Qian Liu
| Snapshot Date: 2025-04-17 13:40 -0400 (Thu, 17 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_21 |
| git_last_commit: 601a107 |
| git_last_commit_date: 2025-04-15 13:01:44 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-18 11:46 -0400 (Fri, 18 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| 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 1758/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.8.0 (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: 1.8.0 |
| 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_1.8.0.tar.gz |
| StartedAt: 2025-04-17 21:13:22 -0400 (Thu, 17 Apr 2025) |
| EndedAt: 2025-04-17 21:14:14 -0400 (Thu, 17 Apr 2025) |
| EllapsedTime: 52.6 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* 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 ‘1.8.0’
* 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 ‘1.8.0’ ** 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 version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
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...
1581e32402b9a_GRCh38.primary_assembly.genome.fa.1.bt2 added
1581e12eea53c_GRCh38.primary_assembly.genome.fa.2.bt2 added
1581e71a20fd9_GRCh38.primary_assembly.genome.fa.3.bt2 added
1581e46bea9d7_GRCh38.primary_assembly.genome.fa.4.bt2 added
1581ef80868a_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1581e3f00d5f9_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1581e4fdfeebf_outfile.txt added
1581e76b36690_GRCh37_to_GRCh38.chain added
1581e7c12b4d1_GRCh37_to_NCBI34.chain added
1581e301d44fa_GRCh37_to_NCBI35.chain added
1581e519b91c3_GRCh37_to_NCBI36.chain added
1581e3c7ec310_GRCh38_to_GRCh37.chain added
1581e26386e77_GRCh38_to_NCBI34.chain added
1581e42dc5a3b_GRCh38_to_NCBI35.chain added
1581e10a7f9c8_GRCh38_to_NCBI36.chain added
1581e3ffc203_NCBI34_to_GRCh37.chain added
1581ec1a5502_NCBI34_to_GRCh38.chain added
1581e14c2fc83_NCBI35_to_GRCh37.chain added
1581ed50071b_NCBI35_to_GRCh38.chain added
1581e1028471_NCBI36_to_GRCh37.chain added
1581e4c45173b_NCBI36_to_GRCh38.chain added
1581e4bf8499b_GRCm38_to_NCBIM36.chain added
1581e19a88614_GRCm38_to_NCBIM37.chain added
1581e6fa9835_NCBIM36_to_GRCm38.chain added
1581e2e1ec327_NCBIM37_to_GRCm38.chain added
1581e659e4d18_1000G_omni2.5.b37.vcf.gz added
1581e7bd796c6_1000G_omni2.5.b37.vcf.gz.tbi added
1581e6ebe0af_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1581e67ec04b5_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1581e38293c60_1000G_omni2.5.hg38.vcf.gz added
1581e1b3adf6e_1000G_omni2.5.hg38.vcf.gz.tbi added
1581e3622bcb9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1581e22943173_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1581e2f3a86c1_af-only-gnomad.raw.sites.vcf added
1581e2b650120_af-only-gnomad.raw.sites.vcf.idx added
1581e742cf221_Mutect2-exome-panel.vcf.idx added
1581e32cc901d_Mutect2-WGS-panel-b37.vcf added
1581e140979f9_Mutect2-WGS-panel-b37.vcf.idx added
1581e7a26d4b5_small_exac_common_3.vcf added
1581eb56f5ba_small_exac_common_3.vcf.idx added
1581e7a1e8c26_1000g_pon.hg38.vcf.gz added
1581e6b83516c_1000g_pon.hg38.vcf.gz.tbi added
1581e7a56c098_af-only-gnomad.hg38.vcf.gz added
1581e557e79e7_af-only-gnomad.hg38.vcf.gz.tbi added
1581e6275588a_small_exac_common_3.hg38.vcf.gz added
1581e607fe86_small_exac_common_3.hg38.vcf.gz.tbi added
1581e76d71281_gencode.v41.annotation.gtf added
1581e2200101b_gencode.v42.annotation.gtf added
1581e32216e0d_gencode.vM30.annotation.gtf added
1581e30c03131_gencode.vM31.annotation.gtf added
1581e19dda0f8_gencode.v41.transcripts.fa added
1581e2573070c_gencode.v41.transcripts.fa.fai added
1581e22d3b809_gencode.v42.transcripts.fa added
1581e79d768bb_gencode.v42.transcripts.fa.fai added
1581e2d1d0b7b_gencode.vM30.pc_transcripts.fa added
1581e4ddccf60_gencode.vM30.pc_transcripts.fa.fai added
1581e5bb2cf8f_gencode.vM31.pc_transcripts.fa added
1581e3858e451_gencode.vM31.pc_transcripts.fa.fai added
1581e53f59ebd_GRCh38.primary_assembly.genome.fa.1.ht2 added
1581e2288b55b_GRCh38.primary_assembly.genome.fa.2.ht2 added
1581e3d3a7b13_GRCh38.primary_assembly.genome.fa.3.ht2 added
1581e4a663bcc_GRCh38.primary_assembly.genome.fa.4.ht2 added
1581e7ddff43c_GRCh38.primary_assembly.genome.fa.5.ht2 added
1581e7a1bcfb3_GRCh38.primary_assembly.genome.fa.6.ht2 added
1581e37e12f66_GRCh38.primary_assembly.genome.fa.7.ht2 added
1581e20eeee33_GRCh38.primary_assembly.genome.fa.8.ht2 added
1581e26586729_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1581e75dcc869_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1581e71e9a1f2_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1581e2187514b_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1581e3aea241f_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1581e61e98d70_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1581e2c44e648_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1581e5f6a97ac_GRCh38.primary_assembly.genome.fa.fai added
1581e4f0bce24_GRCh38.primary_assembly.genome.fa.amb added
1581e100ac607_GRCh38.primary_assembly.genome.fa.ann added
1581e334efdcb_GRCh38.primary_assembly.genome.fa.bwt added
1581e6f834be_GRCh38.primary_assembly.genome.fa.pac added
1581e114ea985_GRCh38.primary_assembly.genome.fa.sa added
1581e435b63a3_GRCh38.primary_assembly.genome.fa added
1581e24ea84e1_hs37d5.fa.fai added
1581e20b9e2b6_hs37d5.fa.amb added
1581ebd32b83_hs37d5.fa.ann added
1581e54cdab85_hs37d5.fa.bwt added
1581eab7d442_hs37d5.fa.pac added
1581e2ad03e8d_hs37d5.fa.sa added
1581e4dbab0f0_hs37d5.fa added
1581e1bb6846e_complete_ref_lens.bin added
1581e6bb05ff8_ctable.bin added
1581e86cca04_ctg_offsets.bin added
1581e1e42d0ee_duplicate_clusters.tsv added
1581e34a2c8c7_info.json added
1581e2b2b9bd0_mphf.bin added
1581e3c028ad4_pos.bin added
1581e4ae88313_pre_indexing.log added
1581e66f57ad0_rank.bin added
1581e7e52227e_ref_indexing.log added
1581e4256befc_refAccumLengths.bin added
1581e4d14b46a_reflengths.bin added
1581ea50c2af_refseq.bin added
1581e3c1d7473_seq.bin added
1581e31c848da_versionInfo.json added
1581e5426f9be_salmon_index added
1581e4ad6541b_chrLength.txt added
1581e3d2bdeff_chrName.txt added
1581eb3d56b9_chrNameLength.txt added
1581e68089172_chrStart.txt added
1581ea8508ba_exonGeTrInfo.tab added
1581e23fff0bb_exonInfo.tab added
1581e78159773_geneInfo.tab added
1581e518a3c9c_Genome added
1581e4a914f96_genomeParameters.txt added
1581ea002719_Log.out added
1581e1006df70_SA added
1581e33373a48_SAindex added
1581e6ed3673c_sjdbInfo.txt added
1581e791eccfb_sjdbList.fromGTF.out.tab added
1581e5523b0dc_sjdbList.out.tab added
1581e1a30672f_transcriptInfo.tab added
1581e5fc64c17_GRCh38.GENCODE.v42_100 added
1581e53adab20_knownGene_hg38.sql added
1581e2ebdeccb_knownGene_hg38.txt added
1581e37051b66_refGene_hg38.sql added
1581e3049e1c2_refGene_hg38.txt added
1581e4284a052_knownGene_mm39.sql added
1581e1139899c_knownGene_mm39.txt added
1581e58796999_refGene_mm39.sql added
1581eb03e930_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//RtmpL70dyM/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
8.036 1.210 9.743
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.078 | 0.256 | 2.463 | |
| dataSearch | 0.342 | 0.016 | 0.359 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.989 | 0.061 | 1.951 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.038 | 0.008 | 0.046 | |
| recipeLoad | 0.404 | 0.033 | 0.440 | |
| recipeMake | 0.001 | 0.000 | 0.000 | |
| recipeSearch | 0.166 | 0.014 | 0.180 | |
| recipeUpdate | 0 | 0 | 0 | |