Qian Liu
| Snapshot Date: 2025-12-04 13:40 -0500 (Thu, 04 Dec 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 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-05 11:35 -0500 (Fri, 05 Dec 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" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4576 |
| 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 1753/2331 | 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 | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 2025-12-05 03:15:04 -0500 (Fri, 05 Dec 2025) |
| EndedAt: 2025-12-05 03:17:50 -0500 (Fri, 05 Dec 2025) |
| EllapsedTime: 166.3 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 6.003 0.346 6.35
* 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...
25db66ab4aa21_GRCh38.primary_assembly.genome.fa.1.bt2 added
25db632d09fe8_GRCh38.primary_assembly.genome.fa.2.bt2 added
25db6fa12d2a_GRCh38.primary_assembly.genome.fa.3.bt2 added
25db611ef18a2_GRCh38.primary_assembly.genome.fa.4.bt2 added
25db61922bc72_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
25db67298a02a_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
25db67ddd324e_outfile.txt added
25db66e2bbb44_GRCh37_to_GRCh38.chain added
25db65ef05976_GRCh37_to_NCBI34.chain added
25db621c51d49_GRCh37_to_NCBI35.chain added
25db636b128dd_GRCh37_to_NCBI36.chain added
25db658a68f16_GRCh38_to_GRCh37.chain added
25db656e08978_GRCh38_to_NCBI34.chain added
25db6bda6638_GRCh38_to_NCBI35.chain added
25db632e69d94_GRCh38_to_NCBI36.chain added
25db63a62bfae_NCBI34_to_GRCh37.chain added
25db67e509ca0_NCBI34_to_GRCh38.chain added
25db625e5065d_NCBI35_to_GRCh37.chain added
25db6e7292aa_NCBI35_to_GRCh38.chain added
25db61ab42702_NCBI36_to_GRCh37.chain added
25db63a53f7f7_NCBI36_to_GRCh38.chain added
25db64a94b6e1_GRCm38_to_NCBIM36.chain added
25db671bec181_GRCm38_to_NCBIM37.chain added
25db65a391a95_NCBIM36_to_GRCm38.chain added
25db671566268_NCBIM37_to_GRCm38.chain added
25db6450758ec_1000G_omni2.5.b37.vcf.gz added
25db6748b5b21_1000G_omni2.5.b37.vcf.gz.tbi added
25db613e7e5f3_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
25db675e98f29_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
25db6230d1ee5_1000G_omni2.5.hg38.vcf.gz added
25db6563ddd42_1000G_omni2.5.hg38.vcf.gz.tbi added
25db6609e394b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
25db655ddbecd_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
25db665df0a6c_af-only-gnomad.raw.sites.vcf added
25db6728d51ed_af-only-gnomad.raw.sites.vcf.idx added
25db66f007b40_Mutect2-exome-panel.vcf.idx added
25db65877aa96_Mutect2-WGS-panel-b37.vcf added
25db6706a843b_Mutect2-WGS-panel-b37.vcf.idx added
25db65d2c3684_small_exac_common_3.vcf added
25db63768040d_small_exac_common_3.vcf.idx added
25db6122fa184_1000g_pon.hg38.vcf.gz added
25db613dd5f61_1000g_pon.hg38.vcf.gz.tbi added
25db6100e9323_af-only-gnomad.hg38.vcf.gz added
25db669102afd_af-only-gnomad.hg38.vcf.gz.tbi added
25db61fb7c599_small_exac_common_3.hg38.vcf.gz added
25db642f530b7_small_exac_common_3.hg38.vcf.gz.tbi added
25db62372eaab_gencode.v41.annotation.gtf added
25db61e08623a_gencode.v42.annotation.gtf added
25db668da3714_gencode.vM30.annotation.gtf added
25db631e57d56_gencode.vM31.annotation.gtf added
25db638bc893c_gencode.v41.transcripts.fa added
25db6232e2f0b_gencode.v41.transcripts.fa.fai added
25db67c7a3437_gencode.v42.transcripts.fa added
25db62a7b4abd_gencode.v42.transcripts.fa.fai added
25db67d6749a1_gencode.vM30.pc_transcripts.fa added
25db66dd0969f_gencode.vM30.pc_transcripts.fa.fai added
25db66f82a3aa_gencode.vM31.pc_transcripts.fa added
25db671f2a4c2_gencode.vM31.pc_transcripts.fa.fai added
