Qian Liu
| Snapshot Date: 2025-02-03 13:00 -0500 (Mon, 03 Feb 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 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-02-06 12:09 -0500 (Thu, 06 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4753 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4501 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4524 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4476 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4407 |
| 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: 2025-02-04 08:50:43 -0500 (Tue, 04 Feb 2025) |
| EndedAt: 2025-02-04 08:55:15 -0500 (Tue, 04 Feb 2025) |
| EllapsedTime: 271.6 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 4.4.2 (2024-10-31)
* 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 12.415 1.301 15.02
getCloudData 4.649 0.218 6.20
* 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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...
c5a470fe31ed_GRCh38.primary_assembly.genome.fa.1.bt2 added
c5a4407ff88f_GRCh38.primary_assembly.genome.fa.2.bt2 added
c5a41197955e_GRCh38.primary_assembly.genome.fa.3.bt2 added
c5a476cf5757_GRCh38.primary_assembly.genome.fa.4.bt2 added
c5a4266f4db1_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
c5a45555b32d_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
c5a46d667b1f_outfile.txt added
c5a4631d6855_GRCh37_to_GRCh38.chain added
c5a41facd749_GRCh37_to_NCBI34.chain added
c5a4c6a09de_GRCh37_to_NCBI35.chain added
c5a45add430_GRCh37_to_NCBI36.chain added
c5a457459e39_GRCh38_to_GRCh37.chain added
c5a41b96dcf2_GRCh38_to_NCBI34.chain added
c5a44d83a204_GRCh38_to_NCBI35.chain added
c5a47d01dc5d_GRCh38_to_NCBI36.chain added
c5a452a9dc9_NCBI34_to_GRCh37.chain added
c5a430dcf9c5_NCBI34_to_GRCh38.chain added
c5a47b920d92_NCBI35_to_GRCh37.chain added
c5a431b92b9f_NCBI35_to_GRCh38.chain added
c5a473deed39_NCBI36_to_GRCh37.chain added
c5a430a8749d_NCBI36_to_GRCh38.chain added
c5a43800860_GRCm38_to_NCBIM36.chain added
c5a44aa5d86b_GRCm38_to_NCBIM37.chain added
c5a44e237f16_NCBIM36_to_GRCm38.chain added
c5a47c6ca56d_NCBIM37_to_GRCm38.chain added
c5a440e0d6ec_1000G_omni2.5.b37.vcf.gz added
c5a4693e413a_1000G_omni2.5.b37.vcf.gz.tbi added
c5a4762c7cd0_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
c5a462b6784c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
c5a43993f835_1000G_omni2.5.hg38.vcf.gz added
c5a4218c7d1b_1000G_omni2.5.hg38.vcf.gz.tbi added
c5a4e6988d2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
c5a432959a62_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
c5a47bcab1df_af-only-gnomad.raw.sites.vcf added
c5a43863e6f7_af-only-gnomad.raw.sites.vcf.idx added
c5a426d07f0d_Mutect2-exome-panel.vcf.idx added
c5a442454263_Mutect2-WGS-panel-b37.vcf added
c5a451099392_Mutect2-WGS-panel-b37.vcf.idx added
c5a44bb77fce_small_exac_common_3.vcf added
c5a47c27d437_small_exac_common_3.vcf.idx added
c5a41adda68f_1000g_pon.hg38.vcf.gz added
c5a44de20410_1000g_pon.hg38.vcf.gz.tbi added
c5a43178de62_af-only-gnomad.hg38.vcf.gz added
c5a476500d4d_af-only-gnomad.hg38.vcf.gz.tbi added
c5a419976ea_small_exac_common_3.hg38.vcf.gz added
c5a424dfd78_small_exac_common_3.hg38.vcf.gz.tbi added
c5a44e3bd276_gencode.v41.annotation.gtf added
c5a43976691a_gencode.v42.annotation.gtf added
c5a4cee476f_gencode.vM30.annotation.gtf added
c5a46f93cf0a_gencode.vM31.annotation.gtf added
c5a450fdd2c0_gencode.v41.transcripts.fa added
c5a4481764ca_gencode.v41.transcripts.fa.fai added
c5a477da2ebf_gencode.v42.transcripts.fa added
c5a415333b12_gencode.v42.transcripts.fa.fai added
c5a4566b259d_gencode.vM30.pc_transcripts.fa added
c5a4147292be_gencode.vM30.pc_transcripts.fa.fai added
c5a46e00026e_gencode.vM31.pc_transcripts.fa added
c5a4429fbc2d_gencode.vM31.pc_transcripts.fa.fai added
c5a44fb5087_GRCh38.primary_assembly.genome.fa.1.ht2 added
c5a4f63d19f_GRCh38.primary_assembly.genome.fa.2.ht2 added
c5a46257259d_GRCh38.primary_assembly.genome.fa.3.ht2 added
c5a4476698db_GRCh38.primary_assembly.genome.fa.4.ht2 added
c5a420bd767c_GRCh38.primary_assembly.genome.fa.5.ht2 added
c5a476add7ae_GRCh38.primary_assembly.genome.fa.6.ht2 added
c5a4f2b1d61_GRCh38.primary_assembly.genome.fa.7.ht2 added
c5a45795d30e_GRCh38.primary_assembly.genome.fa.8.ht2 added
c5a42d53690e_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
c5a43f162d61_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
c5a448fd5ba2_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
c5a4718b0e1d_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
c5a4604bcc27_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
c5a4104845d5_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
c5a478e0ab4c_GRCh38_full_analysis_set_plus_decoy_hla.fa added
c5a4660e4893_GRCh38.primary_assembly.genome.fa.fai added
c5a433bedf3d_GRCh38.primary_assembly.genome.fa.amb added
c5a438323855_GRCh38.primary_assembly.genome.fa.ann added
c5a469107145_GRCh38.primary_assembly.genome.fa.bwt added
c5a4367c9ee6_GRCh38.primary_assembly.genome.fa.pac added
c5a42fa429fc_GRCh38.primary_assembly.genome.fa.sa added
c5a442c077d3_GRCh38.primary_assembly.genome.fa added
c5a469fadfe1_hs37d5.fa.fai added
c5a455806322_hs37d5.fa.amb added
c5a45fec7908_hs37d5.fa.ann added
c5a41dfe2d6b_hs37d5.fa.bwt added
c5a41a57db2f_hs37d5.fa.pac added
c5a47df6f82b_hs37d5.fa.sa added
c5a4611f0fa8_hs37d5.fa added
c5a43e3d1068_complete_ref_lens.bin added
c5a41b003bc4_ctable.bin added
c5a42c53ceb5_ctg_offsets.bin added
c5a43227e3cf_duplicate_clusters.tsv added
c5a458dd44c2_info.json added
c5a426cd4a22_mphf.bin added
c5a46fbe1214_pos.bin added
c5a42795185c_pre_indexing.log added
c5a42d725451_rank.bin added
c5a42cfda926_ref_indexing.log added
c5a4416c14dd_refAccumLengths.bin added
c5a41ecddab9_reflengths.bin added
c5a45cd2b77b_refseq.bin added
c5a4e0c1bd9_seq.bin added
c5a43cf84ac3_versionInfo.json added
c5a450f4677a_salmon_index added
c5a45db5a41b_chrLength.txt added
c5a4402918ad_chrName.txt added
c5a44a1326c3_chrNameLength.txt added
c5a42f55f233_chrStart.txt added
c5a433900a8c_exonGeTrInfo.tab added
c5a435a487c6_exonInfo.tab added
c5a444cdf3ad_geneInfo.tab added
c5a42d390625_Genome added
c5a47ac27e54_genomeParameters.txt added
c5a476f3fbc2_Log.out added
c5a4c15ba91_SA added
c5a4668b8bc9_SAindex added
c5a453866db7_sjdbInfo.txt added
c5a41e8d3438_sjdbList.fromGTF.out.tab added
c5a4485f5833_sjdbList.out.tab added
c5a46b97a163_transcriptInfo.tab added
c5a42fe4a1c4_GRCh38.GENCODE.v42_100 added
c5a44b38636c_knownGene_hg38.sql added
c5a463076e08_knownGene_hg38.txt added
c5a47cc90202_refGene_hg38.sql added
c5a470a3114e_refGene_hg38.txt added
c5a461c551a7_knownGene_mm39.sql added
c5a46173dd16_knownGene_mm39.txt added
c5a47db80155_refGene_mm39.sql added
c5a43b5fb3ee_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/RtmpNmVghL/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
40.798 4.603 48.015
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 12.415 | 1.301 | 15.020 | |
| dataSearch | 2.448 | 0.081 | 2.652 | |
| dataUpdate | 0.000 | 0.001 | 0.002 | |
| getCloudData | 4.649 | 0.218 | 6.200 | |
| getData | 0.000 | 0.001 | 0.001 | |
| meta_data | 0.001 | 0.001 | 0.002 | |
| recipeHub-class | 0.261 | 0.020 | 0.296 | |
| recipeLoad | 2.858 | 0.146 | 3.243 | |
| recipeMake | 0.001 | 0.002 | 0.003 | |
| recipeSearch | 1.186 | 0.058 | 1.286 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |