Qian Liu
| Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_18 |
| git_last_commit: 836e03f |
| git_last_commit_date: 2023-12-08 16:02:19 -0400 (Fri, 08 Dec 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:36:18 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 1725/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.2.2 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.2.2 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ReUseData_1.2.2.tar.gz |
| StartedAt: 2024-04-16 02:56:43 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 03:00:19 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 215.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ReUseData_1.2.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ReUseData.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.2.2’
* 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 R 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 loading without being on the library search path ... 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 6.191 0.292 6.487
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘ReUseData_data.Rmd’ using ‘UTF-8’... OK
‘ReUseData_quickStart.Rmd’ using ‘UTF-8’... OK
‘ReUseData_recipe.Rmd’ using ‘UTF-8’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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...
1778794225919e_GRCh38.primary_assembly.genome.fa.1.bt2 added
177879367781dd_GRCh38.primary_assembly.genome.fa.2.bt2 added
17787955ecbc16_GRCh38.primary_assembly.genome.fa.3.bt2 added
177879338c087a_GRCh38.primary_assembly.genome.fa.4.bt2 added
1778795ee73948_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
177879e9b743b_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1778798fc2e50_outfile.txt added
1778796897ad72_GRCh37_to_GRCh38.chain added
1778797fca1d90_GRCh37_to_NCBI34.chain added
17787972eb369d_GRCh37_to_NCBI35.chain added
177879fc9959e_GRCh37_to_NCBI36.chain added
177879648ddf28_GRCh38_to_GRCh37.chain added
177879622f3253_GRCh38_to_NCBI34.chain added
17787961e2fb83_GRCh38_to_NCBI35.chain added
1778796e5596c_GRCh38_to_NCBI36.chain added
17787974f033b0_NCBI34_to_GRCh37.chain added
177879e56dec5_NCBI34_to_GRCh38.chain added
1778793a2b35ee_NCBI35_to_GRCh37.chain added
177879306b41fb_NCBI35_to_GRCh38.chain added
17787953c83372_NCBI36_to_GRCh37.chain added
1778797d0d3392_NCBI36_to_GRCh38.chain added
177879119a0bf_GRCm38_to_NCBIM36.chain added
177879421736c7_GRCm38_to_NCBIM37.chain added
177879795f5159_NCBIM36_to_GRCm38.chain added
177879147507e7_NCBIM37_to_GRCm38.chain added
1778791cd6f982_1000G_omni2.5.b37.vcf.gz added
1778792b509a4f_1000G_omni2.5.b37.vcf.gz.tbi added
1778793fe847a1_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1778796884de56_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
17787978eec706_1000G_omni2.5.hg38.vcf.gz added
17787966e5e5a2_1000G_omni2.5.hg38.vcf.gz.tbi added
1778792aaa6ff5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1778792f6648e4_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1778793cd2a1b9_af-only-gnomad.raw.sites.vcf added
1778795e36786f_af-only-gnomad.raw.sites.vcf.idx added
177879e4d822c_Mutect2-exome-panel.vcf.idx added
1778794b6e15f4_Mutect2-WGS-panel-b37.vcf added
1778796732a6bf_Mutect2-WGS-panel-b37.vcf.idx added
17787976e52f9e_small_exac_common_3.vcf added
1778794b383384_small_exac_common_3.vcf.idx added
1778795a1ddd5c_1000g_pon.hg38.vcf.gz added
1778796aec53c_1000g_pon.hg38.vcf.gz.tbi added
1778792fc612ac_af-only-gnomad.hg38.vcf.gz added
1778793c4d0fb0_af-only-gnomad.hg38.vcf.gz.tbi added
1778796891c0c0_small_exac_common_3.hg38.vcf.gz added
17787936ab6c18_small_exac_common_3.hg38.vcf.gz.tbi added
177879313d4360_gencode.v41.annotation.gtf added
17787976e89f85_gencode.v42.annotation.gtf added
17787970d6a206_gencode.vM30.annotation.gtf added
17787961a8855b_gencode.vM31.annotation.gtf added
1778794ab0d2f7_gencode.v41.transcripts.fa added
1778796de3d599_gencode.v41.transcripts.fa.fai added
17787962c2261a_gencode.v42.transcripts.fa added
177879cc809be_gencode.v42.transcripts.fa.fai added
177879674326f2_gencode.vM30.pc_transcripts.fa added
17787977372e01_gencode.vM30.pc_transcripts.fa.fai added
177879299f0341_gencode.vM31.pc_transcripts.fa added
1778791293c141_gencode.vM31.pc_transcripts.fa.fai added
177879371f75a3_GRCh38.primary_assembly.genome.fa.1.ht2 added
1778791223e197_GRCh38.primary_assembly.genome.fa.2.ht2 added
177879b828848_GRCh38.primary_assembly.genome.fa.3.ht2 added
1778791e055b45_GRCh38.primary_assembly.genome.fa.4.ht2 added
1778793cce518c_GRCh38.primary_assembly.genome.fa.5.ht2 added
1778793ae8d12c_GRCh38.primary_assembly.genome.fa.6.ht2 added
1778795ad7fcfe_GRCh38.primary_assembly.genome.fa.7.ht2 added
1778791b04c9fc_GRCh38.primary_assembly.genome.fa.8.ht2 added
17787949365358_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
177879264612f2_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
17787923770bb_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
177879401b82f7_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
177879717e4677_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1778795c554e18_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
17787946ca4833_GRCh38_full_analysis_set_plus_decoy_hla.fa added
17787921445923_GRCh38.primary_assembly.genome.fa.fai added
17787918a25dc8_GRCh38.primary_assembly.genome.fa.amb added
1778792f5c08f3_GRCh38.primary_assembly.genome.fa.ann added
17787957efc53c_GRCh38.primary_assembly.genome.fa.bwt added
17787949dfa128_GRCh38.primary_assembly.genome.fa.pac added
1778792644a878_GRCh38.primary_assembly.genome.fa.sa added
17787948c66742_GRCh38.primary_assembly.genome.fa added
1778792b882683_hs37d5.fa.fai added
17787970f57b6f_hs37d5.fa.amb added
17787936aa3cdb_hs37d5.fa.ann added
177879e4a4c9e_hs37d5.fa.bwt added
1778797dbd852e_hs37d5.fa.pac added
1778791ded63cd_hs37d5.fa.sa added
1778795817a9f_hs37d5.fa added
177879275c886f_complete_ref_lens.bin added
1778793081250f_ctable.bin added
1778793ca0f042_ctg_offsets.bin added
17787939806a06_duplicate_clusters.tsv added
1778793c03ad57_info.json added
1778795aa64b88_mphf.bin added
177879764ebb93_pos.bin added
17787976ec7e83_pre_indexing.log added
177879357e4886_rank.bin added
1778791153858f_ref_indexing.log added
1778794022d1db_refAccumLengths.bin added
1778795bc45b79_reflengths.bin added
177879138af64a_refseq.bin added
1778793e54d2_seq.bin added
1778794d42a1f0_versionInfo.json added
1778796fe04462_salmon_index added
17787947089d06_chrLength.txt added
1778796e86fb13_chrName.txt added
177879882a22a_chrNameLength.txt added
1778797664a5f9_chrStart.txt added
1778794676c04f_exonGeTrInfo.tab added
17787952624352_exonInfo.tab added
1778791ca94e72_geneInfo.tab added
177879f3d2792_Genome added
1778797dea69d6_genomeParameters.txt added
177879d9ec9e1_Log.out added
17787945e7646d_SA added
177879c34b674_SAindex added
177879b5c4f0f_sjdbInfo.txt added
17787963d4c83b_sjdbList.fromGTF.out.tab added
17787911b63113_sjdbList.out.tab added
17787932b8d77e_transcriptInfo.tab added
1778791455ed4a_GRCh38.GENCODE.v42_100 added
1778794e572156_knownGene_hg38.sql added
1778796c394185_knownGene_hg38.txt added
17787950599aa1_refGene_hg38.sql added
17787928fd6cde_refGene_hg38.txt added
1778796287fd18_knownGene_mm39.sql added
17787947461924_knownGene_mm39.txt added
1778795e7bb564_refGene_mm39.sql added
17787973db82a7_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/Rtmpgrc0f5/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
20.284 1.273 21.876
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.191 | 0.292 | 6.487 | |
| dataSearch | 1.100 | 0.028 | 1.128 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.883 | 0.188 | 3.723 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.131 | 0.000 | 0.131 | |
| recipeLoad | 1.314 | 0.055 | 1.371 | |
| recipeMake | 0.001 | 0.000 | 0.000 | |
| recipeSearch | 0.545 | 0.011 | 0.557 | |
| recipeUpdate | 0 | 0 | 0 | |