25db61b87c92_GRCh38.primary_assembly.genome.fa.1.ht2 added
25db6656c32d3_GRCh38.primary_assembly.genome.fa.2.ht2 added
25db614ffc3a7_GRCh38.primary_assembly.genome.fa.3.ht2 added
25db657f659d4_GRCh38.primary_assembly.genome.fa.4.ht2 added
25db6460a6c1e_GRCh38.primary_assembly.genome.fa.5.ht2 added
25db66add8274_GRCh38.primary_assembly.genome.fa.6.ht2 added
25db63dd56440_GRCh38.primary_assembly.genome.fa.7.ht2 added
25db63897be0b_GRCh38.primary_assembly.genome.fa.8.ht2 added
25db659ddfdb4_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
25db6164d0ed7_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
25db629024247_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
25db6370a3438_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
25db64db512e4_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
25db63b31e3cb_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
25db64ae79399_GRCh38_full_analysis_set_plus_decoy_hla.fa added
25db65dc3a607_GRCh38.primary_assembly.genome.fa.fai added
25db624420ec8_GRCh38.primary_assembly.genome.fa.amb added
25db66a9f5933_GRCh38.primary_assembly.genome.fa.ann added
25db620b8d6be_GRCh38.primary_assembly.genome.fa.bwt added
25db647b4f974_GRCh38.primary_assembly.genome.fa.pac added
25db68a7bb6d_GRCh38.primary_assembly.genome.fa.sa added
25db69930dd2_GRCh38.primary_assembly.genome.fa added
25db6799a76ca_hs37d5.fa.fai added
25db6416444a9_hs37d5.fa.amb added
25db62cc13cdd_hs37d5.fa.ann added
25db67614ab01_hs37d5.fa.bwt added
25db66bdf8f66_hs37d5.fa.pac added
25db62a28867e_hs37d5.fa.sa added
25db663e541a0_hs37d5.fa added
25db65b623310_complete_ref_lens.bin added
25db61c1b2b40_ctable.bin added
25db6659dbe33_ctg_offsets.bin added
25db640ce65e4_duplicate_clusters.tsv added
25db6311aeee7_info.json added
25db63d941807_mphf.bin added
25db66d8d202_pos.bin added
25db61bf8715c_pre_indexing.log added
25db67b697c48_rank.bin added
25db63f70900e_ref_indexing.log added
25db675d66f10_refAccumLengths.bin added
25db611b68b1f_reflengths.bin added
25db66872d255_refseq.bin added
25db62ce0a349_seq.bin added
25db65f6b9e03_versionInfo.json added
25db623a4b620_salmon_index added
25db677c836e2_chrLength.txt added
25db63d2f440a_chrName.txt added
25db647e6c4e9_chrNameLength.txt added
25db662679015_chrStart.txt added
25db65de81ac8_exonGeTrInfo.tab added
25db6f9bbe5d_exonInfo.tab added
25db66b0f4b82_geneInfo.tab added
25db6677b289a_Genome added
25db69363527_genomeParameters.txt added
25db62c73902b_Log.out added
25db6143c6577_SA added
25db67f4ae028_SAindex added
25db618531f92_sjdbInfo.txt added
25db63e64ebf6_sjdbList.fromGTF.out.tab added
25db6633021c8_sjdbList.out.tab added
25db673b552a2_transcriptInfo.tab added
25db65a801736_GRCh38.GENCODE.v42_100 added
25db648cddffb_knownGene_hg38.sql added
25db63483b886_knownGene_hg38.txt added
25db6b9b061e_refGene_hg38.sql added
25db6661f803_refGene_hg38.txt added
25db63b5c8a89_knownGene_mm39.sql added
25db62793777a_knownGene_mm39.txt added
25db61cb744b_refGene_mm39.sql added
25db67acd1a97_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/RtmpEkj0Ep/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
18.036 1.208 19.900
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.003 | 0.346 | 6.350 | |
| dataSearch | 1.107 | 0.040 | 1.148 | |
| dataUpdate | 0.000 | 0.001 | 0.000 | |
| getCloudData | 2.580 | 0.134 | 3.812 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.127 | 0.004 | 0.131 | |
| recipeLoad | 1.258 | 0.057 | 1.317 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.511 | 0.009 | 0.519 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |