Qian Liu
| Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_20 |
| git_last_commit: 5d8c0ee |
| git_last_commit_date: 2024-10-29 11:17:22 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-04-02 19:32 -0400 (Wed, 02 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
| 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 1727/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.6.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | 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 | | ||||||||
| 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: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2025-04-01 07:56:45 -0400 (Tue, 01 Apr 2025) |
| EndedAt: 2025-04-01 08:00:56 -0400 (Tue, 01 Apr 2025) |
| EllapsedTime: 250.5 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* 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 ‘1.6.0’
* 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 12.232 1.273 14.315
getCloudData 4.680 0.214 5.612
* 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-3.20-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/4.4-x86_64/Resources/library’ * installing *source* package ‘ReUseData’ ... ** 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 4.4.3 (2025-02-28) -- "Trophy Case"
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...
e1ce3e11f4b9_GRCh38.primary_assembly.genome.fa.1.bt2 added
e1cecd9bd85_GRCh38.primary_assembly.genome.fa.2.bt2 added
e1ce2b296d5a_GRCh38.primary_assembly.genome.fa.3.bt2 added
e1ce2cca45d9_GRCh38.primary_assembly.genome.fa.4.bt2 added
e1ce13afc088_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
e1ce77892ad0_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
e1ce4e59faff_outfile.txt added
e1ce756da388_GRCh37_to_GRCh38.chain added
e1ce710b71f2_GRCh37_to_NCBI34.chain added
e1ce266600d9_GRCh37_to_NCBI35.chain added
e1ce72c1ba40_GRCh37_to_NCBI36.chain added
e1cecaafa9c_GRCh38_to_GRCh37.chain added
e1ce2d2b1e43_GRCh38_to_NCBI34.chain added
e1ce69cfd7df_GRCh38_to_NCBI35.chain added
e1ce4c65a7be_GRCh38_to_NCBI36.chain added
e1ce25e7d221_NCBI34_to_GRCh37.chain added
e1ce169487f8_NCBI34_to_GRCh38.chain added
e1ce716ab65c_NCBI35_to_GRCh37.chain added
e1ce14ea8c30_NCBI35_to_GRCh38.chain added
e1ce3299ae0a_NCBI36_to_GRCh37.chain added
e1ce7712c7a_NCBI36_to_GRCh38.chain added
e1ce171f0167_GRCm38_to_NCBIM36.chain added
e1ce74951d0c_GRCm38_to_NCBIM37.chain added
e1ce69a63a9f_NCBIM36_to_GRCm38.chain added
e1ce2052d2e9_NCBIM37_to_GRCm38.chain added
e1ce1d94cf93_1000G_omni2.5.b37.vcf.gz added
e1ce14c7cb11_1000G_omni2.5.b37.vcf.gz.tbi added
e1ce48e4d3bf_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
e1ce2709c5fc_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
e1ce72a53769_1000G_omni2.5.hg38.vcf.gz added
e1ce3cd9094c_1000G_omni2.5.hg38.vcf.gz.tbi added
e1ce4cf17bc9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
e1ce1f5f096_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
e1ce398608db_af-only-gnomad.raw.sites.vcf added
e1ceeaf7f5e_af-only-gnomad.raw.sites.vcf.idx added
e1ce23d2fbda_Mutect2-exome-panel.vcf.idx added
e1ce7094b795_Mutect2-WGS-panel-b37.vcf added
e1ce33a0d0f1_Mutect2-WGS-panel-b37.vcf.idx added
e1ce2f598b2_small_exac_common_3.vcf added
e1ce49fbcfa2_small_exac_common_3.vcf.idx added
e1ce32fcbaa0_1000g_pon.hg38.vcf.gz added
e1ce6e407886_1000g_pon.hg38.vcf.gz.tbi added
e1ce4aa8ddf6_af-only-gnomad.hg38.vcf.gz added
e1ce148467c5_af-only-gnomad.hg38.vcf.gz.tbi added
e1ceb8c109_small_exac_common_3.hg38.vcf.gz added
e1ce6189363d_small_exac_common_3.hg38.vcf.gz.tbi added
e1ce774810d1_gencode.v41.annotation.gtf added
e1ce1c484685_gencode.v42.annotation.gtf added
e1ce4d0dd444_gencode.vM30.annotation.gtf added
e1ce46eae3e1_gencode.vM31.annotation.gtf added
e1ce6716ed26_gencode.v41.transcripts.fa added
e1ce122b8eaa_gencode.v41.transcripts.fa.fai added
e1ce69a34437_gencode.v42.transcripts.fa added
e1ce5dd3ad0f_gencode.v42.transcripts.fa.fai added
e1ce7406e3e8_gencode.vM30.pc_transcripts.fa added
e1ce705ccfda_gencode.vM30.pc_transcripts.fa.fai added
e1ce5d522ad7_gencode.vM31.pc_transcripts.fa added
e1ce3d7ab91e_gencode.vM31.pc_transcripts.fa.fai added
e1ce440f801a_GRCh38.primary_assembly.genome.fa.1.ht2 added
e1ce55a34dde_GRCh38.primary_assembly.genome.fa.2.ht2 added
e1ce544d55be_GRCh38.primary_assembly.genome.fa.3.ht2 added
e1ce2138582f_GRCh38.primary_assembly.genome.fa.4.ht2 added
e1ce7a2586b2_GRCh38.primary_assembly.genome.fa.5.ht2 added
e1ce35ae4ec4_GRCh38.primary_assembly.genome.fa.6.ht2 added
e1ce46b54164_GRCh38.primary_assembly.genome.fa.7.ht2 added
e1ce25d83080_GRCh38.primary_assembly.genome.fa.8.ht2 added
e1ce145836e9_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
e1ce2b7d056e_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
e1ce1cef8f10_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
e1ce33997247_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
e1ce1f1dadc8_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
e1ce557c356d_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
e1ce4d97b2f3_GRCh38_full_analysis_set_plus_decoy_hla.fa added
e1ce22659751_GRCh38.primary_assembly.genome.fa.fai added
e1ce3bb1587b_GRCh38.primary_assembly.genome.fa.amb added
e1ce782811da_GRCh38.primary_assembly.genome.fa.ann added
e1ceeac3cd7_GRCh38.primary_assembly.genome.fa.bwt added
e1ce4dce4ec7_GRCh38.primary_assembly.genome.fa.pac added
e1ce239612b9_GRCh38.primary_assembly.genome.fa.sa added
e1ce51a741ef_GRCh38.primary_assembly.genome.fa added
e1ce3bd9dbca_hs37d5.fa.fai added
e1ce5becc978_hs37d5.fa.amb added
e1ce169f146e_hs37d5.fa.ann added
e1ce25f64d5c_hs37d5.fa.bwt added
e1ce4d50e67c_hs37d5.fa.pac added
e1ce7a4bfe8b_hs37d5.fa.sa added
e1ce13349667_hs37d5.fa added
e1ce617e4e0a_complete_ref_lens.bin added
e1ce2b35a487_ctable.bin added
e1ce4ec4b13a_ctg_offsets.bin added
e1ce534f7f3c_duplicate_clusters.tsv added
e1ce82a66df_info.json added
e1ce17c7bea9_mphf.bin added
e1ce3ab65571_pos.bin added
e1ce18a38bd4_pre_indexing.log added
e1ce193117ef_rank.bin added
e1ce661a58d4_ref_indexing.log added
e1ce4bbdfaaa_refAccumLengths.bin added
e1ce2593d5bf_reflengths.bin added
e1cecb601df_refseq.bin added
e1ce134ddfe_seq.bin added
e1ce35da4f50_versionInfo.json added
e1cef8d28cf_salmon_index added
e1ce7c723602_chrLength.txt added
e1ce2e37fd22_chrName.txt added
e1ce5dcbdae2_chrNameLength.txt added
e1ce728f5b89_chrStart.txt added
e1ce21c2ba21_exonGeTrInfo.tab added
e1ce7749ddd7_exonInfo.tab added
e1ce12838b70_geneInfo.tab added
e1ce7a376f8e_Genome added
e1ce4d7d1251_genomeParameters.txt added
e1ce4e3dab95_Log.out added
e1ce32cbeb54_SA added
e1ce69c6f1d9_SAindex added
e1ce43013d0_sjdbInfo.txt added
e1ce7064bed5_sjdbList.fromGTF.out.tab added
e1ce662ccb98_sjdbList.out.tab added
e1ce6ea9c90_transcriptInfo.tab added
e1ce14ccb57c_GRCh38.GENCODE.v42_100 added
e1ceb9eea8f_knownGene_hg38.sql added
e1ce6e39583e_knownGene_hg38.txt added
e1ce76d086fa_refGene_hg38.sql added
e1ce744dc406_refGene_hg38.txt added
e1ce1d80a191_knownGene_mm39.sql added
e1ce67ef45b8_knownGene_mm39.txt added
e1cedca6857_refGene_mm39.sql added
e1ce63882ed3_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/RtmpdS5FKZ/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
39.225 4.279 44.823
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 12.232 | 1.273 | 14.315 | |
| dataSearch | 2.403 | 0.074 | 2.487 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 4.680 | 0.214 | 5.612 | |
| getData | 0.001 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.001 | 0.002 | |
| recipeHub-class | 0.268 | 0.022 | 0.297 | |
| recipeLoad | 2.836 | 0.141 | 3.248 | |
| recipeMake | 0.001 | 0.001 | 0.002 | |
| recipeSearch | 1.144 | 0.053 | 1.221 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |