##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:iClusterPlus.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings iClusterPlus_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/iClusterPlus.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* 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 '1.38.0'
* 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
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used Fortran compiler: 'GNU Fortran (GCC) 12.3.0'
* checking installed package size ... NOTE
  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 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 ... 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
File 'F:/biocbuild/bbs-3.18-bioc/R/library/iClusterPlus/libs/x64/iClusterPlus.dll':
  Found '_assert', possibly from 'assert' (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 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 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 13.3   0.14   13.45
* 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: 4 NOTEs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/iClusterPlus.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL iClusterPlus
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'iClusterPlus' ...
** using staged installation

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


** libs
using C compiler: 'gcc.exe (GCC) 12.3.0'
using Fortran compiler: 'GNU Fortran (GCC) 12.3.0'
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -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:1452:20: warning: 'gb4' may be used uninitialized [-Wmaybe-uninitialized]
 1452 |            gb4[ID] = b4[ID]*gamma4[j];
      |            ~~~~~~~~^~~~~~~~~~~~~~~~~~
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;
      |                                                                                                                                                                                   ^~~
iClusterBayes.c:1437:20: warning: 'gb3' may be used uninitialized [-Wmaybe-uninitialized]
 1437 |            gb3[ID] = b3[ID]*gamma3[j];
      |            ~~~~~~~~^~~~~~~~~~~~~~~~~~
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: '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: '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: '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:1467:20: warning: 'gb5' may be used uninitialized [-Wmaybe-uninitialized]
 1467 |            gb5[ID] = b5[ID]*gamma5[j];
      |            ~~~~~~~~^~~~~~~~~~~~~~~~~~
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;
      |                                                                                                                                                                                        ^~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -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 -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -lgfortran -lm -lquadmath -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-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 version 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 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 -- Tue Apr 16 01:48:14 2024 
*********************************************** 
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 
  86.56    0.25   87.04