Qian Liu
| Snapshot Date: 2024-11-08 13:40 -0500 (Fri, 08 Nov 2024) |
| 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 2024-11-09 21:31 -0500 (Sat, 09 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 2024-11-09 11:15:14 -0500 (Sat, 09 Nov 2024) |
| EndedAt: 2024-11-09 11:19:42 -0500 (Sat, 09 Nov 2024) |
| EllapsedTime: 267.7 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 4.4.1 (2024-06-14)
* 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 13.6.7
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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...
9ed7347a54fb_GRCh38.primary_assembly.genome.fa.1.bt2 added
9ed74b6145a7_GRCh38.primary_assembly.genome.fa.2.bt2 added
9ed75f23fd9a_GRCh38.primary_assembly.genome.fa.3.bt2 added
9ed733deba42_GRCh38.primary_assembly.genome.fa.4.bt2 added
9ed763965da8_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
9ed724def3ac_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
9ed7294fb41d_outfile.txt added
9ed72fb9f11b_GRCh37_to_GRCh38.chain added
9ed758843c17_GRCh37_to_NCBI34.chain added
9ed751853767_GRCh37_to_NCBI35.chain added
9ed7f87501_GRCh37_to_NCBI36.chain added
9ed737c99526_GRCh38_to_GRCh37.chain added
9ed7135f0e67_GRCh38_to_NCBI34.chain added
9ed745aa9620_GRCh38_to_NCBI35.chain added
9ed74266329b_GRCh38_to_NCBI36.chain added
9ed74384802b_NCBI34_to_GRCh37.chain added
9ed72ffaa9ae_NCBI34_to_GRCh38.chain added
9ed77199f71d_NCBI35_to_GRCh37.chain added
9ed7332ecb2f_NCBI35_to_GRCh38.chain added
9ed7451d94e9_NCBI36_to_GRCh37.chain added
9ed7191b7072_NCBI36_to_GRCh38.chain added
9ed75873593e_GRCm38_to_NCBIM36.chain added
9ed77ce822cf_GRCm38_to_NCBIM37.chain added
9ed76c458419_NCBIM36_to_GRCm38.chain added
9ed747e3bcd7_NCBIM37_to_GRCm38.chain added
9ed73882ec20_1000G_omni2.5.b37.vcf.gz added
9ed71b5c45dc_1000G_omni2.5.b37.vcf.gz.tbi added
9ed746ee7c8c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
9ed75332efb5_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
9ed735177ebf_1000G_omni2.5.hg38.vcf.gz added
9ed7198248d4_1000G_omni2.5.hg38.vcf.gz.tbi added
9ed7387b6361_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
9ed72cb9923f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
9ed74b307d09_af-only-gnomad.raw.sites.vcf added
9ed75c61006f_af-only-gnomad.raw.sites.vcf.idx added
9ed76463a6ca_Mutect2-exome-panel.vcf.idx added
9ed74a5b4b43_Mutect2-WGS-panel-b37.vcf added
9ed72faa41d8_Mutect2-WGS-panel-b37.vcf.idx added
9ed752c8e45a_small_exac_common_3.vcf added
9ed7307fb2c_small_exac_common_3.vcf.idx added
9ed7fb0742_1000g_pon.hg38.vcf.gz added
9ed760997e8e_1000g_pon.hg38.vcf.gz.tbi added
9ed77d43ce2d_af-only-gnomad.hg38.vcf.gz added
9ed76e952c9a_af-only-gnomad.hg38.vcf.gz.tbi added
9ed73a36b2e_small_exac_common_3.hg38.vcf.gz added
9ed75dd19adf_small_exac_common_3.hg38.vcf.gz.tbi added
9ed76c0ed697_gencode.v41.annotation.gtf added
9ed7422a8aed_gencode.v42.annotation.gtf added
9ed77706ef8a_gencode.vM30.annotation.gtf added
9ed768588a12_gencode.vM31.annotation.gtf added
9ed7cd0d943_gencode.v41.transcripts.fa added
9ed76367c447_gencode.v41.transcripts.fa.fai added
9ed73187444d_gencode.v42.transcripts.fa added
9ed7279534a2_gencode.v42.transcripts.fa.fai added
9ed734b28bfb_gencode.vM30.pc_transcripts.fa added
9ed7360426c4_gencode.vM30.pc_transcripts.fa.fai added
9ed74a8d2990_gencode.vM31.pc_transcripts.fa added
9ed779a3d32c_gencode.vM31.pc_transcripts.fa.fai added
9ed7727d2c17_GRCh38.primary_assembly.genome.fa.1.ht2 added
