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R CMD BUILD
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* checking for file G4SNVHunter/DESCRIPTION ... OK
* preparing G4SNVHunter:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a data/datalist file should be added
* building G4SNVHunter_0.99.0.tar.gz
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BiocCheckGitClone('G4SNVHunter')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3623/G4SNVHunter_20241122195408/G4SNVHunter
BiocVersion: 3.21
Package: G4SNVHunter
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3623/G4SNVHunter_20241122195408/G4SNVHunter.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3623/G4SNVHunter_20241122195408/G4SNVHunter
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
! WARNING: System files in '/inst' should not be Git tracked.
inst/.DS_Store
inst/extdata/.DS_Store
ERROR: System files found that should not be Git tracked.
data/.DS_Store
...
vignettes/images/.DS_Store
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
BiocCheck v1.43.2 results
1 ERRORS | 1 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3623/G4SNVHunter_20241122195408/G4SNVHunter.Rcheck
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file G4SNVHunter/DESCRIPTION ... OK
* checking extension type ... Package
* this is package G4SNVHunter version 0.99.0
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 G4SNVHunter can be installed ... OK
* used C++ compiler: g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking build directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] 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 ... [11s/11s] OK
* checking Rd files ... [0s/0s] NOTE
checkRd: (-1) SNVImpactG4.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SNVImpactG4.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SNVImpactG4.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SNVImpactG4.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SNVImpactG4.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SNVImpactG4.Rd:60-61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SNVImpactG4.Rd:62-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SNVImpactG4.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SNVImpactG4.Rd:65-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SNVImpactG4.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SNVImpactG4.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SNVImpactG4.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SNVImpactG4.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SNVImpactG4.Rd:79-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SNVImpactG4.Rd:81-82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SNVImpactG4.Rd:83-84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SNVImpactG4.Rd:85-86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SNVImpactG4.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SNVImpactG4.Rd:88-91: Lost braces in \itemize; \value handles \item{}{} directly
* 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 contents of data directory ... OK
* checking data for non-ASCII characters ... [2s/2s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in vignettes ... OK
* checking examples ... [120s/120s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SNVImpactG4 72.329 2.015 74.352
plotSNVImpact 15.727 1.153 16.882
filterSNVImpact 14.555 1.098 15.654
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [33s/33s]
[33s/33s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [3s/3s] OK
* DONE
Status: 3 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3623/G4SNVHunter_20241122195408/G4SNVHunter.Rcheck/00check.log
for details.
===============================
BiocCheck('G4SNVHunter_0.99.0.tar.gz')
===============================
Error: package or namespace load failed for BiocCheck in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called RBGL
Execution halted