Qian Liu
| Snapshot Date: 2025-02-05 13:48 -0500 (Wed, 05 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: 85fc756 |
| git_last_commit_date: 2024-10-29 11:17:22 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-06 11:44 -0500 (Thu, 06 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4719 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4480 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4491 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4444 |
| 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 1728/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.7.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 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: 1.7.0 |
| 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_1.7.0.tar.gz |
| StartedAt: 2025-02-05 21:01:59 -0500 (Wed, 05 Feb 2025) |
| EndedAt: 2025-02-05 21:02:48 -0500 (Wed, 05 Feb 2025) |
| EllapsedTime: 48.6 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.7.0’
* 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
* 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-3.21-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/4.5-arm64/Resources/library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.7.0’ ** 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 Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 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...
1fef386e7d58_GRCh38.primary_assembly.genome.fa.1.bt2 added
1fef5de73959_GRCh38.primary_assembly.genome.fa.2.bt2 added
1fef77663238_GRCh38.primary_assembly.genome.fa.3.bt2 added
1fef566b37c5_GRCh38.primary_assembly.genome.fa.4.bt2 added
1fef191a92d6_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1fef1f9e2c7a_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1fef497a0dcd_outfile.txt added
1fef6c20336a_GRCh37_to_GRCh38.chain added
1fef360fab9b_GRCh37_to_NCBI34.chain added
1fef3ecb68d7_GRCh37_to_NCBI35.chain added
1fef1c501b76_GRCh37_to_NCBI36.chain added
1fef4f3aee7f_GRCh38_to_GRCh37.chain added
1fef25fffc7c_GRCh38_to_NCBI34.chain added
1fef49194461_GRCh38_to_NCBI35.chain added
1fef19d861c5_GRCh38_to_NCBI36.chain added
1fef4cfad9c4_NCBI34_to_GRCh37.chain added
1fef68eefa57_NCBI34_to_GRCh38.chain added
1fef21759b93_NCBI35_to_GRCh37.chain added
1fef3038e10e_NCBI35_to_GRCh38.chain added
1fef663f76dd_NCBI36_to_GRCh37.chain added
1fef5094db9c_NCBI36_to_GRCh38.chain added
1fef5cde0818_GRCm38_to_NCBIM36.chain added
1fef74e58f49_GRCm38_to_NCBIM37.chain added
1fefb223d94_NCBIM36_to_GRCm38.chain added
1fef74f8c541_NCBIM37_to_GRCm38.chain added
1fef785e6a65_1000G_omni2.5.b37.vcf.gz added
1fef7e9b4a9f_1000G_omni2.5.b37.vcf.gz.tbi added
1fef5404da9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1fef40aa94f0_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1fef7f1839ba_1000G_omni2.5.hg38.vcf.gz added
1feff762386_1000G_omni2.5.hg38.vcf.gz.tbi added
1fef15163a58_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1fef66507238_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1fef2b7aef02_af-only-gnomad.raw.sites.vcf added
1fef13e1829b_af-only-gnomad.raw.sites.vcf.idx added
1fef3a45984f_Mutect2-exome-panel.vcf.idx added
1fef2f12886c_Mutect2-WGS-panel-b37.vcf added
1fef69ba8298_Mutect2-WGS-panel-b37.vcf.idx added
1fef53d3ff62_small_exac_common_3.vcf added
1fef323a5ed_small_exac_common_3.vcf.idx added
1fef19626c37_1000g_pon.hg38.vcf.gz added
1fefcae9be6_1000g_pon.hg38.vcf.gz.tbi added
1fef1b7d1f8b_af-only-gnomad.hg38.vcf.gz added
1fef33a1ecc6_af-only-gnomad.hg38.vcf.gz.tbi added
1fef4bbfd5a5_small_exac_common_3.hg38.vcf.gz added
1fef1f636a7d_small_exac_common_3.hg38.vcf.gz.tbi added
1fef37e444a4_gencode.v41.annotation.gtf added
1fef6b5687a6_gencode.v42.annotation.gtf added
1fef7de3da57_gencode.vM30.annotation.gtf added
1fef7a13c652_gencode.vM31.annotation.gtf added
1fef2841701b_gencode.v41.transcripts.fa added
1fef60271142_gencode.v41.transcripts.fa.fai added
1fef24de355f_gencode.v42.transcripts.fa added
1fef788202e1_gencode.v42.transcripts.fa.fai added
1fef1f8b3f96_gencode.vM30.pc_transcripts.fa added
1fef6efba107_gencode.vM30.pc_transcripts.fa.fai added
1fef4a090b7d_gencode.vM31.pc_transcripts.fa added
1fef17d16184_gencode.vM31.pc_transcripts.fa.fai added
1fef33592d53_GRCh38.primary_assembly.genome.fa.1.ht2 added
1fef23aebe7b_GRCh38.primary_assembly.genome.fa.2.ht2 added
1fef255b8f8a_GRCh38.primary_assembly.genome.fa.3.ht2 added
1fef1e2cc02f_GRCh38.primary_assembly.genome.fa.4.ht2 added
1fefbfd5d23_GRCh38.primary_assembly.genome.fa.5.ht2 added
1fef26edaafb_GRCh38.primary_assembly.genome.fa.6.ht2 added
1fef3d7458b4_GRCh38.primary_assembly.genome.fa.7.ht2 added
1fef216bb0f1_GRCh38.primary_assembly.genome.fa.8.ht2 added
1fef252daf5b_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1fef5a53926e_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1fef24b2a216_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1fef4baf652c_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1fef681b5285_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1fef59c6cf28_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1fefb4a7924_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1fef46573046_GRCh38.primary_assembly.genome.fa.fai added
1fef62267be_GRCh38.primary_assembly.genome.fa.amb added
1fef3cc8ee17_GRCh38.primary_assembly.genome.fa.ann added
1fef2b87472e_GRCh38.primary_assembly.genome.fa.bwt added
1fef3e523355_GRCh38.primary_assembly.genome.fa.pac added
1fef6a8316a_GRCh38.primary_assembly.genome.fa.sa added
1fefc442990_GRCh38.primary_assembly.genome.fa added
1fef4f04b33a_hs37d5.fa.fai added
1fef3d92cd5d_hs37d5.fa.amb added
1fef70e8b43f_hs37d5.fa.ann added
1fef3d91ce02_hs37d5.fa.bwt added
1fef2f6c04e2_hs37d5.fa.pac added
1fef5cb4a9c0_hs37d5.fa.sa added
1fef58f4abcc_hs37d5.fa added
1fef273b0bb4_complete_ref_lens.bin added
1fef157d6a8b_ctable.bin added
1fef5cddd6b2_ctg_offsets.bin added
1fef683a6fbf_duplicate_clusters.tsv added
1fef547e9a0e_info.json added
1fef43b43878_mphf.bin added
1fef6ce77101_pos.bin added
1fef4eac3082_pre_indexing.log added
1fefaa4cf28_rank.bin added
1fef4a1c508d_ref_indexing.log added
1fef8ec7efe_refAccumLengths.bin added
1fef5e855a45_reflengths.bin added
1fef4e9987e_refseq.bin added
1fef41a7ab7_seq.bin added
1fef666e867b_versionInfo.json added
1fef623f29c6_salmon_index added
1fef20cfb88e_chrLength.txt added
1fef255d8376_chrName.txt added
1fef1e61cb24_chrNameLength.txt added
1fef265fb811_chrStart.txt added
1fef562d77c5_exonGeTrInfo.tab added
1fef431252b6_exonInfo.tab added
1fef67f44d20_geneInfo.tab added
1fef57f3a531_Genome added
1fef3ce26113_genomeParameters.txt added
1fef3253459f_Log.out added
1fef78ffe388_SA added
1fef67b333c7_SAindex added
1fef260c8301_sjdbInfo.txt added
1fef7f6cca2a_sjdbList.fromGTF.out.tab added
1fef3f4cccc1_sjdbList.out.tab added
1fef4b16b35e_transcriptInfo.tab added
1fef3f5a06d5_GRCh38.GENCODE.v42_100 added
1fef2f76aa71_knownGene_hg38.sql added
1fef17aff90f_knownGene_hg38.txt added
1fef220853ef_refGene_hg38.sql added
1fef50be815d_refGene_hg38.txt added
1fefb1f2a15_knownGene_mm39.sql added
1fef2b03ce67_knownGene_mm39.txt added
1fef6e3e241_refGene_mm39.sql added
1fef5b1b1cef_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:
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpVWUQZ3/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
6.829 0.904 8.284
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.901 | 0.235 | 2.161 | |
| dataSearch | 0.347 | 0.019 | 0.366 | |
| dataUpdate | 0.000 | 0.001 | 0.000 | |
| getCloudData | 0.859 | 0.059 | 1.498 | |
| getData | 0.001 | 0.000 | 0.001 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.038 | 0.006 | 0.045 | |
| recipeLoad | 0.390 | 0.031 | 0.426 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.167 | 0.010 | 0.178 | |
| recipeUpdate | 0 | 0 | 0 | |