Qian Liu
| Snapshot Date: 2025-10-30 13:40 -0400 (Thu, 30 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: 4a5d06b |
| git_last_commit_date: 2025-10-29 11:20:44 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-10-31 08:34 -0400 (Fri, 31 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4428 |
| 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 1745/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.11.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | 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: 1.11.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.11.0.tar.gz |
| StartedAt: 2025-10-30 23:43:30 -0400 (Thu, 30 Oct 2025) |
| EndedAt: 2025-10-30 23:46:15 -0400 (Thu, 30 Oct 2025) |
| EllapsedTime: 165.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘1.11.0’
* 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 5.715 0.34 6.056
* 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-3.23-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.11.0’ ** 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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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...
2943c861105c8_GRCh38.primary_assembly.genome.fa.1.bt2 added
2943c82bfab3fe_GRCh38.primary_assembly.genome.fa.2.bt2 added
2943c8596da00e_GRCh38.primary_assembly.genome.fa.3.bt2 added
2943c86db30b1f_GRCh38.primary_assembly.genome.fa.4.bt2 added
2943c87265c825_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2943c87b33d4e9_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2943c841916e0d_outfile.txt added
2943c84059d689_GRCh37_to_GRCh38.chain added
2943c862a8b0c2_GRCh37_to_NCBI34.chain added
2943c879941179_GRCh37_to_NCBI35.chain added
2943c83fc124a3_GRCh37_to_NCBI36.chain added
2943c87df83fd4_GRCh38_to_GRCh37.chain added
2943c84420393f_GRCh38_to_NCBI34.chain added
2943c8267c5c8f_GRCh38_to_NCBI35.chain added
2943c876373843_GRCh38_to_NCBI36.chain added
2943c8e669e38_NCBI34_to_GRCh37.chain added
2943c835e9389f_NCBI34_to_GRCh38.chain added
2943c81515f7b7_NCBI35_to_GRCh37.chain added
2943c83d02d2fc_NCBI35_to_GRCh38.chain added
2943c857a8cae0_NCBI36_to_GRCh37.chain added
2943c84f16b3eb_NCBI36_to_GRCh38.chain added
2943c81a202006_GRCm38_to_NCBIM36.chain added
2943c8560ba123_GRCm38_to_NCBIM37.chain added
2943c83e97085e_NCBIM36_to_GRCm38.chain added
2943c86eb4d61f_NCBIM37_to_GRCm38.chain added
2943c8de20a72_1000G_omni2.5.b37.vcf.gz added
2943c855f5b295_1000G_omni2.5.b37.vcf.gz.tbi added
2943c87c8854bd_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2943c840a6ae50_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2943c87806dad5_1000G_omni2.5.hg38.vcf.gz added
2943c84f23654a_1000G_omni2.5.hg38.vcf.gz.tbi added
2943c846b7b418_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2943c824018ed3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2943c828910558_af-only-gnomad.raw.sites.vcf added
2943c8346abf37_af-only-gnomad.raw.sites.vcf.idx added
2943c8166756f9_Mutect2-exome-panel.vcf.idx added
2943c823c4da41_Mutect2-WGS-panel-b37.vcf added
2943c875fc2d44_Mutect2-WGS-panel-b37.vcf.idx added
2943c856c12d82_small_exac_common_3.vcf added
2943c866d8b04_small_exac_common_3.vcf.idx added
2943c86f903ebe_1000g_pon.hg38.vcf.gz added
2943c816825226_1000g_pon.hg38.vcf.gz.tbi added
2943c8465cad8_af-only-gnomad.hg38.vcf.gz added
2943c833b077fd_af-only-gnomad.hg38.vcf.gz.tbi added
2943c83cfeaeb5_small_exac_common_3.hg38.vcf.gz added
2943c87a9d031b_small_exac_common_3.hg38.vcf.gz.tbi added
2943c842171635_gencode.v41.annotation.gtf added
2943c872e7e754_gencode.v42.annotation.gtf added
2943c8fb2fad3_gencode.vM30.annotation.gtf added
2943c87f19e931_gencode.vM31.annotation.gtf added
2943c84a90b234_gencode.v41.transcripts.fa added
2943c85ec9aebe_gencode.v41.transcripts.fa.fai added
2943c8193a0937_gencode.v42.transcripts.fa added
2943c8209c5358_gencode.v42.transcripts.fa.fai added
2943c81d60b71c_gencode.vM30.pc_transcripts.fa added
2943c87eedf56_gencode.vM30.pc_transcripts.fa.fai added
2943c82e7e5dca_gencode.vM31.pc_transcripts.fa added
2943c8735669b1_gencode.vM31.pc_transcripts.fa.fai added
2943c84773414_GRCh38.primary_assembly.genome.fa.1.ht2 added
2943c86f250c1a_GRCh38.primary_assembly.genome.fa.2.ht2 added
2943c86b5d4486_GRCh38.primary_assembly.genome.fa.3.ht2 added
2943c8539a995e_GRCh38.primary_assembly.genome.fa.4.ht2 added
2943c835dcc032_GRCh38.primary_assembly.genome.fa.5.ht2 added
2943c8f5ed35a_GRCh38.primary_assembly.genome.fa.6.ht2 added
2943c87c2b9eb6_GRCh38.primary_assembly.genome.fa.7.ht2 added
2943c86a477f69_GRCh38.primary_assembly.genome.fa.8.ht2 added
2943c825c62a53_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2943c81ff078f8_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2943c86043acad_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2943c87c8757d5_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2943c8265e03fc_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2943c84fd3eb6b_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2943c81309a9fb_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2943c82ac3ced4_GRCh38.primary_assembly.genome.fa.fai added
2943c83846369_GRCh38.primary_assembly.genome.fa.amb added
2943c8500858b0_GRCh38.primary_assembly.genome.fa.ann added
2943c82560d1f0_GRCh38.primary_assembly.genome.fa.bwt added
2943c8459b799e_GRCh38.primary_assembly.genome.fa.pac added
2943c842f04004_GRCh38.primary_assembly.genome.fa.sa added
2943c83513ccc3_GRCh38.primary_assembly.genome.fa added
2943c844b562d0_hs37d5.fa.fai added
2943c8d80f239_hs37d5.fa.amb added
2943c813dd7b81_hs37d5.fa.ann added
2943c85def6c07_hs37d5.fa.bwt added
2943c82e1d4591_hs37d5.fa.pac added
2943c8313e329d_hs37d5.fa.sa added
2943c865de4b5e_hs37d5.fa added
2943c85c9ba35b_complete_ref_lens.bin added
2943c824949c4f_ctable.bin added
2943c86a557f72_ctg_offsets.bin added
2943c84bc0af75_duplicate_clusters.tsv added
2943c8ff1e0d5_info.json added
2943c83df018d0_mphf.bin added
2943c819d6fa7_pos.bin added
2943c81f50b42f_pre_indexing.log added
2943c83a1bb786_rank.bin added
2943c86be4ef10_ref_indexing.log added
2943c84516de82_refAccumLengths.bin added
2943c85a0c307e_reflengths.bin added
2943c84c289bbd_refseq.bin added
2943c8419e3658_seq.bin added
2943c86a347a_versionInfo.json added
2943c81bfc8729_salmon_index added
2943c854a7e053_chrLength.txt added
2943c82b2e034f_chrName.txt added
2943c81f80ea92_chrNameLength.txt added
2943c824b03904_chrStart.txt added
2943c8508ed53f_exonGeTrInfo.tab added
2943c8651c6430_exonInfo.tab added
2943c867a07908_geneInfo.tab added
2943c85a2a202_Genome added
2943c829d1c700_genomeParameters.txt added
2943c875216b41_Log.out added
2943c819801d83_SA added
2943c87c13308_SAindex added
2943c8233eb0d2_sjdbInfo.txt added
2943c84abe5020_sjdbList.fromGTF.out.tab added
2943c86d9f7e66_sjdbList.out.tab added
2943c87fda542d_transcriptInfo.tab added
2943c86f52ec6f_GRCh38.GENCODE.v42_100 added
2943c857f4fdd8_knownGene_hg38.sql added
2943c84b9b03a2_knownGene_hg38.txt added
2943c87f44cd45_refGene_hg38.sql added
2943c815e516a8_refGene_hg38.txt added
2943c84d387349_knownGene_mm39.sql added
2943c81e958174_knownGene_mm39.txt added
2943c85000ce2e_refGene_mm39.sql added
2943c8391d6259_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/RtmpUOkaEe/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
17.857 1.153 19.495
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.715 | 0.340 | 6.056 | |
| dataSearch | 1.105 | 0.034 | 1.139 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.609 | 0.143 | 3.601 | |
| getData | 0.000 | 0.001 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.125 | 0.003 | 0.127 | |
| recipeLoad | 1.318 | 0.099 | 1.418 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.542 | 0.020 | 0.563 | |
| recipeUpdate | 0 | 0 | 0 | |