 | 0.420 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.175 | 0.012 | 0.186 | |
| recipeUpdate | 0 | 0 | 0 | |