Qian Liu
| Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: c5927b9 |
| git_last_commit_date: 2025-04-15 13:01:44 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-04 12:13 -0400 (Mon, 04 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4536 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
| 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 1737/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.9.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | 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 | | ||||||||
| 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: 1.9.0 |
| 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_1.9.0.tar.gz |
| StartedAt: 2025-08-01 10:14:04 -0000 (Fri, 01 Aug 2025) |
| EndedAt: 2025-08-01 10:17:04 -0000 (Fri, 01 Aug 2025) |
| EllapsedTime: 180.2 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_1.9.0.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 ‘1.9.0’
* 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 8.333 0.332 10.014
getCloudData 3.021 0.208 6.130
* 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 ‘1.9.0’ ** 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...
149734535a8eae_GRCh38.primary_assembly.genome.fa.1.bt2 added
14973426f6dddf_GRCh38.primary_assembly.genome.fa.2.bt2 added
14973459d57a9f_GRCh38.primary_assembly.genome.fa.3.bt2 added
14973475aa6192_GRCh38.primary_assembly.genome.fa.4.bt2 added
1497344a0290c1_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1497345dff2108_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
149734267e55de_outfile.txt added
1497346660119f_GRCh37_to_GRCh38.chain added
1497347b44e9f2_GRCh37_to_NCBI34.chain added
1497343e1ee0f_GRCh37_to_NCBI35.chain added
1497343e8ba216_GRCh37_to_NCBI36.chain added
14973476b85d0c_GRCh38_to_GRCh37.chain added
14973411dc0b05_GRCh38_to_NCBI34.chain added
1497343a7f6f76_GRCh38_to_NCBI35.chain added
1497342b6a444d_GRCh38_to_NCBI36.chain added
1497346d8ca256_NCBI34_to_GRCh37.chain added
1497341a8991b6_NCBI34_to_GRCh38.chain added
14973470a039f6_NCBI35_to_GRCh37.chain added
1497341f0b91b4_NCBI35_to_GRCh38.chain added
1497342ac56f37_NCBI36_to_GRCh37.chain added
1497344938ea92_NCBI36_to_GRCh38.chain added
14973433bd1af8_GRCm38_to_NCBIM36.chain added
1497341cb6c6a2_GRCm38_to_NCBIM37.chain added
14973424f88a33_NCBIM36_to_GRCm38.chain added
1497344e333d00_NCBIM37_to_GRCm38.chain added
149734737c5cb1_1000G_omni2.5.b37.vcf.gz added
1497348a3bffe_1000G_omni2.5.b37.vcf.gz.tbi added
1497345b0001ed_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1497346ba99466_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
14973456f88f52_1000G_omni2.5.hg38.vcf.gz added
14973454528794_1000G_omni2.5.hg38.vcf.gz.tbi added
1497343f042314_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1497347def6d31_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1497342e280233_af-only-gnomad.raw.sites.vcf added
14973434ae84a6_af-only-gnomad.raw.sites.vcf.idx added
14973447f1fdf2_Mutect2-exome-panel.vcf.idx added
149734c27233b_Mutect2-WGS-panel-b37.vcf added
1497345b2cda84_Mutect2-WGS-panel-b37.vcf.idx added
1497342e520f92_small_exac_common_3.vcf added
14973476c0d2d_small_exac_common_3.vcf.idx added
1497345f0ec893_1000g_pon.hg38.vcf.gz added
1497346cddb1a8_1000g_pon.hg38.vcf.gz.tbi added
1497347e246a3a_af-only-gnomad.hg38.vcf.gz added
14973470ead399_af-only-gnomad.hg38.vcf.gz.tbi added
149734275d211e_small_exac_common_3.hg38.vcf.gz added
149734298eae87_small_exac_common_3.hg38.vcf.gz.tbi added
1497345e7775ef_gencode.v41.annotation.gtf added
14973441e6b2d4_gencode.v42.annotation.gtf added
1497341a2ee87d_gencode.vM30.annotation.gtf added
1497347d8307a3_gencode.vM31.annotation.gtf added
1497346cac220b_gencode.v41.transcripts.fa added
1497346367d310_gencode.v41.transcripts.fa.fai added
1497343140229b_gencode.v42.transcripts.fa added
149734962e8ae_gencode.v42.transcripts.fa.fai added
1497348605d43_gencode.vM30.pc_transcripts.fa added
1497347f735f9b_gencode.vM30.pc_transcripts.fa.fai added
1497347cdf455f_gencode.vM31.pc_transcripts.fa added
14973411041d41_gencode.vM31.pc_transcripts.fa.fai added
1497345a736188_GRCh38.primary_assembly.genome.fa.1.ht2 added
1497346888d9c5_GRCh38.primary_assembly.genome.fa.2.ht2 added
14973467fcac93_GRCh38.primary_assembly.genome.fa.3.ht2 added
1497342ec5e91d_GRCh38.primary_assembly.genome.fa.4.ht2 added
149734278cfcd9_GRCh38.primary_assembly.genome.fa.5.ht2 added
14973465ec19c5_GRCh38.primary_assembly.genome.fa.6.ht2 added
1497345cedeb50_GRCh38.primary_assembly.genome.fa.7.ht2 added
1497345c3b8180_GRCh38.primary_assembly.genome.fa.8.ht2 added
1497342dde17b7_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
14973469150e8c_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
14973437685c04_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1497345c302749_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
14973470811bb9_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
14973416772498_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
149734490dd8f1_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1497346ea585f3_GRCh38.primary_assembly.genome.fa.fai added
149734761f831_GRCh38.primary_assembly.genome.fa.amb added
149734706afa0f_GRCh38.primary_assembly.genome.fa.ann added
1497341834347a_GRCh38.primary_assembly.genome.fa.bwt added
14973465d96e20_GRCh38.primary_assembly.genome.fa.pac added
1497343251ace4_GRCh38.primary_assembly.genome.fa.sa added
14973432631cf8_GRCh38.primary_assembly.genome.fa added
149734635c75c3_hs37d5.fa.fai added
1497341efdceef_hs37d5.fa.amb added
14973415caf008_hs37d5.fa.ann added
149734149c985e_hs37d5.fa.bwt added
1497342860b79d_hs37d5.fa.pac added
1497341e2b4d4b_hs37d5.fa.sa added
149734140ff7fa_hs37d5.fa added
149734253ffcfd_complete_ref_lens.bin added
1497342f2f6a8c_ctable.bin added
1497346e835982_ctg_offsets.bin added
149734dc8d6c2_duplicate_clusters.tsv added
149734172c171f_info.json added
1497341d49429f_mphf.bin added
1497343555d39c_pos.bin added
1497347d1830e4_pre_indexing.log added
1497347a372df0_rank.bin added
1497341191551c_ref_indexing.log added
1497342af6489c_refAccumLengths.bin added
149734634c3c7c_reflengths.bin added
14973448f9b120_refseq.bin added
1497347266fe5_seq.bin added
14973453cd5835_versionInfo.json added
1497345f70d5b8_salmon_index added
149734503448d7_chrLength.txt added
1497344272de29_chrName.txt added
14973466d2cde9_chrNameLength.txt added
149734409f42e6_chrStart.txt added
1497345aa712a3_exonGeTrInfo.tab added
1497344cac3c09_exonInfo.tab added
14973472f0efca_geneInfo.tab added
149734d0a2f9b_Genome added
1497343008b1cc_genomeParameters.txt added
14973411eebeba_Log.out added
14973422d51fa3_SA added
14973444a54a2b_SAindex added
1497343a4f7657_sjdbInfo.txt added
14973441006cee_sjdbList.fromGTF.out.tab added
14973458b54225_sjdbList.out.tab added
1497345f8f7354_transcriptInfo.tab added
149734702fd77a_GRCh38.GENCODE.v42_100 added
14973447389ba7_knownGene_hg38.sql added
1497346d584a17_knownGene_hg38.txt added
14973475bee9a_refGene_hg38.sql added
1497346481de47_refGene_hg38.txt added
14973422ae1db3_knownGene_mm39.sql added
1497344741f7e_knownGene_mm39.txt added
1497345eb90c37_refGene_mm39.sql added
149734343f72cf_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/RtmpjUGyqa/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
25.041 1.776 35.081
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 8.333 | 0.332 | 10.014 | |
| dataSearch | 1.602 | 0.012 | 2.017 | |
| dataUpdate | 0.001 | 0.000 | 0.000 | |
| getCloudData | 3.021 | 0.208 | 6.130 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.169 | 0.003 | 0.200 | |
| recipeLoad | 1.822 | 0.079 | 2.422 | |
| recipeMake | 0.000 | 0.000 | 0.005 | |
| recipeSearch | 0.776 | 0.036 | 1.037 | |
| recipeUpdate | 0 | 0 | 0 | |