Qian Liu
| Snapshot Date: 2025-07-14 13:25 -0400 (Mon, 14 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 2025-07-15 12:05 -0400 (Tue, 15 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" | 4785 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4524 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4565 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4508 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4509 |
| 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 1736/2311 | 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: 2025-07-15 01:45:30 -0400 (Tue, 15 Jul 2025) |
| EndedAt: 2025-07-15 01:48:14 -0400 (Tue, 15 Jul 2025) |
| EllapsedTime: 164.3 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 6.087 0.245 6.335
* 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...
3acc685c8c65_GRCh38.primary_assembly.genome.fa.1.bt2 added
3acc6900fdd7_GRCh38.primary_assembly.genome.fa.2.bt2 added
3acc189c82ce_GRCh38.primary_assembly.genome.fa.3.bt2 added
3acc30a41d00_GRCh38.primary_assembly.genome.fa.4.bt2 added
3acc3bf8e2a8_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3acc18e4abfe_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3acc222c9c57_outfile.txt added
3acc7dea969c_GRCh37_to_GRCh38.chain added
3acc6715799a_GRCh37_to_NCBI34.chain added
3acc5fd68b86_GRCh37_to_NCBI35.chain added
3accb53ba65_GRCh37_to_NCBI36.chain added
3accdde3ca3_GRCh38_to_GRCh37.chain added
3acc5397c223_GRCh38_to_NCBI34.chain added
3acc38d6f93a_GRCh38_to_NCBI35.chain added
3acc196cd60e_GRCh38_to_NCBI36.chain added
3acc7a83f5e_NCBI34_to_GRCh37.chain added
3acc778bafc_NCBI34_to_GRCh38.chain added
3acc4d789fa5_NCBI35_to_GRCh37.chain added
3acc716f07c4_NCBI35_to_GRCh38.chain added
3acc521c85ce_NCBI36_to_GRCh37.chain added
3acc7004404b_NCBI36_to_GRCh38.chain added
3accdd22f54_GRCm38_to_NCBIM36.chain added
3acc117cdaf4_GRCm38_to_NCBIM37.chain added
3acc1222a3ef_NCBIM36_to_GRCm38.chain added
3acc4a2f3d18_NCBIM37_to_GRCm38.chain added
3acc270c8487_1000G_omni2.5.b37.vcf.gz added
3acc557acffd_1000G_omni2.5.b37.vcf.gz.tbi added
3acc7a96761_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3acc74c46716_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3acc78166cd1_1000G_omni2.5.hg38.vcf.gz added
3acc6cda2d32_1000G_omni2.5.hg38.vcf.gz.tbi added
3acc5d20f37c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3acc61176aa8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3acc576b000_af-only-gnomad.raw.sites.vcf added
3accdc5107c_af-only-gnomad.raw.sites.vcf.idx added
3acc1d104d50_Mutect2-exome-panel.vcf.idx added
3acc1e5b5bfe_Mutect2-WGS-panel-b37.vcf added
3acc2ff1acd4_Mutect2-WGS-panel-b37.vcf.idx added
3acc1afae3ec_small_exac_common_3.vcf added
3acc570d599_small_exac_common_3.vcf.idx added
3accfc8385a_1000g_pon.hg38.vcf.gz added
3acc264e9e52_1000g_pon.hg38.vcf.gz.tbi added
3acc134f123c_af-only-gnomad.hg38.vcf.gz added
3acc635ffa7e_af-only-gnomad.hg38.vcf.gz.tbi added
3acc5f25978c_small_exac_common_3.hg38.vcf.gz added
3acc2cbbe84a_small_exac_common_3.hg38.vcf.gz.tbi added
3acc6b0839dc_gencode.v41.annotation.gtf added
3acc669e5289_gencode.v42.annotation.gtf added
3acc7a3487f0_gencode.vM30.annotation.gtf added
3acc5c7741a0_gencode.vM31.annotation.gtf added
3acc38bad857_gencode.v41.transcripts.fa added
3acc6a38c83b_gencode.v41.transcripts.fa.fai added
3acc6a4970f5_gencode.v42.transcripts.fa added
3acc4a37b34b_gencode.v42.transcripts.fa.fai added
3acc7c5b6c2a_gencode.vM30.pc_transcripts.fa added
3acc3478ae0d_gencode.vM30.pc_transcripts.fa.fai added
3acc714437d3_gencode.vM31.pc_transcripts.fa added
