Qian Liu
| Snapshot Date: 2025-03-17 13:00 -0400 (Mon, 17 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 2025-03-20 12:11 -0400 (Thu, 20 Mar 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" | 4756 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4514 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4441 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4406 |
| 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: 2025-03-19 06:33:10 -0400 (Wed, 19 Mar 2025) |
| EndedAt: 2025-03-19 06:35:31 -0400 (Wed, 19 Mar 2025) |
| EllapsedTime: 140.6 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_1.6.0.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: aarch64-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 Ventura 13.7.1
* 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 7.009 0.776 7.892
* 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-arm64/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: 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...
b815c9aa9ee_GRCh38.primary_assembly.genome.fa.1.bt2 added
b812e0a77c1_GRCh38.primary_assembly.genome.fa.2.bt2 added
b81313c3784_GRCh38.primary_assembly.genome.fa.3.bt2 added
b816860d45c_GRCh38.primary_assembly.genome.fa.4.bt2 added
b812d16198d_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
b815e78f1b_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
b81256438a4_outfile.txt added
b8156c2aa29_GRCh37_to_GRCh38.chain added
b81631963f_GRCh37_to_NCBI34.chain added
b81217f0546_GRCh37_to_NCBI35.chain added
b811a3347d8_GRCh37_to_NCBI36.chain added
b811cb1c358_GRCh38_to_GRCh37.chain added
b815a8fd51f_GRCh38_to_NCBI34.chain added
b8118f114ac_GRCh38_to_NCBI35.chain added
b817b8434fe_GRCh38_to_NCBI36.chain added
b8124b34f0c_NCBI34_to_GRCh37.chain added
b81780aafa6_NCBI34_to_GRCh38.chain added
b81591f8dc_NCBI35_to_GRCh37.chain added
b813269365f_NCBI35_to_GRCh38.chain added
b811970b0d4_NCBI36_to_GRCh37.chain added
b8135693b58_NCBI36_to_GRCh38.chain added
b81fb729cd_GRCm38_to_NCBIM36.chain added
b81421959ca_GRCm38_to_NCBIM37.chain added
b81e55fead_NCBIM36_to_GRCm38.chain added
b812fc31735_NCBIM37_to_GRCm38.chain added
b813128b112_1000G_omni2.5.b37.vcf.gz added
b8166812df4_1000G_omni2.5.b37.vcf.gz.tbi added
b812af022bf_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
b817b793f9e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
b81553fdd66_1000G_omni2.5.hg38.vcf.gz added
b8153e07f43_1000G_omni2.5.hg38.vcf.gz.tbi added
b8137c332ba_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
b8170376def_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
b8147129f77_af-only-gnomad.raw.sites.vcf added
b8117a36215_af-only-gnomad.raw.sites.vcf.idx added
b81677c5cd2_Mutect2-exome-panel.vcf.idx added
b8115b21412_Mutect2-WGS-panel-b37.vcf added
b815e43b4de_Mutect2-WGS-panel-b37.vcf.idx added
b812f178b2b_small_exac_common_3.vcf added
b8132b1cc34_small_exac_common_3.vcf.idx added
b8136d583ec_1000g_pon.hg38.vcf.gz added
b817bc81713_1000g_pon.hg38.vcf.gz.tbi added
b81d631fe2_af-only-gnomad.hg38.vcf.gz added
b8166c2354b_af-only-gnomad.hg38.vcf.gz.tbi added
b81583903a1_small_exac_common_3.hg38.vcf.gz added
b8171d6c47_small_exac_common_3.hg38.vcf.gz.tbi added
b811cafacf7_gencode.v41.annotation.gtf added
b8151849ad7_gencode.v42.annotation.gtf added
b8158d1c310_gencode.vM30.annotation.gtf added
b81335d7cfe_gencode.vM31.annotation.gtf added
b813eb9220a_gencode.v41.transcripts.fa added
b816c69deb1_gencode.v41.transcripts.fa.fai added
b811a9b6e12_gencode.v42.transcripts.fa added
b8152576d63_gencode.v42.transcripts.fa.fai added
b8169cea8d0_gencode.vM30.pc_transcripts.fa added
b817ead25f4_gencode.vM30.pc_transcripts.fa.fai added
b811996f725_gencode.vM31.pc_transcripts.fa added
b8163bab43_gencode.vM31.pc_transcripts.fa.fai added
b813768bee7_GRCh38.primary_assembly.genome.fa.1.ht2 added
b813dcd4c1c_GRCh38.primary_assembly.genome.fa.2.ht2 added
b81713fe1f6_GRCh38.primary_assembly.genome.fa.3.ht2 added
b81190c1790_GRCh38.primary_assembly.genome.fa.4.ht2 added
b8168defbc8_GRCh38.primary_assembly.genome.fa.5.ht2 added
b817643d42_GRCh38.primary_assembly.genome.fa.6.ht2 added
b8145f1bbd8_GRCh38.primary_assembly.genome.fa.7.ht2 added
b8116385c8_GRCh38.primary_assembly.genome.fa.8.ht2 added
b812ce40e2e_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
b81305f0508_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
b812e436907_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
b814ba4624b_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
b81153150b9_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
b8158aaac8d_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
b812d268a75_GRCh38_full_analysis_set_plus_decoy_hla.fa added
b813d4c1e7b_GRCh38.primary_assembly.genome.fa.fai added
b8150653cad_GRCh38.primary_assembly.genome.fa.amb added
b812672ab17_GRCh38.primary_assembly.genome.fa.ann added
b81323e86b9_GRCh38.primary_assembly.genome.fa.bwt added
b8126fef574_GRCh38.primary_assembly.genome.fa.pac added
b812ca4a6ac_GRCh38.primary_assembly.genome.fa.sa added
b816dba7d19_GRCh38.primary_assembly.genome.fa added
b816e6b2c96_hs37d5.fa.fai added
b813e3c647c_hs37d5.fa.amb added
b816ee928cf_hs37d5.fa.ann added
b81d7666ec_hs37d5.fa.bwt added
b81585f16db_hs37d5.fa.pac added
b814ad5b130_hs37d5.fa.sa added
b811363ecb2_hs37d5.fa added
b81548a410_complete_ref_lens.bin added
b81640b1925_ctable.bin added
b81149fff73_ctg_offsets.bin added
b81143be199_duplicate_clusters.tsv added
b8167580e2f_info.json added
b81460b64aa_mphf.bin added
b8115fdf8d3_pos.bin added
b8154daefec_pre_indexing.log added
b8171bd9a79_rank.bin added
b8156e8b845_ref_indexing.log added
b814899e696_refAccumLengths.bin added
b816ff1a716_reflengths.bin added
b816210cec4_refseq.bin added
b813d76d828_seq.bin added
b814569499e_versionInfo.json added
b8136047ac_salmon_index added
b8126016eef_chrLength.txt added
b81281a2067_chrName.txt added
b814b455ec2_chrNameLength.txt added
b8137503929_chrStart.txt added
b8173d8cf1d_exonGeTrInfo.tab added
b811f05b456_exonInfo.tab added
b812f828a03_geneInfo.tab added
b812332e353_Genome added
b8161ea7032_genomeParameters.txt added
b81666c14d6_Log.out added
b8141cc2222_SA added
b8140d507ed_SAindex added
b8161fb79db_sjdbInfo.txt added
b8144fd4b1e_sjdbList.fromGTF.out.tab added
b81514ec1f4_sjdbList.out.tab added
b8199fa3e0_transcriptInfo.tab added
b814fbfcc0f_GRCh38.GENCODE.v42_100 added
b8138ee15b0_knownGene_hg38.sql added
b8116d1f303_knownGene_hg38.txt added
b8131a955a9_refGene_hg38.sql added
b816436e3b7_refGene_hg38.txt added
b814fa036c7_knownGene_mm39.sql added
b811f6c6ba8_knownGene_mm39.txt added
b8170ff2b6_refGene_mm39.sql added
b8128078e59_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/RtmpEqFsC0/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
22.831 2.646 27.700
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.009 | 0.776 | 7.892 | |
| dataSearch | 1.213 | 0.055 | 1.269 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.311 | 0.155 | 4.609 | |
| getData | 0.000 | 0.001 | 0.001 | |
| meta_data | 0.001 | 0.001 | 0.001 | |
| recipeHub-class | 0.104 | 0.010 | 0.140 | |
| recipeLoad | 0.819 | 0.058 | 0.972 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.351 | 0.025 | 0.407 | |
| recipeUpdate | 0 | 0 | 0 | |