Qian Liu
| Snapshot Date: 2025-12-01 13:45 -0500 (Mon, 01 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_22 |
| git_last_commit: 2d4066b |
| git_last_commit_date: 2025-10-29 11:20:44 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-04 12:02 -0500 (Thu, 04 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4878 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4624 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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 1773/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.10.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: ReUseData |
| Version: 1.10.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReUseData_1.10.0.tar.gz |
| StartedAt: 2025-12-02 13:40:32 -0000 (Tue, 02 Dec 2025) |
| EndedAt: 2025-12-02 13:43:18 -0000 (Tue, 02 Dec 2025) |
| EllapsedTime: 166.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReUseData_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.10.0’
* 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 loading without being on the library search path ... 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 8.686 0.570 9.295
getCloudData 3.059 0.104 6.494
* 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
‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.10.0’ ** 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 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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...
36977753f84c42_GRCh38.primary_assembly.genome.fa.1.bt2 added
36977772c265d7_GRCh38.primary_assembly.genome.fa.2.bt2 added
369777cc5a7c0_GRCh38.primary_assembly.genome.fa.3.bt2 added
369777659fea7b_GRCh38.primary_assembly.genome.fa.4.bt2 added
3697774c26af0b_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
36977777f9b46f_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
36977724ab65e9_outfile.txt added
3697773baab855_GRCh37_to_GRCh38.chain added
3697771359692f_GRCh37_to_NCBI34.chain added
36977777a2a9db_GRCh37_to_NCBI35.chain added
3697774a63eed_GRCh37_to_NCBI36.chain added
3697772a59dd79_GRCh38_to_GRCh37.chain added
369777b926c25_GRCh38_to_NCBI34.chain added
3697775f7d316c_GRCh38_to_NCBI35.chain added
36977758ab4265_GRCh38_to_NCBI36.chain added
36977747209fd_NCBI34_to_GRCh37.chain added
36977722579da8_NCBI34_to_GRCh38.chain added
36977734129fde_NCBI35_to_GRCh37.chain added
3697777e1d1dad_NCBI35_to_GRCh38.chain added
369777ecf5dd4_NCBI36_to_GRCh37.chain added
3697771ad83e1e_NCBI36_to_GRCh38.chain added
36977719078a9d_GRCm38_to_NCBIM36.chain added
3697771e615fc_GRCm38_to_NCBIM37.chain added
36977757366df0_NCBIM36_to_GRCm38.chain added
369777722f0300_NCBIM37_to_GRCm38.chain added
3697771d7e7a47_1000G_omni2.5.b37.vcf.gz added
369777448afc6a_1000G_omni2.5.b37.vcf.gz.tbi added
36977721a1296d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3697775854213a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3697776d06cb22_1000G_omni2.5.hg38.vcf.gz added
369777c10fe94_1000G_omni2.5.hg38.vcf.gz.tbi added
3697772c4c6d7d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3697775fc930f9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
36977718d6a654_af-only-gnomad.raw.sites.vcf added
36977711ec57f8_af-only-gnomad.raw.sites.vcf.idx added
3697772befe004_Mutect2-exome-panel.vcf.idx added
36977710d05ac3_Mutect2-WGS-panel-b37.vcf added
3697773697bde2_Mutect2-WGS-panel-b37.vcf.idx added
369777679a985a_small_exac_common_3.vcf added
3697772429c3f2_small_exac_common_3.vcf.idx added
3697772e3a67bd_1000g_pon.hg38.vcf.gz added
3697776c40d747_1000g_pon.hg38.vcf.gz.tbi added
3697774e83a16b_af-only-gnomad.hg38.vcf.gz added
36977739ccd3e2_af-only-gnomad.hg38.vcf.gz.tbi added
3697774bbe08b4_small_exac_common_3.hg38.vcf.gz added
369777272ee3d1_small_exac_common_3.hg38.vcf.gz.tbi added
3697773e3edddf_gencode.v41.annotation.gtf added
3697776e15a65c_gencode.v42.annotation.gtf added
3697775b4183af_gencode.vM30.annotation.gtf added
3697773c5bfb8c_gencode.vM31.annotation.gtf added
3697777ce50430_gencode.v41.transcripts.fa added
3697777619c1cd_gencode.v41.transcripts.fa.fai added
3697775563862a_gencode.v42.transcripts.fa added
3697777ecb1a2c_gencode.v42.transcripts.fa.fai added
3697774d502fbd_gencode.vM30.pc_transcripts.fa added
3697774792892a_gencode.vM30.pc_transcripts.fa.fai added
3697771c499473_gencode.vM31.pc_transcripts.fa added
36977711db2c28_gencode.vM31.pc_transcripts.fa.fai added
3697776933b297_GRCh38.primary_assembly.genome.fa.1.ht2 added
369777749db5ae_GRCh38.primary_assembly.genome.fa.2.ht2 added
3697777ee1f74a_GRCh38.primary_assembly.genome.fa.3.ht2 added
3697777544b12b_GRCh38.primary_assembly.genome.fa.4.ht2 added
36977720ea232b_GRCh38.primary_assembly.genome.fa.5.ht2 added
3697775eab2844_GRCh38.primary_assembly.genome.fa.6.ht2 added
369777e1b577f_GRCh38.primary_assembly.genome.fa.7.ht2 added
36977732d67b23_GRCh38.primary_assembly.genome.fa.8.ht2 added
369777a9b0848_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3697771eebb243_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
369777696e3905_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3697777235a0a2_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
36977743157635_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
36977717a8a0c2_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3697775e7677ea_GRCh38_full_analysis_set_plus_decoy_hla.fa added
369777119917a1_GRCh38.primary_assembly.genome.fa.fai added
369777517574a4_GRCh38.primary_assembly.genome.fa.amb added
3697772a34809e_GRCh38.primary_assembly.genome.fa.ann added
36977738c7fb72_GRCh38.primary_assembly.genome.fa.bwt added
369777fb45284_GRCh38.primary_assembly.genome.fa.pac added
369777184a26fa_GRCh38.primary_assembly.genome.fa.sa added
36977714097f21_GRCh38.primary_assembly.genome.fa added
3697774c104e10_hs37d5.fa.fai added
369777152f2b2a_hs37d5.fa.amb added
369777a2340ee_hs37d5.fa.ann added
3697772173d43a_hs37d5.fa.bwt added
36977713fa4556_hs37d5.fa.pac added
369777577370ab_hs37d5.fa.sa added
36977769065d64_hs37d5.fa added
3697773043d9ca_complete_ref_lens.bin added
369777694e9cd3_ctable.bin added
369777523a0ffc_ctg_offsets.bin added
36977724e18f78_duplicate_clusters.tsv added
3697776830941e_info.json added
369777477ec127_mphf.bin added
36977745cbb2a3_pos.bin added
36977746dbbc62_pre_indexing.log added
369777559a18a7_rank.bin added
36977778a22dc6_ref_indexing.log added
3697775176c4aa_refAccumLengths.bin added
3697777485caea_reflengths.bin added
369777621066cc_refseq.bin added
36977743ac654d_seq.bin added
369777379b411f_versionInfo.json added
36977779b9078e_salmon_index added
3697772222dd37_chrLength.txt added
369777493458c0_chrName.txt added
3697774b2e7c33_chrNameLength.txt added
3697774c575dd5_chrStart.txt added
3697771fc5432_exonGeTrInfo.tab added
3697775ae2ceb7_exonInfo.tab added
36977764a184cf_geneInfo.tab added
3697771605d353_Genome added
36977726f31cc7_genomeParameters.txt added
36977779d0aff9_Log.out added
36977720291441_SA added
3697774866f102_SAindex added
369777dcaf54f_sjdbInfo.txt added
369777779c84ed_sjdbList.fromGTF.out.tab added
369777316d4e66_sjdbList.out.tab added
3697773e0ecf19_transcriptInfo.tab added
36977760eb21c0_GRCh38.GENCODE.v42_100 added
3697773a75e62_knownGene_hg38.sql added
36977762f05e91_knownGene_hg38.txt added
369777491bb5de_refGene_hg38.sql added
3697774b261f8a_refGene_hg38.txt added
36977728bc1134_knownGene_mm39.sql added
369777ff77240_knownGene_mm39.txt added
36977720c03831_refGene_mm39.sql added
369777215e3efb_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:
/home/biocbuild/tmp/RtmphMte9G/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
24.353 1.536 29.292
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 8.686 | 0.570 | 9.295 | |
| dataSearch | 1.705 | 0.012 | 1.721 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 3.059 | 0.104 | 6.494 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.167 | 0.015 | 0.186 | |
| recipeLoad | 1.826 | 0.052 | 1.889 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.783 | 0.012 | 0.796 | |
| recipeUpdate | 0 | 0 | 0 | |