Qian Liu
| Snapshot Date: 2025-08-05 13:25 -0400 (Tue, 05 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 2025-08-06 13:55 -0400 (Wed, 06 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" | 4813 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4550 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4592 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4534 |
| 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 1737/2315 | 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 | | ||||||||
|
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: 2025-08-05 23:22:47 -0400 (Tue, 05 Aug 2025) |
| EndedAt: 2025-08-05 23:25:13 -0400 (Tue, 05 Aug 2025) |
| EllapsedTime: 145.7 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 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataHub-class 7.624 0.907 8.651
* 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-x86_64/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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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...
d9b029e99596_GRCh38.primary_assembly.genome.fa.1.bt2 added
d9b0265bc059_GRCh38.primary_assembly.genome.fa.2.bt2 added
d9b051b126bb_GRCh38.primary_assembly.genome.fa.3.bt2 added
d9b04565e8e3_GRCh38.primary_assembly.genome.fa.4.bt2 added
d9b0259cb2ad_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
d9b052968f25_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
d9b01a8ff07f_outfile.txt added
d9b05ff62f78_GRCh37_to_GRCh38.chain added
d9b01ba6a080_GRCh37_to_NCBI34.chain added
d9b0587341ae_GRCh37_to_NCBI35.chain added
d9b076dd33df_GRCh37_to_NCBI36.chain added
d9b03478b270_GRCh38_to_GRCh37.chain added
d9b0600af1f9_GRCh38_to_NCBI34.chain added
d9b06e9443b1_GRCh38_to_NCBI35.chain added
d9b047e8522e_GRCh38_to_NCBI36.chain added
d9b0656b6ee3_NCBI34_to_GRCh37.chain added
d9b0703d2d19_NCBI34_to_GRCh38.chain added
d9b0405bfde0_NCBI35_to_GRCh37.chain added
d9b057789e22_NCBI35_to_GRCh38.chain added
d9b02fd5f70b_NCBI36_to_GRCh37.chain added
d9b084e0bb6_NCBI36_to_GRCh38.chain added
d9b03be2ddfc_GRCm38_to_NCBIM36.chain added
d9b02b5bea1b_GRCm38_to_NCBIM37.chain added
d9b01f66a8da_NCBIM36_to_GRCm38.chain added
d9b0cd79051_NCBIM37_to_GRCm38.chain added
d9b01c43bc6d_1000G_omni2.5.b37.vcf.gz added
d9b02307a69a_1000G_omni2.5.b37.vcf.gz.tbi added
d9b04b4ada6d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
d9b01f4a50b9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
d9b047f9b1bb_1000G_omni2.5.hg38.vcf.gz added
d9b05a0390e7_1000G_omni2.5.hg38.vcf.gz.tbi added
d9b0201e5bdc_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
d9b02920d8fd_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
d9b02b85df23_af-only-gnomad.raw.sites.vcf added
d9b061fc8927_af-only-gnomad.raw.sites.vcf.idx added
d9b0a9091b3_Mutect2-exome-panel.vcf.idx added
d9b0194d8430_Mutect2-WGS-panel-b37.vcf added
d9b03021784a_Mutect2-WGS-panel-b37.vcf.idx added
d9b065605af5_small_exac_common_3.vcf added
d9b018f3bed2_small_exac_common_3.vcf.idx added
d9b02a74d9ca_1000g_pon.hg38.vcf.gz added
d9b05d86728c_1000g_pon.hg38.vcf.gz.tbi added
d9b025ca754c_af-only-gnomad.hg38.vcf.gz added
d9b0edae3f6_af-only-gnomad.hg38.vcf.gz.tbi added
d9b044ac3318_small_exac_common_3.hg38.vcf.gz added
d9b054e8fe1_small_exac_common_3.hg38.vcf.gz.tbi added
d9b068c7ff7f_gencode.v41.annotation.gtf added
d9b022572097_gencode.v42.annotation.gtf added
d9b061cab1e_gencode.vM30.annotation.gtf added
d9b0442641b4_gencode.vM31.annotation.gtf added
d9b02ba3b360_gencode.v41.transcripts.fa added
d9b08557a02_gencode.v41.transcripts.fa.fai added
d9b023bd1d94_gencode.v42.transcripts.fa added
d9b054e0f1e0_gencode.v42.transcripts.fa.fai added
