Qian Liu
| Snapshot Date: 2025-02-14 13:40 -0500 (Fri, 14 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 2025-02-15 11:43 -0500 (Sat, 15 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" | 4720 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4482 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4493 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4446 |
| 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: 2025-02-14 22:37:14 -0500 (Fri, 14 Feb 2025) |
| EndedAt: 2025-02-14 22:39:47 -0500 (Fri, 14 Feb 2025) |
| EllapsedTime: 152.5 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) (2025-01-22 r87618)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.7.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataHub-class 7.121 0.822 8.04
* 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-x86_64/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) (2025-01-22 r87618) -- "Unsuffered Consequences"
Copyright (C) 2025 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...
3b774de463d9_GRCh38.primary_assembly.genome.fa.1.bt2 added
3b774d576382_GRCh38.primary_assembly.genome.fa.2.bt2 added
3b7724461379_GRCh38.primary_assembly.genome.fa.3.bt2 added
3b7774a87f89_GRCh38.primary_assembly.genome.fa.4.bt2 added
3b77624d3734_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3b773b636957_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3b777b98ed36_outfile.txt added
3b7774fdb39e_GRCh37_to_GRCh38.chain added
3b773c1b8613_GRCh37_to_NCBI34.chain added
3b7732ff6839_GRCh37_to_NCBI35.chain added
3b771e139057_GRCh37_to_NCBI36.chain added
3b7716694f2e_GRCh38_to_GRCh37.chain added
3b775bcd6080_GRCh38_to_NCBI34.chain added
3b7787aa296_GRCh38_to_NCBI35.chain added
3b772b482a33_GRCh38_to_NCBI36.chain added
3b77eca9078_NCBI34_to_GRCh37.chain added
3b7714d2bdde_NCBI34_to_GRCh38.chain added
3b7717af4480_NCBI35_to_GRCh37.chain added
3b7773ba3ba5_NCBI35_to_GRCh38.chain added
3b7747a208fe_NCBI36_to_GRCh37.chain added
3b775efc806f_NCBI36_to_GRCh38.chain added
3b7713542821_GRCm38_to_NCBIM36.chain added
3b777a169870_GRCm38_to_NCBIM37.chain added
3b7761721fae_NCBIM36_to_GRCm38.chain added
3b77b7e0a7d_NCBIM37_to_GRCm38.chain added
3b777fe29a6f_1000G_omni2.5.b37.vcf.gz added
3b7776092f00_1000G_omni2.5.b37.vcf.gz.tbi added
3b7754ece58a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3b77cd1f295_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3b772b8d1ac6_1000G_omni2.5.hg38.vcf.gz added
3b773cd8d380_1000G_omni2.5.hg38.vcf.gz.tbi added
3b773f2597b5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3b773d0b0c76_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3b77205f3649_af-only-gnomad.raw.sites.vcf added
3b774ae50339_af-only-gnomad.raw.sites.vcf.idx added
3b77136b999_Mutect2-exome-panel.vcf.idx added
3b772fd2ec6e_Mutect2-WGS-panel-b37.vcf added
3b7740a04249_Mutect2-WGS-panel-b37.vcf.idx added
3b77595fe7c4_small_exac_common_3.vcf added
3b77276922b3_small_exac_common_3.vcf.idx added
3b77676529fb_1000g_pon.hg38.vcf.gz added
3b7722a752c5_1000g_pon.hg38.vcf.gz.tbi added
3b77172b1549_af-only-gnomad.hg38.vcf.gz added
3b77d827781_af-only-gnomad.hg38.vcf.gz.tbi added
3b777073bd14_small_exac_common_3.hg38.vcf.gz added
3b773e82a5b9_small_exac_common_3.hg38.vcf.gz.tbi added
3b77734e34be_gencode.v41.annotation.gtf added
3b771368e116_gencode.v42.annotation.gtf added
3b774a91754e_gencode.vM30.annotation.gtf added
3b7713ac7a21_gencode.vM31.annotation.gtf added
3b772086169e_gencode.v41.transcripts.fa added
3b774336efc0_gencode.v41.transcripts.fa.fai added
3b774bb648b9_gencode.v42.transcripts.fa added
3b772c609084_gencode.v42.transcripts.fa.fai added
3b7777afe0de_gencode.vM30.pc_transcripts.fa added
3b773bd44c35_gencode.vM30.pc_transcripts.fa.fai added
3b776ed74a42_gencode.vM31.pc_transcripts.fa added
3b77784c6be7_gencode.vM31.pc_transcripts.fa.fai added
3b7761404864_GRCh38.primary_assembly.genome.fa.1.ht2 added
3b774350cf1d_GRCh38.primary_assembly.genome.fa.2.ht2 added
3b776e4d9b71_GRCh38.primary_assembly.genome.fa.3.ht2 added
3b772918504a_GRCh38.primary_assembly.genome.fa.4.ht2 added
3b777b3f3f59_GRCh38.primary_assembly.genome.fa.5.ht2 added
3b7775582b45_GRCh38.primary_assembly.genome.fa.6.ht2 added
3b776f80fb32_GRCh38.primary_assembly.genome.fa.7.ht2 added
3b777cebc8ce_GRCh38.primary_assembly.genome.fa.8.ht2 added
3b775bcc8c74_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3b77521942c1_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3b77786db702_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3b776b0a2212_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3b77664302a4_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3b773962916f_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3b77763a2bd7_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3b7765146ce4_GRCh38.primary_assembly.genome.fa.fai added
3b771ff92094_GRCh38.primary_assembly.genome.fa.amb added
3b771cc9e4f2_GRCh38.primary_assembly.genome.fa.ann added
3b77ad5daa2_GRCh38.primary_assembly.genome.fa.bwt added
3b775e04c73c_GRCh38.primary_assembly.genome.fa.pac added
3b77bb4645d_GRCh38.primary_assembly.genome.fa.sa added
3b7770291bab_GRCh38.primary_assembly.genome.fa added
3b771ad7b114_hs37d5.fa.fai added
3b7746aaa5d0_hs37d5.fa.amb added
3b776d6c1eee_hs37d5.fa.ann added
3b775562d361_hs37d5.fa.bwt added
3b774b23b112_hs37d5.fa.pac added
3b77143e3b48_hs37d5.fa.sa added
3b771a5fe5a_hs37d5.fa added
3b7738ddc78e_complete_ref_lens.bin added
3b77685858cc_ctable.bin added
3b772dee99_ctg_offsets.bin added
3b77478b7ee6_duplicate_clusters.tsv added
3b77173852bc_info.json added
3b7772bfc08c_mphf.bin added
3b77afa622f_pos.bin added
3b773c44014a_pre_indexing.log added
3b7714b0c02f_rank.bin added
3b7760195845_ref_indexing.log added
3b771ff24b4d_refAccumLengths.bin added
3b775c2dbc9d_reflengths.bin added
3b773eba16b2_refseq.bin added
3b772b28204a_seq.bin added
3b77575ff068_versionInfo.json added
3b775ba068a8_salmon_index added
3b77371c97_chrLength.txt added
3b772235fd9d_chrName.txt added
3b7769d5ff7_chrNameLength.txt added
3b7746075485_chrStart.txt added
3b77b3e0bae_exonGeTrInfo.tab added
3b771670d246_exonInfo.tab added
3b7748fcfd2c_geneInfo.tab added
3b7759517923_Genome added
3b7773e816a4_genomeParameters.txt added
3b77a26a46f_Log.out added
3b776ef5789d_SA added
3b7735c1c454_SAindex added
3b774440825e_sjdbInfo.txt added
3b77672f0c53_sjdbList.fromGTF.out.tab added
3b7741d25211_sjdbList.out.tab added
3b775709fbd9_transcriptInfo.tab added
3b7750759033_GRCh38.GENCODE.v42_100 added
3b77564e2d89_knownGene_hg38.sql added
3b77268fa9a3_knownGene_hg38.txt added
3b7721ca201c_refGene_hg38.sql added
3b775d021f98_refGene_hg38.txt added
3b77366863dc_knownGene_mm39.sql added
3b777f741c6b_knownGene_mm39.txt added
3b771ff5f62c_refGene_mm39.sql added
3b774cf4d318_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/RtmpjO4Bzj/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
24.232 3.596 28.829
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.121 | 0.822 | 8.040 | |
| dataSearch | 1.301 | 0.055 | 1.364 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.682 | 0.162 | 3.592 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.002 | |
| recipeHub-class | 0.153 | 0.014 | 0.169 | |
| recipeLoad | 1.523 | 0.095 | 1.629 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.631 | 0.038 | 0.673 | |
| recipeUpdate | 0 | 0 | 0 | |