Qian Liu
| Snapshot Date: 2025-09-29 13:40 -0400 (Mon, 29 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 2025-10-02 11:39 -0400 (Thu, 02 Oct 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" | 4831 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4612 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4584 |
| 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: 2025-09-30 08:53:50 -0400 (Tue, 30 Sep 2025) |
| EndedAt: 2025-09-30 08:58:06 -0400 (Tue, 30 Sep 2025) |
| EllapsedTime: 256.6 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 RC (2025-06-05 r88288)
* 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 ‘1.8.0’
* 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 12.381 1.285 14.188
getCloudData 4.770 0.226 6.144
* 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-x86_64/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 RC (2025-06-05 r88288) -- "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...
22b23a3bf6a8_GRCh38.primary_assembly.genome.fa.1.bt2 added
22b236bead76_GRCh38.primary_assembly.genome.fa.2.bt2 added
22b2206e3a0e_GRCh38.primary_assembly.genome.fa.3.bt2 added
22b224a57dc4_GRCh38.primary_assembly.genome.fa.4.bt2 added
22b26ce3e1a7_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
22b264f3d2ca_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
22b24393ff8d_outfile.txt added
22b2296ea4a4_GRCh37_to_GRCh38.chain added
22b21efb203c_GRCh37_to_NCBI34.chain added
22b279015307_GRCh37_to_NCBI35.chain added
22b245f22ea1_GRCh37_to_NCBI36.chain added
22b21ed36fe7_GRCh38_to_GRCh37.chain added
22b24b57b680_GRCh38_to_NCBI34.chain added
22b26b8eb424_GRCh38_to_NCBI35.chain added
22b265d4dea6_GRCh38_to_NCBI36.chain added
22b27a659884_NCBI34_to_GRCh37.chain added
22b2240040e3_NCBI34_to_GRCh38.chain added
22b2ca4098c_NCBI35_to_GRCh37.chain added
22b2656ecccf_NCBI35_to_GRCh38.chain added
22b24d485e0f_NCBI36_to_GRCh37.chain added
22b24a17526c_NCBI36_to_GRCh38.chain added
22b241245674_GRCm38_to_NCBIM36.chain added
22b238a7fb15_GRCm38_to_NCBIM37.chain added
22b21c553cc2_NCBIM36_to_GRCm38.chain added
22b22007f316_NCBIM37_to_GRCm38.chain added
22b269e839c7_1000G_omni2.5.b37.vcf.gz added
22b2d296e23_1000G_omni2.5.b37.vcf.gz.tbi added
22b21afdc295_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
22b29f1d20b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
22b26314d546_1000G_omni2.5.hg38.vcf.gz added
22b26cbe197b_1000G_omni2.5.hg38.vcf.gz.tbi added
22b2347b1203_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
22b27bdb9ddf_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
22b2f59db00_af-only-gnomad.raw.sites.vcf added
22b25438e4df_af-only-gnomad.raw.sites.vcf.idx added
22b2633a17ab_Mutect2-exome-panel.vcf.idx added
22b27ae80e71_Mutect2-WGS-panel-b37.vcf added
22b2190c5bc1_Mutect2-WGS-panel-b37.vcf.idx added
22b27a5be8bf_small_exac_common_3.vcf added
22b2280d925b_small_exac_common_3.vcf.idx added
22b21303a8e8_1000g_pon.hg38.vcf.gz added
22b255462118_1000g_pon.hg38.vcf.gz.tbi added
22b26f26da64_af-only-gnomad.hg38.vcf.gz added
22b25fcc143e_af-only-gnomad.hg38.vcf.gz.tbi added
22b24f452394_small_exac_common_3.hg38.vcf.gz added
22b24422f234_small_exac_common_3.hg38.vcf.gz.tbi added
22b2524b56de_gencode.v41.annotation.gtf added
22b250343307_gencode.v42.annotation.gtf added
22b2130239b4_gencode.vM30.annotation.gtf added
22b2771a622b_gencode.vM31.annotation.gtf added
22b265233223_gencode.v41.transcripts.fa added
22b269b0cbb4_gencode.v41.transcripts.fa.fai added
22b2560dcca1_gencode.v42.transcripts.fa added
22b223f58a2a_gencode.v42.transcripts.fa.fai added
22b24d41ddd7_gencode.vM30.pc_transcripts.fa added
22b21f4b75e1_gencode.vM30.pc_transcripts.fa.fai added
22b2132816d4_gencode.vM31.pc_transcripts.fa added
22b22cf2c21f_gencode.vM31.pc_transcripts.fa.fai added
22b275a69846_GRCh38.primary_assembly.genome.fa.1.ht2 added
22b2c575802_GRCh38.primary_assembly.genome.fa.2.ht2 added
22b23a52f1a2_GRCh38.primary_assembly.genome.fa.3.ht2 added
22b21b75e098_GRCh38.primary_assembly.genome.fa.4.ht2 added
22b257ec293d_GRCh38.primary_assembly.genome.fa.5.ht2 added
22b2518790e3_GRCh38.primary_assembly.genome.fa.6.ht2 added
22b21b3950e6_GRCh38.primary_assembly.genome.fa.7.ht2 added
22b24fee3a00_GRCh38.primary_assembly.genome.fa.8.ht2 added
22b22121feff_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
22b23eec2857_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
22b224c8807_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
22b26e7684be_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
22b227050e9a_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
22b23d01b479_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
22b23aef9339_GRCh38_full_analysis_set_plus_decoy_hla.fa added
22b246aaa169_GRCh38.primary_assembly.genome.fa.fai added
22b26c4b18bd_GRCh38.primary_assembly.genome.fa.amb added
22b2364557d6_GRCh38.primary_assembly.genome.fa.ann added
22b2289be70_GRCh38.primary_assembly.genome.fa.bwt added
22b22135ac5d_GRCh38.primary_assembly.genome.fa.pac added
22b24ac71eb3_GRCh38.primary_assembly.genome.fa.sa added
22b256b0a01f_GRCh38.primary_assembly.genome.fa added
22b265e07faf_hs37d5.fa.fai added
22b275deee69_hs37d5.fa.amb added
22b27ef66bf3_hs37d5.fa.ann added
22b264295fa3_hs37d5.fa.bwt added
22b25845f9b4_hs37d5.fa.pac added
22b25a0cc5b2_hs37d5.fa.sa added
22b27c87574d_hs37d5.fa added
22b21974c01a_complete_ref_lens.bin added
22b23feff804_ctable.bin added
22b22383ef67_ctg_offsets.bin added
22b22ada6568_duplicate_clusters.tsv added
22b26837a4d2_info.json added
22b21d260c72_mphf.bin added
22b22cfb1f51_pos.bin added
22b21ac515e9_pre_indexing.log added
22b212181ba_rank.bin added
22b23ecbdaea_ref_indexing.log added
22b2399158db_refAccumLengths.bin added
22b27560af63_reflengths.bin added
22b21e9ac8c9_refseq.bin added
22b243f413d1_seq.bin added
22b24d412131_versionInfo.json added
22b26eea3f96_salmon_index added
22b254f4c9bd_chrLength.txt added
22b212e8c2de_chrName.txt added
22b26f518684_chrNameLength.txt added
22b251567d34_chrStart.txt added
22b25360aa4_exonGeTrInfo.tab added
22b21ef497a8_exonInfo.tab added
22b24c10a678_geneInfo.tab added
22b25921374b_Genome added
22b213b54aa4_genomeParameters.txt added
22b263375f17_Log.out added
22b2484411e4_SA added
22b26cf2b4cc_SAindex added
22b2323bf4f5_sjdbInfo.txt added
22b27e4f1a96_sjdbList.fromGTF.out.tab added
22b27b5aaea2_sjdbList.out.tab added
22b27e7f4cf2_transcriptInfo.tab added
22b25794e4bf_GRCh38.GENCODE.v42_100 added
22b27035e484_knownGene_hg38.sql added
22b2622dcfa9_knownGene_hg38.txt added
22b22d9c929a_refGene_hg38.sql added
22b225cd3db_refGene_hg38.txt added
22b21c58d013_knownGene_mm39.sql added
22b2ac49def_knownGene_mm39.txt added
22b2725cbb6e_refGene_mm39.sql added
22b226156d6a_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/RtmpMLFi49/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
43.417 5.441 51.299
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 12.381 | 1.285 | 14.188 | |
| dataSearch | 2.499 | 0.085 | 2.606 | |
| dataUpdate | 0.000 | 0.001 | 0.002 | |
| getCloudData | 4.770 | 0.226 | 6.144 | |
| getData | 0.000 | 0.001 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.002 | |
| recipeHub-class | 0.274 | 0.027 | 0.313 | |
| recipeLoad | 2.884 | 0.142 | 3.050 | |
| recipeMake | 0.001 | 0.002 | 0.003 | |
| recipeSearch | 1.144 | 0.053 | 1.200 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |