##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:iClusterPlus.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings iClusterPlus_1.43.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/iClusterPlus.Rcheck'
* using R Under development (unstable) (2025-03-01 r87860 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'iClusterPlus/DESCRIPTION' ... OK
* this is package 'iClusterPlus' version '1.43.1'
* 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
* used C compiler: 'gcc.exe (GCC) 14.2.0'
* used Fortran compiler: 'GNU Fortran (GCC) 14.2.0'
* checking installed package size ... INFO
  installed size is 18.1Mb
  sub-directories of 1Mb or more:
    data  12.4Mb
    doc    4.8Mb
* 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 code 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 ... OK
* 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
* checking usage of KIND in Fortran files ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
iCluster 14.18   0.42   14.58
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.R'
 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 ... OK
* DONE

Status: 3 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/iClusterPlus.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL iClusterPlus
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'iClusterPlus' ...
** this is package 'iClusterPlus' version '1.43.1'
** using staged installation

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


** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
using Fortran compiler: 'GNU Fortran (GCC) 14.2.0'
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c iClusterBayes.c -o iClusterBayes.o
iClusterBayes.c: In function 'mcmcBayes':
iClusterBayes.c:1218:28: warning: variable 'Zdraw' set but not used [-Wunused-but-set-variable]
 1218 |   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:1218:20: warning: variable 'Zburnin' set but not used [-Wunused-but-set-variable]
 1218 |   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:1374:6: warning: 'gb5' may be used uninitialized [-Wmaybe-uninitialized]
 1374 |      mcmcMix6d(meanZ,lastZ,nkZbd,sdev,
      |      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1375 |                &ty0,&p0,a0,gb0,con0,cat0,sigma0,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1376 |                &ty1,&p1,a1,gb1,con1,cat1,sigma1,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1377 |                &ty2,&p2,a2,gb2,con2,cat2,sigma2,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1378 |                &ty3,&p3,a3,gb3,con3,cat3,sigma3,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1379 |                &ty4,&p4,a4,gb4,con4,cat4,sigma4,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1380 |                &ty5,&p5,a5,gb5,con5,cat5,sigma5,acceptZ);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iClusterBayes.c:1220:184: note: 'gb5' was declared here
 1220 |   double *sumMeanZ,*suma0,*sumb0,*suma1,*sumb1,*suma2,*sumb2,*suma3,*sumb3,*suma4,*sumb4,*suma5,*sumb5,*sumsig0,*sumsig1,*sumsig2,*sumsig3,*sumsig4,*sumsig5,*gb0,*gb1,*gb2,*gb3,*gb4,*gb5;
      |                                                                                                                                                                                        ^~~
iClusterBayes.c:1374:6: warning: 'gb0' may be used uninitialized [-Wmaybe-uninitialized]
 1374 |      mcmcMix6d(meanZ,lastZ,nkZbd,sdev,
      |      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1375 |                &ty0,&p0,a0,gb0,con0,cat0,sigma0,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1376 |                &ty1,&p1,a1,gb1,con1,cat1,sigma1,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1377 |                &ty2,&p2,a2,gb2,con2,cat2,sigma2,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1378 |                &ty3,&p3,a3,gb3,con3,cat3,sigma3,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1379 |                &ty4,&p4,a4,gb4,con4,cat4,sigma4,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1380 |                &ty5,&p5,a5,gb5,con5,cat5,sigma5,acceptZ);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iClusterBayes.c:1220:159: note: 'gb0' was declared here
 1220 |   double *sumMeanZ,*suma0,*sumb0,*suma1,*sumb1,*suma2,*sumb2,*suma3,*sumb3,*suma4,*sumb4,*suma5,*sumb5,*sumsig0,*sumsig1,*sumsig2,*sumsig3,*sumsig4,*sumsig5,*gb0,*gb1,*gb2,*gb3,*gb4,*gb5;
      |                                                                                                                                                               ^~~
iClusterBayes.c:1374:6: warning: 'gb1' may be used uninitialized [-Wmaybe-uninitialized]
 1374 |      mcmcMix6d(meanZ,lastZ,nkZbd,sdev,
      |      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1375 |                &ty0,&p0,a0,gb0,con0,cat0,sigma0,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1376 |                &ty1,&p1,a1,gb1,con1,cat1,sigma1,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1377 |                &ty2,&p2,a2,gb2,con2,cat2,sigma2,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1378 |                &ty3,&p3,a3,gb3,con3,cat3,sigma3,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1379 |                &ty4,&p4,a4,gb4,con4,cat4,sigma4,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1380 |                &ty5,&p5,a5,gb5,con5,cat5,sigma5,acceptZ);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iClusterBayes.c:1220:164: note: 'gb1' was declared here
 1220 |   double *sumMeanZ,*suma0,*sumb0,*suma1,*sumb1,*suma2,*sumb2,*suma3,*sumb3,*suma4,*sumb4,*suma5,*sumb5,*sumsig0,*sumsig1,*sumsig2,*sumsig3,*sumsig4,*sumsig5,*gb0,*gb1,*gb2,*gb3,*gb4,*gb5;
      |                                                                                                                                                                    ^~~
iClusterBayes.c:1374:6: warning: 'gb2' may be used uninitialized [-Wmaybe-uninitialized]
 1374 |      mcmcMix6d(meanZ,lastZ,nkZbd,sdev,
      |      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1375 |                &ty0,&p0,a0,gb0,con0,cat0,sigma0,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1376 |                &ty1,&p1,a1,gb1,con1,cat1,sigma1,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1377 |                &ty2,&p2,a2,gb2,con2,cat2,sigma2,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1378 |                &ty3,&p3,a3,gb3,con3,cat3,sigma3,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1379 |                &ty4,&p4,a4,gb4,con4,cat4,sigma4,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1380 |                &ty5,&p5,a5,gb5,con5,cat5,sigma5,acceptZ);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iClusterBayes.c:1220:169: note: 'gb2' was declared here
 1220 |   double *sumMeanZ,*suma0,*sumb0,*suma1,*sumb1,*suma2,*sumb2,*suma3,*sumb3,*suma4,*sumb4,*suma5,*sumb5,*sumsig0,*sumsig1,*sumsig2,*sumsig3,*sumsig4,*sumsig5,*gb0,*gb1,*gb2,*gb3,*gb4,*gb5;
      |                                                                                                                                                                         ^~~
iClusterBayes.c:1374:6: warning: 'gb3' may be used uninitialized [-Wmaybe-uninitialized]
 1374 |      mcmcMix6d(meanZ,lastZ,nkZbd,sdev,
      |      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1375 |                &ty0,&p0,a0,gb0,con0,cat0,sigma0,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1376 |                &ty1,&p1,a1,gb1,con1,cat1,sigma1,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1377 |                &ty2,&p2,a2,gb2,con2,cat2,sigma2,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1378 |                &ty3,&p3,a3,gb3,con3,cat3,sigma3,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1379 |                &ty4,&p4,a4,gb4,con4,cat4,sigma4,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1380 |                &ty5,&p5,a5,gb5,con5,cat5,sigma5,acceptZ);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iClusterBayes.c:1220:174: note: 'gb3' was declared here
 1220 |   double *sumMeanZ,*suma0,*sumb0,*suma1,*sumb1,*suma2,*sumb2,*suma3,*sumb3,*suma4,*sumb4,*suma5,*sumb5,*sumsig0,*sumsig1,*sumsig2,*sumsig3,*sumsig4,*sumsig5,*gb0,*gb1,*gb2,*gb3,*gb4,*gb5;
      |                                                                                                                                                                              ^~~
iClusterBayes.c:1374:6: warning: 'gb4' may be used uninitialized [-Wmaybe-uninitialized]
 1374 |      mcmcMix6d(meanZ,lastZ,nkZbd,sdev,
      |      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1375 |                &ty0,&p0,a0,gb0,con0,cat0,sigma0,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1376 |                &ty1,&p1,a1,gb1,con1,cat1,sigma1,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1377 |                &ty2,&p2,a2,gb2,con2,cat2,sigma2,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1378 |                &ty3,&p3,a3,gb3,con3,cat3,sigma3,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1379 |                &ty4,&p4,a4,gb4,con4,cat4,sigma4,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1380 |                &ty5,&p5,a5,gb5,con5,cat5,sigma5,acceptZ);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iClusterBayes.c:1220:179: note: 'gb4' was declared here
 1220 |   double *sumMeanZ,*suma0,*sumb0,*suma1,*sumb1,*suma2,*sumb2,*suma3,*sumb3,*suma4,*sumb4,*suma5,*sumb5,*sumsig0,*sumsig1,*sumsig2,*sumsig3,*sumsig4,*sumsig5,*gb0,*gb1,*gb2,*gb3,*gb4,*gb5;
      |                                                                                                                                                                                   ^~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c iClusterPlus.c -o iClusterPlus.o
gfortran   -fdefault-real-8 -ffixed-form   -O2  -mfpmath=sse -msse2 -mstackrealign  -c  newGLMnet.f90 -o newGLMnet.o
gcc -shared -s -static-libgcc -o iClusterPlus.dll tmp.def iClusterBayes.o iClusterPlus.o newGLMnet.o -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lRlapack -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lRblas -lgfortran -lquadmath -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -lgfortran -lquadmath -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-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
** 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)

R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 -- Fri Mar 28 02:46:39 2025 
*********************************************** 
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 
 100.21    0.34  100.59