Qian Liu
| Snapshot Date: 2026-01-08 13:40 -0500 (Thu, 08 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: 4a5d06b |
| git_last_commit_date: 2025-10-29 11:20:44 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-09 12:02 -0500 (Fri, 09 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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 1754/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.11.0 (landing page) Qian Liu
| kjohnson3 | macOS 13.7.7 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: 1.11.0 |
| 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_1.11.0.tar.gz |
| StartedAt: 2026-01-08 22:02:10 -0500 (Thu, 08 Jan 2026) |
| EndedAt: 2026-01-08 22:03:05 -0500 (Thu, 08 Jan 2026) |
| EllapsedTime: 54.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* 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 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.11.0’
* 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-3.23-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/4.6-arm64/Resources/library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.11.0’ ** 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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
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...
457428d67676_GRCh38.primary_assembly.genome.fa.1.bt2 added
457417fb51ec_GRCh38.primary_assembly.genome.fa.2.bt2 added
457474bf6940_GRCh38.primary_assembly.genome.fa.3.bt2 added
4574429724a1_GRCh38.primary_assembly.genome.fa.4.bt2 added
457450e5e82e_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
457425ee4d80_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
4574402221f4_outfile.txt added
4574e33b11_GRCh37_to_GRCh38.chain added
4574463ad98b_GRCh37_to_NCBI34.chain added
457441a058b2_GRCh37_to_NCBI35.chain added
457461f2fc7_GRCh37_to_NCBI36.chain added
45746979b4f4_GRCh38_to_GRCh37.chain added
457435573545_GRCh38_to_NCBI34.chain added
4574706a605e_GRCh38_to_NCBI35.chain added
457457dcf4fa_GRCh38_to_NCBI36.chain added
45746b577626_NCBI34_to_GRCh37.chain added
45743b0defd8_NCBI34_to_GRCh38.chain added
4574ffd6c32_NCBI35_to_GRCh37.chain added
457446ca4ed1_NCBI35_to_GRCh38.chain added
4574bfc9fa6_NCBI36_to_GRCh37.chain added
45747655516f_NCBI36_to_GRCh38.chain added
45745b558b1a_GRCm38_to_NCBIM36.chain added
45744d1f86ce_GRCm38_to_NCBIM37.chain added
457450cb65f0_NCBIM36_to_GRCm38.chain added
457459919900_NCBIM37_to_GRCm38.chain added
457465d3fcf0_1000G_omni2.5.b37.vcf.gz added
4574408324ca_1000G_omni2.5.b37.vcf.gz.tbi added
457461e46adc_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
45745b23c3b9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
4574906d56e_1000G_omni2.5.hg38.vcf.gz added
45741fa62d63_1000G_omni2.5.hg38.vcf.gz.tbi added
457456edced0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
457416a4e646_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
4574240a0947_af-only-gnomad.raw.sites.vcf added
4574ee726cd_af-only-gnomad.raw.sites.vcf.idx added
457469a4645f_Mutect2-exome-panel.vcf.idx added
457427b9cf28_Mutect2-WGS-panel-b37.vcf added
457417cf5f78_Mutect2-WGS-panel-b37.vcf.idx added
45742f84cb7e_small_exac_common_3.vcf added
4574374bd591_small_exac_common_3.vcf.idx added
457453b23ef3_1000g_pon.hg38.vcf.gz added
45745b42ee72_1000g_pon.hg38.vcf.gz.tbi added
4574734ad2d_af-only-gnomad.hg38.vcf.gz added
45741355690d_af-only-gnomad.hg38.vcf.gz.tbi added
45744c63de65_small_exac_common_3.hg38.vcf.gz added
4574309de011_small_exac_common_3.hg38.vcf.gz.tbi added
45744ce19506_gencode.v41.annotation.gtf added
45746dfee458_gencode.v42.annotation.gtf added
4574794185d2_gencode.vM30.annotation.gtf added
45743cb8dc2f_gencode.vM31.annotation.gtf added
4574c7fb0ce_gencode.v41.transcripts.fa added
45741330aacb_gencode.v41.transcripts.fa.fai added
4574601cff44_gencode.v42.transcripts.fa added
4574fbafaa8_gencode.v42.transcripts.fa.fai added
45743c9e33a9_gencode.vM30.pc_transcripts.fa added
45743651bb56_gencode.vM30.pc_transcripts.fa.fai added
45742fe226f6_gencode.vM31.pc_transcripts.fa added
4574286bf909_gencode.vM31.pc_transcripts.fa.fai added
457448aad29a_GRCh38.primary_assembly.genome.fa.1.ht2 added
457446e8a1bb_GRCh38.primary_assembly.genome.fa.2.ht2 added
457452d2205b_GRCh38.primary_assembly.genome.fa.3.ht2 added
4574614a60d7_GRCh38.primary_assembly.genome.fa.4.ht2 added
45745a1bf527_GRCh38.primary_assembly.genome.fa.5.ht2 added
4574617c01a8_GRCh38.primary_assembly.genome.fa.6.ht2 added
45741450ee98_GRCh38.primary_assembly.genome.fa.7.ht2 added
45744d604793_GRCh38.primary_assembly.genome.fa.8.ht2 added
45746bfb2b94_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
457436ea38ee_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
45744b3fad6c_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
45744192b40c_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
457466aa176_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
4574428e4d44_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
4574c72cd7f_GRCh38_full_analysis_set_plus_decoy_hla.fa added
45744511533b_GRCh38.primary_assembly.genome.fa.fai added
4574746f69e9_GRCh38.primary_assembly.genome.fa.amb added
45743e927bb7_GRCh38.primary_assembly.genome.fa.ann added
45742f84b79_GRCh38.primary_assembly.genome.fa.bwt added
45747b22f674_GRCh38.primary_assembly.genome.fa.pac added
4574346278d4_GRCh38.primary_assembly.genome.fa.sa added
45742ceac12a_GRCh38.primary_assembly.genome.fa added
4574682fc36f_hs37d5.fa.fai added
457417c7e1d9_hs37d5.fa.amb added
457443bc79c1_hs37d5.fa.ann added
4574add90a5_hs37d5.fa.bwt added
457458434635_hs37d5.fa.pac added
457428b66ed8_hs37d5.fa.sa added
457461273bc9_hs37d5.fa added
457456c63af3_complete_ref_lens.bin added
457470485406_ctable.bin added
45741c848f81_ctg_offsets.bin added
457442e96cc7_duplicate_clusters.tsv added
45746ae49f22_info.json added
4574478ba801_mphf.bin added
457421c2fe59_pos.bin added
45748c89660_pre_indexing.log added
457429087d21_rank.bin added
45746c4f1692_ref_indexing.log added
45743c5302cb_refAccumLengths.bin added
45746ddc7c5d_reflengths.bin added
45742668f604_refseq.bin added
457434ef944f_seq.bin added
45745cf1e9af_versionInfo.json added
4574e250fd5_salmon_index added
457423327034_chrLength.txt added
4574446477f9_chrName.txt added
457420009f83_chrNameLength.txt added
45748e861df_chrStart.txt added
457450717c0a_exonGeTrInfo.tab added
45744a869dc8_exonInfo.tab added
45744be0dbb1_geneInfo.tab added
457417776862_Genome added
4574206605f7_genomeParameters.txt added
4574a11abbf_Log.out added
4574e228dc3_SA added
45747e890474_SAindex added
457455839c92_sjdbInfo.txt added
4574339c611a_sjdbList.fromGTF.out.tab added
45745fab0c6e_sjdbList.out.tab added
457456bd3ad3_transcriptInfo.tab added
457421611f22_GRCh38.GENCODE.v42_100 added
45746f43024c_knownGene_hg38.sql added
4574184c04a5_knownGene_hg38.txt added
457426c4f919_refGene_hg38.sql added
45744dbdec31_refGene_hg38.txt added
45746fddacd6_knownGene_mm39.sql added
4574427e4efa_knownGene_mm39.txt added
457472732130_refGene_mm39.sql added
457464881103_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//RtmpOpK4m5/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
6.875 0.828 8.737
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.090 | 0.268 | 2.410 | |
| dataSearch | 0.360 | 0.017 | 0.396 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.922 | 0.059 | 2.069 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.040 | 0.006 | 0.047 | |
| recipeLoad | 0.433 | 0.030 | 0.478 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.171 | 0.011 | 0.183 | |
| recipeUpdate | 0.001 | 0.000 | 0.001 | |