##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:iClusterPlus.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings iClusterPlus_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/iClusterPlus.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 'iClusterPlus/DESCRIPTION' ... OK
* this is package 'iClusterPlus' version '1.31.0'
* 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 whether package 'iClusterPlus' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 22.9Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
    doc    4.2Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Found a 'configure.in' file: 'configure.ac' has long been preferred.
* 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
CNregions: no visible binding for global variable 'chromosome'
CNregions: no visible binding for global variable 'num.mark'
CNregions: no visible global function definition for 'GRanges'
CNregions: no visible global function definition for 'IRanges'
CNregions: no visible global function definition for 'findOverlaps'
CNregions : get.medoid: no visible global function definition for 'pam'
classError: no visible global function definition for 'mapClass'
plotHMBayes: no visible global function definition for 'bluered'
plotHMBayes : my.panel.levelplot: no visible global function definition
  for 'panel.levelplot'
plotHMBayes : my.panel.levelplot: no visible global function definition
  for 'panel.abline'
plotHMBayes : my.panel.levelplot.2: no visible global function
  definition for 'panel.levelplot'
plotHMBayes : my.panel.levelplot.2: no visible global function
  definition for 'panel.abline'
plotHMBayes: no visible global function definition for 'levelplot'
plotHeatmap: no visible global function definition for 'bluered'
plotHeatmap : my.panel.levelplot: no visible global function definition
  for 'panel.levelplot'
plotHeatmap : my.panel.levelplot: no visible global function definition
  for 'panel.abline'
plotHeatmap : my.panel.levelplot.2: no visible global function
  definition for 'panel.levelplot'
plotHeatmap : my.panel.levelplot.2: no visible global function
  definition for 'panel.abline'
plotHeatmap: no visible global function definition for 'levelplot'
tune.iCluster2: no visible binding for global variable 'glp'
tune.iClusterPlus: no visible binding for global variable 'glp'
Undefined global functions or variables:
  GRanges IRanges bluered chromosome findOverlaps glp levelplot
  mapClass num.mark pam panel.abline panel.levelplot
* 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 ... WARNING
  LazyData DB of 17.8 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... 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 for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/iClusterPlus/libs/x64/iClusterPlus.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  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. 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 'tests' ... OK
* checking tests ...
  Running 'runTests.R'
 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: 1 WARNING, 4 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/iClusterPlus.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL iClusterPlus
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'iClusterPlus' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** 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 iClusterBayes.c -o iClusterBayes.o
iClusterBayes.c: In function 'mcmcBayes':
iClusterBayes.c:1212:28: warning: variable 'Zdraw' set but not used [-Wunused-but-set-variable]
   int i,j,h,n,k,ID,Zburnin,Zdraw,ndt,nk,thin,nthin,remainder,ty0,p0,ty1,p1,ty2,p2,ty3,p3,ty4,p4,ty5,p5,betaBurnin,betaDraw,p0k,p1k,p2k,p3k,p4k,p5k;
                            ^~~~~
iClusterBayes.c:1212:20: warning: variable 'Zburnin' set but not used [-Wunused-but-set-variable]
   int i,j,h,n,k,ID,Zburnin,Zdraw,ndt,nk,thin,nthin,remainder,ty0,p0,ty1,p1,ty2,p2,ty3,p3,ty4,p4,ty5,p5,betaBurnin,betaDraw,p0k,p1k,p2k,p3k,p4k,p5k;
                    ^~~~~~~
iClusterBayes.c:1446:13: warning: 'gb4' may be used uninitialized in this function [-Wmaybe-uninitialized]
     gb4[ID] = b4[ID]*gamma4[j];
     ~~~~~~~~^~~~~~~~~~~~~~~~~~
iClusterBayes.c:1431:13: warning: 'gb3' may be used uninitialized in this function [-Wmaybe-uninitialized]
     gb3[ID] = b3[ID]*gamma3[j];
     ~~~~~~~~^~~~~~~~~~~~~~~~~~
iClusterBayes.c:1475:5: warning: 'gb2' may be used uninitialized in this function [-Wmaybe-uninitialized]
     mcmcMix6d(meanZ,lastZ,nkZbd,sdev,
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
         &ty0,&p0,a0,gb0,con0,cat0,sigma0,
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
         &ty1,&p1,a1,gb1,con1,cat1,sigma1,
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
         &ty2,&p2,a2,gb2,con2,cat2,sigma2,
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
         &ty3,&p3,a3,gb3,con3,cat3,sigma3,
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
         &ty4,&p4,a4,gb4,con4,cat4,sigma4,
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
         &ty5,&p5,a5,gb5,con5,cat5,sigma5,acceptZ);
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iClusterBayes.c:1475:5: warning: 'gb1' may be used uninitialized in this function [-Wmaybe-uninitialized]
iClusterBayes.c:1475:5: warning: 'gb0' may be used uninitialized in this function [-Wmaybe-uninitialized]
iClusterBayes.c:1461:13: warning: 'gb5' may be used uninitialized in this function [-Wmaybe-uninitialized]
     gb5[ID] = b5[ID]*gamma5[j];
     ~~~~~~~~^~~~~~~~~~~~~~~~~~
"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 iClusterPlus.c -o iClusterPlus.o
"C:/rtools40/mingw64/bin/"gfortran  -fno-optimize-sibling-calls -fdefault-real-8 -ffixed-form   -O2  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c  newGLMnet.f90 -o newGLMnet.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o iClusterPlus.dll tmp.def iClusterBayes.o iClusterPlus.o newGLMnet.o -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -lgfortran -lm -lquadmath -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-iClusterPlus/00new/iClusterPlus/libs/x64
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'iClusterPlus'
    finding HTML links ... done
    CNregions                               html  
    breast.chr17                            html  
    compute.pod                             html  
    coord                                   html  
    gbm                                     html  
    glp                                     html  
    iCluster                                html  
    iCluster2                               html  
    iClusterBayes                           html  
    iClusterPlus                            html  
    plotHMBayes                             html  
    plotHeatmap                             html  
    plotRI                                  html  
    plotiCluster                            html  
    simuResult                              html  
    tune.iCluster2                          html  
    tune.iClusterBayes                      html  
    tune.iClusterPlus                       html  
    utility                                 html  
    variation.hg18.v10.nov.2010             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 (iClusterPlus)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'parody' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("iClusterPlus")


RUNIT TEST PROTOCOL -- Thu Mar 17 19:23:23 2022 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
iClusterPlus RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> 
> proc.time()
   user  system elapsed 
  78.17    0.15   78.31