9ed777d9d4b9_GRCh38.primary_assembly.genome.fa.2.ht2 added
9ed77e1cfb27_GRCh38.primary_assembly.genome.fa.3.ht2 added
9ed720acfe20_GRCh38.primary_assembly.genome.fa.4.ht2 added
9ed73d5ff7a2_GRCh38.primary_assembly.genome.fa.5.ht2 added
9ed7677acc28_GRCh38.primary_assembly.genome.fa.6.ht2 added
9ed72ef18b2b_GRCh38.primary_assembly.genome.fa.7.ht2 added
9ed773e7cc20_GRCh38.primary_assembly.genome.fa.8.ht2 added
9ed7770a8452_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
9ed75375608c_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
9ed73f15b222_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
9ed72961f689_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
9ed75e80b198_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
9ed7530ba2a0_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
9ed720e1e0f8_GRCh38_full_analysis_set_plus_decoy_hla.fa added
9ed74d78caa5_GRCh38.primary_assembly.genome.fa.fai added
9ed735403e5f_GRCh38.primary_assembly.genome.fa.amb added
9ed7cbeea49_GRCh38.primary_assembly.genome.fa.ann added
9ed74a076528_GRCh38.primary_assembly.genome.fa.bwt added
9ed72b824b10_GRCh38.primary_assembly.genome.fa.pac added
9ed7770e1dc0_GRCh38.primary_assembly.genome.fa.sa added
9ed73fc36550_GRCh38.primary_assembly.genome.fa added
9ed7353087e4_hs37d5.fa.fai added
9ed7529a504_hs37d5.fa.amb added
9ed77110ac41_hs37d5.fa.ann added
9ed77d9d1964_hs37d5.fa.bwt added
9ed754ee34a9_hs37d5.fa.pac added
9ed762c36ece_hs37d5.fa.sa added
9ed7c9fc90a_hs37d5.fa added
9ed74e47b5ff_complete_ref_lens.bin added
9ed745fda07f_ctable.bin added
9ed7e3415bf_ctg_offsets.bin added
9ed77d7fb5e1_duplicate_clusters.tsv added
9ed74b7e0725_info.json added
9ed73f0734db_mphf.bin added
9ed7721f3630_pos.bin added
9ed75f1ec3d8_pre_indexing.log added
9ed75ccbcab1_rank.bin added
9ed747685a0f_ref_indexing.log added
9ed713f0b369_refAccumLengths.bin added
9ed71f92bcb9_reflengths.bin added
9ed75aa425e0_refseq.bin added
9ed74eb2c39d_seq.bin added
9ed73a48a0c8_versionInfo.json added
9ed77633c85c_salmon_index added
9ed741a74ca4_chrLength.txt added
9ed74e98c4a8_chrName.txt added
9ed7f9719e8_chrNameLength.txt added
9ed7925d657_chrStart.txt added
9ed7131aee72_exonGeTrInfo.tab added
9ed74d1c882a_exonInfo.tab added
9ed7c2fa4f3_geneInfo.tab added
9ed7bf653c5_Genome added
9ed758f5b0a5_genomeParameters.txt added
9ed76a204e43_Log.out added
9ed76ef24723_SA added
9ed7641c83bc_SAindex added
9ed7c0cdefd_sjdbInfo.txt added
9ed72103ba39_sjdbList.fromGTF.out.tab added
9ed77bb7051d_sjdbList.out.tab added
9ed72cb0f25f_transcriptInfo.tab added
9ed714f851e5_GRCh38.GENCODE.v42_100 added
9ed73ac89c24_knownGene_hg38.sql added
9ed748831da2_knownGene_hg38.txt added
9ed7180e9bdf_refGene_hg38.sql added
9ed7671b59cf_refGene_hg38.txt added
9ed734a559eb_knownGene_mm39.sql added
9ed753b26e4d_knownGene_mm39.txt added
9ed76767ac28_refGene_mm39.sql added
9ed74757ab21_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:
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpABvij5/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
6.408 0.738 7.672
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.589 | 0.167 | 1.760 | |
| dataSearch | 0.282 | 0.014 | 0.297 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 0.739 | 0.044 | 1.597 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.033 | 0.005 | 0.038 | |
| recipeLoad | 0.374 | 0.022 | 0.398 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.159 | 0.009 | 0.169 | |
| recipeUpdate | 0 | 0 | 0 | |