Qian Liu
| Snapshot Date: 2025-02-03 13:00 -0500 (Mon, 03 Feb 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 2025-02-06 12:10 -0500 (Thu, 06 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" | 4753 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4501 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4524 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4476 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4407 |
| 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. |
| Package: ReUseData |
| Version: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2025-02-05 07:19:15 -0500 (Wed, 05 Feb 2025) |
| EndedAt: 2025-02-05 07:21:42 -0500 (Wed, 05 Feb 2025) |
| EllapsedTime: 147.0 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* 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 ‘1.6.0’
* 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 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 6.847 0.812 7.751
getCloudData 2.781 0.155 5.057
* 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-3.20-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/4.4-arm64/Resources/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-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...
f73253e4ee7f_GRCh38.primary_assembly.genome.fa.1.bt2 added
f7325ae5fee0_GRCh38.primary_assembly.genome.fa.2.bt2 added
f73231c052bf_GRCh38.primary_assembly.genome.fa.3.bt2 added
f7324978931d_GRCh38.primary_assembly.genome.fa.4.bt2 added
f732b027a9a_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
f7324fbf1a1b_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
f732b4b0b84_outfile.txt added
f7326be10ce6_GRCh37_to_GRCh38.chain added
f732416075f_GRCh37_to_NCBI34.chain added
f732423df011_GRCh37_to_NCBI35.chain added
f732705c0e10_GRCh37_to_NCBI36.chain added
f7322b9f7611_GRCh38_to_GRCh37.chain added
f73272006c76_GRCh38_to_NCBI34.chain added
f73279d0f172_GRCh38_to_NCBI35.chain added
f73249bb1d9_GRCh38_to_NCBI36.chain added
f7329b91fec_NCBI34_to_GRCh37.chain added
f73258dec3f0_NCBI34_to_GRCh38.chain added
f732911ef25_NCBI35_to_GRCh37.chain added
f732786b6ac9_NCBI35_to_GRCh38.chain added
f732542fefe2_NCBI36_to_GRCh37.chain added
f732172e099c_NCBI36_to_GRCh38.chain added
f7324f78eca7_GRCm38_to_NCBIM36.chain added
f732bf8f0b4_GRCm38_to_NCBIM37.chain added
f732482bf90_NCBIM36_to_GRCm38.chain added
f73223ee8940_NCBIM37_to_GRCm38.chain added
f732174db2e_1000G_omni2.5.b37.vcf.gz added
f7321ee1a9c1_1000G_omni2.5.b37.vcf.gz.tbi added
f732714fcdbd_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
f7322e4c6d69_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
f7321ba3203e_1000G_omni2.5.hg38.vcf.gz added
f7327299d49e_1000G_omni2.5.hg38.vcf.gz.tbi added
f73251560bd9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
f7326823fd46_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
f73212c93414_af-only-gnomad.raw.sites.vcf added
f732577a16ae_af-only-gnomad.raw.sites.vcf.idx added
f73210672660_Mutect2-exome-panel.vcf.idx added
f73264087109_Mutect2-WGS-panel-b37.vcf added
f7326635392d_Mutect2-WGS-panel-b37.vcf.idx added
f732303cedc7_small_exac_common_3.vcf added
f732701ebc8e_small_exac_common_3.vcf.idx added
f73271ed4823_1000g_pon.hg38.vcf.gz added
f732111b2c44_1000g_pon.hg38.vcf.gz.tbi added
f732ef72d22_af-only-gnomad.hg38.vcf.gz added
f7325b41adb_af-only-gnomad.hg38.vcf.gz.tbi added
f732734f22c9_small_exac_common_3.hg38.vcf.gz added
f7325074f543_small_exac_common_3.hg38.vcf.gz.tbi added
f7322e922af9_gencode.v41.annotation.gtf added
f7327e435951_gencode.v42.annotation.gtf added
f732779d1599_gencode.vM30.annotation.gtf added
f73269f52d28_gencode.vM31.annotation.gtf added
f7325f67d370_gencode.v41.transcripts.fa added
f732196a8eff_gencode.v41.transcripts.fa.fai added
f73222d21462_gencode.v42.transcripts.fa added
f732e383fca_gencode.v42.transcripts.fa.fai added
f732ee3ee11_gencode.vM30.pc_transcripts.fa added
f7321622a5ba_gencode.vM30.pc_transcripts.fa.fai added
f7323cae61b0_gencode.vM31.pc_transcripts.fa added
f7325c8f88ef_gencode.vM31.pc_transcripts.fa.fai added
f73253673262_GRCh38.primary_assembly.genome.fa.1.ht2 added
f7321c1ceab5_GRCh38.primary_assembly.genome.fa.2.ht2 added
f7322e751f7e_GRCh38.primary_assembly.genome.fa.3.ht2 added
f732b66a106_GRCh38.primary_assembly.genome.fa.4.ht2 added
f7327ed596c2_GRCh38.primary_assembly.genome.fa.5.ht2 added
f732789cdb9b_GRCh38.primary_assembly.genome.fa.6.ht2 added
f732215dafa_GRCh38.primary_assembly.genome.fa.7.ht2 added
f73268db5427_GRCh38.primary_assembly.genome.fa.8.ht2 added
f73217720239_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
f7323deff835_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
f73255907f57_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
f73219854a4_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
f73237dcdbcd_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
f7324e28c62_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
f732356e786f_GRCh38_full_analysis_set_plus_decoy_hla.fa added
f73267a4dad0_GRCh38.primary_assembly.genome.fa.fai added
f7327819c2d8_GRCh38.primary_assembly.genome.fa.amb added
f73263473081_GRCh38.primary_assembly.genome.fa.ann added
f73256c19812_GRCh38.primary_assembly.genome.fa.bwt added
f7323fe6f23d_GRCh38.primary_assembly.genome.fa.pac added
f7325329a391_GRCh38.primary_assembly.genome.fa.sa added
f73252b1af3e_GRCh38.primary_assembly.genome.fa added
f732f6839dc_hs37d5.fa.fai added
f7323aea26b_hs37d5.fa.amb added
f7323e2920b0_hs37d5.fa.ann added
f7327e2122b1_hs37d5.fa.bwt added
f732316cd328_hs37d5.fa.pac added
f7325f9b0071_hs37d5.fa.sa added
f732393a2bc0_hs37d5.fa added
f7321a0e679a_complete_ref_lens.bin added
f73227b3bcd3_ctable.bin added
f732931d502_ctg_offsets.bin added
f73226977b05_duplicate_clusters.tsv added
f732230d990e_info.json added
f73251bb781c_mphf.bin added
f7326acaa02f_pos.bin added
f7321cdaa46f_pre_indexing.log added
f73256618235_rank.bin added
f7321bab91e1_ref_indexing.log added
f7321cf658f8_refAccumLengths.bin added
f732714b10a2_reflengths.bin added
f732773135c9_refseq.bin added
f7323fc25c41_seq.bin added
f7327136d01a_versionInfo.json added
f73245989507_salmon_index added
f73224602243_chrLength.txt added
f73223696f5d_chrName.txt added
f7325f0e54d4_chrNameLength.txt added
f73225e35b0d_chrStart.txt added
f732716ec5e9_exonGeTrInfo.tab added
f7321f837e2d_exonInfo.tab added
f73271d0cc84_geneInfo.tab added
f7324323287c_Genome added
f73239370753_genomeParameters.txt added
f7324bc1f77d_Log.out added
f7322b5f5666_SA added
f7322158c9_SAindex added
f732d4bf430_sjdbInfo.txt added
f732758c8221_sjdbList.fromGTF.out.tab added
f7325bb380d1_sjdbList.out.tab added
f73265ce485f_transcriptInfo.tab added
f73249f18930_GRCh38.GENCODE.v42_100 added
f7321065d43d_knownGene_hg38.sql added
f732d50f934_knownGene_hg38.txt added
f7323f18cbc0_refGene_hg38.sql added
f73274e8ca9c_refGene_hg38.txt added
f7325f4e03ba_knownGene_mm39.sql added
f7327ad6d937_knownGene_mm39.txt added
f7322f4ee8e2_refGene_mm39.sql added
f732659b65b1_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/RtmpXTF3YQ/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
23.221 2.951 28.045
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.847 | 0.812 | 7.751 | |
| dataSearch | 1.184 | 0.052 | 1.242 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.781 | 0.155 | 5.057 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0.001 | 0.001 | 0.001 | |
| recipeHub-class | 0.157 | 0.015 | 0.173 | |
| recipeLoad | 1.381 | 0.095 | 1.499 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.601 | 0.036 | 0.637 | |
| recipeUpdate | 0 | 0 | 0 | |