Qian Liu
| Snapshot Date: 2025-10-24 13:45 -0400 (Fri, 24 Oct 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 2025-10-25 12:04 -0400 (Sat, 25 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 1.9.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | NA | NA | ||||||||||
|
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: 2025-10-25 03:19:05 -0400 (Sat, 25 Oct 2025) |
| EndedAt: 2025-10-25 03:21:47 -0400 (Sat, 25 Oct 2025) |
| EllapsedTime: 162.1 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 Patched (2025-08-23 r88802)
* 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 24.04.3 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 5.867 0.227 6.097
* 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 Patched (2025-08-23 r88802) -- "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...
23353361efff33_GRCh38.primary_assembly.genome.fa.1.bt2 added
233533232cfe88_GRCh38.primary_assembly.genome.fa.2.bt2 added
233533317f6d64_GRCh38.primary_assembly.genome.fa.3.bt2 added
2335332d3fcb1d_GRCh38.primary_assembly.genome.fa.4.bt2 added
2335332aa099dd_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
233533136aeb39_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2335337b142fd_outfile.txt added
23353366b02537_GRCh37_to_GRCh38.chain added
23353321bc5845_GRCh37_to_NCBI34.chain added
2335336623424d_GRCh37_to_NCBI35.chain added
23353347a6f9a6_GRCh37_to_NCBI36.chain added
2335337c94c3c9_GRCh38_to_GRCh37.chain added
23353350d1a389_GRCh38_to_NCBI34.chain added
2335334b9c5d27_GRCh38_to_NCBI35.chain added
2335337a4a4b0_GRCh38_to_NCBI36.chain added
2335337a96bbfd_NCBI34_to_GRCh37.chain added
2335337466151b_NCBI34_to_GRCh38.chain added
233533a17255f_NCBI35_to_GRCh37.chain added
2335332f632715_NCBI35_to_GRCh38.chain added
2335338a75568_NCBI36_to_GRCh37.chain added
233533289e4534_NCBI36_to_GRCh38.chain added
2335332b6c96cd_GRCm38_to_NCBIM36.chain added
2335331f2cbf5e_GRCm38_to_NCBIM37.chain added
233533627b70c2_NCBIM36_to_GRCm38.chain added
2335335ea956b9_NCBIM37_to_GRCm38.chain added
233533263724c2_1000G_omni2.5.b37.vcf.gz added
23353340546f9f_1000G_omni2.5.b37.vcf.gz.tbi added
233533441339fb_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2335334c7f5607_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
233533571be86d_1000G_omni2.5.hg38.vcf.gz added
2335333bab05f5_1000G_omni2.5.hg38.vcf.gz.tbi added
2335332e6f553b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2335337a48e6f5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2335336d2a735a_af-only-gnomad.raw.sites.vcf added
2335335baf2058_af-only-gnomad.raw.sites.vcf.idx added
23353324e980d2_Mutect2-exome-panel.vcf.idx added
233533955e93_Mutect2-WGS-panel-b37.vcf added
23353363606355_Mutect2-WGS-panel-b37.vcf.idx added
233533b99a609_small_exac_common_3.vcf added
2335332251b6d8_small_exac_common_3.vcf.idx added
2335334983a5a2_1000g_pon.hg38.vcf.gz added
23353353409faf_1000g_pon.hg38.vcf.gz.tbi added
2335331ee67aa1_af-only-gnomad.hg38.vcf.gz added
2335331a55492b_af-only-gnomad.hg38.vcf.gz.tbi added
2335331edcfcd6_small_exac_common_3.hg38.vcf.gz added
233533268b1f52_small_exac_common_3.hg38.vcf.gz.tbi added
23353314ec0529_gencode.v41.annotation.gtf added
233533134311f2_gencode.v42.annotation.gtf added
23353330a244b1_gencode.vM30.annotation.gtf added
233533444f2c3e_gencode.vM31.annotation.gtf added
2335331bea675a_gencode.v41.transcripts.fa added
233533594089e5_gencode.v41.transcripts.fa.fai added
2335336fbbc30b_gencode.v42.transcripts.fa added
2335333b1726b8_gencode.v42.transcripts.fa.fai added
2335333bbbfaa7_gencode.vM30.pc_transcripts.fa added
2335334e6519c4_gencode.vM30.pc_transcripts.fa.fai added
233533614e4b7a_gencode.vM31.pc_transcripts.fa added
2335337c106a46_gencode.vM31.pc_transcripts.fa.fai added
233533127853bf_GRCh38.primary_assembly.genome.fa.1.ht2 added
2335332dcda182_GRCh38.primary_assembly.genome.fa.2.ht2 added
233533532c52b3_GRCh38.primary_assembly.genome.fa.3.ht2 added
2335334e2359b5_GRCh38.primary_assembly.genome.fa.4.ht2 added
2335335c3cf6bd_GRCh38.primary_assembly.genome.fa.5.ht2 added
2335334d7539a9_GRCh38.primary_assembly.genome.fa.6.ht2 added
2335333b4dcd0f_GRCh38.primary_assembly.genome.fa.7.ht2 added
23353337ec1715_GRCh38.primary_assembly.genome.fa.8.ht2 added
233533725eba7b_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2335333be32ba2_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2335331b4c7a6a_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2335337df86085_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2335335e34e27a_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
23353364d0200d_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
23353351390034_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2335337d1b5d1b_GRCh38.primary_assembly.genome.fa.fai added
2335337f256938_GRCh38.primary_assembly.genome.fa.amb added
2335337015fd0b_GRCh38.primary_assembly.genome.fa.ann added
23353323a67c6d_GRCh38.primary_assembly.genome.fa.bwt added
23353314116e61_GRCh38.primary_assembly.genome.fa.pac added
2335333590efd_GRCh38.primary_assembly.genome.fa.sa added
2335335448c11e_GRCh38.primary_assembly.genome.fa added
23353358609a9f_hs37d5.fa.fai added
2335331f437657_hs37d5.fa.amb added
2335332d894b03_hs37d5.fa.ann added
233533481c5daa_hs37d5.fa.bwt added
2335335a5a9d0f_hs37d5.fa.pac added
233533694545ab_hs37d5.fa.sa added
2335331681776e_hs37d5.fa added
2335333ba8e88a_complete_ref_lens.bin added
2335336555aff1_ctable.bin added
23353328f9cb2e_ctg_offsets.bin added
23353369768a0c_duplicate_clusters.tsv added
233533388202a5_info.json added
233533771d24e3_mphf.bin added
23353345b380c9_pos.bin added
2335335f73c4e_pre_indexing.log added
233533326af1f2_rank.bin added
2335337d9f97de_ref_indexing.log added
2335337855f6c9_refAccumLengths.bin added
2335336e4e1d94_reflengths.bin added
23353318ec1248_refseq.bin added
233533764e574e_seq.bin added
2335334c83000e_versionInfo.json added
2335337dbc3255_salmon_index added
23353347875783_chrLength.txt added
233533499e5d29_chrName.txt added
2335337ce19b8e_chrNameLength.txt added
233533379d548e_chrStart.txt added
2335336d44d997_exonGeTrInfo.tab added
23353310f309ef_exonInfo.tab added
2335333af6638b_geneInfo.tab added
233533418d9ab5_Genome added
2335336953a48f_genomeParameters.txt added
2335335a39d9e2_Log.out added
2335336f16e5b9_SA added
23353331700239_SAindex added
233533349476f1_sjdbInfo.txt added
233533585c2b64_sjdbList.fromGTF.out.tab added
23353347f179a8_sjdbList.out.tab added
233533703d5f7b_transcriptInfo.tab added
2335333db1db55_GRCh38.GENCODE.v42_100 added
23353370eb44d6_knownGene_hg38.sql added
23353359b3e987_knownGene_hg38.txt added
2335337633ddfa_refGene_hg38.sql added
233533680869b9_refGene_hg38.txt added
2335331f676a50_knownGene_mm39.sql added
2335337c2b1a48_knownGene_mm39.txt added
2335331a735bab_refGene_mm39.sql added
2335331d07022e_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/Rtmpxpfsw4/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
17.351 0.870 18.646
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.867 | 0.227 | 6.097 | |
| dataSearch | 1.067 | 0.009 | 1.076 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.682 | 0.094 | 3.981 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.122 | 0.000 | 0.122 | |
| recipeLoad | 1.222 | 0.011 | 1.234 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.519 | 0.009 | 0.528 | |
| recipeUpdate | 0 | 0 | 0 | |