Qian Liu
| Snapshot Date: 2025-10-02 13:40 -0400 (Thu, 02 Oct 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 2025-10-06 11:41 -0400 (Mon, 06 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4832 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4613 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4554 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4585 |
| 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 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: 2025-10-04 09:10:55 -0400 (Sat, 04 Oct 2025) |
| EndedAt: 2025-10-04 09:13:27 -0400 (Sat, 04 Oct 2025) |
| EllapsedTime: 152.0 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 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataHub-class 7.412 0.928 8.473
* 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 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
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...
7fa05b9cd628_GRCh38.primary_assembly.genome.fa.1.bt2 added
7fa015b00b15_GRCh38.primary_assembly.genome.fa.2.bt2 added
7fa058a79ad2_GRCh38.primary_assembly.genome.fa.3.bt2 added
7fa063a57e76_GRCh38.primary_assembly.genome.fa.4.bt2 added
7fa0611a816_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
7fa071323f76_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
7fa019e49609_outfile.txt added
7fa06e363626_GRCh37_to_GRCh38.chain added
7fa0291d3151_GRCh37_to_NCBI34.chain added
7fa03b90d1ed_GRCh37_to_NCBI35.chain added
7fa020c63d28_GRCh37_to_NCBI36.chain added
7fa036d91de7_GRCh38_to_GRCh37.chain added
7fa0683a44d2_GRCh38_to_NCBI34.chain added
7fa0497c6c73_GRCh38_to_NCBI35.chain added
7fa07b417b6_GRCh38_to_NCBI36.chain added
7fa04080b1ad_NCBI34_to_GRCh37.chain added
7fa04110f5f0_NCBI34_to_GRCh38.chain added
7fa0408280ef_NCBI35_to_GRCh37.chain added
7fa037deebff_NCBI35_to_GRCh38.chain added
7fa0c57cf01_NCBI36_to_GRCh37.chain added
7fa058d750fb_NCBI36_to_GRCh38.chain added
7fa02005bc4e_GRCm38_to_NCBIM36.chain added
7fa0588db54e_GRCm38_to_NCBIM37.chain added
7fa03f7a414d_NCBIM36_to_GRCm38.chain added
7fa0735546c9_NCBIM37_to_GRCm38.chain added
7fa0639a7146_1000G_omni2.5.b37.vcf.gz added
7fa03082ddc0_1000G_omni2.5.b37.vcf.gz.tbi added
7fa05fac8121_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
7fa03651ce99_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
7fa034d2baab_1000G_omni2.5.hg38.vcf.gz added
7fa076dd4ba4_1000G_omni2.5.hg38.vcf.gz.tbi added
7fa03a9138f3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
7fa01431f78f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
7fa05c73d7a4_af-only-gnomad.raw.sites.vcf added
7fa039527f67_af-only-gnomad.raw.sites.vcf.idx added
7fa0572a6097_Mutect2-exome-panel.vcf.idx added
7fa01f2b8636_Mutect2-WGS-panel-b37.vcf added
7fa062785336_Mutect2-WGS-panel-b37.vcf.idx added
7fa0499f30bb_small_exac_common_3.vcf added
7fa072386abf_small_exac_common_3.vcf.idx added
7fa055e85c2e_1000g_pon.hg38.vcf.gz added
7fa09fbfc12_1000g_pon.hg38.vcf.gz.tbi added
7fa07e6206dc_af-only-gnomad.hg38.vcf.gz added
7fa055b09656_af-only-gnomad.hg38.vcf.gz.tbi added
7fa03c5e140d_small_exac_common_3.hg38.vcf.gz added
7fa044768071_small_exac_common_3.hg38.vcf.gz.tbi added
7fa03fea9dd4_gencode.v41.annotation.gtf added
7fa0441fea14_gencode.v42.annotation.gtf added
7fa0b40e9fd_gencode.vM30.annotation.gtf added
7fa052c1e6d0_gencode.vM31.annotation.gtf added
7fa038188c22_gencode.v41.transcripts.fa added
7fa0539828f3_gencode.v41.transcripts.fa.fai added
7fa02aa89465_gencode.v42.transcripts.fa added
7fa021a688c4_gencode.v42.transcripts.fa.fai added
7fa03c5d0d1e_gencode.vM30.pc_transcripts.fa added
7fa01084b88_gencode.vM30.pc_transcripts.fa.fai added
