Qian Liu
| Snapshot Date: 2025-10-24 13:45 -0400 (Fri, 24 Oct 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 2025-10-25 12:06 -0400 (Sat, 25 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 1773/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.9.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | NA | NA | ||||||||||
|
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: 2025-10-24 21:38:33 -0400 (Fri, 24 Oct 2025) |
| EndedAt: 2025-10-24 21:39:23 -0400 (Fri, 24 Oct 2025) |
| EllapsedTime: 49.5 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 Patched (2025-09-10 r88807)
* 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 13.7.7
* 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
* 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-arm64/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 Patched (2025-09-10 r88807) -- "Great Square Root"
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...
e7a2f652f0_GRCh38.primary_assembly.genome.fa.1.bt2 added
e7a22bbf0b0e_GRCh38.primary_assembly.genome.fa.2.bt2 added
e7a2b6eda92_GRCh38.primary_assembly.genome.fa.3.bt2 added
e7a21acfad1b_GRCh38.primary_assembly.genome.fa.4.bt2 added
e7a2386dd55d_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
e7a232d2e99c_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
e7a234e71ad5_outfile.txt added
e7a23092b115_GRCh37_to_GRCh38.chain added
e7a26ea7f29c_GRCh37_to_NCBI34.chain added
e7a254291885_GRCh37_to_NCBI35.chain added
e7a25608eeed_GRCh37_to_NCBI36.chain added
e7a2647e35bb_GRCh38_to_GRCh37.chain added
e7a219f9bb88_GRCh38_to_NCBI34.chain added
e7a25a86eb0a_GRCh38_to_NCBI35.chain added
e7a24fb10bf4_GRCh38_to_NCBI36.chain added
e7a27087e90b_NCBI34_to_GRCh37.chain added
e7a26ad50ae4_NCBI34_to_GRCh38.chain added
e7a248be3587_NCBI35_to_GRCh37.chain added
e7a23fac5760_NCBI35_to_GRCh38.chain added
e7a24b9c8048_NCBI36_to_GRCh37.chain added
e7a2faa1dc0_NCBI36_to_GRCh38.chain added
e7a269873048_GRCm38_to_NCBIM36.chain added
e7a22a72fd18_GRCm38_to_NCBIM37.chain added
e7a26346486d_NCBIM36_to_GRCm38.chain added
e7a21b3d1f06_NCBIM37_to_GRCm38.chain added
e7a249bfd0e2_1000G_omni2.5.b37.vcf.gz added
e7a2502acb41_1000G_omni2.5.b37.vcf.gz.tbi added
e7a229864185_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
e7a22d37980f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
e7a21ce017fa_1000G_omni2.5.hg38.vcf.gz added
e7a23c462ce5_1000G_omni2.5.hg38.vcf.gz.tbi added
e7a2232d8d4d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
e7a2397cc46_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
e7a262e40981_af-only-gnomad.raw.sites.vcf added
e7a2692c26df_af-only-gnomad.raw.sites.vcf.idx added
e7a251ac306a_Mutect2-exome-panel.vcf.idx added
e7a27f9ea909_Mutect2-WGS-panel-b37.vcf added
e7a296bcf54_Mutect2-WGS-panel-b37.vcf.idx added
e7a24f898a1_small_exac_common_3.vcf added
e7a25cec7493_small_exac_common_3.vcf.idx added
e7a227d98e8e_1000g_pon.hg38.vcf.gz added
e7a23c1e2112_1000g_pon.hg38.vcf.gz.tbi added
e7a25e0d4393_af-only-gnomad.hg38.vcf.gz added
e7a238cf9822_af-only-gnomad.hg38.vcf.gz.tbi added
e7a2450cfd51_small_exac_common_3.hg38.vcf.gz added
e7a257caf441_small_exac_common_3.hg38.vcf.gz.tbi added
e7a24d6a046e_gencode.v41.annotation.gtf added
e7a26b48f976_gencode.v42.annotation.gtf added
e7a23f1e901_gencode.vM30.annotation.gtf added
e7a27ef842ac_gencode.vM31.annotation.gtf added
e7a25ce16b53_gencode.v41.transcripts.fa added
e7a2534d45c8_gencode.v41.transcripts.fa.fai added
e7a276207831_gencode.v42.transcripts.fa added
e7a24db3158d_gencode.v42.transcripts.fa.fai added
e7a2284c03d5_gencode.vM30.pc_transcripts.fa added
e7a2168fa99e_gencode.vM30.pc_transcripts.fa.fai added
e7a231c8cfa4_gencode.vM31.pc_transcripts.fa added
e7a276b83184_gencode.vM31.pc_transcripts.fa.fai added
e7a236bb0e00_GRCh38.primary_assembly.genome.fa.1.ht2 added
e7a232943e12_GRCh38.primary_assembly.genome.fa.2.ht2 added
e7a2227729af_GRCh38.primary_assembly.genome.fa.3.ht2 added
e7a23d51b1d6_GRCh38.primary_assembly.genome.fa.4.ht2 added
e7a23e72780d_GRCh38.primary_assembly.genome.fa.5.ht2 added
e7a24d27bd82_GRCh38.primary_assembly.genome.fa.6.ht2 added
e7a26c0ac960_GRCh38.primary_assembly.genome.fa.7.ht2 added
e7a2382af50a_GRCh38.primary_assembly.genome.fa.8.ht2 added
e7a2c3d8055_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
e7a219b452ba_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
e7a2da33e85_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
e7a2585d94c1_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
e7a267d13839_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
e7a258c25b6e_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
e7a24000c048_GRCh38_full_analysis_set_plus_decoy_hla.fa added
e7a2714fd7cb_GRCh38.primary_assembly.genome.fa.fai added
e7a230e08a8b_GRCh38.primary_assembly.genome.fa.amb added
e7a265a7c4be_GRCh38.primary_assembly.genome.fa.ann added
e7a26965ca15_GRCh38.primary_assembly.genome.fa.bwt added
e7a219b65ec2_GRCh38.primary_assembly.genome.fa.pac added
e7a214071fbe_GRCh38.primary_assembly.genome.fa.sa added
e7a25fb4fd37_GRCh38.primary_assembly.genome.fa added
e7a2635c56f7_hs37d5.fa.fai added
e7a24351a517_hs37d5.fa.amb added
e7a2252dab88_hs37d5.fa.ann added
e7a2595880c9_hs37d5.fa.bwt added
e7a2416f39f2_hs37d5.fa.pac added
e7a26d45606d_hs37d5.fa.sa added
e7a265bdcc26_hs37d5.fa added
e7a2fa606f9_complete_ref_lens.bin added
e7a25d13cd75_ctable.bin added
e7a23f15ec10_ctg_offsets.bin added
e7a2383d2ecb_duplicate_clusters.tsv added
e7a238cb2e45_info.json added
e7a2234ad124_mphf.bin added
e7a24e8a496_pos.bin added
e7a2458d765e_pre_indexing.log added
e7a24a5638fe_rank.bin added
e7a262b7d1d2_ref_indexing.log added
e7a2123064a0_refAccumLengths.bin added
e7a2271e4db4_reflengths.bin added
e7a2367f787c_refseq.bin added
e7a26abf30d7_seq.bin added
e7a22e1faa01_versionInfo.json added
e7a220d23f4f_salmon_index added
e7a24b3a6c5e_chrLength.txt added
e7a268a0b5e7_chrName.txt added
e7a2f06865b_chrNameLength.txt added
e7a2755ec811_chrStart.txt added
e7a221a1104a_exonGeTrInfo.tab added
e7a255347b85_exonInfo.tab added
e7a268998476_geneInfo.tab added
e7a236c794a0_Genome added
e7a268eeb078_genomeParameters.txt added
e7a2e83cc1a_Log.out added
e7a26eccc667_SA added
e7a245f5cd05_SAindex added
e7a2c672725_sjdbInfo.txt added
e7a2483af47f_sjdbList.fromGTF.out.tab added
e7a21689e2e5_sjdbList.out.tab added
e7a2368f33f2_transcriptInfo.tab added
e7a2739b70d9_GRCh38.GENCODE.v42_100 added
e7a2620df1da_knownGene_hg38.sql added
e7a21815181_knownGene_hg38.txt added
e7a2510decec_refGene_hg38.sql added
e7a2693da386_refGene_hg38.txt added
e7a24dbae864_knownGene_mm39.sql added
e7a229ef251a_knownGene_mm39.txt added
e7a2136ce378_refGene_mm39.sql added
e7a251c9e53e_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//Rtmptw4sD6/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
6.364 0.669 7.818
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.905 | 0.210 | 2.130 | |
| dataSearch | 0.349 | 0.016 | 0.367 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.857 | 0.055 | 2.084 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.037 | 0.005 | 0.043 | |
| recipeLoad | 0.385 | 0.023 | 0.410 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.161 | 0.009 | 0.170 | |
| recipeUpdate | 0 | 0 | 0 | |