Qian Liu
| Snapshot Date: 2024-06-30 14:00 -0400 (Sun, 30 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 2024-07-03 10:22 -0400 (Wed, 03 Jul 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" | 4757 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4480 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4511 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4469 |
| 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 | | ||||||||
| palomino7 | 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: 2024-07-01 10:31:43 -0400 (Mon, 01 Jul 2024) |
| EndedAt: 2024-07-01 10:37:14 -0400 (Mon, 01 Jul 2024) |
| EllapsedTime: 330.9 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_1.4.0.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 13.449 1.343 17.880
getCloudData 5.116 0.213 13.528
* 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...
13692891c091_GRCh38.primary_assembly.genome.fa.1.bt2 added
1369218f973fc_GRCh38.primary_assembly.genome.fa.2.bt2 added
13692212db233_GRCh38.primary_assembly.genome.fa.3.bt2 added
136923f0e4349_GRCh38.primary_assembly.genome.fa.4.bt2 added
1369241638df6_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
136926efd3303_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
13692312042e2_outfile.txt added
136923d071ca0_GRCh37_to_GRCh38.chain added
136921de86bad_GRCh37_to_NCBI34.chain added
136925f53a32_GRCh37_to_NCBI35.chain added
1369226bfabac_GRCh37_to_NCBI36.chain added
13692719fbd13_GRCh38_to_GRCh37.chain added
136922e3664ac_GRCh38_to_NCBI34.chain added
13692750b6fe7_GRCh38_to_NCBI35.chain added
1369241dfe2b9_GRCh38_to_NCBI36.chain added
13692519e0178_NCBI34_to_GRCh37.chain added
136925c729724_NCBI34_to_GRCh38.chain added
136926720ebe6_NCBI35_to_GRCh37.chain added
13692225f7def_NCBI35_to_GRCh38.chain added
136922b44e78a_NCBI36_to_GRCh37.chain added
1369238bd2b37_NCBI36_to_GRCh38.chain added
13692b6044fb_GRCm38_to_NCBIM36.chain added
136925d50c092_GRCm38_to_NCBIM37.chain added
136926092e11a_NCBIM36_to_GRCm38.chain added
136924af8a37e_NCBIM37_to_GRCm38.chain added
136929b5cba6_1000G_omni2.5.b37.vcf.gz added
136927e4d0444_1000G_omni2.5.b37.vcf.gz.tbi added
1369272534d23_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
136923aed6f78_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
136923a314d81_1000G_omni2.5.hg38.vcf.gz added
136927ad76dff_1000G_omni2.5.hg38.vcf.gz.tbi added
136925576bf5a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
13692670cd98b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
136927c9e6987_af-only-gnomad.raw.sites.vcf added
136924225dfc_af-only-gnomad.raw.sites.vcf.idx added
136926c484d82_Mutect2-exome-panel.vcf.idx added
136927ed8c957_Mutect2-WGS-panel-b37.vcf added
136924a8aafd0_Mutect2-WGS-panel-b37.vcf.idx added
13692571ca6eb_small_exac_common_3.vcf added
136921a12bafb_small_exac_common_3.vcf.idx added
1369243b1c21c_1000g_pon.hg38.vcf.gz added
136924b3edefc_1000g_pon.hg38.vcf.gz.tbi added
13692ca198fc_af-only-gnomad.hg38.vcf.gz added
136924542cede_af-only-gnomad.hg38.vcf.gz.tbi added
13692251b7458_small_exac_common_3.hg38.vcf.gz added
136922d735070_small_exac_common_3.hg38.vcf.gz.tbi added
136926da6005f_gencode.v41.annotation.gtf added
136922d629536_gencode.v42.annotation.gtf added
1369223322381_gencode.vM30.annotation.gtf added
1369230b8fc34_gencode.vM31.annotation.gtf added
1369240b5d2e9_gencode.v41.transcripts.fa added
136926129e02f_gencode.v41.transcripts.fa.fai added
1369243d5f7f_gencode.v42.transcripts.fa added
1369259488d05_gencode.v42.transcripts.fa.fai added
136922a22710e_gencode.vM30.pc_transcripts.fa added
136923b2c63be_gencode.vM30.pc_transcripts.fa.fai added
136925f486d4b_gencode.vM31.pc_transcripts.fa added
13692bff87cc_gencode.vM31.pc_transcripts.fa.fai added
13692352c683b_GRCh38.primary_assembly.genome.fa.1.ht2 added
13692766f14c2_GRCh38.primary_assembly.genome.fa.2.ht2 added
1369276bc094c_GRCh38.primary_assembly.genome.fa.3.ht2 added
136923306997a_GRCh38.primary_assembly.genome.fa.4.ht2 added
13692764632c1_GRCh38.primary_assembly.genome.fa.5.ht2 added
136927aae5990_GRCh38.primary_assembly.genome.fa.6.ht2 added
136924c7a3bdc_GRCh38.primary_assembly.genome.fa.7.ht2 added
136926cf00fbd_GRCh38.primary_assembly.genome.fa.8.ht2 added
13692499792b_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1369277e1f868_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
13692147bb155_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1369244b74df4_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
136925e5ef16a_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
136922b3b968d_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1369255191927_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1369262c27b16_GRCh38.primary_assembly.genome.fa.fai added
136924e1f1401_GRCh38.primary_assembly.genome.fa.amb added
136925a5a75b8_GRCh38.primary_assembly.genome.fa.ann added
1369268e6b15f_GRCh38.primary_assembly.genome.fa.bwt added
1369218709c7_GRCh38.primary_assembly.genome.fa.pac added
136924892e899_GRCh38.primary_assembly.genome.fa.sa added
1369224e4ba08_GRCh38.primary_assembly.genome.fa added
1369224717624_hs37d5.fa.fai added
136921503482d_hs37d5.fa.amb added
13692a778d22_hs37d5.fa.ann added
136922ed2b88c_hs37d5.fa.bwt added
13692c520758_hs37d5.fa.pac added
136925d6028b9_hs37d5.fa.sa added
136925411b993_hs37d5.fa added
1369257ae8d03_complete_ref_lens.bin added
136924abecee_ctable.bin added
13692334fffa7_ctg_offsets.bin added
1369249194742_duplicate_clusters.tsv added
136921a95638c_info.json added
1369245ba89f6_mphf.bin added
1369259b7993d_pos.bin added
1369224ada1cf_pre_indexing.log added
1369235a2fd9_rank.bin added
1369215fb5147_ref_indexing.log added
1369226951797_refAccumLengths.bin added
1369263fce4b_reflengths.bin added
136924700a121_refseq.bin added
136927a52a1f1_seq.bin added
13692470613f4_versionInfo.json added
1369260081c99_salmon_index added
13692348db210_chrLength.txt added
1369242a55364_chrName.txt added
136927405ec6a_chrNameLength.txt added
1369230e45ea8_chrStart.txt added
13692610280ab_exonGeTrInfo.tab added
136926b4d8c4e_exonInfo.tab added
1369230368beb_geneInfo.tab added
136924d1c0a07_Genome added
136926bd6791d_genomeParameters.txt added
136924da9963a_Log.out added
1369238c5e1ab_SA added
136924762beab_SAindex added
1369223d3f12a_sjdbInfo.txt added
136922f7e0ec6_sjdbList.fromGTF.out.tab added
136927cfc0185_sjdbList.out.tab added
136924c802de_transcriptInfo.tab added
1369267343f45_GRCh38.GENCODE.v42_100 added
136921725fff2_knownGene_hg38.sql added
136923fc674bd_knownGene_hg38.txt added
136927e1a4500_refGene_hg38.sql added
136926ea843ad_refGene_hg38.txt added
1369268f34b9c_knownGene_mm39.sql added
136923ce92498_knownGene_mm39.txt added
136926e619665_refGene_mm39.sql added
1369248d8f980_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/RtmphtAPgd/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
46.180 5.621 61.615
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 13.449 | 1.343 | 17.880 | |
| dataSearch | 2.749 | 0.089 | 3.381 | |
| dataUpdate | 0.001 | 0.001 | 0.001 | |
| getCloudData | 5.116 | 0.213 | 13.528 | |
| getData | 0.000 | 0.001 | 0.002 | |
| meta_data | 0.001 | 0.001 | 0.002 | |
| recipeHub-class | 0.292 | 0.019 | 0.347 | |
| recipeLoad | 3.082 | 0.144 | 3.562 | |
| recipeMake | 0.000 | 0.002 | 0.003 | |
| recipeSearch | 1.313 | 0.063 | 1.527 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |