##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:GOsummaries.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings GOsummaries_2.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GOsummaries.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘GOsummaries/DESCRIPTION’ ... OK
* this is package ‘GOsummaries’ version ‘2.37.0’
* 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 ‘GOsummaries’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* 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 R 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 ... NOTE
adjust_wordcloud_appearance: no visible global function definition for
  ‘colorRampPalette’
annotate.gosummaries: no visible global function definition for
  ‘packageVersion’
gen_wordcloud_legend: no visible global function definition for
  ‘colorRampPalette’
open_file_con : <anonymous>: no visible global function definition for
  ‘pdf’
open_file_con : <anonymous>: no visible global function definition for
  ‘png’
open_file_con : <anonymous>: no visible global function definition for
  ‘jpeg’
open_file_con : <anonymous>: no visible global function definition for
  ‘tiff’
open_file_con : <anonymous>: no visible global function definition for
  ‘bmp’
panel_boxplot : qq: no visible global function definition for
  ‘boxplot.stats’
panel_boxplot: no visible binding for global variable ‘x’
panel_boxplot: no visible binding for global variable ‘y’
panel_boxplot: no visible binding for global variable ‘Class’
panel_dummy: no visible binding for global variable ‘y’
panel_dummy: no visible binding for global variable ‘x’
plotWordcloud: no visible global function definition for
  ‘colorRampPalette’
plotWordcloud: no visible global function definition for ‘runif’
plot_motor: no visible global function definition for ‘dev.off’
print.gosummaries: no visible global function definition for ‘head’
pspearman: no visible global function definition for ‘pt’
spearman_mds: no visible global function definition for ‘cor’
Undefined global functions or variables:
  Class bmp boxplot.stats colorRampPalette cor dev.off head jpeg
  packageVersion pdf png pt runif tiff x y
Consider adding
  importFrom("grDevices", "bmp", "boxplot.stats", "colorRampPalette",
             "dev.off", "jpeg", "pdf", "png", "tiff")
  importFrom("stats", "cor", "pt", "runif")
  importFrom("utils", "head", "packageVersion")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘GOsummaries-basics.Rnw’... failed
 WARNING
Errors in running code in vignettes:
when running code in ‘GOsummaries-basics.Rnw’
  ...

> BiocStyle::latex()

  When sourcing ‘GOsummaries-basics.R’:
Error: there is no package called ‘BiocStyle’
Execution halted

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
  ...
--- re-building ‘GOsummaries-basics.Rnw’ using Sweave

Error: processing vignette 'GOsummaries-basics.Rnw' failed with diagnostics:
 chunk 1 (label = style-Sweave) 
Error in loadNamespace(x) : there is no package called ‘BiocStyle’

--- failed re-building ‘GOsummaries-basics.Rnw’

SUMMARY: processing the following file failed:
  ‘GOsummaries-basics.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/GOsummaries.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL GOsummaries
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘GOsummaries’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -c findCoordinates.cpp -o findCoordinates.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o GOsummaries.so findCoordinates.o -L/home/biocbuild/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-GOsummaries/00new/GOsummaries/libs
** R
** data
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GOsummaries)