Qian Liu
| Snapshot Date: 2025-01-13 13:00 -0500 (Mon, 13 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 2025-01-16 12:10 -0500 (Thu, 16 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" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4489 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4387 |
| 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: 2025-01-15 06:19:46 -0500 (Wed, 15 Jan 2025) |
| EndedAt: 2025-01-15 06:22:11 -0500 (Wed, 15 Jan 2025) |
| EllapsedTime: 145.1 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 6.806 0.797 7.665
* 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...
13e6161444f76_GRCh38.primary_assembly.genome.fa.1.bt2 added
13e614bbcfddd_GRCh38.primary_assembly.genome.fa.2.bt2 added
13e6164bedf03_GRCh38.primary_assembly.genome.fa.3.bt2 added
13e612f2371a1_GRCh38.primary_assembly.genome.fa.4.bt2 added
13e613ff91934_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
13e617ae5c5bb_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
13e61318b706_outfile.txt added
13e614b97ec80_GRCh37_to_GRCh38.chain added
13e616327ee45_GRCh37_to_NCBI34.chain added
13e61528c26de_GRCh37_to_NCBI35.chain added
13e616f4be328_GRCh37_to_NCBI36.chain added
13e615f2e902d_GRCh38_to_GRCh37.chain added
13e6169fbab2c_GRCh38_to_NCBI34.chain added
13e619a30c10_GRCh38_to_NCBI35.chain added
13e612f6cf361_GRCh38_to_NCBI36.chain added
13e6119de7d9a_NCBI34_to_GRCh37.chain added
13e615e0816ba_NCBI34_to_GRCh38.chain added
13e61650c3d90_NCBI35_to_GRCh37.chain added
13e6169decc4_NCBI35_to_GRCh38.chain added
13e616a233b40_NCBI36_to_GRCh37.chain added
13e612f071d30_NCBI36_to_GRCh38.chain added
13e617c0d526e_GRCm38_to_NCBIM36.chain added
13e614e9ef362_GRCm38_to_NCBIM37.chain added
13e61257ccf41_NCBIM36_to_GRCm38.chain added
13e61250ac7a1_NCBIM37_to_GRCm38.chain added
13e6166b82e06_1000G_omni2.5.b37.vcf.gz added
13e6145d5c099_1000G_omni2.5.b37.vcf.gz.tbi added
13e615457a0a0_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
13e6144f293a2_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
13e6111ba940b_1000G_omni2.5.hg38.vcf.gz added
13e61704d6744_1000G_omni2.5.hg38.vcf.gz.tbi added
13e6169b6daf5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
13e6163e1410b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
13e6159756c67_af-only-gnomad.raw.sites.vcf added
13e612c200c13_af-only-gnomad.raw.sites.vcf.idx added
13e616bf8ca06_Mutect2-exome-panel.vcf.idx added
13e611a97874b_Mutect2-WGS-panel-b37.vcf added
13e6152335a90_Mutect2-WGS-panel-b37.vcf.idx added
13e61297ece19_small_exac_common_3.vcf added
13e61440ce097_small_exac_common_3.vcf.idx added
13e61296cfc68_1000g_pon.hg38.vcf.gz added
13e61322f2517_1000g_pon.hg38.vcf.gz.tbi added
13e61352c22be_af-only-gnomad.hg38.vcf.gz added
13e61649d0337_af-only-gnomad.hg38.vcf.gz.tbi added
13e613e437c_small_exac_common_3.hg38.vcf.gz added
13e6177c08203_small_exac_common_3.hg38.vcf.gz.tbi added
13e617f97d060_gencode.v41.annotation.gtf added
13e6147f19011_gencode.v42.annotation.gtf added
13e61442970fd_gencode.vM30.annotation.gtf added
13e617cb91500_gencode.vM31.annotation.gtf added
13e615b11f2f8_gencode.v41.transcripts.fa added
13e617766a67d_gencode.v41.transcripts.fa.fai added
13e61743c95c8_gencode.v42.transcripts.fa added
13e61358db916_gencode.v42.transcripts.fa.fai added
13e616b726ed1_gencode.vM30.pc_transcripts.fa added
13e6125c99273_gencode.vM30.pc_transcripts.fa.fai added
13e6154adcf66_gencode.vM31.pc_transcripts.fa added
13e615f0b5cf8_gencode.vM31.pc_transcripts.fa.fai added
13e616304ce87_GRCh38.primary_assembly.genome.fa.1.ht2 added
13e61509333da_GRCh38.primary_assembly.genome.fa.2.ht2 added
13e6170315689_GRCh38.primary_assembly.genome.fa.3.ht2 added
13e61372875ea_GRCh38.primary_assembly.genome.fa.4.ht2 added
13e61415571f0_GRCh38.primary_assembly.genome.fa.5.ht2 added
13e6150ab6512_GRCh38.primary_assembly.genome.fa.6.ht2 added
13e612478aa1e_GRCh38.primary_assembly.genome.fa.7.ht2 added
13e616de8aa46_GRCh38.primary_assembly.genome.fa.8.ht2 added
13e6146031209_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
13e61739530c7_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
13e6147b59419_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
13e61620e1a16_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
13e61bd2cca5_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
13e613c796ab3_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
13e61474c2cc9_GRCh38_full_analysis_set_plus_decoy_hla.fa added
13e615a1064b0_GRCh38.primary_assembly.genome.fa.fai added
13e616a428d01_GRCh38.primary_assembly.genome.fa.amb added
13e6137377327_GRCh38.primary_assembly.genome.fa.ann added
13e61196921c3_GRCh38.primary_assembly.genome.fa.bwt added
13e614527963d_GRCh38.primary_assembly.genome.fa.pac added
13e6129f8a243_GRCh38.primary_assembly.genome.fa.sa added
13e61264f23c_GRCh38.primary_assembly.genome.fa added
13e61315b425e_hs37d5.fa.fai added
13e615e6242a2_hs37d5.fa.amb added
13e61504ca17_hs37d5.fa.ann added
13e617d6fae93_hs37d5.fa.bwt added
13e612f2e753b_hs37d5.fa.pac added
13e6113128cb0_hs37d5.fa.sa added
13e6126d28098_hs37d5.fa added
13e6145f88f11_complete_ref_lens.bin added
13e614178c8fa_ctable.bin added
13e6160d2b6aa_ctg_offsets.bin added
13e6129d6848f_duplicate_clusters.tsv added
13e614298ddbe_info.json added
13e614206071a_mphf.bin added
13e6119bc5dd3_pos.bin added
13e611db3d4d8_pre_indexing.log added
13e6195ac024_rank.bin added
13e6124fc8048_ref_indexing.log added
13e613d4a09f0_refAccumLengths.bin added
13e6147d28aff_reflengths.bin added
13e614fa3902f_refseq.bin added
13e617b4f2681_seq.bin added
13e619691e66_versionInfo.json added
13e61544abf5d_salmon_index added
13e6177599de6_chrLength.txt added
13e611c8da441_chrName.txt added
13e61171ab60c_chrNameLength.txt added
13e615aa5d9ad_chrStart.txt added
13e613e761b59_exonGeTrInfo.tab added
13e613bfd9018_exonInfo.tab added
13e613ff366d_geneInfo.tab added
13e61684e3027_Genome added
13e61653b85f0_genomeParameters.txt added
13e6126d6837c_Log.out added
13e614d5255cf_SA added
13e61587fb0b1_SAindex added
13e61272961db_sjdbInfo.txt added
13e61dd784f3_sjdbList.fromGTF.out.tab added
13e614059749e_sjdbList.out.tab added
13e6130f75213_transcriptInfo.tab added
13e613d2d7682_GRCh38.GENCODE.v42_100 added
13e6173bf702e_knownGene_hg38.sql added
13e611d5e1760_knownGene_hg38.txt added
13e61c50aeb0_refGene_hg38.sql added
13e614fcab21_refGene_hg38.txt added
13e6168470615_knownGene_mm39.sql added
13e61ee0822f_knownGene_mm39.txt added
13e613582e34a_refGene_mm39.sql added
13e6124182ab8_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/RtmpYHOI8a/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
23.052 2.689 26.973
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.806 | 0.797 | 7.665 | |
| dataSearch | 1.093 | 0.048 | 1.141 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.669 | 0.145 | 4.655 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.135 | 0.012 | 0.151 | |
| recipeLoad | 1.391 | 0.094 | 1.490 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.603 | 0.042 | 0.646 | |
| recipeUpdate | 0 | 0 | 0 | |