Bioconductor Single Package Builder - Build History
nebbiolo1 Summary
| Package: concordexR |
| Version: 0.99.1 |
| RVersion: 4.3 |
| BiocVersion: 3.17 |
| BuildCommand: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data concordexR |
| BuildTime: 1 minutes 8.13 seconds |
| CheckCommand: BiocCheckGitClone('concordexR') && /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3006/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3006/adf6e72227084414cbdac47b18916d2ce78371aa/concordexR.install-out.txt concordexR_0.99.1.tar.gz && BiocCheck('concordexR_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 1 minutes 47.65 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 1472.53 KiB |
| BuildID:: concordexR_20230403190816 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: concordexR. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. |
nebbiolo1 BUILD SRC output
=============================== R CMD BUILD =============================== * checking for file ‘concordexR/DESCRIPTION’ ... OK * preparing ‘concordexR’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘concordexR_0.99.1.tar.gz’
nebbiolo1 CHECK output
===============================
BiocCheckGitClone('concordexR')
===============================
─ BiocCheckVersion: 1.35.17
─ BiocVersion: 3.17
─ Package: concordexR
─ PackageVersion: 0.99.1
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3006/adf6e72227084414cbdac47b18916d2ce78371aa/concordexR
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3006/adf6e72227084414cbdac47b18916d2ce78371aa/concordexR.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘concordexR/DESCRIPTION’ ... OK
* this is package ‘concordexR’ version ‘0.99.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘concordexR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the package can be unloaded cleanly ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
* checking loading without being on the library search path ... [4s/4s] OK
* checking use of S3 registration ... 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 ... [14s/14s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... [6s/6s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [6s/6s]
[6s/6s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [2s/2s] OK
* DONE
Status: OK
===============================
BiocCheck('concordexR_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.35.17
─ BiocVersion: 3.17
─ Package: concordexR
─ PackageVersion: 0.99.1
─ sourceDir: /tmp/RtmpEEdUFL/filed02e23324e389/concordexR
─ installDir: /tmp/RtmpEEdUFL/filed02e261b553c1
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3006/adf6e72227084414cbdac47b18916d2ce78371aa/concordexR.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
Error in loadNamespace(x) : there is no package called ‘BiocFileCache’
Calls: BiocCheck ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted