Qian Liu
| Snapshot Date: 2025-03-20 13:00 -0400 (Thu, 20 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 2025-03-24 12:09 -0400 (Mon, 24 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" | 4763 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4494 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4521 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4448 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4414 |
| 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: 2025-03-21 08:00:15 -0400 (Fri, 21 Mar 2025) |
| EndedAt: 2025-03-21 08:04:28 -0400 (Fri, 21 Mar 2025) |
| EllapsedTime: 253.2 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_1.6.0.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 12.289 1.296 14.350
getCloudData 4.571 0.211 5.566
* 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...
16ded4c8701a0_GRCh38.primary_assembly.genome.fa.1.bt2 added
16ded337bd6a0_GRCh38.primary_assembly.genome.fa.2.bt2 added
16ded747bcc8_GRCh38.primary_assembly.genome.fa.3.bt2 added
16ded76baf233_GRCh38.primary_assembly.genome.fa.4.bt2 added
16ded6b732f2a_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
16ded571da582_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
16ded5b5d267c_outfile.txt added
16ded4089c5c0_GRCh37_to_GRCh38.chain added
16ded1515e15a_GRCh37_to_NCBI34.chain added
16ded4f7de686_GRCh37_to_NCBI35.chain added
16ded52a9902f_GRCh37_to_NCBI36.chain added
16ded7a39280e_GRCh38_to_GRCh37.chain added
16ded3e74edd2_GRCh38_to_NCBI34.chain added
16ded6ea99606_GRCh38_to_NCBI35.chain added
16ded3fb89cac_GRCh38_to_NCBI36.chain added
16ded713600e2_NCBI34_to_GRCh37.chain added
16ded10742f7f_NCBI34_to_GRCh38.chain added
16ded3bda4349_NCBI35_to_GRCh37.chain added
16ded76778c51_NCBI35_to_GRCh38.chain added
16ded229d569a_NCBI36_to_GRCh37.chain added
16ded7a0aa37_NCBI36_to_GRCh38.chain added
16ded450704ca_GRCm38_to_NCBIM36.chain added
16ded4fcb8d2d_GRCm38_to_NCBIM37.chain added
16ded3ca1ae48_NCBIM36_to_GRCm38.chain added
16ded1ab91811_NCBIM37_to_GRCm38.chain added
16ded6ddb11cb_1000G_omni2.5.b37.vcf.gz added
16ded496d5ec5_1000G_omni2.5.b37.vcf.gz.tbi added
16ded2b68fd2c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
16ded79c569f7_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
16dedfb01596_1000G_omni2.5.hg38.vcf.gz added
16ded715932e5_1000G_omni2.5.hg38.vcf.gz.tbi added
16ded171c9286_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
16ded54d7a744_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
16ded1a268ce0_af-only-gnomad.raw.sites.vcf added
16ded58ead389_af-only-gnomad.raw.sites.vcf.idx added
16ded20e5f4fa_Mutect2-exome-panel.vcf.idx added
16ded593659f5_Mutect2-WGS-panel-b37.vcf added
16ded7f4c1194_Mutect2-WGS-panel-b37.vcf.idx added
16ded5b164cd6_small_exac_common_3.vcf added
16ded150ea452_small_exac_common_3.vcf.idx added
16ded74460e4a_1000g_pon.hg38.vcf.gz added
16ded235457e9_1000g_pon.hg38.vcf.gz.tbi added
16ded7657941d_af-only-gnomad.hg38.vcf.gz added
16ded6fbd389d_af-only-gnomad.hg38.vcf.gz.tbi added
16ded6fd004ba_small_exac_common_3.hg38.vcf.gz added
16ded41e688af_small_exac_common_3.hg38.vcf.gz.tbi added
16ded617baf6_gencode.v41.annotation.gtf added
16ded7ff36f99_gencode.v42.annotation.gtf added
16ded4723e76f_gencode.vM30.annotation.gtf added
16ded62f4ce6_gencode.vM31.annotation.gtf added
16dedb619336_gencode.v41.transcripts.fa added
16ded3307c410_gencode.v41.transcripts.fa.fai added
16ded42d9109c_gencode.v42.transcripts.fa added
16ded38d1940d_gencode.v42.transcripts.fa.fai added
16ded474efe9f_gencode.vM30.pc_transcripts.fa added
16ded132e9d4c_gencode.vM30.pc_transcripts.fa.fai added
16ded5958f26a_gencode.vM31.pc_transcripts.fa added
