Qian Liu
| Snapshot Date: 2025-08-11 13:40 -0400 (Mon, 11 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_21 |
| git_last_commit: 601a107 |
| git_last_commit_date: 2025-04-15 13:01:44 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-08-14 11:46 -0400 (Thu, 14 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4566 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 1758/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.8.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | 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: 1.8.0 |
| 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_1.8.0.tar.gz |
| StartedAt: 2025-08-13 07:50:22 -0400 (Wed, 13 Aug 2025) |
| EndedAt: 2025-08-13 07:52:52 -0400 (Wed, 13 Aug 2025) |
| EllapsedTime: 150.2 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* 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 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.8.0’
* 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 7.176 0.799 8.081
getCloudData 2.907 0.173 5.093
* 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-3.21-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 ‘1.8.0’ ** 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 (2025-06-14 r88325) -- "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...
50729902710_GRCh38.primary_assembly.genome.fa.1.bt2 added
50736f4a0c1_GRCh38.primary_assembly.genome.fa.2.bt2 added
5077665fb16_GRCh38.primary_assembly.genome.fa.3.bt2 added
50721479e14_GRCh38.primary_assembly.genome.fa.4.bt2 added
50764db441d_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
5077754ffa5_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
5076d5be6d7_outfile.txt added
5072c906558_GRCh37_to_GRCh38.chain added
5073bed8b43_GRCh37_to_NCBI34.chain added
5076851fa71_GRCh37_to_NCBI35.chain added
5075e114638_GRCh37_to_NCBI36.chain added
507401936c7_GRCh38_to_GRCh37.chain added
507375b63b1_GRCh38_to_NCBI34.chain added
50750ee15db_GRCh38_to_NCBI35.chain added
5073edd065f_GRCh38_to_NCBI36.chain added
50720cd6737_NCBI34_to_GRCh37.chain added
507d335cb4_NCBI34_to_GRCh38.chain added
507270b3431_NCBI35_to_GRCh37.chain added
507508f90fd_NCBI35_to_GRCh38.chain added
507177fb5d_NCBI36_to_GRCh37.chain added
5076c17976b_NCBI36_to_GRCh38.chain added
507d6293e_GRCm38_to_NCBIM36.chain added
5076c2da5df_GRCm38_to_NCBIM37.chain added
50728e50af5_NCBIM36_to_GRCm38.chain added
50755326fcc_NCBIM37_to_GRCm38.chain added
5076249e5c6_1000G_omni2.5.b37.vcf.gz added
507618c5c93_1000G_omni2.5.b37.vcf.gz.tbi added
5074611e8ed_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
50741d3438b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
50714f77c70_1000G_omni2.5.hg38.vcf.gz added
50740aa7d1_1000G_omni2.5.hg38.vcf.gz.tbi added
507578f8c69_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
507114b6e68_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
5076f3d76b6_af-only-gnomad.raw.sites.vcf added
5072c3cdfc8_af-only-gnomad.raw.sites.vcf.idx added
5075087da28_Mutect2-exome-panel.vcf.idx added
507703a166_Mutect2-WGS-panel-b37.vcf added
5077f593322_Mutect2-WGS-panel-b37.vcf.idx added
507392c3e7f_small_exac_common_3.vcf added
5077bb212c_small_exac_common_3.vcf.idx added
507e7ed3ab_1000g_pon.hg38.vcf.gz added
507287a86fc_1000g_pon.hg38.vcf.gz.tbi added
5074341f27_af-only-gnomad.hg38.vcf.gz added
50779e93b98_af-only-gnomad.hg38.vcf.gz.tbi added
5073f47b6af_small_exac_common_3.hg38.vcf.gz added
5077d2abb9d_small_exac_common_3.hg38.vcf.gz.tbi added
50783809e_gencode.v41.annotation.gtf added
50739710555_gencode.v42.annotation.gtf added
5072b152ce9_gencode.vM30.annotation.gtf added
5077b378b17_gencode.vM31.annotation.gtf added
5077b8cd233_gencode.v41.transcripts.fa added
5075a3c51a3_gencode.v41.transcripts.fa.fai added
5072e13d29d_gencode.v42.transcripts.fa added
5071768590d_gencode.v42.transcripts.fa.fai added
50743ae707c_gencode.vM30.pc_transcripts.fa added
507715aff9a_gencode.vM30.pc_transcripts.fa.fai added
507d43119a_gencode.vM31.pc_transcripts.fa added
5072e389c43_gencode.vM31.pc_transcripts.fa.fai added
50769b0a6a_GRCh38.primary_assembly.genome.fa.1.ht2 added
5072cc8b889_GRCh38.primary_assembly.genome.fa.2.ht2 added
5072dcb4157_GRCh38.primary_assembly.genome.fa.3.ht2 added
5077b2ece3d_GRCh38.primary_assembly.genome.fa.4.ht2 added
5073de645f9_GRCh38.primary_assembly.genome.fa.5.ht2 added
50758fbfe2e_GRCh38.primary_assembly.genome.fa.6.ht2 added
5077ecaba6_GRCh38.primary_assembly.genome.fa.7.ht2 added
50742f9235a_GRCh38.primary_assembly.genome.fa.8.ht2 added
50772800c0f_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
5073497e783_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
50760e0646e_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
5072be1a372_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
5076ab1a7df_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
50735845832_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
5073ba5611_GRCh38_full_analysis_set_plus_decoy_hla.fa added
5073e687800_GRCh38.primary_assembly.genome.fa.fai added
5073c9e6802_GRCh38.primary_assembly.genome.fa.amb added
50743be7a65_GRCh38.primary_assembly.genome.fa.ann added
507e559fa2_GRCh38.primary_assembly.genome.fa.bwt added
50717634c08_GRCh38.primary_assembly.genome.fa.pac added
5077814ad36_GRCh38.primary_assembly.genome.fa.sa added
5071577f1d1_GRCh38.primary_assembly.genome.fa added
50775a4db59_hs37d5.fa.fai added
5071a3cec66_hs37d5.fa.amb added
50715c429ff_hs37d5.fa.ann added
5071a12f83_hs37d5.fa.bwt added
5077d36424a_hs37d5.fa.pac added
507753a487e_hs37d5.fa.sa added
507456d8452_hs37d5.fa added
507190a471a_complete_ref_lens.bin added
50771c208cd_ctable.bin added
50779d00513_ctg_offsets.bin added
50747fd60df_duplicate_clusters.tsv added
5074be2f565_info.json added
507215ce0cf_mphf.bin added
50758ab4725_pos.bin added
50754cbfb9d_pre_indexing.log added
5071bf42be9_rank.bin added
5073b6edc55_ref_indexing.log added
5076b436eee_refAccumLengths.bin added
50718280246_reflengths.bin added
5076aad4e0d_refseq.bin added
50717df6e32_seq.bin added
5074dbba0dc_versionInfo.json added
507593df362_salmon_index added
5077235d4b3_chrLength.txt added
5072c1f6e59_chrName.txt added
5074385abb0_chrNameLength.txt added
5077ccad271_chrStart.txt added
50767be38b8_exonGeTrInfo.tab added
507797ded3d_exonInfo.tab added
5073a627e1b_geneInfo.tab added
50718453c8f_Genome added
507698adcbb_genomeParameters.txt added
5071ba1af1f_Log.out added
50713f02a65_SA added
5077c6f571c_SAindex added
50771c02f16_sjdbInfo.txt added
5075387b2_sjdbList.fromGTF.out.tab added
5076bf1b748_sjdbList.out.tab added
5074a380f55_transcriptInfo.tab added
5072676bb84_GRCh38.GENCODE.v42_100 added
5073d10ead6_knownGene_hg38.sql added
50721a9a6ec_knownGene_hg38.txt added
50790de138_refGene_hg38.sql added
5076e3d282c_refGene_hg38.txt added
5077118993e_knownGene_mm39.sql added
5075f4ef74_knownGene_mm39.txt added
5071394abba_refGene_mm39.sql added
5075964a61_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/Rtmp7fCMFe/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
25.677 3.760 31.684
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.176 | 0.799 | 8.081 | |
| dataSearch | 1.225 | 0.052 | 1.285 | |
| dataUpdate | 0.000 | 0.001 | 0.000 | |
| getCloudData | 2.907 | 0.173 | 5.093 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.149 | 0.018 | 0.173 | |
| recipeLoad | 1.484 | 0.103 | 1.625 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.604 | 0.036 | 0.644 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |