Qian Liu
| Snapshot Date: 2024-05-01 14:05:06 -0400 (Wed, 01 May 2024) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: cbe4e73 |
| git_last_commit_date: 2024-04-30 11:46:52 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-03 11:38:45 -0400 (Fri, 03 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4660 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4391 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4422 |
| 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 1687/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.5.0 (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 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: 1.5.0 |
| 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_1.5.0.tar.gz |
| StartedAt: 2024-05-02 10:07:04 -0400 (Thu, 02 May 2024) |
| EndedAt: 2024-05-02 10:12:22 -0400 (Thu, 02 May 2024) |
| EllapsedTime: 317.9 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 ‘1.5.0’
* 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 13.548 1.359 18.173
getCloudData 5.004 0.219 6.927
* 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 4.4.0 Patched (2024-04-24 r86482) -- "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...
3bafbef17b1_GRCh38.primary_assembly.genome.fa.1.bt2 added
3baf7dfc6b95_GRCh38.primary_assembly.genome.fa.2.bt2 added
3baf46fb43d1_GRCh38.primary_assembly.genome.fa.3.bt2 added
3baf1a2172bf_GRCh38.primary_assembly.genome.fa.4.bt2 added
3baf9f46700_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3bafc96361b_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3baf59ba2d11_outfile.txt added
3baf4de4e51c_GRCh37_to_GRCh38.chain added
3baf6e7db937_GRCh37_to_NCBI34.chain added
3bafb028d_GRCh37_to_NCBI35.chain added
3baf52d47700_GRCh37_to_NCBI36.chain added
3baf7ad0cb7b_GRCh38_to_GRCh37.chain added
3baf21df373b_GRCh38_to_NCBI34.chain added
3baf45a313dc_GRCh38_to_NCBI35.chain added
3baf556cf43b_GRCh38_to_NCBI36.chain added
3baf6416794d_NCBI34_to_GRCh37.chain added
3baf7f75e190_NCBI34_to_GRCh38.chain added
3baf142bf650_NCBI35_to_GRCh37.chain added
3baf52380888_NCBI35_to_GRCh38.chain added
3baf5cb842e3_NCBI36_to_GRCh37.chain added
3baf452f74a3_NCBI36_to_GRCh38.chain added
3baf2e929cd1_GRCm38_to_NCBIM36.chain added
3baf1b75753a_GRCm38_to_NCBIM37.chain added
3baf3c6340eb_NCBIM36_to_GRCm38.chain added
3baf183b2346_NCBIM37_to_GRCm38.chain added
3baf5288d517_1000G_omni2.5.b37.vcf.gz added
3baf155e0356_1000G_omni2.5.b37.vcf.gz.tbi added
3baf4f2d0e0f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3baf16f62365_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3baf798dc7a9_1000G_omni2.5.hg38.vcf.gz added
3baf4b2f6697_1000G_omni2.5.hg38.vcf.gz.tbi added
3baf14f86a11_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3baf40fb8cd8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3baf42dbda3c_af-only-gnomad.raw.sites.vcf added
3baf6fd4bb6e_af-only-gnomad.raw.sites.vcf.idx added
3baf775d6c1d_Mutect2-exome-panel.vcf.idx added
3baf16652124_Mutect2-WGS-panel-b37.vcf added
3baf4962cdf8_Mutect2-WGS-panel-b37.vcf.idx added
3baf75c07a6b_small_exac_common_3.vcf added
3baf2fa54332_small_exac_common_3.vcf.idx added
3bafadea00e_1000g_pon.hg38.vcf.gz added
3baf1dddfcb5_1000g_pon.hg38.vcf.gz.tbi added
3baf58f9de64_af-only-gnomad.hg38.vcf.gz added
3baf7c77a4de_af-only-gnomad.hg38.vcf.gz.tbi added
3baf12e92aa9_small_exac_common_3.hg38.vcf.gz added
3baf9efc6f2_small_exac_common_3.hg38.vcf.gz.tbi added
3baf5cee3ef6_gencode.v41.annotation.gtf added
3baf1d67b824_gencode.v42.annotation.gtf added
3baf46a5291_gencode.vM30.annotation.gtf added
3baf6052afda_gencode.vM31.annotation.gtf added
3baf5497429d_gencode.v41.transcripts.fa added
3baf16967cce_gencode.v41.transcripts.fa.fai added
3baf71dbc3f7_gencode.v42.transcripts.fa added
3baf131ec787_gencode.v42.transcripts.fa.fai added
