Qian Liu
| Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 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 2025-04-02 19:34 -0400 (Wed, 02 Apr 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" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
| 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: 2025-04-02 06:00:45 -0400 (Wed, 02 Apr 2025) |
| EndedAt: 2025-04-02 06:03:09 -0400 (Wed, 02 Apr 2025) |
| EllapsedTime: 143.5 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: 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 7.170 0.790 8.052
getCloudData 2.836 0.154 5.428
* 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 4.4.3 (2025-02-28) -- "Trophy Case"
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...
bf482b21b239_GRCh38.primary_assembly.genome.fa.1.bt2 added
bf48313bd24e_GRCh38.primary_assembly.genome.fa.2.bt2 added
bf484e6c1822_GRCh38.primary_assembly.genome.fa.3.bt2 added
bf481aa48867_GRCh38.primary_assembly.genome.fa.4.bt2 added
bf4827f72fdb_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
bf485566e75c_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
bf4856df74d1_outfile.txt added
bf48686e71e5_GRCh37_to_GRCh38.chain added
bf482af7a6f3_GRCh37_to_NCBI34.chain added
bf4868f1b18e_GRCh37_to_NCBI35.chain added
bf4853c01775_GRCh37_to_NCBI36.chain added
bf4868442d47_GRCh38_to_GRCh37.chain added
bf4853f8c5cb_GRCh38_to_NCBI34.chain added
bf487181bd7e_GRCh38_to_NCBI35.chain added
bf487cbfd569_GRCh38_to_NCBI36.chain added
bf481654207b_NCBI34_to_GRCh37.chain added
bf486d2076b0_NCBI34_to_GRCh38.chain added
bf486e5054c8_NCBI35_to_GRCh37.chain added
bf485bee4f0c_NCBI35_to_GRCh38.chain added
bf487a87cbfa_NCBI36_to_GRCh37.chain added
bf486960c8ee_NCBI36_to_GRCh38.chain added
bf485127b74e_GRCm38_to_NCBIM36.chain added
bf486738b82_GRCm38_to_NCBIM37.chain added
bf48bcc071d_NCBIM36_to_GRCm38.chain added
bf487fe706f7_NCBIM37_to_GRCm38.chain added
bf48187a83bb_1000G_omni2.5.b37.vcf.gz added
bf48135e768b_1000G_omni2.5.b37.vcf.gz.tbi added
bf481eb8a99c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
bf486d875085_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
bf484eb783f0_1000G_omni2.5.hg38.vcf.gz added
bf48723729ef_1000G_omni2.5.hg38.vcf.gz.tbi added
bf483a2447e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
bf48123eae0f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
bf4851156424_af-only-gnomad.raw.sites.vcf added
bf485361a112_af-only-gnomad.raw.sites.vcf.idx added
bf482e95cf82_Mutect2-exome-panel.vcf.idx added
bf486d6a77b2_Mutect2-WGS-panel-b37.vcf added
bf4868d87f3c_Mutect2-WGS-panel-b37.vcf.idx added
bf485d8971ea_small_exac_common_3.vcf added
bf486a95e99f_small_exac_common_3.vcf.idx added
bf48181cfc64_1000g_pon.hg38.vcf.gz added
bf4816fe159a_1000g_pon.hg38.vcf.gz.tbi added
bf4833c3d41_af-only-gnomad.hg38.vcf.gz added
bf4867d9780f_af-only-gnomad.hg38.vcf.gz.tbi added
bf487659560c_small_exac_common_3.hg38.vcf.gz added
bf4863206a87_small_exac_common_3.hg38.vcf.gz.tbi added
bf486531f7e8_gencode.v41.annotation.gtf added
bf48338ad43f_gencode.v42.annotation.gtf added
bf485f748e88_gencode.vM30.annotation.gtf added
bf485d39b3ad_gencode.vM31.annotation.gtf added
bf48774352ab_gencode.v41.transcripts.fa added
bf4864e895b8_gencode.v41.transcripts.fa.fai added
bf4861bd96c9_gencode.v42.transcripts.fa added
bf4865f69840_gencode.v42.transcripts.fa.fai added
bf482085c60c_gencode.vM30.pc_transcripts.fa added
bf482e8d4e82_gencode.vM30.pc_transcripts.fa.fai added
bf483f1d50ae_gencode.vM31.pc_transcripts.fa added
bf481d9befe1_gencode.vM31.pc_transcripts.fa.fai added
bf4868a1abf6_GRCh38.primary_assembly.genome.fa.1.ht2 added
bf484e20d924_GRCh38.primary_assembly.genome.fa.2.ht2 added
bf484e8ff28e_GRCh38.primary_assembly.genome.fa.3.ht2 added
bf484c7d70ed_GRCh38.primary_assembly.genome.fa.4.ht2 added
bf483f80fed6_GRCh38.primary_assembly.genome.fa.5.ht2 added
bf482ddab42c_GRCh38.primary_assembly.genome.fa.6.ht2 added
bf48716acc38_GRCh38.primary_assembly.genome.fa.7.ht2 added
bf481a85aab4_GRCh38.primary_assembly.genome.fa.8.ht2 added
bf483d8a1d06_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
bf483677947a_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
bf4864b4f185_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
bf48235c866a_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
bf48f7cab49_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
bf4841d14d90_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
bf48143b4ab2_GRCh38_full_analysis_set_plus_decoy_hla.fa added
bf4840a4f67e_GRCh38.primary_assembly.genome.fa.fai added
bf48e32eb5a_GRCh38.primary_assembly.genome.fa.amb added
bf4830f968fe_GRCh38.primary_assembly.genome.fa.ann added
bf48465c14d0_GRCh38.primary_assembly.genome.fa.bwt added
bf48475a87c6_GRCh38.primary_assembly.genome.fa.pac added
bf48887fcc3_GRCh38.primary_assembly.genome.fa.sa added
bf4817e36a95_GRCh38.primary_assembly.genome.fa added
bf48536a6873_hs37d5.fa.fai added
bf486eef80cd_hs37d5.fa.amb added
bf482df14ba1_hs37d5.fa.ann added
bf483c9c4e97_hs37d5.fa.bwt added
bf4839ebba97_hs37d5.fa.pac added
bf4823272d36_hs37d5.fa.sa added
bf4861094641_hs37d5.fa added
bf4827e3872c_complete_ref_lens.bin added
bf484abf6e29_ctable.bin added
bf485dd96c15_ctg_offsets.bin added
bf486d4706d5_duplicate_clusters.tsv added
bf485211c1ff_info.json added
bf48bd77671_mphf.bin added
bf486ea0fac9_pos.bin added
bf48ab0dadd_pre_indexing.log added
bf4860f0e8a6_rank.bin added
bf48683a1c02_ref_indexing.log added
bf483f04fcc3_refAccumLengths.bin added
bf48606e8687_reflengths.bin added
bf4878423a86_refseq.bin added
bf4844107118_seq.bin added
bf4813710191_versionInfo.json added
bf48601de08f_salmon_index added
bf484981fd95_chrLength.txt added
bf48752f66e6_chrName.txt added
bf487b0cc224_chrNameLength.txt added
bf4829e0899_chrStart.txt added
bf4855467626_exonGeTrInfo.tab added
bf484f6e487_exonInfo.tab added
bf486d155d9c_geneInfo.tab added
bf4815b4e4b7_Genome added
bf481713b583_genomeParameters.txt added
bf48ef1b74b_Log.out added
bf481f38a497_SA added
bf483fbdc584_SAindex added
bf4843f27dcd_sjdbInfo.txt added
bf4865214094_sjdbList.fromGTF.out.tab added
bf486a16e86a_sjdbList.out.tab added
bf485f4bd90_transcriptInfo.tab added
bf486c93bfe_GRCh38.GENCODE.v42_100 added
bf48581a42d_knownGene_hg38.sql added
bf48241892e_knownGene_hg38.txt added
bf481c952c2a_refGene_hg38.sql added
bf48586880f_refGene_hg38.txt added
bf48434e939e_knownGene_mm39.sql added
bf485bbd8c97_knownGene_mm39.txt added
bf4879593c8e_refGene_mm39.sql added
bf485196ccdf_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/RtmpFRijZr/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
23.857 2.771 28.030
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.170 | 0.790 | 8.052 | |
| dataSearch | 1.153 | 0.048 | 1.201 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.836 | 0.154 | 5.428 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.135 | 0.011 | 0.147 | |
| recipeLoad | 1.444 | 0.088 | 1.542 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.617 | 0.039 | 0.656 | |
| recipeUpdate | 0 | 0 | 0 | |