7fa04796ce3f_gencode.vM31.pc_transcripts.fa added
7fa07dbeaed0_gencode.vM31.pc_transcripts.fa.fai added
7fa071c71a2e_GRCh38.primary_assembly.genome.fa.1.ht2 added
7fa04687fc5d_GRCh38.primary_assembly.genome.fa.2.ht2 added
7fa09c961d8_GRCh38.primary_assembly.genome.fa.3.ht2 added
7fa0436b0ed_GRCh38.primary_assembly.genome.fa.4.ht2 added
7fa0229999c4_GRCh38.primary_assembly.genome.fa.5.ht2 added
7fa0123e249b_GRCh38.primary_assembly.genome.fa.6.ht2 added
7fa02dd54578_GRCh38.primary_assembly.genome.fa.7.ht2 added
7fa0cc3e0ca_GRCh38.primary_assembly.genome.fa.8.ht2 added
7fa0fdaf452_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
7fa06fde3b9f_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
7fa0671c7d19_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
7fa07f592931_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
7fa0369f9148_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
7fa025fb29fc_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
7fa0c8172df_GRCh38_full_analysis_set_plus_decoy_hla.fa added
7fa069c94e3_GRCh38.primary_assembly.genome.fa.fai added
7fa011f2c679_GRCh38.primary_assembly.genome.fa.amb added
7fa059c43b23_GRCh38.primary_assembly.genome.fa.ann added
7fa06206a4df_GRCh38.primary_assembly.genome.fa.bwt added
7fa022325ec0_GRCh38.primary_assembly.genome.fa.pac added
7fa018eaa0ca_GRCh38.primary_assembly.genome.fa.sa added
7fa053e23a8d_GRCh38.primary_assembly.genome.fa added
7fa029722a01_hs37d5.fa.fai added
7fa0623bce9_hs37d5.fa.amb added
7fa014476825_hs37d5.fa.ann added
7fa05c065f89_hs37d5.fa.bwt added
7fa0266a4a92_hs37d5.fa.pac added
7fa0c45caf2_hs37d5.fa.sa added
7fa03a0edc29_hs37d5.fa added
7fa025982586_complete_ref_lens.bin added
7fa027c793b2_ctable.bin added
7fa01fb19f85_ctg_offsets.bin added
7fa0465fe504_duplicate_clusters.tsv added
7fa041b48db4_info.json added
7fa034c3461f_mphf.bin added
7fa030b849_pos.bin added
7fa07e92c0b7_pre_indexing.log added
7fa054aa6f4c_rank.bin added
7fa01711201_ref_indexing.log added
7fa026550064_refAccumLengths.bin added
7fa0168cb8e5_reflengths.bin added
7fa070becdf3_refseq.bin added
7fa07ec34658_seq.bin added
7fa0463f7c6c_versionInfo.json added
7fa07201ba7b_salmon_index added
7fa04f7a1bb6_chrLength.txt added
7fa059b1727d_chrName.txt added
7fa010d39a8c_chrNameLength.txt added
7fa0344765f5_chrStart.txt added
7fa03b76d2a3_exonGeTrInfo.tab added
7fa075fee9d4_exonInfo.tab added
7fa032a999d1_geneInfo.tab added
7fa01cb18253_Genome added
7fa049e325dc_genomeParameters.txt added
7fa05fcab469_Log.out added
7fa0750a8aa0_SA added
7fa07134a68_SAindex added
7fa0379f579_sjdbInfo.txt added
7fa03be2dcb7_sjdbList.fromGTF.out.tab added
7fa02b089118_sjdbList.out.tab added
7fa03f6dd4ba_transcriptInfo.tab added
7fa043a91fde_GRCh38.GENCODE.v42_100 added
7fa0146b4a86_knownGene_hg38.sql added
7fa0fe9ade3_knownGene_hg38.txt added
7fa036971a3e_refGene_hg38.sql added
7fa07a3bf871_refGene_hg38.txt added
7fa077340168_knownGene_mm39.sql added
7fa077488ffb_knownGene_mm39.txt added
7fa03ce4e4eb_refGene_mm39.sql added
7fa057711f88_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/RtmpPKAkls/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
26.598 3.707 32.126
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.412 | 0.928 | 8.473 | |
| dataSearch | 1.273 | 0.060 | 1.357 | |
| dataUpdate | 0.000 | 0.001 | 0.000 | |
| getCloudData | 2.867 | 0.184 | 4.421 | |
| getData | 0.001 | 0.001 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.159 | 0.021 | 0.185 | |
| recipeLoad | 1.500 | 0.125 | 1.647 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.648 | 0.041 | 0.693 | |
| recipeUpdate | 0 | 0 | 0 | |