3baf49bd79df_gencode.vM30.pc_transcripts.fa added
3baf368c454b_gencode.vM30.pc_transcripts.fa.fai added
3baf33195ae7_gencode.vM31.pc_transcripts.fa added
3baf459f0de6_gencode.vM31.pc_transcripts.fa.fai added
3baf4d499abf_GRCh38.primary_assembly.genome.fa.1.ht2 added
3baf1b4e993d_GRCh38.primary_assembly.genome.fa.2.ht2 added
3baf452e81cc_GRCh38.primary_assembly.genome.fa.3.ht2 added
3baf704b9b8f_GRCh38.primary_assembly.genome.fa.4.ht2 added
3baf73d202e1_GRCh38.primary_assembly.genome.fa.5.ht2 added
3baf60bb3d2e_GRCh38.primary_assembly.genome.fa.6.ht2 added
3baf24adc89f_GRCh38.primary_assembly.genome.fa.7.ht2 added
3bafd4e5189_GRCh38.primary_assembly.genome.fa.8.ht2 added
3baf10cb0032_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3baf7f79db3a_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3baf1927fe38_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3baf10a31b6f_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3baf445e1cf1_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3baf7ebe3547_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3baf799c0952_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3baf732824dd_GRCh38.primary_assembly.genome.fa.fai added
3baf508c643b_GRCh38.primary_assembly.genome.fa.amb added
3baf310886cd_GRCh38.primary_assembly.genome.fa.ann added
3baf26ca15e1_GRCh38.primary_assembly.genome.fa.bwt added
3baf1d627aac_GRCh38.primary_assembly.genome.fa.pac added
3baf2c63c146_GRCh38.primary_assembly.genome.fa.sa added
3baf4925f16e_GRCh38.primary_assembly.genome.fa added
3baf5a0d9246_hs37d5.fa.fai added
3baf30fe5fda_hs37d5.fa.amb added
3bafc46fa57_hs37d5.fa.ann added
3baf7dd6c0d_hs37d5.fa.bwt added
3baf59e0cd83_hs37d5.fa.pac added
3baf35d4818e_hs37d5.fa.sa added
3baf1285ad3e_hs37d5.fa added
3baf630caf2_complete_ref_lens.bin added
3baf6d5bd90a_ctable.bin added
3baf2906579d_ctg_offsets.bin added
3baf5f621975_duplicate_clusters.tsv added
3baf2175813f_info.json added
3baf29786042_mphf.bin added
3baf1df7a253_pos.bin added
3baf6cc20683_pre_indexing.log added
3baf3639ba3d_rank.bin added
3baf7f2169b_ref_indexing.log added
3baf26aa1e30_refAccumLengths.bin added
3baf6aa3f524_reflengths.bin added
3baf3233452e_refseq.bin added
3baf4402e8c1_seq.bin added
3baf1afef9c9_versionInfo.json added
3baf59c108f7_salmon_index added
3baf1033be2a_chrLength.txt added
3baf3509bfb5_chrName.txt added
3baf13091f47_chrNameLength.txt added
3baf3be47814_chrStart.txt added
3baf148787c4_exonGeTrInfo.tab added
3baf4de25f63_exonInfo.tab added
3baf48e48487_geneInfo.tab added
3baf12b8e074_Genome added
3baf2797e946_genomeParameters.txt added
3baf665406f8_Log.out added
3baf1695b844_SA added
3baf3f7483f1_SAindex added
3baf7a8263c2_sjdbInfo.txt added
3baf6639464_sjdbList.fromGTF.out.tab added
3baf73a33482_sjdbList.out.tab added
3baf5fcc7e1d_transcriptInfo.tab added
3baf6a6bd30d_GRCh38.GENCODE.v42_100 added
3baf4ced3110_knownGene_hg38.sql added
3baf683038e4_knownGene_hg38.txt added
3baf35e7362c_refGene_hg38.sql added
3baf5e959e59_refGene_hg38.txt added
3baf30cf1592_knownGene_mm39.sql added
3baf6b913d46_knownGene_mm39.txt added
3bafc4df5d6_refGene_mm39.sql added
3baf5246bae9_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/RtmpRvXKOl/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
45.074 5.516 61.431
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 13.548 | 1.359 | 18.173 | |
| dataSearch | 2.703 | 0.088 | 3.131 | |
| dataUpdate | 0.001 | 0.002 | 0.002 | |
| getCloudData | 5.004 | 0.219 | 6.927 | |
| getData | 0.000 | 0.001 | 0.002 | |
| meta_data | 0.001 | 0.001 | 0.002 | |
| recipeHub-class | 0.284 | 0.019 | 0.345 | |
| recipeLoad | 3.108 | 0.146 | 3.888 | |
| recipeMake | 0.000 | 0.002 | 0.003 | |
| recipeSearch | 1.242 | 0.059 | 1.540 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |