Qian Liu
| Snapshot Date: 2025-12-21 13:40 -0500 (Sun, 21 Dec 2025) |
| 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 Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-22 11:35 -0500 (Mon, 22 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4878 |
| 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
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| 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: 2025-12-21 21:43:47 -0500 (Sun, 21 Dec 2025) |
| EndedAt: 2025-12-21 21:44:45 -0500 (Sun, 21 Dec 2025) |
| EllapsedTime: 57.8 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_1.11.0.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...
b7705cd2c020_GRCh38.primary_assembly.genome.fa.1.bt2 added
b7701043a47c_GRCh38.primary_assembly.genome.fa.2.bt2 added
b77048e3d13b_GRCh38.primary_assembly.genome.fa.3.bt2 added
b77064bd9ddf_GRCh38.primary_assembly.genome.fa.4.bt2 added
b7705cc7cf24_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
b77041f07412_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
b77011546b90_outfile.txt added
b7703d61c3d3_GRCh37_to_GRCh38.chain added
b7705d7f7120_GRCh37_to_NCBI34.chain added
b77059dc1bd4_GRCh37_to_NCBI35.chain added
b7701a72963_GRCh37_to_NCBI36.chain added
b77058e236e_GRCh38_to_GRCh37.chain added
b77036b80d9b_GRCh38_to_NCBI34.chain added
b7706d85572d_GRCh38_to_NCBI35.chain added
b7704d1e8387_GRCh38_to_NCBI36.chain added
b770e4d3b9f_NCBI34_to_GRCh37.chain added
b77070854b0e_NCBI34_to_GRCh38.chain added
b7703f02bdd8_NCBI35_to_GRCh37.chain added
b7704cfdd039_NCBI35_to_GRCh38.chain added
b7702b7175ac_NCBI36_to_GRCh37.chain added
b77025e4857c_NCBI36_to_GRCh38.chain added
b7703df7a353_GRCm38_to_NCBIM36.chain added
b7704d03bded_GRCm38_to_NCBIM37.chain added
b77030aa3a1b_NCBIM36_to_GRCm38.chain added
b77077ccdb92_NCBIM37_to_GRCm38.chain added
b7702a638bb0_1000G_omni2.5.b37.vcf.gz added
b7706d67e58d_1000G_omni2.5.b37.vcf.gz.tbi added
b770400fc418_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
b7704b132483_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
b77055c23af6_1000G_omni2.5.hg38.vcf.gz added
b77042ad1876_1000G_omni2.5.hg38.vcf.gz.tbi added
b77072210d2c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
b77057e7fe3d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
b7703fe483e1_af-only-gnomad.raw.sites.vcf added
b770338e498c_af-only-gnomad.raw.sites.vcf.idx added
b770427ea0c5_Mutect2-exome-panel.vcf.idx added
b77076d079e_Mutect2-WGS-panel-b37.vcf added
b77070f19e1_Mutect2-WGS-panel-b37.vcf.idx added
b770706c0665_small_exac_common_3.vcf added
b77044180a8c_small_exac_common_3.vcf.idx added
b77065c9041_1000g_pon.hg38.vcf.gz added
b77027029eaa_1000g_pon.hg38.vcf.gz.tbi added
b7701cfebee8_af-only-gnomad.hg38.vcf.gz added
b77018a78037_af-only-gnomad.hg38.vcf.gz.tbi added
b7701cd2a786_small_exac_common_3.hg38.vcf.gz added
b77049f45d32_small_exac_common_3.hg38.vcf.gz.tbi added
b7704a12a38c_gencode.v41.annotation.gtf added
b770daf6252_gencode.v42.annotation.gtf added
b770755ffc82_gencode.vM30.annotation.gtf added
b77070baf701_gencode.vM31.annotation.gtf added
b7702ae9c79_gencode.v41.transcripts.fa added
b77015a2cd4f_gencode.v41.transcripts.fa.fai added
b770735508a1_gencode.v42.transcripts.fa added
b77053a9bd2e_gencode.v42.transcripts.fa.fai added
b7702cc341eb_gencode.vM30.pc_transcripts.fa added
b770471cc242_gencode.vM30.pc_transcripts.fa.fai added
b77031159f87_gencode.vM31.pc_transcripts.fa added
b77029c713e_gencode.vM31.pc_transcripts.fa.fai added
b7706cce9ec8_GRCh38.primary_assembly.genome.fa.1.ht2 added
b770711a9446_GRCh38.primary_assembly.genome.fa.2.ht2 added
b7707fcb9ad_GRCh38.primary_assembly.genome.fa.3.ht2 added
b770610210f3_GRCh38.primary_assembly.genome.fa.4.ht2 added
b7704ea6f346_GRCh38.primary_assembly.genome.fa.5.ht2 added
b77032ada101_GRCh38.primary_assembly.genome.fa.6.ht2 added
b770252562a5_GRCh38.primary_assembly.genome.fa.7.ht2 added
b770396f51b0_GRCh38.primary_assembly.genome.fa.8.ht2 added
b7703b5c1745_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
b7701afbd175_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
b770a74662a_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
b7705fdf54c2_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
b7703f35bdba_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
b770613b1ec1_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
b770706042c5_GRCh38_full_analysis_set_plus_decoy_hla.fa added
b7703fbfcd26_GRCh38.primary_assembly.genome.fa.fai added
b77049359a7c_GRCh38.primary_assembly.genome.fa.amb added
b7705e316870_GRCh38.primary_assembly.genome.fa.ann added
b7707dbfc15f_GRCh38.primary_assembly.genome.fa.bwt added
b77038308478_GRCh38.primary_assembly.genome.fa.pac added
b7707948ff19_GRCh38.primary_assembly.genome.fa.sa added
b77027640084_GRCh38.primary_assembly.genome.fa added
b770165dee50_hs37d5.fa.fai added
b77070c8d1a8_hs37d5.fa.amb added
b770103ca671_hs37d5.fa.ann added
b7707dd34d0a_hs37d5.fa.bwt added
b7703b670c0f_hs37d5.fa.pac added
b7706a48cb40_hs37d5.fa.sa added
b77051180d43_hs37d5.fa added
b77020ed34d_complete_ref_lens.bin added
b7701b526549_ctable.bin added
b7703e77a9a2_ctg_offsets.bin added
b7702221eab8_duplicate_clusters.tsv added
b77060b8e789_info.json added
b770b6904fb_mphf.bin added
b7701bc60097_pos.bin added
b7706450c7bf_pre_indexing.log added
b770736a000c_rank.bin added
b77034294f06_ref_indexing.log added
b7704032dab_refAccumLengths.bin added
b7706cab379b_reflengths.bin added
b7705ccfd8d9_refseq.bin added
b77051a5be29_seq.bin added
b77058679f9f_versionInfo.json added
b7707b20ad10_salmon_index added
b7701e423497_chrLength.txt added
b770c8ab506_chrName.txt added
b7706672a358_chrNameLength.txt added
b77070421af3_chrStart.txt added
b7703f78119_exonGeTrInfo.tab added
b7706e3c9257_exonInfo.tab added
b7704aabc64b_geneInfo.tab added
b77053678c39_Genome added
b77033271cf6_genomeParameters.txt added
b7704cde74b6_Log.out added
b77020c08027_SA added
b7703e1d913d_SAindex added
b77072a5ba7_sjdbInfo.txt added
b7706de7349d_sjdbList.fromGTF.out.tab added
b770662f67c9_sjdbList.out.tab added
b7703246f188_transcriptInfo.tab added
b7704f9b3181_GRCh38.GENCODE.v42_100 added
b77055cf34fb_knownGene_hg38.sql added
b770169f76c0_knownGene_hg38.txt added
b7703f2d42da_refGene_hg38.sql added
b7703480169d_refGene_hg38.txt added
b770454cb858_knownGene_mm39.sql added
b7702fdabcf3_knownGene_mm39.txt added
b77041ab0e10_refGene_mm39.sql added
b77045285e1e_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//RtmpheTvk5/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
6.905 0.843 8.748
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.076 | 0.281 | 2.480 | |
| dataSearch | 0.360 | 0.017 | 0.395 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.910 | 0.063 | 2.150 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.041 | 0.004 | 0.047 | |
| recipeLoad | 0.417 | 0.031 | 0.465 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.174 | 0.013 | 0.219 | |
| recipeUpdate | 0.000 | 0.000 | 0.007 | |