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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:snapCGH.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings snapCGH_1.65.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/snapCGH.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 'snapCGH/DESCRIPTION' ... OK
* this is package 'snapCGH' version '1.65.0'
* 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 'snapCGH' can be installed ... OK
* 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 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
heatmapGenome: no visible binding for global variable 'floor.func'
readPositionalInfo: no visible binding for global variable 'RGList'
Undefined global functions or variables:
  RGList floor.func
* 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 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/snapCGH/libs/x64/snapCGH.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 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: 2 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/snapCGH.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL snapCGH
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'snapCGH' ...
** 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 optimizer.c -o optimizer.o
optimizer.c: In function 'fr_two':
optimizer.c:26:30: warning: unused variable 'temp3' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                              ^~~~~
optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^~~~~
optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^~~~~
optimizer.c: In function 'fr_three':
optimizer.c:195:30: warning: unused variable 'temp3' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                              ^~~~~
optimizer.c:195:23: warning: unused variable 'temp2' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^~~~~
optimizer.c:195:10: warning: unused variable 'denom' [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^~~~~
optimizer.c:194:69: warning: unused variable 'alphahat' [-Wunused-variable]
   double gammaA[3][3], gammaB[3][3], gammaC[3][3], alpha[3][nrow1], alphahat[3][nrow1], emis_prob[3][nrow1];
                                                                     ^~~~~~~~
optimizer.c: In function 'fr_four':
optimizer.c:413:30: warning: unused variable 'temp3' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                              ^~~~~
optimizer.c:413:23: warning: unused variable 'temp2' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^~~~~
optimizer.c:413:10: warning: unused variable 'denom' [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^~~~~
optimizer.c:412:69: warning: unused variable 'alphahat' [-Wunused-variable]
   double gammaA[4][4], gammaB[4][4], gammaC[4][4], alpha[4][nrow1], alphahat[4][nrow1], emis_prob[4][nrow1];
                                                                     ^~~~~~~~
optimizer.c: In function 'fr_five':
optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                              ^~~~~
optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^~~~~
optimizer.c:687:10: warning: unused variable 'denom' [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^~~~~
optimizer.c:686:69: warning: unused variable 'alphahat' [-Wunused-variable]
   double gammaA[5][5], gammaB[5][5], gammaC[5][5], alpha[5][nrow1], alphahat[5][nrow1], emis_prob[5][nrow1];
                                                                     ^~~~~~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.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-snapCGH/00new/snapCGH/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'snapCGH'
    finding HTML links ... done
    IDProbes                                html  
    LargeDataObject                         html  
    SegList                                 html  
    Viterbi.five                            html  
    Viterbi.four                            html  
    Viterbi.three                           html  
    Viterbi.two                             html  
    cbind                                   html  
    chrominfo.Mb                            html  
    compareSegmentations                    html  
    convert.output                          html  
    dim                                     html  
    dimnames                                html  
    filter                                  html  
    find.param.five                         html  
    find.param.four                         html  
    find.param.one                          html  
    find.param.three                        html  
    find.param.two                          html  
    findBreakPoints                         html  
    fit.model                               html  
    genomePlot                              html  
    heatmapGenome                           html  
    imputeMissingValues                     html  
    log2ratios                              html  
    mergeStates                             html  
    plotSegmentedGenome                     html  
    processCGH                              html  
    read.clonesinfo                         html  
    readPositionalInfo                      html  
    removeByWeights                         html  
    runBioHMM                               html  
    runDNAcopy                              html  
    runGLAD                                 html  
    runHMM                                  html  
    runTilingArray                          html  
    sim.structure                           html  
    zoomChromosome                          html  
    zoomGenome                              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 (snapCGH)
Making 'packages.html' ... done