Qian Liu
| Snapshot Date: 2025-09-18 13:40 -0400 (Thu, 18 Sep 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 2025-09-22 11:41 -0400 (Mon, 22 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" | 4827 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4581 |
| 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: 2025-09-20 08:48:09 -0400 (Sat, 20 Sep 2025) |
| EndedAt: 2025-09-20 08:50:39 -0400 (Sat, 20 Sep 2025) |
| EllapsedTime: 149.6 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_1.8.0.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 7.311 0.844 8.251
getCloudData 2.763 0.152 5.113
* 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...
4b9d1541c45b_GRCh38.primary_assembly.genome.fa.1.bt2 added
4b9d10c23d44_GRCh38.primary_assembly.genome.fa.2.bt2 added
4b9d404443f4_GRCh38.primary_assembly.genome.fa.3.bt2 added
4b9d41c96922_GRCh38.primary_assembly.genome.fa.4.bt2 added
4b9de1558ec_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
4b9d1b80f52d_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
4b9d2f606b76_outfile.txt added
4b9d632f2846_GRCh37_to_GRCh38.chain added
4b9d2cfd3e89_GRCh37_to_NCBI34.chain added
4b9d2614ab72_GRCh37_to_NCBI35.chain added
4b9d1703dce6_GRCh37_to_NCBI36.chain added
4b9d7e9b8bd7_GRCh38_to_GRCh37.chain added
4b9d15fa1131_GRCh38_to_NCBI34.chain added
4b9d547eb33c_GRCh38_to_NCBI35.chain added
4b9d4a29537a_GRCh38_to_NCBI36.chain added
4b9d5f27949f_NCBI34_to_GRCh37.chain added
4b9d1f8e8387_NCBI34_to_GRCh38.chain added
4b9d455d2440_NCBI35_to_GRCh37.chain added
4b9d65f70953_NCBI35_to_GRCh38.chain added
4b9d3d855c71_NCBI36_to_GRCh37.chain added
4b9d7e781e44_NCBI36_to_GRCh38.chain added
4b9db433a_GRCm38_to_NCBIM36.chain added
4b9d636a94db_GRCm38_to_NCBIM37.chain added
4b9d6a52e8da_NCBIM36_to_GRCm38.chain added
4b9d693576be_NCBIM37_to_GRCm38.chain added
4b9d3506e9e8_1000G_omni2.5.b37.vcf.gz added
4b9d58e6998a_1000G_omni2.5.b37.vcf.gz.tbi added
4b9db6a609f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
4b9d74ed6c93_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
4b9df7362de_1000G_omni2.5.hg38.vcf.gz added
4b9d605fe4be_1000G_omni2.5.hg38.vcf.gz.tbi added
4b9d37a2a760_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
4b9d179aac29_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
4b9d2b9cc3da_af-only-gnomad.raw.sites.vcf added
4b9d40fe3394_af-only-gnomad.raw.sites.vcf.idx added
4b9d70ec5ae1_Mutect2-exome-panel.vcf.idx added
4b9d2d42a3b2_Mutect2-WGS-panel-b37.vcf added
4b9d72091254_Mutect2-WGS-panel-b37.vcf.idx added
4b9d31928349_small_exac_common_3.vcf added
4b9d9e9470c_small_exac_common_3.vcf.idx added
4b9d323769e9_1000g_pon.hg38.vcf.gz added
4b9d540a59c0_1000g_pon.hg38.vcf.gz.tbi added
4b9d738a775a_af-only-gnomad.hg38.vcf.gz added
4b9d7a1f0f9_af-only-gnomad.hg38.vcf.gz.tbi added
4b9d18d36f59_small_exac_common_3.hg38.vcf.gz added
4b9d613348ca_small_exac_common_3.hg38.vcf.gz.tbi added
4b9d6deff7a0_gencode.v41.annotation.gtf added
4b9d256a61c3_gencode.v42.annotation.gtf added
4b9d6b385c65_gencode.vM30.annotation.gtf added
4b9d413a21e1_gencode.vM31.annotation.gtf added
4b9d4f865c3b_gencode.v41.transcripts.fa added
4b9d7e114e46_gencode.v41.transcripts.fa.fai added
4b9d222a1653_gencode.v42.transcripts.fa added
4b9d791fb4aa_gencode.v42.transcripts.fa.fai added
4b9d108e4306_gencode.vM30.pc_transcripts.fa added
4b9d6bd24767_gencode.vM30.pc_transcripts.fa.fai added
4b9d3a4df27e_gencode.vM31.pc_transcripts.fa added
4b9d536b4c19_gencode.vM31.pc_transcripts.fa.fai added
4b9d29512818_GRCh38.primary_assembly.genome.fa.1.ht2 added
4b9df1f54d9_GRCh38.primary_assembly.genome.fa.2.ht2 added
4b9d51fb7a50_GRCh38.primary_assembly.genome.fa.3.ht2 added
4b9d551b443c_GRCh38.primary_assembly.genome.fa.4.ht2 added
4b9d711ceaca_GRCh38.primary_assembly.genome.fa.5.ht2 added
4b9d217aadca_GRCh38.primary_assembly.genome.fa.6.ht2 added
4b9d7d27b9f1_GRCh38.primary_assembly.genome.fa.7.ht2 added
4b9d3b20bd68_GRCh38.primary_assembly.genome.fa.8.ht2 added
4b9d6273152b_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
4b9d7172ec8b_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
4b9d3007d3dd_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
4b9d51e66acd_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
4b9d6e6de2bc_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
4b9d7040dd47_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
4b9d327f99e4_GRCh38_full_analysis_set_plus_decoy_hla.fa added
4b9d575061a2_GRCh38.primary_assembly.genome.fa.fai added
4b9d5e39ff76_GRCh38.primary_assembly.genome.fa.amb added
4b9d31b2cc4e_GRCh38.primary_assembly.genome.fa.ann added
4b9d51832e5f_GRCh38.primary_assembly.genome.fa.bwt added
4b9d7b5988c7_GRCh38.primary_assembly.genome.fa.pac added
4b9d33230015_GRCh38.primary_assembly.genome.fa.sa added
4b9d3eda7ced_GRCh38.primary_assembly.genome.fa added
4b9d7a3fcbd7_hs37d5.fa.fai added
4b9d725fcef4_hs37d5.fa.amb added
4b9d700c2fd5_hs37d5.fa.ann added
4b9d3018826b_hs37d5.fa.bwt added
4b9d191a5778_hs37d5.fa.pac added
4b9d10649428_hs37d5.fa.sa added
4b9d3b3ad680_hs37d5.fa added
4b9d13d88be1_complete_ref_lens.bin added
4b9d6dc76af4_ctable.bin added
4b9d3f3ef17a_ctg_offsets.bin added
4b9d3d5fa106_duplicate_clusters.tsv added
4b9d5144b064_info.json added
4b9d74989eea_mphf.bin added
4b9d4fe95073_pos.bin added
4b9d5ea0d701_pre_indexing.log added
4b9d1183b330_rank.bin added
4b9d5d691d4b_ref_indexing.log added
4b9d200256d6_refAccumLengths.bin added
4b9d79930c04_reflengths.bin added
4b9d24fa18f7_refseq.bin added
4b9d1f7d1318_seq.bin added
4b9d4c709cce_versionInfo.json added
4b9d7546bf96_salmon_index added
4b9d77cc4d00_chrLength.txt added
4b9d5d37872_chrName.txt added
4b9d7e88875a_chrNameLength.txt added
4b9d356e669c_chrStart.txt added
4b9d6312a72b_exonGeTrInfo.tab added
4b9d5d9d2add_exonInfo.tab added
4b9d7969432e_geneInfo.tab added
4b9d6db9bf47_Genome added
4b9d3dbd0698_genomeParameters.txt added
4b9d44fc04d2_Log.out added
4b9d7da09a5f_SA added
4b9d3af71368_SAindex added
4b9d331b2f16_sjdbInfo.txt added
4b9d3db06790_sjdbList.fromGTF.out.tab added
4b9d85f3e94_sjdbList.out.tab added
4b9d25056ad7_transcriptInfo.tab added
4b9d6a95c3e_GRCh38.GENCODE.v42_100 added
4b9d58e6eddc_knownGene_hg38.sql added
4b9d210a341d_knownGene_hg38.txt added
4b9d24e36cdd_refGene_hg38.sql added
4b9d4f003416_refGene_hg38.txt added
4b9d165bb8df_knownGene_mm39.sql added
4b9d5fc643f0_knownGene_mm39.txt added
4b9d519672af_refGene_mm39.sql added
4b9d6c436901_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/RtmpjoA9Lf/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
26.060 3.341 31.282
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.311 | 0.844 | 8.251 | |
| dataSearch | 1.278 | 0.057 | 1.339 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.763 | 0.152 | 5.113 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.001 | 0.001 | |
| recipeHub-class | 0.144 | 0.016 | 0.160 | |
| recipeLoad | 1.458 | 0.103 | 1.574 | |
| recipeMake | 0.001 | 0.000 | 0.000 | |
| recipeSearch | 0.597 | 0.040 | 0.638 | |
| recipeUpdate | 0 | 0 | 0 | |