Qian Liu
| Snapshot Date: 2025-01-23 13:40 -0500 (Thu, 23 Jan 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 2025-01-24 11:43 -0500 (Fri, 24 Jan 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" | 4609 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4393 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 3839 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 3835 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4408 |
| 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 1722/2286 | 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 | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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. |
| 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: 2025-01-23 19:02:15 -0500 (Thu, 23 Jan 2025) |
| EndedAt: 2025-01-23 19:03:02 -0500 (Thu, 23 Jan 2025) |
| EllapsedTime: 47.6 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...
124ae6854fac9_GRCh38.primary_assembly.genome.fa.1.bt2 added
124ae231cd7a2_GRCh38.primary_assembly.genome.fa.2.bt2 added
124ae3a90deb0_GRCh38.primary_assembly.genome.fa.3.bt2 added
124ae7d0c12d9_GRCh38.primary_assembly.genome.fa.4.bt2 added
124ae23a9a4b2_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
124ae567bb468_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
124ae53814433_outfile.txt added
124ae4ba49b19_GRCh37_to_GRCh38.chain added
124ae23c2ad1b_GRCh37_to_NCBI34.chain added
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124ae2d7cb668_NCBI34_to_GRCh37.chain added
124ae56ab7d2c_NCBI34_to_GRCh38.chain added
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124ae5ffb4caf_NCBI35_to_GRCh38.chain added
124ae6b67a663_NCBI36_to_GRCh37.chain added
124ae61dce4ab_NCBI36_to_GRCh38.chain added
124ae6d28c8be_GRCm38_to_NCBIM36.chain added
124ae109369ef_GRCm38_to_NCBIM37.chain added
124ae3e0fd269_NCBIM36_to_GRCm38.chain added
124aebf0b54_NCBIM37_to_GRCm38.chain added
124ae7e80b82d_1000G_omni2.5.b37.vcf.gz added
124ae34bbd33d_1000G_omni2.5.b37.vcf.gz.tbi added
124ae172964d7_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
124ae1e9b6b22_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
124ae6d9694e0_1000G_omni2.5.hg38.vcf.gz added
124ae39083655_1000G_omni2.5.hg38.vcf.gz.tbi added
124ae4a2723b3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
124ae4f98e2cd_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
124ae3e52298e_af-only-gnomad.raw.sites.vcf added
124ae4264999_af-only-gnomad.raw.sites.vcf.idx added
124ae6da9ddef_Mutect2-exome-panel.vcf.idx added
124ae2b29ae28_Mutect2-WGS-panel-b37.vcf added
124ae3d68da3b_Mutect2-WGS-panel-b37.vcf.idx added
124ae2ecf76fc_small_exac_common_3.vcf added
124ae368cb266_small_exac_common_3.vcf.idx added
124ae4f146284_1000g_pon.hg38.vcf.gz added
124ae434ff0ab_1000g_pon.hg38.vcf.gz.tbi added
124ae35418d13_af-only-gnomad.hg38.vcf.gz added
124ae6294f5b5_af-only-gnomad.hg38.vcf.gz.tbi added
124ae218f70a3_small_exac_common_3.hg38.vcf.gz added
124ae502bee8b_small_exac_common_3.hg38.vcf.gz.tbi added
124ae743a10cb_gencode.v41.annotation.gtf added
124ae1024bb0a_gencode.v42.annotation.gtf added
124ae5b7395cd_gencode.vM30.annotation.gtf added
124ae16ff4a3_gencode.vM31.annotation.gtf added
124ae5d25fa11_gencode.v41.transcripts.fa added
124ae6844a1dd_gencode.v41.transcripts.fa.fai added
124ae71dee9a5_gencode.v42.transcripts.fa added
124ae61bd8a0a_gencode.v42.transcripts.fa.fai added
124ae62b1c8a7_gencode.vM30.pc_transcripts.fa added
124ae5ec7e90_gencode.vM30.pc_transcripts.fa.fai added
124ae696922f9_gencode.vM31.pc_transcripts.fa added
124ae75773f7f_gencode.vM31.pc_transcripts.fa.fai added
124ae67e9e718_GRCh38.primary_assembly.genome.fa.1.ht2 added
124ae2d430df4_GRCh38.primary_assembly.genome.fa.2.ht2 added
124aed492563_GRCh38.primary_assembly.genome.fa.3.ht2 added
124ae3d358d65_GRCh38.primary_assembly.genome.fa.4.ht2 added
124ae6d60148_GRCh38.primary_assembly.genome.fa.5.ht2 added
124ae4bee2179_GRCh38.primary_assembly.genome.fa.6.ht2 added
124ae7ed7b5e0_GRCh38.primary_assembly.genome.fa.7.ht2 added
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124ae623639a8_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
124ae560376f7_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
124ae7d777e3e_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
124ae300158cc_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
124ae286cd1b3_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
124ae3b5381_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
124ae36e73a45_GRCh38_full_analysis_set_plus_decoy_hla.fa added
124ae6a2a42c_GRCh38.primary_assembly.genome.fa.fai added
124ae1fc8481b_GRCh38.primary_assembly.genome.fa.amb added
124ae15f5f4ea_GRCh38.primary_assembly.genome.fa.ann added
124ae46a239e9_GRCh38.primary_assembly.genome.fa.bwt added
124ae44881439_GRCh38.primary_assembly.genome.fa.pac added
124ae41e7cd55_GRCh38.primary_assembly.genome.fa.sa added
124ae5959a940_GRCh38.primary_assembly.genome.fa added
124aed76d694_hs37d5.fa.fai added
124ae75019573_hs37d5.fa.amb added
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124ae3cfc0aac_ctable.bin added
124ae4720c17b_ctg_offsets.bin added
124ae377e96b8_duplicate_clusters.tsv added
124ae57d9267e_info.json added
124ae716e4740_mphf.bin added
124ae7f07f4ed_pos.bin added
124ae636134c2_pre_indexing.log added
124ae2cedf87_rank.bin added
124ae5bb51981_ref_indexing.log added
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124ae4b2a5ca2_reflengths.bin added
124ae4a27b63b_refseq.bin added
124ae752d0185_seq.bin added
124ae5dbefedc_versionInfo.json added
124ae264e4d99_salmon_index added
124ae5ec88b74_chrLength.txt added
124ae403b9d49_chrName.txt added
124ae9d34491_chrNameLength.txt added
124aed3a90a1_chrStart.txt added
124ae7fed40cf_exonGeTrInfo.tab added
124ae313a17a6_exonInfo.tab added
124ae5ce6ac89_geneInfo.tab added
124ae2c498605_Genome added
124aeefdc8fa_genomeParameters.txt added
124ae37959cc6_Log.out added
124ae3f67a7ac_SA added
124ae2e312db9_SAindex added
124ae1eb0e460_sjdbInfo.txt added
124ae6f616a5d_sjdbList.fromGTF.out.tab added
124ae648e38cb_sjdbList.out.tab added
124ae3532cb00_transcriptInfo.tab added
124ae19ad8849_GRCh38.GENCODE.v42_100 added
124ae4fce7dca_knownGene_hg38.sql added
124ae7da481b4_knownGene_hg38.txt added
124ae3b3f90dd_refGene_hg38.sql added
124ae4a3fbb8e_refGene_hg38.txt added
124ae1e328db7_knownGene_mm39.sql added
124ae8f5f8de_knownGene_mm39.txt added
124ae4ca5bb6a_refGene_mm39.sql added
124ae14b35376_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//RtmpvGArxi/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
6.610 0.862 7.879
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.823 | 0.225 | 2.067 | |
| dataSearch | 0.293 | 0.016 | 0.309 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.819 | 0.052 | 1.370 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.036 | 0.004 | 0.041 | |
| recipeLoad | 0.383 | 0.027 | 0.412 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.167 | 0.012 | 0.180 | |
| recipeUpdate | 0 | 0 | 0 | |