Qian Liu
| Snapshot Date: 2025-03-17 13:00 -0400 (Mon, 17 Mar 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 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-20 12:09 -0400 (Thu, 20 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4756 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4514 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4441 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4406 |
| 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 | 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: 1.6.0 |
| 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: 2025-03-18 08:45:21 -0400 (Tue, 18 Mar 2025) |
| EndedAt: 2025-03-18 08:49:37 -0400 (Tue, 18 Mar 2025) |
| EllapsedTime: 255.5 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 12.132 1.235 13.758
getCloudData 4.609 0.205 5.720
* 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 4.4.3 (2025-02-28) -- "Trophy Case"
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...
dbad68c6e6fb_GRCh38.primary_assembly.genome.fa.1.bt2 added
dbad5a669e7a_GRCh38.primary_assembly.genome.fa.2.bt2 added
dbad72e89f4_GRCh38.primary_assembly.genome.fa.3.bt2 added
dbad62f5db_GRCh38.primary_assembly.genome.fa.4.bt2 added
dbad60fafd0f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
dbad7dfc1586_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
dbad30e95108_outfile.txt added
dbad25c6fd4e_GRCh37_to_GRCh38.chain added
dbad2b201f42_GRCh37_to_NCBI34.chain added
dbad49e43c2c_GRCh37_to_NCBI35.chain added
dbad272a929a_GRCh37_to_NCBI36.chain added
dbad5bfed08c_GRCh38_to_GRCh37.chain added
dbad362dc683_GRCh38_to_NCBI34.chain added
dbad7743de3e_GRCh38_to_NCBI35.chain added
dbad8b3f59e_GRCh38_to_NCBI36.chain added
dbad5ec25c88_NCBI34_to_GRCh37.chain added
dbad2a491552_NCBI34_to_GRCh38.chain added
dbad2416d02e_NCBI35_to_GRCh37.chain added
dbad55bd8e84_NCBI35_to_GRCh38.chain added
dbadfd7a816_NCBI36_to_GRCh37.chain added
dbad175c447a_NCBI36_to_GRCh38.chain added
dbad2a93b191_GRCm38_to_NCBIM36.chain added
dbad466ebc6d_GRCm38_to_NCBIM37.chain added
dbad1014bc3b_NCBIM36_to_GRCm38.chain added
dbad4151cdbc_NCBIM37_to_GRCm38.chain added
dbad619a1324_1000G_omni2.5.b37.vcf.gz added
dbad4a5ed28b_1000G_omni2.5.b37.vcf.gz.tbi added
dbad1750c9d2_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
dbad38f205f3_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
dbad1964b1ba_1000G_omni2.5.hg38.vcf.gz added
dbad21d0375c_1000G_omni2.5.hg38.vcf.gz.tbi added
dbad6ce28a5b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
dbadce99436_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
dbad3b016bd9_af-only-gnomad.raw.sites.vcf added
dbad5a4f91d2_af-only-gnomad.raw.sites.vcf.idx added
dbad1deea050_Mutect2-exome-panel.vcf.idx added
dbad1d5ef38a_Mutect2-WGS-panel-b37.vcf added
dbad44c6f816_Mutect2-WGS-panel-b37.vcf.idx added
dbad62c98fa0_small_exac_common_3.vcf added
dbad1ef4840b_small_exac_common_3.vcf.idx added
dbad4708fe0d_1000g_pon.hg38.vcf.gz added
dbad1f5f2bea_1000g_pon.hg38.vcf.gz.tbi added
dbad213c1fbd_af-only-gnomad.hg38.vcf.gz added
dbad7247c256_af-only-gnomad.hg38.vcf.gz.tbi added
dbad4527d6b7_small_exac_common_3.hg38.vcf.gz added
dbad3a81abd9_small_exac_common_3.hg38.vcf.gz.tbi added
dbad17395191_gencode.v41.annotation.gtf added
dbad341a1280_gencode.v42.annotation.gtf added
dbad1bb4ac39_gencode.vM30.annotation.gtf added
dbad7296e064_gencode.vM31.annotation.gtf added
dbadf660002_gencode.v41.transcripts.fa added
dbad718a8b33_gencode.v41.transcripts.fa.fai added
dbad3eb8fb81_gencode.v42.transcripts.fa added
dbad6287f252_gencode.v42.transcripts.fa.fai added
dbad4b361807_gencode.vM30.pc_transcripts.fa added
dbad4c639a24_gencode.vM30.pc_transcripts.fa.fai added
dbad1f1cd8aa_gencode.vM31.pc_transcripts.fa added
dbad1ed490db_gencode.vM31.pc_transcripts.fa.fai added
dbad157229ad_GRCh38.primary_assembly.genome.fa.1.ht2 added
dbad7a0e27da_GRCh38.primary_assembly.genome.fa.2.ht2 added
dbad375a97d0_GRCh38.primary_assembly.genome.fa.3.ht2 added
dbad1ca4f514_GRCh38.primary_assembly.genome.fa.4.ht2 added
dbad11d602bd_GRCh38.primary_assembly.genome.fa.5.ht2 added
dbad794dcf70_GRCh38.primary_assembly.genome.fa.6.ht2 added
dbad636e0047_GRCh38.primary_assembly.genome.fa.7.ht2 added
dbad4ad46850_GRCh38.primary_assembly.genome.fa.8.ht2 added
dbad3f0c8291_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
dbad4e501ded_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
dbad6ddcdac5_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
dbad3e9ef3dc_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
dbad359c10a2_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
dbad1908172d_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
dbad62299831_GRCh38_full_analysis_set_plus_decoy_hla.fa added
dbad18c6eb50_GRCh38.primary_assembly.genome.fa.fai added
dbad2b82dde5_GRCh38.primary_assembly.genome.fa.amb added
dbad1cb5fbb4_GRCh38.primary_assembly.genome.fa.ann added
dbad6f9ff525_GRCh38.primary_assembly.genome.fa.bwt added
dbad6e978963_GRCh38.primary_assembly.genome.fa.pac added
dbad1ebcfb4e_GRCh38.primary_assembly.genome.fa.sa added
dbad916cda6_GRCh38.primary_assembly.genome.fa added
dbad381751f3_hs37d5.fa.fai added
dbad305454a_hs37d5.fa.amb added
dbad4f07fed2_hs37d5.fa.ann added
dbad15eab587_hs37d5.fa.bwt added
dbad6433bd4e_hs37d5.fa.pac added
dbadd17f47_hs37d5.fa.sa added
dbad39fb0ebc_hs37d5.fa added
dbad11847661_complete_ref_lens.bin added
dbadf77e343_ctable.bin added
dbad7e94ba4_ctg_offsets.bin added
dbad6565000a_duplicate_clusters.tsv added
dbad49e5c487_info.json added
dbadbc9a0f8_mphf.bin added
dbad6266ffd3_pos.bin added
dbad5825a81d_pre_indexing.log added
dbad10403521_rank.bin added
dbad676011dc_ref_indexing.log added
dbad5434b789_refAccumLengths.bin added
dbad50fdae8f_reflengths.bin added
dbad3ecf57d3_refseq.bin added
dbad1e8efddc_seq.bin added
dbad3dbc8630_versionInfo.json added
dbad240dd8fa_salmon_index added
dbad9201794_chrLength.txt added
dbad19ebfa3a_chrName.txt added
dbad53790321_chrNameLength.txt added
dbad2dbc9657_chrStart.txt added
dbad38324136_exonGeTrInfo.tab added
dbad6b575d0c_exonInfo.tab added
dbad349df5e2_geneInfo.tab added
dbad6e79e36a_Genome added
dbad4417cd0_genomeParameters.txt added
dbad67693dde_Log.out added
dbad2e5ceedc_SA added
dbad5745c54b_SAindex added
dbad259bebb0_sjdbInfo.txt added
dbad1f8e831a_sjdbList.fromGTF.out.tab added
dbad45413025_sjdbList.out.tab added
dbad3abff0a8_transcriptInfo.tab added
dbadf50c3ba_GRCh38.GENCODE.v42_100 added
dbad7f61f030_knownGene_hg38.sql added
dbad76e020a5_knownGene_hg38.txt added
dbad747f6d9b_refGene_hg38.sql added
dbad59f516dd_refGene_hg38.txt added
dbad69b0354e_knownGene_mm39.sql added
dbad2f7bca17_knownGene_mm39.txt added
dbad6810c45b_refGene_mm39.sql added
dbad24cb67bd_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/RtmpTldJBY/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
39.856 4.332 46.082
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 12.132 | 1.235 | 13.758 | |
| dataSearch | 2.444 | 0.078 | 2.559 | |
| dataUpdate | 0.001 | 0.001 | 0.002 | |
| getCloudData | 4.609 | 0.205 | 5.720 | |
| getData | 0.001 | 0.002 | 0.001 | |
| meta_data | 0.001 | 0.001 | 0.002 | |
| recipeHub-class | 0.259 | 0.021 | 0.284 | |
| recipeLoad | 2.836 | 0.138 | 3.189 | |
| recipeMake | 0.001 | 0.001 | 0.003 | |
| recipeSearch | 1.161 | 0.054 | 1.284 | |
| recipeUpdate | 0.000 | 0.001 | 0.001 | |