3acc51d63c27_gencode.vM31.pc_transcripts.fa.fai added
3acc3c22156e_GRCh38.primary_assembly.genome.fa.1.ht2 added
3acc66089ee9_GRCh38.primary_assembly.genome.fa.2.ht2 added
3acc49eca8f8_GRCh38.primary_assembly.genome.fa.3.ht2 added
3acc28fc42a1_GRCh38.primary_assembly.genome.fa.4.ht2 added
3acc43299265_GRCh38.primary_assembly.genome.fa.5.ht2 added
3acc2b0413a1_GRCh38.primary_assembly.genome.fa.6.ht2 added
3acc2e72f2a1_GRCh38.primary_assembly.genome.fa.7.ht2 added
3acc50eea2e2_GRCh38.primary_assembly.genome.fa.8.ht2 added
3acc481460f1_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3acc4cce4ea0_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3acce04fb6_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3acc630f44de_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3acc523f2439_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3acc10a88810_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3acc95de330_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3acc658e3675_GRCh38.primary_assembly.genome.fa.fai added
3acc7408828e_GRCh38.primary_assembly.genome.fa.amb added
3acc68837abc_GRCh38.primary_assembly.genome.fa.ann added
3acc124a1ebf_GRCh38.primary_assembly.genome.fa.bwt added
3acc5f10bc6b_GRCh38.primary_assembly.genome.fa.pac added
3acc4f21cd45_GRCh38.primary_assembly.genome.fa.sa added
3accc7ea6af_GRCh38.primary_assembly.genome.fa added
3acc3b87fe0b_hs37d5.fa.fai added
3acc7dca59c_hs37d5.fa.amb added
3acc76b76eeb_hs37d5.fa.ann added
3acc25d16f00_hs37d5.fa.bwt added
3acc521458e8_hs37d5.fa.pac added
3acc7312db15_hs37d5.fa.sa added
3acc5a4a1d0d_hs37d5.fa added
3acc435890bb_complete_ref_lens.bin added
3acc44e9173d_ctable.bin added
3acc166c327c_ctg_offsets.bin added
3acc29612fa4_duplicate_clusters.tsv added
3acced5c035_info.json added
3acc3f68751d_mphf.bin added
3acc6c8ac20a_pos.bin added
3acc39d9d3d6_pre_indexing.log added
3acc6ddb67be_rank.bin added
3acc3d7964ec_ref_indexing.log added
3acc1ee34c8_refAccumLengths.bin added
3acc3aa9b65e_reflengths.bin added
3acc3e59b4a2_refseq.bin added
3acc64fd79a6_seq.bin added
3accce8da97_versionInfo.json added
3acc4f023cb2_salmon_index added
3acc6e5b5cd6_chrLength.txt added
3acc7277110c_chrName.txt added
3acc430abf41_chrNameLength.txt added
3acc56ded792_chrStart.txt added
3acc4c12fcc_exonGeTrInfo.tab added
3acc221b7bac_exonInfo.tab added
3acc2600a4d8_geneInfo.tab added
3acc113fd67b_Genome added
3acc5da379b7_genomeParameters.txt added
3acc2ddd4a74_Log.out added
3acc7f74566_SA added
3acc374e8b8_SAindex added
3acc7ff1a35c_sjdbInfo.txt added
3acc7b0a207c_sjdbList.fromGTF.out.tab added
3acc5dbf05c5_sjdbList.out.tab added
3acc434a3417_transcriptInfo.tab added
3acc3ff337b9_GRCh38.GENCODE.v42_100 added
3acc742b3841_knownGene_hg38.sql added
3acc6cab63bc_knownGene_hg38.txt added
3acc4ec8f7ee_refGene_hg38.sql added
3acc3393ad5e_refGene_hg38.txt added
3acc593625c6_knownGene_mm39.sql added
3acc8a2cbc5_knownGene_mm39.txt added
3acc216f151d_refGene_mm39.sql added
3acc16af8ab2_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/Rtmp4YxWkq/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
18.677 1.437 20.441
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.087 | 0.245 | 6.335 | |
| dataSearch | 1.093 | 0.012 | 1.105 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.669 | 0.097 | 3.721 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.121 | 0.002 | 0.124 | |
| recipeLoad | 1.271 | 0.013 | 1.284 | |
| recipeMake | 0.001 | 0.000 | 0.000 | |
| recipeSearch | 0.533 | 0.007 | 0.540 | |
| recipeUpdate | 0 | 0 | 0 | |