Qian Liu
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 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 2024-06-11 14:40 -0400 (Tue, 11 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" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
| 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 ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ReUseData_1.4.0.tar.gz |
| StartedAt: 2024-06-10 02:37:24 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 02:40:16 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 172.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ReUseData_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* 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 ‘1.4.0’
* 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 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 5.872 0.287 6.161
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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...
1c0ac0518c0803_GRCh38.primary_assembly.genome.fa.1.bt2 added
1c0ac02d57afb1_GRCh38.primary_assembly.genome.fa.2.bt2 added
1c0ac0f5f4751_GRCh38.primary_assembly.genome.fa.3.bt2 added
1c0ac03218cb34_GRCh38.primary_assembly.genome.fa.4.bt2 added
1c0ac05020f3de_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1c0ac0565f008a_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1c0ac060042182_outfile.txt added
1c0ac063ccf7f9_GRCh37_to_GRCh38.chain added
1c0ac064177ff_GRCh37_to_NCBI34.chain added
1c0ac06cf4194b_GRCh37_to_NCBI35.chain added
1c0ac03b94fb8c_GRCh37_to_NCBI36.chain added
1c0ac07101eaef_GRCh38_to_GRCh37.chain added
1c0ac04e8250fc_GRCh38_to_NCBI34.chain added
1c0ac01b6f21e_GRCh38_to_NCBI35.chain added
1c0ac01eaee13d_GRCh38_to_NCBI36.chain added
1c0ac0562947dc_NCBI34_to_GRCh37.chain added
1c0ac04363765b_NCBI34_to_GRCh38.chain added
1c0ac067ac78d7_NCBI35_to_GRCh37.chain added
1c0ac04c0241df_NCBI35_to_GRCh38.chain added
1c0ac07c1c3fda_NCBI36_to_GRCh37.chain added
1c0ac02896c82d_NCBI36_to_GRCh38.chain added
1c0ac04cb48577_GRCm38_to_NCBIM36.chain added
1c0ac042278fad_GRCm38_to_NCBIM37.chain added
1c0ac049ec807e_NCBIM36_to_GRCm38.chain added
1c0ac05bc92c9b_NCBIM37_to_GRCm38.chain added
1c0ac014675890_1000G_omni2.5.b37.vcf.gz added
1c0ac01a9fb18_1000G_omni2.5.b37.vcf.gz.tbi added
1c0ac02aa0e014_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1c0ac034ac9924_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1c0ac07ab01d18_1000G_omni2.5.hg38.vcf.gz added
1c0ac011c7b46c_1000G_omni2.5.hg38.vcf.gz.tbi added
1c0ac0638a127_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1c0ac02807ccc9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1c0ac02126fbbd_af-only-gnomad.raw.sites.vcf added
1c0ac038516c5b_af-only-gnomad.raw.sites.vcf.idx added
1c0ac07828c0a7_Mutect2-exome-panel.vcf.idx added
1c0ac07785fc48_Mutect2-WGS-panel-b37.vcf added
1c0ac018558dde_Mutect2-WGS-panel-b37.vcf.idx added
1c0ac05bf5b8a0_small_exac_common_3.vcf added
1c0ac07dc77447_small_exac_common_3.vcf.idx added
1c0ac0549a729_1000g_pon.hg38.vcf.gz added
1c0ac0178ab42c_1000g_pon.hg38.vcf.gz.tbi added
1c0ac06ec95f36_af-only-gnomad.hg38.vcf.gz added
1c0ac053cbf826_af-only-gnomad.hg38.vcf.gz.tbi added
1c0ac01941a64b_small_exac_common_3.hg38.vcf.gz added
1c0ac0d784073_small_exac_common_3.hg38.vcf.gz.tbi added
1c0ac029f54002_gencode.v41.annotation.gtf added
1c0ac05ca51ca6_gencode.v42.annotation.gtf added
1c0ac07524b94a_gencode.vM30.annotation.gtf added
1c0ac075f781e2_gencode.vM31.annotation.gtf added
1c0ac058c15c80_gencode.v41.transcripts.fa added
1c0ac01dbb8178_gencode.v41.transcripts.fa.fai added
1c0ac042ac0759_gencode.v42.transcripts.fa added
1c0ac01ae8ec2d_gencode.v42.transcripts.fa.fai added
1c0ac067a801f6_gencode.vM30.pc_transcripts.fa added
1c0ac01e7533f5_gencode.vM30.pc_transcripts.fa.fai added
1c0ac02f5044bd_gencode.vM31.pc_transcripts.fa added
1c0ac06951fd0f_gencode.vM31.pc_transcripts.fa.fai added
1c0ac049161409_GRCh38.primary_assembly.genome.fa.1.ht2 added
1c0ac063fcdde1_GRCh38.primary_assembly.genome.fa.2.ht2 added
1c0ac064021a27_GRCh38.primary_assembly.genome.fa.3.ht2 added
1c0ac05addc875_GRCh38.primary_assembly.genome.fa.4.ht2 added
1c0ac06a357f08_GRCh38.primary_assembly.genome.fa.5.ht2 added
1c0ac0c09e6f0_GRCh38.primary_assembly.genome.fa.6.ht2 added
1c0ac07c04c433_GRCh38.primary_assembly.genome.fa.7.ht2 added
1c0ac02286eb64_GRCh38.primary_assembly.genome.fa.8.ht2 added
1c0ac0432a797_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1c0ac0738ac07b_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1c0ac03adc7942_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1c0ac060286038_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1c0ac0715234c2_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1c0ac04026206b_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1c0ac077b31464_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1c0ac0601b93f8_GRCh38.primary_assembly.genome.fa.fai added
1c0ac013f21891_GRCh38.primary_assembly.genome.fa.amb added
1c0ac010f4baaf_GRCh38.primary_assembly.genome.fa.ann added
1c0ac06d93d46b_GRCh38.primary_assembly.genome.fa.bwt added
1c0ac03de75894_GRCh38.primary_assembly.genome.fa.pac added
1c0ac06d99d755_GRCh38.primary_assembly.genome.fa.sa added
1c0ac062b88db5_GRCh38.primary_assembly.genome.fa added
1c0ac033deda76_hs37d5.fa.fai added
1c0ac0465b33d5_hs37d5.fa.amb added
1c0ac0740f2d_hs37d5.fa.ann added
1c0ac0768ae1cf_hs37d5.fa.bwt added
1c0ac061442003_hs37d5.fa.pac added
1c0ac0681c1124_hs37d5.fa.sa added
1c0ac0150015c4_hs37d5.fa added
1c0ac0109464c0_complete_ref_lens.bin added
1c0ac0516e0e33_ctable.bin added
1c0ac05e1629cd_ctg_offsets.bin added
1c0ac0749142a2_duplicate_clusters.tsv added
1c0ac03570285a_info.json added
1c0ac038f3f243_mphf.bin added
1c0ac05ec6c1aa_pos.bin added
1c0ac0417a0f4a_pre_indexing.log added
1c0ac034f8b676_rank.bin added
1c0ac014dad0e_ref_indexing.log added
1c0ac045acb6e1_refAccumLengths.bin added
1c0ac0288376f1_reflengths.bin added
1c0ac03c2a2650_refseq.bin added
1c0ac025d51719_seq.bin added
1c0ac019d5abb3_versionInfo.json added
1c0ac07c5046bc_salmon_index added
1c0ac01d882b7e_chrLength.txt added
1c0ac079f13fab_chrName.txt added
1c0ac010425f4d_chrNameLength.txt added
1c0ac02e7ce62d_chrStart.txt added
1c0ac067851416_exonGeTrInfo.tab added
1c0ac04e29b7e1_exonInfo.tab added
1c0ac01c16bd83_geneInfo.tab added
1c0ac04a3da1cb_Genome added
1c0ac02089257_genomeParameters.txt added
1c0ac06271f158_Log.out added
1c0ac04ab1b0f9_SA added
1c0ac078937427_SAindex added
1c0ac043b6115b_sjdbInfo.txt added
1c0ac032cdc21d_sjdbList.fromGTF.out.tab added
1c0ac0d9389eb_sjdbList.out.tab added
1c0ac0544a761c_transcriptInfo.tab added
1c0ac043bd050_GRCh38.GENCODE.v42_100 added
1c0ac06ba9b3b9_knownGene_hg38.sql added
1c0ac048dbb8be_knownGene_hg38.txt added
1c0ac039abf8aa_refGene_hg38.sql added
1c0ac0249da5fc_refGene_hg38.txt added
1c0ac027a27a68_knownGene_mm39.sql added
1c0ac07b2607f4_knownGene_mm39.txt added
1c0ac059965c72_refGene_mm39.sql added
1c0ac028f02777_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/Rtmp5vP9er/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
19.818 1.495 21.833
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.872 | 0.287 | 6.161 | |
| dataSearch | 1.118 | 0.028 | 1.146 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.604 | 0.140 | 3.403 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.123 | 0.000 | 0.123 | |
| recipeLoad | 1.202 | 0.128 | 1.331 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.552 | 0.008 | 0.561 | |
| recipeUpdate | 0 | 0 | 0 | |