Qian Liu
| Snapshot Date: 2025-01-02 13:00 -0500 (Thu, 02 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 2025-01-09 12:08 -0500 (Thu, 09 Jan 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" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4358 |
| 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 | ERROR | skipped | ||||||||||
|
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: 2025-01-03 09:14:35 -0500 (Fri, 03 Jan 2025) |
| EndedAt: 2025-01-03 09:19:01 -0500 (Fri, 03 Jan 2025) |
| EllapsedTime: 265.9 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: x86_64-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 Monterey 12.7.6
* 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 12.338 1.255 13.855
getCloudData 4.589 0.218 5.854
* 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-x86_64/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: x86_64-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...
f40d6c0729e5_GRCh38.primary_assembly.genome.fa.1.bt2 added
f40d4a4fb0cb_GRCh38.primary_assembly.genome.fa.2.bt2 added
f40d35e0058a_GRCh38.primary_assembly.genome.fa.3.bt2 added
f40d68bc2a8_GRCh38.primary_assembly.genome.fa.4.bt2 added
f40d4198a6f3_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
f40dcf8bd2a_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
f40d1e4b170d_outfile.txt added
f40d53d66604_GRCh37_to_GRCh38.chain added
f40d20c3bb9c_GRCh37_to_NCBI34.chain added
f40d12520f92_GRCh37_to_NCBI35.chain added
f40d497c43a3_GRCh37_to_NCBI36.chain added
f40d7d3ca805_GRCh38_to_GRCh37.chain added
f40d193b207f_GRCh38_to_NCBI34.chain added
f40d78d27ec9_GRCh38_to_NCBI35.chain added
f40d4381fc17_GRCh38_to_NCBI36.chain added
f40dacd6ca1_NCBI34_to_GRCh37.chain added
f40d3496c391_NCBI34_to_GRCh38.chain added
f40d16017f90_NCBI35_to_GRCh37.chain added
f40d3c5dd239_NCBI35_to_GRCh38.chain added
f40d3394bb25_NCBI36_to_GRCh37.chain added
f40d698a9497_NCBI36_to_GRCh38.chain added
f40d9217ba3_GRCm38_to_NCBIM36.chain added
f40d753c0f03_GRCm38_to_NCBIM37.chain added
f40d39fdca16_NCBIM36_to_GRCm38.chain added
f40d44de8818_NCBIM37_to_GRCm38.chain added
f40d6db902fa_1000G_omni2.5.b37.vcf.gz added
f40dd72a35d_1000G_omni2.5.b37.vcf.gz.tbi added
f40d61433590_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
f40d371b2d3_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
f40d1d933c69_1000G_omni2.5.hg38.vcf.gz added
f40d2d6320aa_1000G_omni2.5.hg38.vcf.gz.tbi added
f40d46f5902d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
f40d23cc9ec0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
f40d4eca619c_af-only-gnomad.raw.sites.vcf added
f40d48ce712d_af-only-gnomad.raw.sites.vcf.idx added
f40d696866b2_Mutect2-exome-panel.vcf.idx added
f40d452e662e_Mutect2-WGS-panel-b37.vcf added
f40d6936797d_Mutect2-WGS-panel-b37.vcf.idx added
f40d77623381_small_exac_common_3.vcf added
f40d50239762_small_exac_common_3.vcf.idx added
f40d50a7cc08_1000g_pon.hg38.vcf.gz added
f40d38444a96_1000g_pon.hg38.vcf.gz.tbi added
f40db7cdab6_af-only-gnomad.hg38.vcf.gz added
f40d31fae89e_af-only-gnomad.hg38.vcf.gz.tbi added
f40d4fbdf6b4_small_exac_common_3.hg38.vcf.gz added
f40d408fcc52_small_exac_common_3.hg38.vcf.gz.tbi added
f40d20af3c9b_gencode.v41.annotation.gtf added
f40d50b3f4e0_gencode.v42.annotation.gtf added
f40d5691c784_gencode.vM30.annotation.gtf added
f40d7cc1d782_gencode.vM31.annotation.gtf added
f40d1a2bd7cb_gencode.v41.transcripts.fa added
f40d34645dd9_gencode.v41.transcripts.fa.fai added
f40d294d6c6e_gencode.v42.transcripts.fa added
f40d1a09bef1_gencode.v42.transcripts.fa.fai added
f40d75d6cd91_gencode.vM30.pc_transcripts.fa added
f40d69522707_gencode.vM30.pc_transcripts.fa.fai added
f40d10807296_gencode.vM31.pc_transcripts.fa added
f40d60e2de50_gencode.vM31.pc_transcripts.fa.fai added
f40d4e7187e1_GRCh38.primary_assembly.genome.fa.1.ht2 added
f40d7f8fed02_GRCh38.primary_assembly.genome.fa.2.ht2 added
f40d42115fbb_GRCh38.primary_assembly.genome.fa.3.ht2 added
f40d2a40fe0_GRCh38.primary_assembly.genome.fa.4.ht2 added
f40d610e3c7a_GRCh38.primary_assembly.genome.fa.5.ht2 added
f40d6da49f5d_GRCh38.primary_assembly.genome.fa.6.ht2 added
f40d52dacae7_GRCh38.primary_assembly.genome.fa.7.ht2 added
f40d1a3f2e30_GRCh38.primary_assembly.genome.fa.8.ht2 added
f40d29f15ec6_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
f40d25852ead_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
f40d4abb7319_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
f40d588194a3_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
f40d234586ba_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
f40d29902f6d_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
f40d3919b26c_GRCh38_full_analysis_set_plus_decoy_hla.fa added
f40d4610edbd_GRCh38.primary_assembly.genome.fa.fai added
f40d168373b_GRCh38.primary_assembly.genome.fa.amb added
f40d61020335_GRCh38.primary_assembly.genome.fa.ann added
f40d4b20be54_GRCh38.primary_assembly.genome.fa.bwt added
f40d52afa354_GRCh38.primary_assembly.genome.fa.pac added
f40d90c0a35_GRCh38.primary_assembly.genome.fa.sa added
f40d75722236_GRCh38.primary_assembly.genome.fa added
f40d18244377_hs37d5.fa.fai added
f40d74c94602_hs37d5.fa.amb added
f40d4a136934_hs37d5.fa.ann added
f40d405ffaea_hs37d5.fa.bwt added
f40d5d5239aa_hs37d5.fa.pac added
f40d4147f7c3_hs37d5.fa.sa added
f40d5bdb44b0_hs37d5.fa added
f40d187aaded_complete_ref_lens.bin added
f40d1e30af29_ctable.bin added
f40de3bbc3b_ctg_offsets.bin added
f40d73c2ccc9_duplicate_clusters.tsv added
f40d7a12db7e_info.json added
f40d6c086bce_mphf.bin added
f40d1cddd8cb_pos.bin added
f40d28c4063b_pre_indexing.log added
f40d5d752065_rank.bin added
f40d34a1f6d2_ref_indexing.log added
f40d75536ffc_refAccumLengths.bin added
f40d38dd4591_reflengths.bin added
f40d47024fc1_refseq.bin added
f40d68c22c52_seq.bin added
f40d23ebf139_versionInfo.json added
f40d5729e79b_salmon_index added
f40d249dd2_chrLength.txt added
f40d63f54610_chrName.txt added
f40d7bcaf7b4_chrNameLength.txt added
f40d4a4c89ea_chrStart.txt added
f40d66f287c1_exonGeTrInfo.tab added
f40d3caec4b4_exonInfo.tab added
f40d75f4248b_geneInfo.tab added
f40d6f8b5e2c_Genome added
f40d26d3d3ea_genomeParameters.txt added
f40d1cfdbb90_Log.out added
f40d5624f9ce_SA added
f40d158c6f91_SAindex added
f40d36f0a3a4_sjdbInfo.txt added
f40d70878029_sjdbList.fromGTF.out.tab added
f40d4fef3d76_sjdbList.out.tab added
f40d63ac36f9_transcriptInfo.tab added
f40d3f4d488e_GRCh38.GENCODE.v42_100 added
f40d6ad68319_knownGene_hg38.sql added
f40d2939151b_knownGene_hg38.txt added
f40d6298b4c1_refGene_hg38.sql added
f40d17831d79_refGene_hg38.txt added
f40d2103fefe_knownGene_mm39.sql added
f40dd59e6a1_knownGene_mm39.txt added
f40d9345ae0_refGene_mm39.sql added
f40d4c3a2cd8_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/Rtmp4fzjwn/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
40.193 4.605 47.796
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 12.338 | 1.255 | 13.855 | |
| dataSearch | 2.497 | 0.081 | 2.939 | |
| dataUpdate | 0.000 | 0.001 | 0.002 | |
| getCloudData | 4.589 | 0.218 | 5.854 | |
| getData | 0.000 | 0.001 | 0.001 | |
| meta_data | 0.002 | 0.001 | 0.002 | |
| recipeHub-class | 0.268 | 0.022 | 0.318 | |
| recipeLoad | 2.818 | 0.142 | 3.231 | |
| recipeMake | 0.001 | 0.002 | 0.002 | |
| recipeSearch | 1.166 | 0.060 | 1.517 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |