===============================
R CMD BUILD
===============================
* checking for file BioGA/DESCRIPTION ... OK
* preparing BioGA:
* 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
Omitted LazyData from DESCRIPTION
* building BioGA_0.99.0.tar.gz
===============================
BiocCheckGitClone('BioGA')
===============================
BiocCheckVersion: 1.39.26
BiocVersion: 3.19
Package: BioGA
PackageVersion: 0.99.0
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3315/BioGA_20240321125947/BioGA
platform: unix
isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be Git tracked.
BioGA.Rproj
* 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...
* 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 results
1 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3315/BioGA_20240321125947/BioGA.Rcheck
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file BioGA/DESCRIPTION ... OK
* checking extension type ... Package
* this is package BioGA version 0.99.0
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package BioGA can be installed ... OK
* used C++ compiler: g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'library' or 'require' call not declared from: animation
'library' or 'require' call to animation in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: SummarizedExperiment
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [4s/4s] NOTE
animate_fitness_history : animate_plot: no visible binding for global
variable Generation
animate_fitness_history : animate_plot: no visible binding for global
variable Fitness
animate_fitness_history : animate_plot: no visible binding for global
variable Variable
animate_fitness_history: no visible global function definition for
ani.options
animate_fitness_history: no visible global function definition for
saveGIF
Undefined global functions or variables:
Fitness Generation Variable ani.options saveGIF
* 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 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
File /home/pkgbuild/packagebuilder/workers/jobs/3315/R-libs/BioGA/libs/BioGA.so:
Found rand, possibly from rand (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See Writing portable packages in the Writing R Extensions manual.
* checking files in vignettes ... OK
* checking examples ... [1s/1s] ERROR
Running examples in BioGA-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: animate_fitness_history
> ### Title: Animate Fitness Change Over Generations
> ### Aliases: animate_fitness_history
>
> ### ** Examples
>
> # example of usage
> fitness_history <- list(c(10, 8, 6, 4, 2), c(9, 7, 5, 3, 1))
> animate_fitness_history(fitness_history)
Error in library(animation) : there is no package called animation
Calls: animate_fitness_history -> library
Execution halted
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [1s/1s]
[1s/1s] 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 ... [2s/2s] OK
* DONE
Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3315/BioGA_20240321125947/BioGA.Rcheck/00check.log
for details.
===============================
BiocCheck('BioGA_0.99.0.tar.gz')
===============================
BiocCheckVersion: 1.39.26
BiocVersion: 3.19
Package: BioGA
PackageVersion: 0.99.0
sourceDir: /tmp/RtmpdO8VvV/filee364321ef9db9/BioGA
installDir: /tmp/RtmpdO8VvV/filee3643207cc6e1
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3315/BioGA_20240321125947/BioGA.BiocCheck
platform: unix
isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (20%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* WARNING: Import SummarizedExperiment in NAMESPACE as well as
DESCRIPTION.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of BioGA...
* WARNING: Avoid the use of 'library' or 'require' in R code
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 5 lines (1%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 82 lines
(11%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package is in the Support Site Watched Tags.
BiocCheck results
0 ERRORS | 2 WARNINGS | 4 NOTES
See the BioGA.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.