Qian Liu
| Snapshot Date: 2025-11-10 13:45 -0500 (Mon, 10 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_22 |
| git_last_commit: 2d4066b |
| git_last_commit_date: 2025-10-29 11:20:44 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-11 12:02 -0500 (Tue, 11 Nov 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" | 4902 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4638 |
| 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 1.10.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
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: 1.10.0 |
| 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_1.10.0.tar.gz |
| StartedAt: 2025-11-11 03:25:44 -0500 (Tue, 11 Nov 2025) |
| EndedAt: 2025-11-11 03:28:26 -0500 (Tue, 11 Nov 2025) |
| EllapsedTime: 162.2 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_1.10.0.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 ‘1.10.0’
* 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 5.677 0.233 5.913
* 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 ‘1.10.0’ ** 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...
30c5b66f70b653_GRCh38.primary_assembly.genome.fa.1.bt2 added
30c5b663b5e63f_GRCh38.primary_assembly.genome.fa.2.bt2 added
30c5b6787dae2_GRCh38.primary_assembly.genome.fa.3.bt2 added
30c5b675f49bde_GRCh38.primary_assembly.genome.fa.4.bt2 added
30c5b664185e5b_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
30c5b624781b48_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
30c5b61aef388d_outfile.txt added
30c5b66b683469_GRCh37_to_GRCh38.chain added
30c5b67dcefce8_GRCh37_to_NCBI34.chain added
30c5b65bd861de_GRCh37_to_NCBI35.chain added
30c5b61b0fce82_GRCh37_to_NCBI36.chain added
30c5b67771bdcf_GRCh38_to_GRCh37.chain added
30c5b6467b4234_GRCh38_to_NCBI34.chain added
30c5b655a432c1_GRCh38_to_NCBI35.chain added
30c5b63d6c1611_GRCh38_to_NCBI36.chain added
30c5b6ed73d1_NCBI34_to_GRCh37.chain added
30c5b631f9fc20_NCBI34_to_GRCh38.chain added
30c5b610c9336a_NCBI35_to_GRCh37.chain added
30c5b668d8d251_NCBI35_to_GRCh38.chain added
30c5b618bfa8a6_NCBI36_to_GRCh37.chain added
30c5b659897ad6_NCBI36_to_GRCh38.chain added
30c5b613eb830d_GRCm38_to_NCBIM36.chain added
30c5b6ffd5592_GRCm38_to_NCBIM37.chain added
30c5b627e994bd_NCBIM36_to_GRCm38.chain added
30c5b65e9e5776_NCBIM37_to_GRCm38.chain added
30c5b64db60d27_1000G_omni2.5.b37.vcf.gz added
30c5b65e6de9d3_1000G_omni2.5.b37.vcf.gz.tbi added
30c5b67e03f65f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
30c5b6126daaf0_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
30c5b649b7673b_1000G_omni2.5.hg38.vcf.gz added
30c5b634d6c9e0_1000G_omni2.5.hg38.vcf.gz.tbi added
30c5b61de6143_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
30c5b62d6d4d7b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
30c5b63c5ea4c2_af-only-gnomad.raw.sites.vcf added
30c5b677d2fd21_af-only-gnomad.raw.sites.vcf.idx added
30c5b61185abd6_Mutect2-exome-panel.vcf.idx added
30c5b660d6c00a_Mutect2-WGS-panel-b37.vcf added
30c5b612c235ae_Mutect2-WGS-panel-b37.vcf.idx added
30c5b67cede03f_small_exac_common_3.vcf added
30c5b65ea5bcf2_small_exac_common_3.vcf.idx added
30c5b66e9a978c_1000g_pon.hg38.vcf.gz added
30c5b617fdaec2_1000g_pon.hg38.vcf.gz.tbi added
30c5b656177ac1_af-only-gnomad.hg38.vcf.gz added
30c5b63515d9c1_af-only-gnomad.hg38.vcf.gz.tbi added
30c5b66da1e183_small_exac_common_3.hg38.vcf.gz added
30c5b6138390d3_small_exac_common_3.hg38.vcf.gz.tbi added
30c5b636034d92_gencode.v41.annotation.gtf added
30c5b61f9bdda3_gencode.v42.annotation.gtf added
30c5b6244cc43d_gencode.vM30.annotation.gtf added
30c5b61edc1fe3_gencode.vM31.annotation.gtf added
30c5b6385b8649_gencode.v41.transcripts.fa added
30c5b67dd63f13_gencode.v41.transcripts.fa.fai added
30c5b632c7a2f0_gencode.v42.transcripts.fa added
30c5b64858dbdc_gencode.v42.transcripts.fa.fai added