d9b07c27d4a8_gencode.vM30.pc_transcripts.fa added
d9b01afaa146_gencode.vM30.pc_transcripts.fa.fai added
d9b03c720880_gencode.vM31.pc_transcripts.fa added
d9b0628c2a80_gencode.vM31.pc_transcripts.fa.fai added
d9b0603a6c0b_GRCh38.primary_assembly.genome.fa.1.ht2 added
d9b01b8b7788_GRCh38.primary_assembly.genome.fa.2.ht2 added
d9b061548fd8_GRCh38.primary_assembly.genome.fa.3.ht2 added
d9b076afdfd3_GRCh38.primary_assembly.genome.fa.4.ht2 added
d9b0148fd285_GRCh38.primary_assembly.genome.fa.5.ht2 added
d9b06e46244e_GRCh38.primary_assembly.genome.fa.6.ht2 added
d9b03ef9b571_GRCh38.primary_assembly.genome.fa.7.ht2 added
d9b07bf72e03_GRCh38.primary_assembly.genome.fa.8.ht2 added
d9b020ee068a_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
d9b06aef5ee9_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
d9b094049d8_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
d9b05bb008a6_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
d9b0207f951_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
d9b0598135e1_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
d9b031f874af_GRCh38_full_analysis_set_plus_decoy_hla.fa added
d9b02eb4a6ca_GRCh38.primary_assembly.genome.fa.fai added
d9b056322fba_GRCh38.primary_assembly.genome.fa.amb added
d9b078db888b_GRCh38.primary_assembly.genome.fa.ann added
d9b014e19baa_GRCh38.primary_assembly.genome.fa.bwt added
d9b067b2c09b_GRCh38.primary_assembly.genome.fa.pac added
d9b0883354d_GRCh38.primary_assembly.genome.fa.sa added
d9b05e205698_GRCh38.primary_assembly.genome.fa added
d9b01d15456f_hs37d5.fa.fai added
d9b05f818953_hs37d5.fa.amb added
d9b0315ed921_hs37d5.fa.ann added
d9b04a011ed9_hs37d5.fa.bwt added
d9b0f905e84_hs37d5.fa.pac added
d9b04f2d3417_hs37d5.fa.sa added
d9b020b6fa9d_hs37d5.fa added
d9b04cff6a32_complete_ref_lens.bin added
d9b01495201c_ctable.bin added
d9b04a6f18d2_ctg_offsets.bin added
d9b043c6a92b_duplicate_clusters.tsv added
d9b0278c68d0_info.json added
d9b0733543f8_mphf.bin added
d9b02e0189df_pos.bin added
d9b06702a711_pre_indexing.log added
d9b05f2681ec_rank.bin added
d9b0591bddc1_ref_indexing.log added
d9b0347bd79b_refAccumLengths.bin added
d9b02e881c08_reflengths.bin added
d9b069e86915_refseq.bin added
d9b0194b1805_seq.bin added
d9b01115fd3c_versionInfo.json added
d9b03aa476e7_salmon_index added
d9b037a55c5_chrLength.txt added
d9b05494fa4b_chrName.txt added
d9b0bc7d4f_chrNameLength.txt added
d9b056c6cde9_chrStart.txt added
d9b015f8a881_exonGeTrInfo.tab added
d9b077feb86b_exonInfo.tab added
d9b073fdb658_geneInfo.tab added
d9b015ce86e6_Genome added
d9b029fa7139_genomeParameters.txt added
d9b0791f6ab6_Log.out added
d9b07d9710d9_SA added
d9b048d356f9_SAindex added
d9b02af31ac9_sjdbInfo.txt added
d9b03e639826_sjdbList.fromGTF.out.tab added
d9b07c9a06c9_sjdbList.out.tab added
d9b06433b607_transcriptInfo.tab added
d9b07ef3b8f5_GRCh38.GENCODE.v42_100 added
d9b032f41df0_knownGene_hg38.sql added
d9b038d991b2_knownGene_hg38.txt added
d9b053ec5a46_refGene_hg38.sql added
d9b0421ad4b5_refGene_hg38.txt added
d9b06f82d8fa_knownGene_mm39.sql added
d9b077733e47_knownGene_mm39.txt added
d9b02efde495_refGene_mm39.sql added
d9b01eaa0a4d_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/RtmpvLHg8B/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
21.664 2.478 25.265
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.624 | 0.907 | 8.651 | |
| dataSearch | 1.417 | 0.064 | 1.492 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.923 | 0.172 | 4.241 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.141 | 0.011 | 0.153 | |
| recipeLoad | 1.567 | 0.102 | 1.680 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.645 | 0.040 | 0.688 | |
| recipeUpdate | 0 | 0 | 0 | |