16ded5e933af9_gencode.vM31.pc_transcripts.fa.fai added
16ded1404e1f1_GRCh38.primary_assembly.genome.fa.1.ht2 added
16ded4c8d9f7b_GRCh38.primary_assembly.genome.fa.2.ht2 added
16ded65e16b80_GRCh38.primary_assembly.genome.fa.3.ht2 added
16ded3258d4c1_GRCh38.primary_assembly.genome.fa.4.ht2 added
16ded65f7e4b9_GRCh38.primary_assembly.genome.fa.5.ht2 added
16ded75c961fb_GRCh38.primary_assembly.genome.fa.6.ht2 added
16ded783fe226_GRCh38.primary_assembly.genome.fa.7.ht2 added
16ded2a186a77_GRCh38.primary_assembly.genome.fa.8.ht2 added
16ded28f5c038_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
16ded1e1eb18a_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
16ded7119ea78_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
16ded5c70a64a_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
16ded67b573af_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
16ded39be1b5a_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
16ded6ff5cf53_GRCh38_full_analysis_set_plus_decoy_hla.fa added
16ded72fe8b91_GRCh38.primary_assembly.genome.fa.fai added
16ded257d1792_GRCh38.primary_assembly.genome.fa.amb added
16ded37968578_GRCh38.primary_assembly.genome.fa.ann added
16ded7b14a5ca_GRCh38.primary_assembly.genome.fa.bwt added
16ded890afe7_GRCh38.primary_assembly.genome.fa.pac added
16ded530c6b15_GRCh38.primary_assembly.genome.fa.sa added
16ded544a5a4b_GRCh38.primary_assembly.genome.fa added
16ded5d6e1d28_hs37d5.fa.fai added
16ded683c5d03_hs37d5.fa.amb added
16ded52fea56b_hs37d5.fa.ann added
16ded4c1e3e5e_hs37d5.fa.bwt added
16ded5590b45c_hs37d5.fa.pac added
16dedf312fe7_hs37d5.fa.sa added
16ded663fee7b_hs37d5.fa added
16ded6f4201ae_complete_ref_lens.bin added
16ded567c7f92_ctable.bin added
16ded79b769a_ctg_offsets.bin added
16ded6f877c5c_duplicate_clusters.tsv added
16ded27f5b538_info.json added
16ded744c8406_mphf.bin added
16ded4b6fe190_pos.bin added
16ded1e41dba1_pre_indexing.log added
16ded75ba368b_rank.bin added
16ded14531c0f_ref_indexing.log added
16ded5c572735_refAccumLengths.bin added
16ded5dcf37ef_reflengths.bin added
16ded4f615c06_refseq.bin added
16dede0b6a1_seq.bin added
16ded20f6047a_versionInfo.json added
16ded779ff67d_salmon_index added
16ded26efc5e6_chrLength.txt added
16ded47a99302_chrName.txt added
16ded4df28d0f_chrNameLength.txt added
16ded6f0afbc3_chrStart.txt added
16ded3a16f829_exonGeTrInfo.tab added
16ded39fe698a_exonInfo.tab added
16ded6dc300c4_geneInfo.tab added
16ded1d677c28_Genome added
16ded7508352c_genomeParameters.txt added
16ded6ddb17ba_Log.out added
16ded4af2ecae_SA added
16ded1290b9f3_SAindex added
16ded5ba00a0a_sjdbInfo.txt added
16ded67f34584_sjdbList.fromGTF.out.tab added
16ded1459126d_sjdbList.out.tab added
16ded63c8bc8a_transcriptInfo.tab added
16dedfd23b34_GRCh38.GENCODE.v42_100 added
16ded332cdb09_knownGene_hg38.sql added
16ded45e0461e_knownGene_hg38.txt added
16ded71b7f69_refGene_hg38.sql added
16ded1e49ca24_refGene_hg38.txt added
16ded7e761104_knownGene_mm39.sql added
16ded79575e78_knownGene_mm39.txt added
16ded56fb5684_refGene_mm39.sql added
16dedeed20b9_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/Rtmp301szl/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
40.393 4.363 46.566
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 12.289 | 1.296 | 14.350 | |
| dataSearch | 2.522 | 0.077 | 2.721 | |
| dataUpdate | 0.000 | 0.001 | 0.002 | |
| getCloudData | 4.571 | 0.211 | 5.566 | |
| getData | 0.001 | 0.001 | 0.002 | |
| meta_data | 0.001 | 0.001 | 0.001 | |
| recipeHub-class | 0.254 | 0.017 | 0.273 | |
| recipeLoad | 2.792 | 0.137 | 2.954 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 1.168 | 0.054 | 1.273 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |