Qian Liu
| Snapshot Date: 2025-08-28 13:40 -0400 (Thu, 28 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_21 |
| git_last_commit: 601a107 |
| git_last_commit_date: 2025-04-15 13:01:44 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-01 11:42 -0400 (Mon, 01 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4606 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4547 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 1758/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.8.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | 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: 1.8.0 |
| 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_1.8.0.tar.gz |
| StartedAt: 2025-08-30 09:15:56 -0400 (Sat, 30 Aug 2025) |
| EndedAt: 2025-08-30 09:18:31 -0400 (Sat, 30 Aug 2025) |
| EllapsedTime: 155.1 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-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 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.8.0’
* 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 7.541 0.850 8.564
getCloudData 2.946 0.164 5.104
* 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-3.21-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 ‘1.8.0’ ** 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...
6ec25bfa8fd4_GRCh38.primary_assembly.genome.fa.1.bt2 added
6ec21ef8d679_GRCh38.primary_assembly.genome.fa.2.bt2 added
6ec262c8b1d1_GRCh38.primary_assembly.genome.fa.3.bt2 added
6ec266124301_GRCh38.primary_assembly.genome.fa.4.bt2 added
6ec238ed2b01_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
6ec25aa26bd9_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
6ec25d56a20b_outfile.txt added
6ec262a8b00c_GRCh37_to_GRCh38.chain added
6ec230be166e_GRCh37_to_NCBI34.chain added
6ec2fb2a8c2_GRCh37_to_NCBI35.chain added
6ec21a65609b_GRCh37_to_NCBI36.chain added
6ec275a96da6_GRCh38_to_GRCh37.chain added
6ec2465de9a3_GRCh38_to_NCBI34.chain added
6ec23f95f06c_GRCh38_to_NCBI35.chain added
6ec2cdb6311_GRCh38_to_NCBI36.chain added
6ec21744f7af_NCBI34_to_GRCh37.chain added
6ec230e10e18_NCBI34_to_GRCh38.chain added
6ec276462ba_NCBI35_to_GRCh37.chain added
6ec24f8da520_NCBI35_to_GRCh38.chain added
6ec25c5400ad_NCBI36_to_GRCh37.chain added
6ec2ef88d36_NCBI36_to_GRCh38.chain added
6ec25ffedbe7_GRCm38_to_NCBIM36.chain added
6ec255174bed_GRCm38_to_NCBIM37.chain added
6ec26c79e03f_NCBIM36_to_GRCm38.chain added
6ec235717fbc_NCBIM37_to_GRCm38.chain added
6ec22e792b0d_1000G_omni2.5.b37.vcf.gz added
6ec214f97a51_1000G_omni2.5.b37.vcf.gz.tbi added
6ec26cd6699_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
6ec2170aca4c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
6ec245674f65_1000G_omni2.5.hg38.vcf.gz added
6ec218d937c_1000G_omni2.5.hg38.vcf.gz.tbi added
6ec275cdb2af_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
6ec2138e3b95_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
6ec25ee9bd3a_af-only-gnomad.raw.sites.vcf added
6ec243865b84_af-only-gnomad.raw.sites.vcf.idx added
6ec229e259be_Mutect2-exome-panel.vcf.idx added
6ec24b71de6d_Mutect2-WGS-panel-b37.vcf added
6ec220c1eccd_Mutect2-WGS-panel-b37.vcf.idx added
6ec21ba19788_small_exac_common_3.vcf added
6ec2de36fe4_small_exac_common_3.vcf.idx added
6ec24ec6e8db_1000g_pon.hg38.vcf.gz added
6ec264e1aa44_1000g_pon.hg38.vcf.gz.tbi added
6ec21b718a1a_af-only-gnomad.hg38.vcf.gz added
6ec23b21bf09_af-only-gnomad.hg38.vcf.gz.tbi added
6ec224850633_small_exac_common_3.hg38.vcf.gz added
6ec2195a1100_small_exac_common_3.hg38.vcf.gz.tbi added
6ec268122400_gencode.v41.annotation.gtf added
6ec27ef9b160_gencode.v42.annotation.gtf added
6ec23aec56c0_gencode.vM30.annotation.gtf added
6ec272337578_gencode.vM31.annotation.gtf added
6ec2106553db_gencode.v41.transcripts.fa added
6ec26c645745_gencode.v41.transcripts.fa.fai added
6ec22f9daa9b_gencode.v42.transcripts.fa added
6ec2182bbe89_gencode.v42.transcripts.fa.fai added
6ec25fea20c4_gencode.vM30.pc_transcripts.fa added
6ec240d550e_gencode.vM30.pc_transcripts.fa.fai added
6ec274b0c36_gencode.vM31.pc_transcripts.fa added
6ec2500eb0f7_gencode.vM31.pc_transcripts.fa.fai added
6ec274845130_GRCh38.primary_assembly.genome.fa.1.ht2 added
6ec21aee6213_GRCh38.primary_assembly.genome.fa.2.ht2 added
6ec21868db35_GRCh38.primary_assembly.genome.fa.3.ht2 added
6ec2c0f8118_GRCh38.primary_assembly.genome.fa.4.ht2 added
6ec24de454d7_GRCh38.primary_assembly.genome.fa.5.ht2 added
6ec2497e1734_GRCh38.primary_assembly.genome.fa.6.ht2 added
6ec275257c9d_GRCh38.primary_assembly.genome.fa.7.ht2 added
6ec270186380_GRCh38.primary_assembly.genome.fa.8.ht2 added
6ec2512ca1fe_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
6ec2493f5454_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
6ec25cb97c5d_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
6ec21593ed3a_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
6ec222bb85e7_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
6ec245541281_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
6ec2128af6b6_GRCh38_full_analysis_set_plus_decoy_hla.fa added
6ec2614b303c_GRCh38.primary_assembly.genome.fa.fai added
6ec2f4be50b_GRCh38.primary_assembly.genome.fa.amb added
6ec23faa3d05_GRCh38.primary_assembly.genome.fa.ann added
6ec2418c33ea_GRCh38.primary_assembly.genome.fa.bwt added
6ec25ba46944_GRCh38.primary_assembly.genome.fa.pac added
6ec26fb1e5d_GRCh38.primary_assembly.genome.fa.sa added
6ec250866f3f_GRCh38.primary_assembly.genome.fa added
6ec229f1ba66_hs37d5.fa.fai added
6ec23d04940d_hs37d5.fa.amb added
6ec2779400c6_hs37d5.fa.ann added
6ec215bf047f_hs37d5.fa.bwt added
6ec22fc03900_hs37d5.fa.pac added
6ec274de477d_hs37d5.fa.sa added
6ec22d279b7c_hs37d5.fa added
6ec2351010d_complete_ref_lens.bin added
6ec23b1bfe2e_ctable.bin added
6ec22acc9c53_ctg_offsets.bin added
6ec25f2b2318_duplicate_clusters.tsv added
6ec290d2d78_info.json added
6ec2402425ec_mphf.bin added
6ec2535c9da_pos.bin added
6ec2e5709e2_pre_indexing.log added
6ec27449dbc8_rank.bin added
6ec21cfc631d_ref_indexing.log added
6ec27dcf13c8_refAccumLengths.bin added
6ec2261befff_reflengths.bin added
6ec2742961e4_refseq.bin added
6ec248d9fb50_seq.bin added
6ec25f02668d_versionInfo.json added
6ec2169ae3b6_salmon_index added
6ec212dbcd52_chrLength.txt added
6ec21c84cc2a_chrName.txt added
6ec25277e806_chrNameLength.txt added
6ec23e220c36_chrStart.txt added
6ec22d4fcd18_exonGeTrInfo.tab added
6ec25221f9e5_exonInfo.tab added
6ec2349d5383_geneInfo.tab added
6ec244d5d871_Genome added
6ec233750605_genomeParameters.txt added
6ec247de4ca7_Log.out added
6ec2537a8ccd_SA added
6ec212b2118c_SAindex added
6ec2689e07ea_sjdbInfo.txt added
6ec25f19c94e_sjdbList.fromGTF.out.tab added
6ec215ef50a9_sjdbList.out.tab added
6ec21298927f_transcriptInfo.tab added
6ec25eb9d962_GRCh38.GENCODE.v42_100 added
6ec27b6ee183_knownGene_hg38.sql added
6ec22c979ec4_knownGene_hg38.txt added
6ec216386cbb_refGene_hg38.sql added
6ec2526a7462_refGene_hg38.txt added
6ec24afef833_knownGene_mm39.sql added
6ec2295902bc_knownGene_mm39.txt added
6ec212c299d9_refGene_mm39.sql added
6ec226027f2e_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/RtmpZb4Q6a/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
27.691 3.748 33.521
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.541 | 0.850 | 8.564 | |
| dataSearch | 1.219 | 0.054 | 1.276 | |
| dataUpdate | 0.000 | 0.001 | 0.000 | |
| getCloudData | 2.946 | 0.164 | 5.104 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.158 | 0.013 | 0.181 | |
| recipeLoad | 1.514 | 0.094 | 1.642 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.630 | 0.039 | 0.692 | |
| recipeUpdate | 0 | 0 | 0 | |