Qian Liu
| Snapshot Date: 2025-07-28 13:25 -0400 (Mon, 28 Jul 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 2025-07-29 12:05 -0400 (Tue, 29 Jul 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" | 4535 |
| 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" | 4516 |
| 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. |
| Package: ReUseData |
| Version: 1.9.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.9.0.tar.gz |
| StartedAt: 2025-07-29 01:56:39 -0400 (Tue, 29 Jul 2025) |
| EndedAt: 2025-07-29 01:59:24 -0400 (Tue, 29 Jul 2025) |
| EllapsedTime: 165.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* 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 5.963 0.242 6.208
* 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 re-building of vignette outputs ... OK
* 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/bbs-3.22-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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...
3aef9f7e60d77_GRCh38.primary_assembly.genome.fa.1.bt2 added
3aef9f58be13fd_GRCh38.primary_assembly.genome.fa.2.bt2 added
3aef9f551a2305_GRCh38.primary_assembly.genome.fa.3.bt2 added
3aef9f176bda0c_GRCh38.primary_assembly.genome.fa.4.bt2 added
3aef9f11f7643f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3aef9fce40cb9_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3aef9f72f7dedd_outfile.txt added
3aef9f35ae428f_GRCh37_to_GRCh38.chain added
3aef9f45896356_GRCh37_to_NCBI34.chain added
3aef9ffc9ec05_GRCh37_to_NCBI35.chain added
3aef9f102d28f7_GRCh37_to_NCBI36.chain added
3aef9f61cab9b_GRCh38_to_GRCh37.chain added
3aef9f45d72bc0_GRCh38_to_NCBI34.chain added
3aef9f160d1b60_GRCh38_to_NCBI35.chain added
3aef9f49b09e62_GRCh38_to_NCBI36.chain added
3aef9f727e6595_NCBI34_to_GRCh37.chain added
3aef9f4c1a5904_NCBI34_to_GRCh38.chain added
3aef9f116d2610_NCBI35_to_GRCh37.chain added
3aef9f2fd5585b_NCBI35_to_GRCh38.chain added
3aef9f2279e32a_NCBI36_to_GRCh37.chain added
3aef9f100befd_NCBI36_to_GRCh38.chain added
3aef9f1634a849_GRCm38_to_NCBIM36.chain added
3aef9f739c9e32_GRCm38_to_NCBIM37.chain added
3aef9f498beaef_NCBIM36_to_GRCm38.chain added
3aef9f662fb1c0_NCBIM37_to_GRCm38.chain added
3aef9f319e81a8_1000G_omni2.5.b37.vcf.gz added
3aef9f6cc858a8_1000G_omni2.5.b37.vcf.gz.tbi added
3aef9f36fe1e14_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3aef9f45027261_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3aef9f7b667d18_1000G_omni2.5.hg38.vcf.gz added
3aef9f5d104f32_1000G_omni2.5.hg38.vcf.gz.tbi added
3aef9f4ce87fd8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3aef9f54249115_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3aef9f322a7238_af-only-gnomad.raw.sites.vcf added
3aef9f645459e5_af-only-gnomad.raw.sites.vcf.idx added
3aef9f661bf554_Mutect2-exome-panel.vcf.idx added
3aef9f3f0e7ef1_Mutect2-WGS-panel-b37.vcf added
3aef9f574c38c2_Mutect2-WGS-panel-b37.vcf.idx added
3aef9f1bca37e4_small_exac_common_3.vcf added
3aef9f497e247_small_exac_common_3.vcf.idx added
3aef9f671624c8_1000g_pon.hg38.vcf.gz added
3aef9f2bf760db_1000g_pon.hg38.vcf.gz.tbi added
3aef9fab48de3_af-only-gnomad.hg38.vcf.gz added
3aef9f2ced5088_af-only-gnomad.hg38.vcf.gz.tbi added
3aef9f42047c3b_small_exac_common_3.hg38.vcf.gz added
3aef9f54652c45_small_exac_common_3.hg38.vcf.gz.tbi added
3aef9f1f6bb61d_gencode.v41.annotation.gtf added
3aef9fe1ed53f_gencode.v42.annotation.gtf added
3aef9f65d25255_gencode.vM30.annotation.gtf added
3aef9f4f410e79_gencode.vM31.annotation.gtf added
3aef9f3098b869_gencode.v41.transcripts.fa added
3aef9f66d31152_gencode.v41.transcripts.fa.fai added
3aef9f6575b6c2_gencode.v42.transcripts.fa added
3aef9f2435569b_gencode.v42.transcripts.fa.fai added
3aef9f305efc41_gencode.vM30.pc_transcripts.fa added
3aef9f4ba56883_gencode.vM30.pc_transcripts.fa.fai added
3aef9f55d3d843_gencode.vM31.pc_transcripts.fa added
3aef9f1d2754e9_gencode.vM31.pc_transcripts.fa.fai added
3aef9f2a38697_GRCh38.primary_assembly.genome.fa.1.ht2 added
3aef9f1ad64aa4_GRCh38.primary_assembly.genome.fa.2.ht2 added
3aef9f188dd201_GRCh38.primary_assembly.genome.fa.3.ht2 added
3aef9f5fb3d5c9_GRCh38.primary_assembly.genome.fa.4.ht2 added
3aef9f67beca7d_GRCh38.primary_assembly.genome.fa.5.ht2 added
3aef9f6cb26317_GRCh38.primary_assembly.genome.fa.6.ht2 added
3aef9f11de4801_GRCh38.primary_assembly.genome.fa.7.ht2 added
3aef9f4c132462_GRCh38.primary_assembly.genome.fa.8.ht2 added
3aef9f52ce586b_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3aef9f50ecc6f2_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3aef9f235f5d24_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3aef9f6e98904f_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3aef9f5584a93a_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3aef9fa7581ec_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3aef9f1a8ff12a_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3aef9f6039371d_GRCh38.primary_assembly.genome.fa.fai added
3aef9f3762d274_GRCh38.primary_assembly.genome.fa.amb added
3aef9f5c946d66_GRCh38.primary_assembly.genome.fa.ann added
3aef9f349e6362_GRCh38.primary_assembly.genome.fa.bwt added
3aef9f56ce8892_GRCh38.primary_assembly.genome.fa.pac added
3aef9f6ab342a5_GRCh38.primary_assembly.genome.fa.sa added
3aef9f1a70b5b8_GRCh38.primary_assembly.genome.fa added
3aef9f260f970b_hs37d5.fa.fai added
3aef9f1b4bfb0f_hs37d5.fa.amb added
3aef9f143c70a_hs37d5.fa.ann added
3aef9fb854dcd_hs37d5.fa.bwt added
3aef9f3f8151aa_hs37d5.fa.pac added
3aef9f31a2c34c_hs37d5.fa.sa added
3aef9f572ab650_hs37d5.fa added
3aef9f155529ee_complete_ref_lens.bin added
3aef9f4eca1835_ctable.bin added
3aef9f59ce3ce7_ctg_offsets.bin added
3aef9f302b7492_duplicate_clusters.tsv added
3aef9f6757ea37_info.json added
3aef9f398212b1_mphf.bin added
3aef9f17ea3f0f_pos.bin added
3aef9f540a4d4e_pre_indexing.log added
3aef9f4b605ab2_rank.bin added
3aef9f63fd6371_ref_indexing.log added
3aef9f26d8a5b9_refAccumLengths.bin added
3aef9f1c4d21a5_reflengths.bin added
3aef9f75cc096_refseq.bin added
3aef9f15713609_seq.bin added
3aef9f71d1cadf_versionInfo.json added
3aef9f11d24282_salmon_index added
3aef9f30012733_chrLength.txt added
3aef9f520b01fc_chrName.txt added
3aef9f493514f7_chrNameLength.txt added
3aef9fc959499_chrStart.txt added
3aef9f6a9655e_exonGeTrInfo.tab added
3aef9f20039d89_exonInfo.tab added
3aef9f7748d73f_geneInfo.tab added
3aef9f211a1b16_Genome added
3aef9f46133494_genomeParameters.txt added
3aef9f1294d24e_Log.out added
3aef9f225de221_SA added
3aef9f51988261_SAindex added
3aef9f521623f8_sjdbInfo.txt added
3aef9f5400a56d_sjdbList.fromGTF.out.tab added
3aef9f28c338b2_sjdbList.out.tab added
3aef9f676b4de6_transcriptInfo.tab added
3aef9f22cabda2_GRCh38.GENCODE.v42_100 added
3aef9f2917599_knownGene_hg38.sql added
3aef9f1796c279_knownGene_hg38.txt added
3aef9fa22a7d9_refGene_hg38.sql added
3aef9f3c13884a_refGene_hg38.txt added
3aef9f2f810188_knownGene_mm39.sql added
3aef9f5e2cf527_knownGene_mm39.txt added
3aef9f773e2fd_refGene_mm39.sql added
3aef9f137e64fa_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/RtmpfMwV1z/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
19.202 1.855 21.351
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.963 | 0.242 | 6.208 | |
| dataSearch | 1.113 | 0.013 | 1.126 | |
| dataUpdate | 0.001 | 0.000 | 0.000 | |
| getCloudData | 2.638 | 0.103 | 3.306 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.134 | 0.002 | 0.137 | |
| recipeLoad | 1.238 | 0.011 | 1.251 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.526 | 0.005 | 0.530 | |
| recipeUpdate | 0 | 0 | 0 | |