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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FEAST.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings FEAST_1.3.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/FEAST.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'FEAST/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FEAST' version '1.3.0'
* 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 whether package 'FEAST' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.5Mb
* 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 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
FEAST: multiple local function definitions for 'bp_fun' with different
  formal arguments
SC3_Clust: no visible global function definition for 'metadata'
Visual_Rslt: no visible global function definition for 'ggbarplot'
Visual_Rslt: no visible global function definition for 'theme'
Visual_Rslt: no visible global function definition for 'element_text'
Visual_Rslt: no visible global function definition for 'ggline'
Visual_Rslt: no visible global function definition for 'get_palette'
Visual_Rslt: no visible global function definition for
  'scale_y_continuous'
Visual_Rslt: no visible global function definition for 'guides'
Visual_Rslt: no visible global function definition for 'guide_legend'
Visual_Rslt: no visible global function definition for 'ggarrange'
aricode_NMI : entropy: no visible global function definition for
  'sortPairs'
Undefined global functions or variables:
  element_text get_palette ggarrange ggbarplot ggline guide_legend
  guides metadata scale_y_continuous sortPairs theme
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/FEAST/libs/x64/FEAST.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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. 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 installed files from 'inst/doc' ... OK
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/FEAST.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL FEAST
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'FEAST' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c cal_3_metrics.c -o cal_3_metrics.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o FEAST.dll tmp.def cal_3_metrics.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-FEAST/00new/FEAST/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'FEAST'
    finding HTML links ... done
    Consensus                               html  
    FEAST                                   html  
    FEAST_fast                              html  
    Norm_Y                                  html  
    Purity                                  html  
    SC3_Clust                               html  
    Select_Model_short_SC3                  html  
    Select_Model_short_TSCAN                html  
    TSCAN_Clust                             html  
    Visual_Rslt                             html  
    Y                                       html  
    align_CellType                          html  
    cal_F2                                  html  
    cal_Fisher2                             html  
    cal_MSE                                 html  
    cal_metrics                             html  
    eval_Cluster                            html  
    process_Y                               html  
    setUp_BPPARAM                           html  
    trueclass                               html  
    vector2matrix                           html  
** 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 (FEAST)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'iPAC' is missing or broken
 done