Qian Liu
| Snapshot Date: 2025-01-30 13:00 -0500 (Thu, 30 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_20 |
| git_last_commit: 5d8c0ee |
| git_last_commit_date: 2024-10-29 11:17:22 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-02-03 12:12 -0500 (Mon, 03 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4494 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4400 |
| 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 1727/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.6.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: ReUseData |
| Version: 1.6.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReUseData_1.6.0.tar.gz |
| StartedAt: 2025-01-31 09:38:46 -0000 (Fri, 31 Jan 2025) |
| EndedAt: 2025-01-31 09:41:24 -0000 (Fri, 31 Jan 2025) |
| EllapsedTime: 158.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReUseData_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.6.0’
* 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 8.426 0.370 8.839
getCloudData 3.276 0.132 8.018
* 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
‘/home/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.2/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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...
33fd6722091a82_GRCh38.primary_assembly.genome.fa.1.bt2 added
33fd674589b004_GRCh38.primary_assembly.genome.fa.2.bt2 added
33fd67621f64e3_GRCh38.primary_assembly.genome.fa.3.bt2 added
33fd67445593b8_GRCh38.primary_assembly.genome.fa.4.bt2 added
33fd67209d1be8_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
33fd677f27b5e0_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
33fd67768f302_outfile.txt added
33fd67366bda1b_GRCh37_to_GRCh38.chain added
33fd6754ba5954_GRCh37_to_NCBI34.chain added
33fd6747e4fc86_GRCh37_to_NCBI35.chain added
33fd6739e827cf_GRCh37_to_NCBI36.chain added
33fd67c6ee5ed_GRCh38_to_GRCh37.chain added
33fd674c34e887_GRCh38_to_NCBI34.chain added
33fd67710e3983_GRCh38_to_NCBI35.chain added
33fd6751c66c01_GRCh38_to_NCBI36.chain added
33fd674e5759_NCBI34_to_GRCh37.chain added
33fd677dafa197_NCBI34_to_GRCh38.chain added
33fd676a17cf88_NCBI35_to_GRCh37.chain added
33fd673b66df63_NCBI35_to_GRCh38.chain added
33fd6756ae1d2_NCBI36_to_GRCh37.chain added
33fd67617443c5_NCBI36_to_GRCh38.chain added
33fd67600c1682_GRCm38_to_NCBIM36.chain added
33fd6721183d4_GRCm38_to_NCBIM37.chain added
33fd6717dfdcb4_NCBIM36_to_GRCm38.chain added
33fd6754bd0f93_NCBIM37_to_GRCm38.chain added
33fd673e252109_1000G_omni2.5.b37.vcf.gz added
33fd6723c43bb4_1000G_omni2.5.b37.vcf.gz.tbi added
33fd6719a46eac_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
33fd67798d9244_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
33fd6740c50f66_1000G_omni2.5.hg38.vcf.gz added
33fd672edb7411_1000G_omni2.5.hg38.vcf.gz.tbi added
33fd671b96acc6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
33fd6764ebf6a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
33fd6710fad8f4_af-only-gnomad.raw.sites.vcf added
33fd675fec407e_af-only-gnomad.raw.sites.vcf.idx added
33fd6726ebdb52_Mutect2-exome-panel.vcf.idx added
33fd6710228ed5_Mutect2-WGS-panel-b37.vcf added
33fd6767553380_Mutect2-WGS-panel-b37.vcf.idx added
33fd675d57b56e_small_exac_common_3.vcf added
33fd6764dce829_small_exac_common_3.vcf.idx added
33fd672f3a3006_1000g_pon.hg38.vcf.gz added
33fd67173fdd3d_1000g_pon.hg38.vcf.gz.tbi added
33fd67714bce16_af-only-gnomad.hg38.vcf.gz added
33fd677b6f188d_af-only-gnomad.hg38.vcf.gz.tbi added
33fd6784e16c0_small_exac_common_3.hg38.vcf.gz added
33fd6743123a17_small_exac_common_3.hg38.vcf.gz.tbi added
33fd677bbd6fe7_gencode.v41.annotation.gtf added
33fd675fdb857_gencode.v42.annotation.gtf added
33fd672d2a099f_gencode.vM30.annotation.gtf added
33fd6737244f4a_gencode.vM31.annotation.gtf added
33fd67b689a2a_gencode.v41.transcripts.fa added
33fd67e9e4d64_gencode.v41.transcripts.fa.fai added
33fd67173065cc_gencode.v42.transcripts.fa added
