Qian Liu
| Snapshot Date: 2025-03-17 13:00 -0400 (Mon, 17 Mar 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 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-20 12:12 -0400 (Thu, 20 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4756 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4514 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4441 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4406 |
| 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: 2025-03-18 10:58:40 -0000 (Tue, 18 Mar 2025) |
| EndedAt: 2025-03-18 11:01:15 -0000 (Tue, 18 Mar 2025) |
| EllapsedTime: 155.1 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 4.4.3 (2025-02-28)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* 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 8.305 0.706 9.051
getCloudData 3.352 0.115 6.757
* 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-4.4.3/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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 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...
3a00fb242afec9_GRCh38.primary_assembly.genome.fa.1.bt2 added
3a00fb1ba3b1f1_GRCh38.primary_assembly.genome.fa.2.bt2 added
3a00fb158ed7e_GRCh38.primary_assembly.genome.fa.3.bt2 added
3a00fbcaea14c_GRCh38.primary_assembly.genome.fa.4.bt2 added
3a00fb4021331_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3a00fb597038aa_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3a00fb786e29f1_outfile.txt added
3a00fb39d8bbe8_GRCh37_to_GRCh38.chain added
3a00fb35493ad9_GRCh37_to_NCBI34.chain added
3a00fb158e052_GRCh37_to_NCBI35.chain added
3a00fb1ac11072_GRCh37_to_NCBI36.chain added
3a00fb3f563ac9_GRCh38_to_GRCh37.chain added
3a00fb4124923f_GRCh38_to_NCBI34.chain added
3a00fb41d83961_GRCh38_to_NCBI35.chain added
3a00fb258cf8ae_GRCh38_to_NCBI36.chain added
3a00fb8ef1e1a_NCBI34_to_GRCh37.chain added
3a00fb2935362d_NCBI34_to_GRCh38.chain added
3a00fb31c203ab_NCBI35_to_GRCh37.chain added
3a00fb14ac13f8_NCBI35_to_GRCh38.chain added
3a00fb40c35814_NCBI36_to_GRCh37.chain added
3a00fb24811df7_NCBI36_to_GRCh38.chain added
3a00fb65ece83a_GRCm38_to_NCBIM36.chain added
3a00fb4a6540e9_GRCm38_to_NCBIM37.chain added
3a00fb7dc93047_NCBIM36_to_GRCm38.chain added
3a00fb53dcb391_NCBIM37_to_GRCm38.chain added
3a00fb5531aebe_1000G_omni2.5.b37.vcf.gz added
3a00fbdc2d47f_1000G_omni2.5.b37.vcf.gz.tbi added
3a00fb1dc68ca2_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3a00fb5f4bf390_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3a00fb162166cd_1000G_omni2.5.hg38.vcf.gz added
3a00fb3d73ada_1000G_omni2.5.hg38.vcf.gz.tbi added
3a00fb376f25a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3a00fb31c518be_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3a00fb5302859_af-only-gnomad.raw.sites.vcf added
3a00fb102593a6_af-only-gnomad.raw.sites.vcf.idx added
3a00fb35c72bef_Mutect2-exome-panel.vcf.idx added
3a00fb5ea06103_Mutect2-WGS-panel-b37.vcf added
3a00fb893bd97_Mutect2-WGS-panel-b37.vcf.idx added
3a00fb6f9fe7d7_small_exac_common_3.vcf added
3a00fb13e99bdc_small_exac_common_3.vcf.idx added
3a00fb9ec9de9_1000g_pon.hg38.vcf.gz added
3a00fba60f84a_1000g_pon.hg38.vcf.gz.tbi added
3a00fb533fd6a6_af-only-gnomad.hg38.vcf.gz added
3a00fb4b113028_af-only-gnomad.hg38.vcf.gz.tbi added
3a00fb4c3931ab_small_exac_common_3.hg38.vcf.gz added
3a00fb78cccf54_small_exac_common_3.hg38.vcf.gz.tbi added
3a00fb54004e42_gencode.v41.annotation.gtf added
3a00fb756e67d8_gencode.v42.annotation.gtf added
3a00fb2a8ed2ff_gencode.vM30.annotation.gtf added
3a00fb68ac623a_gencode.vM31.annotation.gtf added
3a00fb3631bfed_gencode.v41.transcripts.fa added
3a00fb4f0ff0f7_gencode.v41.transcripts.fa.fai added
3a00fb4e994a75_gencode.v42.transcripts.fa added
3a00fb9700d6_gencode.v42.transcripts.fa.fai added
3a00fb4cd9213e_gencode.vM30.pc_transcripts.fa added
3a00fb2275fe06_gencode.vM30.pc_transcripts.fa.fai added
3a00fb55c8af94_gencode.vM31.pc_transcripts.fa added
3a00fb5a9bf5be_gencode.vM31.pc_transcripts.fa.fai added
3a00fb403c8aa9_GRCh38.primary_assembly.genome.fa.1.ht2 added
3a00fb3514a325_GRCh38.primary_assembly.genome.fa.2.ht2 added
3a00fb70bd5c8b_GRCh38.primary_assembly.genome.fa.3.ht2 added
3a00fb4413c583_GRCh38.primary_assembly.genome.fa.4.ht2 added
3a00fb388b957f_GRCh38.primary_assembly.genome.fa.5.ht2 added
3a00fb2282754a_GRCh38.primary_assembly.genome.fa.6.ht2 added
3a00fb4943eddc_GRCh38.primary_assembly.genome.fa.7.ht2 added
3a00fb48b12925_GRCh38.primary_assembly.genome.fa.8.ht2 added
3a00fb5849a139_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3a00fb27e44edf_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3a00fb5144e6bc_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3a00fb47e98911_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3a00fb3bcdeabc_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3a00fb5b3184a5_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3a00fb524a815b_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3a00fbf0dc162_GRCh38.primary_assembly.genome.fa.fai added
3a00fb2642b4ce_GRCh38.primary_assembly.genome.fa.amb added
3a00fb1e83b306_GRCh38.primary_assembly.genome.fa.ann added
3a00fb7da90b6_GRCh38.primary_assembly.genome.fa.bwt added
3a00fb7a430310_GRCh38.primary_assembly.genome.fa.pac added
3a00fb13f21adf_GRCh38.primary_assembly.genome.fa.sa added
3a00fb326963b5_GRCh38.primary_assembly.genome.fa added
3a00fb62ef654b_hs37d5.fa.fai added
3a00fb4a23dacc_hs37d5.fa.amb added
3a00fb17954ac_hs37d5.fa.ann added
3a00fb3188afc0_hs37d5.fa.bwt added
3a00fb4abadba2_hs37d5.fa.pac added
3a00fb4e5275eb_hs37d5.fa.sa added
3a00fb53feadc6_hs37d5.fa added
3a00fb20838b37_complete_ref_lens.bin added
3a00fb28ee6ba9_ctable.bin added
3a00fb143b386f_ctg_offsets.bin added
3a00fb55982e5c_duplicate_clusters.tsv added
3a00fb19abc834_info.json added
3a00fb584efdf3_mphf.bin added
3a00fbe23c3db_pos.bin added
3a00fb3c2e3d7e_pre_indexing.log added
3a00fb2192ebcf_rank.bin added
3a00fb56d4ed00_ref_indexing.log added
3a00fb1477deb8_refAccumLengths.bin added
3a00fb49773aaf_reflengths.bin added
3a00fb2819d3bc_refseq.bin added
3a00fb5c6167c9_seq.bin added
3a00fb545256b_versionInfo.json added
3a00fb34b5861_salmon_index added
3a00fb2eabe924_chrLength.txt added
3a00fb1452e6cd_chrName.txt added
3a00fb298e0d2f_chrNameLength.txt added
3a00fb4d2f9c2a_chrStart.txt added
3a00fb1c2d7783_exonGeTrInfo.tab added
3a00fb23d11040_exonInfo.tab added
3a00fb6121b709_geneInfo.tab added
3a00fb4e96db38_Genome added
3a00fb6c0758b_genomeParameters.txt added
3a00fb2b4591d5_Log.out added
3a00fb50102fe5_SA added
3a00fb3849254b_SAindex added
3a00fb76006d78_sjdbInfo.txt added
3a00fb1e62a5d0_sjdbList.fromGTF.out.tab added
3a00fbc47d311_sjdbList.out.tab added
3a00fb1683f8af_transcriptInfo.tab added
3a00fb47511179_GRCh38.GENCODE.v42_100 added
3a00fb20830b81_knownGene_hg38.sql added
3a00fb6c1c270b_knownGene_hg38.txt added
3a00fb60fcd9ad_refGene_hg38.sql added
3a00fb78d20974_refGene_hg38.txt added
3a00fb7a3feae6_knownGene_mm39.sql added
3a00fb1d2b172c_knownGene_mm39.txt added
3a00fb1a64f543_refGene_mm39.sql added
3a00fb5114d7e6_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/RtmpsTjbMv/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
26.721 1.925 30.212
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 8.305 | 0.706 | 9.051 | |
| dataSearch | 1.670 | 0.056 | 1.730 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 3.352 | 0.115 | 6.757 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.168 | 0.008 | 0.179 | |
| recipeLoad | 1.859 | 0.056 | 1.924 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.782 | 0.020 | 0.805 | |
| recipeUpdate | 0 | 0 | 0 | |