Qian Liu
| Snapshot Date: 2025-03-18 13:40 -0400 (Tue, 18 Mar 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 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-19 11:46 -0400 (Wed, 19 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4742 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4459 |
| 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 1740/2313 | 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 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: 1.7.0 |
| 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: 2025-03-18 21:05:16 -0400 (Tue, 18 Mar 2025) |
| EndedAt: 2025-03-18 21:06:05 -0400 (Tue, 18 Mar 2025) |
| EllapsedTime: 49.5 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) (2025-03-02 r87868)
* 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) (2025-03-02 r87868) -- "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...
7aa630f14252_GRCh38.primary_assembly.genome.fa.1.bt2 added
7aa62f392e98_GRCh38.primary_assembly.genome.fa.2.bt2 added
7aa653221560_GRCh38.primary_assembly.genome.fa.3.bt2 added
7aa662a97c43_GRCh38.primary_assembly.genome.fa.4.bt2 added
7aa6651d454f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
7aa664b17965_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
7aa63f990988_outfile.txt added
7aa65840e056_GRCh37_to_GRCh38.chain added
7aa6b485b5e_GRCh37_to_NCBI34.chain added
7aa63b667e1b_GRCh37_to_NCBI35.chain added
7aa645e13d14_GRCh37_to_NCBI36.chain added
7aa646710fe3_GRCh38_to_GRCh37.chain added
7aa628ca2436_GRCh38_to_NCBI34.chain added
7aa66f0f6a25_GRCh38_to_NCBI35.chain added
7aa65d01dc19_GRCh38_to_NCBI36.chain added
7aa625191d03_NCBI34_to_GRCh37.chain added
7aa613bfc2fc_NCBI34_to_GRCh38.chain added
7aa6129a3885_NCBI35_to_GRCh37.chain added
7aa64af4ad4d_NCBI35_to_GRCh38.chain added
7aa659dc0ad_NCBI36_to_GRCh37.chain added
7aa637d4a0bc_NCBI36_to_GRCh38.chain added
7aa66884b346_GRCm38_to_NCBIM36.chain added
7aa66015ee45_GRCm38_to_NCBIM37.chain added
7aa63fce254b_NCBIM36_to_GRCm38.chain added
7aa676f27fa6_NCBIM37_to_GRCm38.chain added
7aa62a9aa84c_1000G_omni2.5.b37.vcf.gz added
7aa6f9f2b6e_1000G_omni2.5.b37.vcf.gz.tbi added
7aa61adc4ac5_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
7aa674b0d949_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
7aa66898379_1000G_omni2.5.hg38.vcf.gz added
7aa62e168049_1000G_omni2.5.hg38.vcf.gz.tbi added
7aa647405042_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
7aa64f554199_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
7aa66645cc7f_af-only-gnomad.raw.sites.vcf added
7aa67074da4d_af-only-gnomad.raw.sites.vcf.idx added
7aa67a82ee9_Mutect2-exome-panel.vcf.idx added
7aa6329fc6ec_Mutect2-WGS-panel-b37.vcf added
7aa617bcc9eb_Mutect2-WGS-panel-b37.vcf.idx added
7aa66b6c6f79_small_exac_common_3.vcf added
7aa61c0aa808_small_exac_common_3.vcf.idx added
7aa67f9db399_1000g_pon.hg38.vcf.gz added
7aa64a7a4343_1000g_pon.hg38.vcf.gz.tbi added
7aa620d609e8_af-only-gnomad.hg38.vcf.gz added
7aa644246f2f_af-only-gnomad.hg38.vcf.gz.tbi added
7aa633ff999c_small_exac_common_3.hg38.vcf.gz added
7aa651bdeb6f_small_exac_common_3.hg38.vcf.gz.tbi added
7aa6babee56_gencode.v41.annotation.gtf added
7aa644ac5616_gencode.v42.annotation.gtf added
7aa6e47e193_gencode.vM30.annotation.gtf added
7aa6112a8138_gencode.vM31.annotation.gtf added
7aa67d898c55_gencode.v41.transcripts.fa added
7aa6515c60d6_gencode.v41.transcripts.fa.fai added
7aa67d9ab55_gencode.v42.transcripts.fa added
7aa6637f5d79_gencode.v42.transcripts.fa.fai added
7aa63ed1e5f7_gencode.vM30.pc_transcripts.fa added
7aa64650db59_gencode.vM30.pc_transcripts.fa.fai added
7aa66670d41f_gencode.vM31.pc_transcripts.fa added
7aa6797673c3_gencode.vM31.pc_transcripts.fa.fai added
7aa64faa4581_GRCh38.primary_assembly.genome.fa.1.ht2 added
7aa633b94103_GRCh38.primary_assembly.genome.fa.2.ht2 added
7aa6475b467c_GRCh38.primary_assembly.genome.fa.3.ht2 added
7aa639709b7d_GRCh38.primary_assembly.genome.fa.4.ht2 added
7aa6ff04901_GRCh38.primary_assembly.genome.fa.5.ht2 added
7aa66848e8d3_GRCh38.primary_assembly.genome.fa.6.ht2 added
7aa6aadaa22_GRCh38.primary_assembly.genome.fa.7.ht2 added
7aa6f7ca3a8_GRCh38.primary_assembly.genome.fa.8.ht2 added
7aa63fdc7289_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
7aa621e3a120_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
7aa667674d41_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
7aa62f011b70_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
7aa671b06e2b_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
7aa67611035c_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
7aa656f3c992_GRCh38_full_analysis_set_plus_decoy_hla.fa added
7aa61f36bcd7_GRCh38.primary_assembly.genome.fa.fai added
7aa642a7d743_GRCh38.primary_assembly.genome.fa.amb added
7aa6192591e5_GRCh38.primary_assembly.genome.fa.ann added
7aa6718d5e48_GRCh38.primary_assembly.genome.fa.bwt added
7aa678290335_GRCh38.primary_assembly.genome.fa.pac added
7aa64c91ca34_GRCh38.primary_assembly.genome.fa.sa added
7aa677724331_GRCh38.primary_assembly.genome.fa added
7aa66e99833a_hs37d5.fa.fai added
7aa620768d90_hs37d5.fa.amb added
7aa64747f996_hs37d5.fa.ann added
7aa646530b69_hs37d5.fa.bwt added
7aa676123e90_hs37d5.fa.pac added
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7aa625416a41_hs37d5.fa added
7aa669a6e482_complete_ref_lens.bin added
7aa64be448fe_ctable.bin added
7aa67874429e_ctg_offsets.bin added
7aa618c1d0da_duplicate_clusters.tsv added
7aa65c76a4e8_info.json added
7aa67144aac4_mphf.bin added
7aa6532763f4_pos.bin added
7aa63f1352d2_pre_indexing.log added
7aa6da27958_rank.bin added
7aa625cc8766_ref_indexing.log added
7aa616cd4ced_refAccumLengths.bin added
7aa675674d_reflengths.bin added
7aa61bd0f077_refseq.bin added
7aa6325b22e5_seq.bin added
7aa67d500236_versionInfo.json added
7aa6fc16780_salmon_index added
7aa662720c94_chrLength.txt added
7aa62d97fb0a_chrName.txt added
7aa654e264e8_chrNameLength.txt added
7aa65b4ee6e1_chrStart.txt added
7aa61917ec9c_exonGeTrInfo.tab added
7aa671af02a2_exonInfo.tab added
7aa618d613fd_geneInfo.tab added
7aa6eba53c8_Genome added
7aa66ad27705_genomeParameters.txt added
7aa61f84200d_Log.out added
7aa61b5445a5_SA added
7aa639a861a7_SAindex added
7aa65da33883_sjdbInfo.txt added
7aa66d3507c_sjdbList.fromGTF.out.tab added
7aa61b490064_sjdbList.out.tab added
7aa655b8b33a_transcriptInfo.tab added
7aa650fed0cd_GRCh38.GENCODE.v42_100 added
7aa693e6c46_knownGene_hg38.sql added
7aa661366c67_knownGene_hg38.txt added
7aa63c07100d_refGene_hg38.sql added
7aa673aee444_refGene_hg38.txt added
7aa65f0c67b1_knownGene_mm39.sql added
7aa6276bc637_knownGene_mm39.txt added
7aa614a25919_refGene_mm39.sql added
7aa62e8782e4_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//RtmpGrtwHY/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
7.278 1.050 8.730
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.881 | 0.227 | 2.149 | |
| dataSearch | 0.334 | 0.013 | 0.394 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.875 | 0.050 | 1.720 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.041 | 0.003 | 0.048 | |
| recipeLoad | 0.388 | 0.030 | 0.461 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.159 | 0.013 | 0.180 | |
| recipeUpdate | 0 | 0 | 0 | |