Qian Liu
| Snapshot Date: 2025-09-01 13:45 -0400 (Mon, 01 Sep 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 2025-09-02 12:02 -0400 (Tue, 02 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| 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 1742/2320 | 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 | NA | NA | |||||||||
| lconway | macOS 12.7.1 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 | 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: 1.9.0 |
| 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: 2025-09-01 23:13:53 -0400 (Mon, 01 Sep 2025) |
| EndedAt: 2025-09-01 23:16:18 -0400 (Mon, 01 Sep 2025) |
| EllapsedTime: 145.5 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 (2025-06-13)
* 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 ‘1.9.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataHub-class 7.496 0.89 8.489
* 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-x86_64/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 (2025-06-13) -- "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...
44333a8bb035_GRCh38.primary_assembly.genome.fa.1.bt2 added
443328dd859a_GRCh38.primary_assembly.genome.fa.2.bt2 added
4433676e566b_GRCh38.primary_assembly.genome.fa.3.bt2 added
44337cebbfd9_GRCh38.primary_assembly.genome.fa.4.bt2 added
443359807fa1_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
443333b50ef_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
44332b3e7c91_outfile.txt added
4433136429c5_GRCh37_to_GRCh38.chain added
443314f24e75_GRCh37_to_NCBI34.chain added
44332ffcee11_GRCh37_to_NCBI35.chain added
4433671b6b4_GRCh37_to_NCBI36.chain added
44331391e6ba_GRCh38_to_GRCh37.chain added
44334fc2c75f_GRCh38_to_NCBI34.chain added
44337caf56e1_GRCh38_to_NCBI35.chain added
44335b710dba_GRCh38_to_NCBI36.chain added
44335b3c5d3c_NCBI34_to_GRCh37.chain added
4433580d3cef_NCBI34_to_GRCh38.chain added
44334d1b9c12_NCBI35_to_GRCh37.chain added
44334fa3894a_NCBI35_to_GRCh38.chain added
4433798a821e_NCBI36_to_GRCh37.chain added
44337464bde8_NCBI36_to_GRCh38.chain added
44331f0060b_GRCm38_to_NCBIM36.chain added
4433351cbd2b_GRCm38_to_NCBIM37.chain added
443371c76d4a_NCBIM36_to_GRCm38.chain added
44335bd84fa1_NCBIM37_to_GRCm38.chain added
443356540222_1000G_omni2.5.b37.vcf.gz added
443325583275_1000G_omni2.5.b37.vcf.gz.tbi added
44334158b27a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
4433262d891a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
443377841d8a_1000G_omni2.5.hg38.vcf.gz added
44332af8c53_1000G_omni2.5.hg38.vcf.gz.tbi added
443353259e85_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
44334aca5868_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
44332a723a34_af-only-gnomad.raw.sites.vcf added
4433314b41b1_af-only-gnomad.raw.sites.vcf.idx added
443343c5e4bf_Mutect2-exome-panel.vcf.idx added
4433752cda5b_Mutect2-WGS-panel-b37.vcf added
443353b3c876_Mutect2-WGS-panel-b37.vcf.idx added
4433402de5e8_small_exac_common_3.vcf added
44335510343_small_exac_common_3.vcf.idx added
44339ad266f_1000g_pon.hg38.vcf.gz added
443346b6465f_1000g_pon.hg38.vcf.gz.tbi added
443368c62b3d_af-only-gnomad.hg38.vcf.gz added
44332a40e788_af-only-gnomad.hg38.vcf.gz.tbi added
4433b20a764_small_exac_common_3.hg38.vcf.gz added
4433ccd9bf1_small_exac_common_3.hg38.vcf.gz.tbi added
4433eb8f1c8_gencode.v41.annotation.gtf added
443310098905_gencode.v42.annotation.gtf added
44336202af7c_gencode.vM30.annotation.gtf added
44331e4f2829_gencode.vM31.annotation.gtf added
44335ed5ab4a_gencode.v41.transcripts.fa added
44331de0b7ea_gencode.v41.transcripts.fa.fai added
4433c4a72f9_gencode.v42.transcripts.fa added
44336bc23fbc_gencode.v42.transcripts.fa.fai added
44331de686e9_gencode.vM30.pc_transcripts.fa added
44339a33a55_gencode.vM30.pc_transcripts.fa.fai added
44333b4aa764_gencode.vM31.pc_transcripts.fa added
44332233b4a5_gencode.vM31.pc_transcripts.fa.fai added
44337098ce2d_GRCh38.primary_assembly.genome.fa.1.ht2 added
44334008261b_GRCh38.primary_assembly.genome.fa.2.ht2 added
443356fdd774_GRCh38.primary_assembly.genome.fa.3.ht2 added
4433334c2d4a_GRCh38.primary_assembly.genome.fa.4.ht2 added
44334e316f95_GRCh38.primary_assembly.genome.fa.5.ht2 added
4433f94c74e_GRCh38.primary_assembly.genome.fa.6.ht2 added
443370a8d9df_GRCh38.primary_assembly.genome.fa.7.ht2 added
44335d77f941_GRCh38.primary_assembly.genome.fa.8.ht2 added
44336f8d4a57_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
4433250bcef8_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
44332a410ec8_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
443315318224_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
44336557145a_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
443337f954b0_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
443352270b85_GRCh38_full_analysis_set_plus_decoy_hla.fa added
443316572e6_GRCh38.primary_assembly.genome.fa.fai added
44332b5a5ac1_GRCh38.primary_assembly.genome.fa.amb added
443338fc4b23_GRCh38.primary_assembly.genome.fa.ann added
44333ba9040f_GRCh38.primary_assembly.genome.fa.bwt added
443355499362_GRCh38.primary_assembly.genome.fa.pac added
4433516b32ac_GRCh38.primary_assembly.genome.fa.sa added
443354cbe3f6_GRCh38.primary_assembly.genome.fa added
443315e356f8_hs37d5.fa.fai added
443362bf02_hs37d5.fa.amb added
443352ea1c80_hs37d5.fa.ann added
44337f54207_hs37d5.fa.bwt added
443376c1dda5_hs37d5.fa.pac added
443331beb88c_hs37d5.fa.sa added
4433604608d7_hs37d5.fa added
443315ee8ca2_complete_ref_lens.bin added
44336052eaed_ctable.bin added
443363bd9f02_ctg_offsets.bin added
443336126f76_duplicate_clusters.tsv added
44337453c7b5_info.json added
4433285c77bd_mphf.bin added
44334eb92dfe_pos.bin added
44335f7aa712_pre_indexing.log added
44336d6ebfb6_rank.bin added
44331ec7ddb_ref_indexing.log added
44334d3ab5d9_refAccumLengths.bin added
44334978e12b_reflengths.bin added
44331f06f3bc_refseq.bin added
443316bcb8e_seq.bin added
44334c00d85c_versionInfo.json added
44334b7ca6ff_salmon_index added
443364b7d610_chrLength.txt added
44336146e818_chrName.txt added
4433762fb18c_chrNameLength.txt added
443335319af2_chrStart.txt added
44334bb3a126_exonGeTrInfo.tab added
44337e18ec9d_exonInfo.tab added
443316567818_geneInfo.tab added
44336e67b1d_Genome added
443359cb075_genomeParameters.txt added
44337204d433_Log.out added
44331b079ac0_SA added
44331040c11d_SAindex added
4433b465f41_sjdbInfo.txt added
44333917aa2f_sjdbList.fromGTF.out.tab added
443340a610f1_sjdbList.out.tab added
443356a25f5f_transcriptInfo.tab added
44333e238268_GRCh38.GENCODE.v42_100 added
4433d4699b7_knownGene_hg38.sql added
44331615c430_knownGene_hg38.txt added
44336f0336a3_refGene_hg38.sql added
44333bf84045_refGene_hg38.txt added
4433274390c5_knownGene_mm39.sql added
443344d589a6_knownGene_mm39.txt added
44331f401498_refGene_mm39.sql added
44332808172f_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/Rtmp4dJCpp/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
21.445 2.345 24.792
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.496 | 0.890 | 8.489 | |
| dataSearch | 1.411 | 0.055 | 1.473 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 2.821 | 0.168 | 4.227 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.001 | 0.001 | |
| recipeHub-class | 0.155 | 0.011 | 0.167 | |
| recipeLoad | 1.488 | 0.098 | 1.597 | |
| recipeMake | 0.001 | 0.001 | 0.001 | |
| recipeSearch | 0.625 | 0.040 | 0.671 | |
| recipeUpdate | 0 | 0 | 0 | |