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 17:44 -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: 2024-06-25 06:38:18 -0400 (Tue, 25 Jun 2024) |
| EndedAt: 2024-06-25 06:40:46 -0400 (Tue, 25 Jun 2024) |
| EllapsedTime: 147.2 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: 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 13.6.6
* 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 6.733 0.717 7.51
* 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-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 4.4.0 (2024-04-24) -- "Puppy Cup"
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...
cf9f1b6222f6_GRCh38.primary_assembly.genome.fa.1.bt2 added
cf9f47e55285_GRCh38.primary_assembly.genome.fa.2.bt2 added
cf9f208cbea3_GRCh38.primary_assembly.genome.fa.3.bt2 added
cf9f7837d006_GRCh38.primary_assembly.genome.fa.4.bt2 added
cf9f183a7793_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
cf9f26806052_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
cf9f3633bb3d_outfile.txt added
cf9f7e49bd97_GRCh37_to_GRCh38.chain added
cf9f1b3e4547_GRCh37_to_NCBI34.chain added
cf9f1536464a_GRCh37_to_NCBI35.chain added
cf9f1e40af27_GRCh37_to_NCBI36.chain added
cf9f28ab38f5_GRCh38_to_GRCh37.chain added
cf9f12871af_GRCh38_to_NCBI34.chain added
cf9f63f98c1_GRCh38_to_NCBI35.chain added
cf9f3945aa1b_GRCh38_to_NCBI36.chain added
cf9fca2effd_NCBI34_to_GRCh37.chain added
cf9f1d39d186_NCBI34_to_GRCh38.chain added
cf9f3eeac367_NCBI35_to_GRCh37.chain added
cf9f26c2bf76_NCBI35_to_GRCh38.chain added
cf9f3ba7efdb_NCBI36_to_GRCh37.chain added
cf9fe743176_NCBI36_to_GRCh38.chain added
cf9f6e5b4163_GRCm38_to_NCBIM36.chain added
cf9f2922032f_GRCm38_to_NCBIM37.chain added
cf9f77ff17c1_NCBIM36_to_GRCm38.chain added
cf9fc70bd73_NCBIM37_to_GRCm38.chain added
cf9f3da5cf66_1000G_omni2.5.b37.vcf.gz added
cf9f50d35128_1000G_omni2.5.b37.vcf.gz.tbi added
cf9f6175428c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
cf9f59642750_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
cf9f3e512309_1000G_omni2.5.hg38.vcf.gz added
cf9f40d343d5_1000G_omni2.5.hg38.vcf.gz.tbi added
cf9f6e0a7632_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
cf9f70d6050e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
cf9f72e61401_af-only-gnomad.raw.sites.vcf added
cf9f5f2b8895_af-only-gnomad.raw.sites.vcf.idx added
cf9f23141f03_Mutect2-exome-panel.vcf.idx added
cf9f7e000ff2_Mutect2-WGS-panel-b37.vcf added
cf9f3617197e_Mutect2-WGS-panel-b37.vcf.idx added
cf9f268abaf0_small_exac_common_3.vcf added
cf9f5df6f654_small_exac_common_3.vcf.idx added
cf9fa634fe_1000g_pon.hg38.vcf.gz added
cf9f1fe11007_1000g_pon.hg38.vcf.gz.tbi added
cf9f70e34bea_af-only-gnomad.hg38.vcf.gz added
cf9f5a8d298c_af-only-gnomad.hg38.vcf.gz.tbi added
cf9f69a2d4c5_small_exac_common_3.hg38.vcf.gz added
cf9f413f07b1_small_exac_common_3.hg38.vcf.gz.tbi added
cf9f111216ee_gencode.v41.annotation.gtf added
cf9f3a9f6c03_gencode.v42.annotation.gtf added
cf9f386c5706_gencode.vM30.annotation.gtf added
cf9f50c567da_gencode.vM31.annotation.gtf added
cf9f502542a3_gencode.v41.transcripts.fa added
cf9f3e3a0470_gencode.v41.transcripts.fa.fai added
cf9f52f974fa_gencode.v42.transcripts.fa added
cf9f776ef3a4_gencode.v42.transcripts.fa.fai added
cf9f153dd13e_gencode.vM30.pc_transcripts.fa added
cf9fd744857_gencode.vM30.pc_transcripts.fa.fai added
cf9f4d394ea7_gencode.vM31.pc_transcripts.fa added
cf9f6d5add8c_gencode.vM31.pc_transcripts.fa.fai added
cf9f68874a6a_GRCh38.primary_assembly.genome.fa.1.ht2 added
cf9fa26aac3_GRCh38.primary_assembly.genome.fa.2.ht2 added
cf9f7094ed69_GRCh38.primary_assembly.genome.fa.3.ht2 added
cf9f416ec23d_GRCh38.primary_assembly.genome.fa.4.ht2 added
cf9f4e92545a_GRCh38.primary_assembly.genome.fa.5.ht2 added
cf9f68e00902_GRCh38.primary_assembly.genome.fa.6.ht2 added
cf9f4c6f9818_GRCh38.primary_assembly.genome.fa.7.ht2 added
cf9f326a76dc_GRCh38.primary_assembly.genome.fa.8.ht2 added
cf9f6ba17f5f_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
cf9f37b16d2d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
cf9f6176c1eb_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
cf9f3bb55d4a_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
cf9f7fffc3e5_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
cf9f70963109_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
cf9f146d7f9e_GRCh38_full_analysis_set_plus_decoy_hla.fa added
cf9f20d5688c_GRCh38.primary_assembly.genome.fa.fai added
cf9f1ac2d02b_GRCh38.primary_assembly.genome.fa.amb added
cf9f6bf0c4c6_GRCh38.primary_assembly.genome.fa.ann added
cf9fc06da87_GRCh38.primary_assembly.genome.fa.bwt added
cf9f15f4db3c_GRCh38.primary_assembly.genome.fa.pac added
cf9f7e654b66_GRCh38.primary_assembly.genome.fa.sa added
cf9f2c39565e_GRCh38.primary_assembly.genome.fa added
cf9f68554c00_hs37d5.fa.fai added
cf9f37f0c983_hs37d5.fa.amb added
cf9f213dd426_hs37d5.fa.ann added
cf9f62331bd6_hs37d5.fa.bwt added
cf9f968b0f8_hs37d5.fa.pac added
cf9f383a6e9b_hs37d5.fa.sa added
cf9f4339ef4_hs37d5.fa added
cf9f5908a753_complete_ref_lens.bin added
cf9f472167cf_ctable.bin added
cf9f62266b84_ctg_offsets.bin added
cf9f485cd973_duplicate_clusters.tsv added
cf9f47c83222_info.json added
cf9f28537aff_mphf.bin added
cf9fb01008_pos.bin added
cf9f26ec7d92_pre_indexing.log added
cf9f70281034_rank.bin added
cf9f563fff72_ref_indexing.log added
cf9f39bc19b_refAccumLengths.bin added
cf9f66c3a8f6_reflengths.bin added
cf9f3789e32f_refseq.bin added
cf9f3da23f25_seq.bin added
cf9f66dfb5bf_versionInfo.json added
cf9f6915435c_salmon_index added
cf9f72f982e9_chrLength.txt added
cf9f5b01c9f7_chrName.txt added
cf9f5272a5ce_chrNameLength.txt added
cf9f64e3a1ab_chrStart.txt added
cf9f1c8b154c_exonGeTrInfo.tab added
cf9f6f233f37_exonInfo.tab added
cf9f730b6ce1_geneInfo.tab added
cf9f731962c8_Genome added
cf9f7a47381_genomeParameters.txt added
cf9f3d9b1e12_Log.out added
cf9f12d34f57_SA added
cf9f6efde268_SAindex added
cf9f5e1b52c5_sjdbInfo.txt added
cf9f53d733c7_sjdbList.fromGTF.out.tab added
cf9f558878d1_sjdbList.out.tab added
cf9f72b40d35_transcriptInfo.tab added
cf9facf4d68_GRCh38.GENCODE.v42_100 added
cf9f2fe2ec63_knownGene_hg38.sql added
cf9f5b0d7024_knownGene_hg38.txt added
cf9f4f3d7a2f_refGene_hg38.sql added
cf9f4d20cc4d_refGene_hg38.txt added
cf9f2444faca_knownGene_mm39.sql added
cf9f2cacf660_knownGene_mm39.txt added
cf9ff632f8a_refGene_mm39.sql added
cf9f38c614ea_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/Rtmp5QoTxQ/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
24.273 2.960 28.421
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.733 | 0.717 | 7.510 | |
| dataSearch | 1.130 | 0.046 | 1.177 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.701 | 0.136 | 4.898 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.136 | 0.011 | 0.147 | |
| recipeLoad | 1.404 | 0.084 | 1.499 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.578 | 0.034 | 0.611 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |