Qian Liu
| Snapshot Date: 2025-12-02 13:40 -0500 (Tue, 02 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 2025-12-03 11:35 -0500 (Wed, 03 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" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4575 |
| 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 1753/2331 | 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: 2025-12-02 22:05:45 -0500 (Tue, 02 Dec 2025) |
| EndedAt: 2025-12-02 22:06:43 -0500 (Tue, 02 Dec 2025) |
| EllapsedTime: 57.6 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_1.11.0.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...
f4703fdefee5_GRCh38.primary_assembly.genome.fa.1.bt2 added
f47049308d25_GRCh38.primary_assembly.genome.fa.2.bt2 added
f47012829dad_GRCh38.primary_assembly.genome.fa.3.bt2 added
f4703d3dd259_GRCh38.primary_assembly.genome.fa.4.bt2 added
f47025bcf078_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
f470174f69a3_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
f4705ea05849_outfile.txt added
f47071045127_GRCh37_to_GRCh38.chain added
f470526c1168_GRCh37_to_NCBI34.chain added
f47034eaed1e_GRCh37_to_NCBI35.chain added
f4702b7567b6_GRCh37_to_NCBI36.chain added
f47028ebf404_GRCh38_to_GRCh37.chain added
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f47045bc3700_GRCh38_to_NCBI36.chain added
f47047bf04c4_NCBI34_to_GRCh37.chain added
f4704dd204a8_NCBI34_to_GRCh38.chain added
f470172fd982_NCBI35_to_GRCh37.chain added
f4704670f1b2_NCBI35_to_GRCh38.chain added
f470210c013f_NCBI36_to_GRCh37.chain added
f4701b25e00c_NCBI36_to_GRCh38.chain added
f470539841c0_GRCm38_to_NCBIM36.chain added
f4703104cf20_GRCm38_to_NCBIM37.chain added
f47032ba5704_NCBIM36_to_GRCm38.chain added
f47067a6e1a0_NCBIM37_to_GRCm38.chain added
f4707d270489_1000G_omni2.5.b37.vcf.gz added
f470c9afe90_1000G_omni2.5.b37.vcf.gz.tbi added
f47013bea667_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
f470499ebe51_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
f47054e0dd99_1000G_omni2.5.hg38.vcf.gz added
f47076f49357_1000G_omni2.5.hg38.vcf.gz.tbi added
f47032f571c4_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
f470100014ff_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
f4707562798d_af-only-gnomad.raw.sites.vcf added
f470141a5430_af-only-gnomad.raw.sites.vcf.idx added
f4704c8d259f_Mutect2-exome-panel.vcf.idx added
f47046a110fc_Mutect2-WGS-panel-b37.vcf added
f4707862349d_Mutect2-WGS-panel-b37.vcf.idx added
f470776c6d29_small_exac_common_3.vcf added
f4706f72dbff_small_exac_common_3.vcf.idx added
f4705dc97b82_1000g_pon.hg38.vcf.gz added
f47056cbc3e8_1000g_pon.hg38.vcf.gz.tbi added
f4705baae0dc_af-only-gnomad.hg38.vcf.gz added
f4702f90ba88_af-only-gnomad.hg38.vcf.gz.tbi added
f47046c64f1d_small_exac_common_3.hg38.vcf.gz added
f4705741d38_small_exac_common_3.hg38.vcf.gz.tbi added
f470a2a4a54_gencode.v41.annotation.gtf added
f4705e75d602_gencode.v42.annotation.gtf added
f470a354dc1_gencode.vM30.annotation.gtf added
f4703183bf23_gencode.vM31.annotation.gtf added
f4704079ac3a_gencode.v41.transcripts.fa added
f470741a34e7_gencode.v41.transcripts.fa.fai added
f4706487653d_gencode.v42.transcripts.fa added
f4707507bb5a_gencode.v42.transcripts.fa.fai added
f4704e9d4dbc_gencode.vM30.pc_transcripts.fa added
f470395a99f6_gencode.vM30.pc_transcripts.fa.fai added
f4706b3202e4_gencode.vM31.pc_transcripts.fa added
f470205bfdb7_gencode.vM31.pc_transcripts.fa.fai added
f470776e09f9_GRCh38.primary_assembly.genome.fa.1.ht2 added
f4705950f7b0_GRCh38.primary_assembly.genome.fa.2.ht2 added
f47052b5719f_GRCh38.primary_assembly.genome.fa.3.ht2 added
f470636a825_GRCh38.primary_assembly.genome.fa.4.ht2 added
f4706e591852_GRCh38.primary_assembly.genome.fa.5.ht2 added
f4701b4be817_GRCh38.primary_assembly.genome.fa.6.ht2 added
f47014724c01_GRCh38.primary_assembly.genome.fa.7.ht2 added
f4705bdbe023_GRCh38.primary_assembly.genome.fa.8.ht2 added
f470405848f2_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
f470641d28de_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
f47036663a2b_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
f4707174f8f3_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
f470368453b6_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
f4702993edb0_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
f4702ed9d323_GRCh38_full_analysis_set_plus_decoy_hla.fa added
f4705eb4b6dc_GRCh38.primary_assembly.genome.fa.fai added
f4702a515617_GRCh38.primary_assembly.genome.fa.amb added
f47041eb15b5_GRCh38.primary_assembly.genome.fa.ann added
f47030de3fe2_GRCh38.primary_assembly.genome.fa.bwt added
f4704f34277e_GRCh38.primary_assembly.genome.fa.pac added
f470690ce9d1_GRCh38.primary_assembly.genome.fa.sa added
f4704ecace38_GRCh38.primary_assembly.genome.fa added
f47064a8e6f1_hs37d5.fa.fai added
f470cd20bd8_hs37d5.fa.amb added
f4703207987b_hs37d5.fa.ann added
f47010abcce6_hs37d5.fa.bwt added
f4707f191896_hs37d5.fa.pac added
f470489d610a_hs37d5.fa.sa added
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f4704c0dd319_complete_ref_lens.bin added
f4701f9e3551_ctable.bin added
f4704bbe690e_ctg_offsets.bin added
f47041e33cfb_duplicate_clusters.tsv added
f4702db8a488_info.json added
f4703539f42b_mphf.bin added
f4706fcd4e59_pos.bin added
f470fd2ee67_pre_indexing.log added
f4706121b44e_rank.bin added
f4706bc49eb3_ref_indexing.log added
f470398f310b_refAccumLengths.bin added
f47067dce6b2_reflengths.bin added
f47057ade563_refseq.bin added
f47059aef38d_seq.bin added
f4706cf7dbfa_versionInfo.json added
f47048b31fa_salmon_index added
f4704e7e166a_chrLength.txt added
f47037f1b168_chrName.txt added
f4705cb63f89_chrNameLength.txt added
f47041056aec_chrStart.txt added
f4704aaecd4d_exonGeTrInfo.tab added
f4701a28a089_exonInfo.tab added
f47061438fc9_geneInfo.tab added
f4701a950702_Genome added
f4702dff21f0_genomeParameters.txt added
f470490d2b27_Log.out added
f4707f8c32e8_SA added
f4704d625ec3_SAindex added
f470753b7be5_sjdbInfo.txt added
f47014433384_sjdbList.fromGTF.out.tab added
f47047eb2980_sjdbList.out.tab added
f4701ff1b763_transcriptInfo.tab added
f470363ed4f7_GRCh38.GENCODE.v42_100 added
f470570fbff3_knownGene_hg38.sql added
f4704b03172c_knownGene_hg38.txt added
f47037e6702d_refGene_hg38.sql added
f47079ceb706_refGene_hg38.txt added
f47072522963_knownGene_mm39.sql added
f470701b5d37_knownGene_mm39.txt added
f4701484ff61_refGene_mm39.sql added
f470279a43cd_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//Rtmphy98Lp/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
7.058 0.817 8.863
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.017 | 0.240 | 2.297 | |
| dataSearch | 0.374 | 0.017 | 0.429 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.916 | 0.061 | 2.346 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.041 | 0.005 | 0.046 | |
| recipeLoad | 0.424 | 0.032 | 0.494 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.177 | 0.013 | 0.196 | |
| recipeUpdate | 0 | 0 | 0 | |