30c5b625bfd3d0_gencode.vM30.pc_transcripts.fa added
30c5b61165fa66_gencode.vM30.pc_transcripts.fa.fai added
30c5b6160ee903_gencode.vM31.pc_transcripts.fa added
30c5b642dbda4_gencode.vM31.pc_transcripts.fa.fai added
30c5b6f69f0c5_GRCh38.primary_assembly.genome.fa.1.ht2 added
30c5b6287c93f3_GRCh38.primary_assembly.genome.fa.2.ht2 added
30c5b64de524df_GRCh38.primary_assembly.genome.fa.3.ht2 added
30c5b64440baa5_GRCh38.primary_assembly.genome.fa.4.ht2 added
30c5b62a5af536_GRCh38.primary_assembly.genome.fa.5.ht2 added
30c5b67b52725a_GRCh38.primary_assembly.genome.fa.6.ht2 added
30c5b69f5f67_GRCh38.primary_assembly.genome.fa.7.ht2 added
30c5b6222df258_GRCh38.primary_assembly.genome.fa.8.ht2 added
30c5b6cd81e31_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
30c5b661761f71_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
30c5b634f02806_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
30c5b69c5fe70_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
30c5b6401bdc63_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
30c5b6238abf93_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
30c5b621c3ad32_GRCh38_full_analysis_set_plus_decoy_hla.fa added
30c5b616335725_GRCh38.primary_assembly.genome.fa.fai added
30c5b658a09954_GRCh38.primary_assembly.genome.fa.amb added
30c5b6f658eb5_GRCh38.primary_assembly.genome.fa.ann added
30c5b629b6e7f8_GRCh38.primary_assembly.genome.fa.bwt added
30c5b6ea3e6e6_GRCh38.primary_assembly.genome.fa.pac added
30c5b62f016c59_GRCh38.primary_assembly.genome.fa.sa added
30c5b64e03ac35_GRCh38.primary_assembly.genome.fa added
30c5b62d8006ca_hs37d5.fa.fai added
30c5b6675cf2a2_hs37d5.fa.amb added
30c5b64bd9eb48_hs37d5.fa.ann added
30c5b66047a9ba_hs37d5.fa.bwt added
30c5b62fb5ce7e_hs37d5.fa.pac added
30c5b67199bf19_hs37d5.fa.sa added
30c5b671ada421_hs37d5.fa added
30c5b645c4b782_complete_ref_lens.bin added
30c5b675c77cbd_ctable.bin added
30c5b611794e6_ctg_offsets.bin added
30c5b66e414b75_duplicate_clusters.tsv added
30c5b643aca19c_info.json added
30c5b645584f8c_mphf.bin added
30c5b6189c40ac_pos.bin added
30c5b63eff13f7_pre_indexing.log added
30c5b645f7aef3_rank.bin added
30c5b63aca3304_ref_indexing.log added
30c5b64bd73228_refAccumLengths.bin added
30c5b6276dce65_reflengths.bin added
30c5b66fba5b0a_refseq.bin added
30c5b6559d3098_seq.bin added
30c5b66789aac8_versionInfo.json added
30c5b613451a9d_salmon_index added
30c5b67760ddcb_chrLength.txt added
30c5b67dbd01ed_chrName.txt added
30c5b66be5b3f1_chrNameLength.txt added
30c5b66c66c80_chrStart.txt added
30c5b62773e9e5_exonGeTrInfo.tab added
30c5b67a899ad8_exonInfo.tab added
30c5b635c7d8d9_geneInfo.tab added
30c5b67577961a_Genome added
30c5b62809a1a2_genomeParameters.txt added
30c5b61d24cb7c_Log.out added
30c5b641518163_SA added
30c5b68514b5c_SAindex added
30c5b64cda99fa_sjdbInfo.txt added
30c5b632eb407c_sjdbList.fromGTF.out.tab added
30c5b679feef7d_sjdbList.out.tab added
30c5b6129f517c_transcriptInfo.tab added
30c5b628b2bd39_GRCh38.GENCODE.v42_100 added
30c5b67b168464_knownGene_hg38.sql added
30c5b6e09cf2_knownGene_hg38.txt added
30c5b66c5f5ed5_refGene_hg38.sql added
30c5b6406ed3f0_refGene_hg38.txt added
30c5b6197cdd9e_knownGene_mm39.sql added
30c5b62b5e72cc_knownGene_mm39.txt added
30c5b666682e3_refGene_mm39.sql added
30c5b6544710a2_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/Rtmp4Mp1nn/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
18.539 1.158 20.081
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.677 | 0.233 | 5.913 | |
| dataSearch | 1.085 | 0.010 | 1.095 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.661 | 0.115 | 3.785 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.117 | 0.003 | 0.121 | |
| recipeLoad | 1.290 | 0.012 | 1.302 | |
| recipeMake | 0.001 | 0.000 | 0.000 | |
| recipeSearch | 0.530 | 0.006 | 0.537 | |
| recipeUpdate | 0 | 0 | 0 | |