33fd67d7a1dfe_gencode.v42.transcripts.fa.fai added
33fd67267e2a18_gencode.vM30.pc_transcripts.fa added
33fd676bed755f_gencode.vM30.pc_transcripts.fa.fai added
33fd674b9f3f07_gencode.vM31.pc_transcripts.fa added
33fd674a4265cc_gencode.vM31.pc_transcripts.fa.fai added
33fd67591e40b_GRCh38.primary_assembly.genome.fa.1.ht2 added
33fd67452cd14b_GRCh38.primary_assembly.genome.fa.2.ht2 added
33fd67b077532_GRCh38.primary_assembly.genome.fa.3.ht2 added
33fd67346d581c_GRCh38.primary_assembly.genome.fa.4.ht2 added
33fd6760c37e11_GRCh38.primary_assembly.genome.fa.5.ht2 added
33fd671156349d_GRCh38.primary_assembly.genome.fa.6.ht2 added
33fd6745683110_GRCh38.primary_assembly.genome.fa.7.ht2 added
33fd6740afbe8f_GRCh38.primary_assembly.genome.fa.8.ht2 added
33fd6738420fef_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
33fd67558abfe5_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
33fd672804f210_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
33fd671599c55d_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
33fd673a67a80e_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
33fd67573f2216_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
33fd672cd9a29b_GRCh38_full_analysis_set_plus_decoy_hla.fa added
33fd672bb37624_GRCh38.primary_assembly.genome.fa.fai added
33fd6752ae3aa4_GRCh38.primary_assembly.genome.fa.amb added
33fd673527b95b_GRCh38.primary_assembly.genome.fa.ann added
33fd676ec5b03b_GRCh38.primary_assembly.genome.fa.bwt added
33fd674e6baa8b_GRCh38.primary_assembly.genome.fa.pac added
33fd673b2571b3_GRCh38.primary_assembly.genome.fa.sa added
33fd671befb9da_GRCh38.primary_assembly.genome.fa added
33fd6758ff9d5_hs37d5.fa.fai added
33fd67468e0bdd_hs37d5.fa.amb added
33fd672a8e073e_hs37d5.fa.ann added
33fd671cc05fa1_hs37d5.fa.bwt added
33fd67540829db_hs37d5.fa.pac added
33fd67510c3157_hs37d5.fa.sa added
33fd678add500_hs37d5.fa added
33fd671fa768e2_complete_ref_lens.bin added
33fd671b4e9723_ctable.bin added
33fd67e3fb90b_ctg_offsets.bin added
33fd6764d43a2e_duplicate_clusters.tsv added
33fd6726560c56_info.json added
33fd6742ad1127_mphf.bin added
33fd674597b83f_pos.bin added
33fd6737ac40f3_pre_indexing.log added
33fd678154237_rank.bin added
33fd6764776cf_ref_indexing.log added
33fd676fee50e2_refAccumLengths.bin added
33fd675da0021d_reflengths.bin added
33fd672e4c68df_refseq.bin added
33fd675881640_seq.bin added
33fd671807aa2b_versionInfo.json added
33fd6758b8af5_salmon_index added
33fd673261b8db_chrLength.txt added
33fd6743bb2050_chrName.txt added
33fd675839c599_chrNameLength.txt added
33fd6767897236_chrStart.txt added
33fd673280d08b_exonGeTrInfo.tab added
33fd6726a57024_exonInfo.tab added
33fd6722aee3e9_geneInfo.tab added
33fd674e708a66_Genome added
33fd672c3569f9_genomeParameters.txt added
33fd67693cefc6_Log.out added
33fd6778fe91a4_SA added
33fd6748f5c99a_SAindex added
33fd673d4519a1_sjdbInfo.txt added
33fd674a0ac2fb_sjdbList.fromGTF.out.tab added
33fd6751a39e9a_sjdbList.out.tab added
33fd675cec8284_transcriptInfo.tab added
33fd6765595a1f_GRCh38.GENCODE.v42_100 added
33fd675fe357a5_knownGene_hg38.sql added
33fd6741c0bcb2_knownGene_hg38.txt added
33fd67baf6675_refGene_hg38.sql added
33fd67229068cc_refGene_hg38.txt added
33fd6775874f1_knownGene_mm39.sql added
33fd67435ba768_knownGene_mm39.txt added
33fd672aa5ab04_refGene_mm39.sql added
33fd67d9febc0_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:
/home/biocbuild/tmp/RtmpPBCVFW/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
26.453 1.816 32.050
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 8.426 | 0.370 | 8.839 | |
| dataSearch | 1.660 | 0.032 | 1.696 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 3.276 | 0.132 | 8.018 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.179 | 0.008 | 0.189 | |
| recipeLoad | 1.925 | 0.048 | 1.983 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.784 | 0.032 | 0.819 | |
| recipeUpdate | 0 | 0 | 0 | |