Qian Liu
| Snapshot Date: 2024-06-23 14:00 -0400 (Sun, 23 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_19 |
| git_last_commit: 801f620 |
| git_last_commit_date: 2024-04-30 11:46:52 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-25 17:42 -0400 (Tue, 25 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
| 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 1745/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.4.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.4.0 |
| 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_1.4.0.tar.gz |
| StartedAt: 2024-06-24 10:22:46 -0400 (Mon, 24 Jun 2024) |
| EndedAt: 2024-06-24 10:28:04 -0400 (Mon, 24 Jun 2024) |
| EllapsedTime: 318.6 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.4.0’
* 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 13.408 1.320 16.653
getCloudData 5.090 0.225 12.623
* 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-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup"
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...
44da66202a69_GRCh38.primary_assembly.genome.fa.1.bt2 added
44da49c087e0_GRCh38.primary_assembly.genome.fa.2.bt2 added
44da7f18a8f3_GRCh38.primary_assembly.genome.fa.3.bt2 added
44da2bfc2ab5_GRCh38.primary_assembly.genome.fa.4.bt2 added
44da3857e7a2_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
44da13285994_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
44da3e110d5f_outfile.txt added
44da5184f7ce_GRCh37_to_GRCh38.chain added
44da70a91f31_GRCh37_to_NCBI34.chain added
44da6f3f03bf_GRCh37_to_NCBI35.chain added
44da120f29a8_GRCh37_to_NCBI36.chain added
44da2177dddb_GRCh38_to_GRCh37.chain added
44da44866607_GRCh38_to_NCBI34.chain added
44da539478b6_GRCh38_to_NCBI35.chain added
44da38811f98_GRCh38_to_NCBI36.chain added
44da25415123_NCBI34_to_GRCh37.chain added
44da6335e3f0_NCBI34_to_GRCh38.chain added
44da6707d472_NCBI35_to_GRCh37.chain added
44da330cbd36_NCBI35_to_GRCh38.chain added
44da95a3e69_NCBI36_to_GRCh37.chain added
44da3b7644b_NCBI36_to_GRCh38.chain added
44da7d1979d4_GRCm38_to_NCBIM36.chain added
44da138d8d76_GRCm38_to_NCBIM37.chain added
44da32424801_NCBIM36_to_GRCm38.chain added
44da1d85536e_NCBIM37_to_GRCm38.chain added
44da1c2869e6_1000G_omni2.5.b37.vcf.gz added
44da2140897b_1000G_omni2.5.b37.vcf.gz.tbi added
44da1401fb4b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
44dae190330_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
44dac204b8b_1000G_omni2.5.hg38.vcf.gz added
44da1c3f98e5_1000G_omni2.5.hg38.vcf.gz.tbi added
44da134ef0e0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
44da23a80c07_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
44da6dadb1da_af-only-gnomad.raw.sites.vcf added
44da26779777_af-only-gnomad.raw.sites.vcf.idx added
44da7579195b_Mutect2-exome-panel.vcf.idx added
44da616fe19d_Mutect2-WGS-panel-b37.vcf added
44da78453c64_Mutect2-WGS-panel-b37.vcf.idx added
44da98006ec_small_exac_common_3.vcf added
44da344674d3_small_exac_common_3.vcf.idx added
44da7d9fe374_1000g_pon.hg38.vcf.gz added
44dac0e151b_1000g_pon.hg38.vcf.gz.tbi added
44da708ba5cb_af-only-gnomad.hg38.vcf.gz added
44da6031ec26_af-only-gnomad.hg38.vcf.gz.tbi added
44da6d86e420_small_exac_common_3.hg38.vcf.gz added
44da32eb290d_small_exac_common_3.hg38.vcf.gz.tbi added
44da6cd42e98_gencode.v41.annotation.gtf added
44da5e3f34f9_gencode.v42.annotation.gtf added
44da7aef7c6_gencode.vM30.annotation.gtf added
44da700cec1a_gencode.vM31.annotation.gtf added
44da6060d86e_gencode.v41.transcripts.fa added
44da76214f30_gencode.v41.transcripts.fa.fai added
44da4d614e7_gencode.v42.transcripts.fa added
44da2f64c2c_gencode.v42.transcripts.fa.fai added
44da7802de38_gencode.vM30.pc_transcripts.fa added
44da44b6c16_gencode.vM30.pc_transcripts.fa.fai added
44da73a51a8d_gencode.vM31.pc_transcripts.fa added
44da5c725a4b_gencode.vM31.pc_transcripts.fa.fai added
44da57862157_GRCh38.primary_assembly.genome.fa.1.ht2 added
44da26f703a5_GRCh38.primary_assembly.genome.fa.2.ht2 added
44da2310599f_GRCh38.primary_assembly.genome.fa.3.ht2 added
44da66be7b5_GRCh38.primary_assembly.genome.fa.4.ht2 added
44da16391f5e_GRCh38.primary_assembly.genome.fa.5.ht2 added
44da3a5fb8_GRCh38.primary_assembly.genome.fa.6.ht2 added
44da78622925_GRCh38.primary_assembly.genome.fa.7.ht2 added
44da747b79e1_GRCh38.primary_assembly.genome.fa.8.ht2 added
44da567ede85_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
44da23431a20_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
44daa683cf6_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
44da417a3fd0_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
44da40f39245_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
44da37081153_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
44da72a97c5e_GRCh38_full_analysis_set_plus_decoy_hla.fa added
44da55243a21_GRCh38.primary_assembly.genome.fa.fai added
44da3d647832_GRCh38.primary_assembly.genome.fa.amb added
44daf0f3a1b_GRCh38.primary_assembly.genome.fa.ann added
44da30afca56_GRCh38.primary_assembly.genome.fa.bwt added
44da650ced12_GRCh38.primary_assembly.genome.fa.pac added
44da33a06c92_GRCh38.primary_assembly.genome.fa.sa added
44da6937ffb8_GRCh38.primary_assembly.genome.fa added
44da5b75beff_hs37d5.fa.fai added
44daf4e8642_hs37d5.fa.amb added
44da6c505ee7_hs37d5.fa.ann added
44da1086c73f_hs37d5.fa.bwt added
44da830193_hs37d5.fa.pac added
44da18dc5a28_hs37d5.fa.sa added
44da2aa304d8_hs37d5.fa added
44da349316c6_complete_ref_lens.bin added
44da24bc3c21_ctable.bin added
44da420fad5e_ctg_offsets.bin added
44da133f1834_duplicate_clusters.tsv added
44da134e07cb_info.json added
44da67e1aa53_mphf.bin added
44da1075646d_pos.bin added
44dab14388c_pre_indexing.log added
44da5c8c7502_rank.bin added
44da95605c6_ref_indexing.log added
44da6e950ef3_refAccumLengths.bin added
44da7c08ac3c_reflengths.bin added
44da1d63d6c2_refseq.bin added
44da5a869a1_seq.bin added
44da73aecbed_versionInfo.json added
44da58ce6ff0_salmon_index added
44da5917231c_chrLength.txt added
44da7e0230f5_chrName.txt added
44da41dc6574_chrNameLength.txt added
44da6c88c473_chrStart.txt added
44da71991b0_exonGeTrInfo.tab added
44da1fabbd74_exonInfo.tab added
44da44231aea_geneInfo.tab added
44da5cbc1b98_Genome added
44da41b7c7b8_genomeParameters.txt added
44da89922bd_Log.out added
44da7db7aab3_SA added
44da25280e40_SAindex added
44da68bf9ece_sjdbInfo.txt added
44da7c531c1b_sjdbList.fromGTF.out.tab added
44da345a7061_sjdbList.out.tab added
44da1d880b21_transcriptInfo.tab added
44da4e92b2ac_GRCh38.GENCODE.v42_100 added
44da1106281_knownGene_hg38.sql added
44da5ab303b2_knownGene_hg38.txt added
44da1eb7c9a3_refGene_hg38.sql added
44da3416fc16_refGene_hg38.txt added
44da51002311_knownGene_mm39.sql added
44da5ffe5aa2_knownGene_mm39.txt added
44da33f072ea_refGene_mm39.sql added
44da6f087b49_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/RtmphYqaNl/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
45.828 5.463 58.938
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 13.408 | 1.320 | 16.653 | |
| dataSearch | 2.689 | 0.080 | 2.976 | |
| dataUpdate | 0.001 | 0.002 | 0.002 | |
| getCloudData | 5.090 | 0.225 | 12.623 | |
| getData | 0.001 | 0.001 | 0.002 | |
| meta_data | 0.001 | 0.001 | 0.002 | |
| recipeHub-class | 0.301 | 0.020 | 0.572 | |
| recipeLoad | 3.131 | 0.147 | 4.234 | |
| recipeMake | 0.000 | 0.002 | 0.002 | |
| recipeSearch | 1.270 | 0.061 | 1.540 | |
| recipeUpdate | 0 | 0 | 0 | |