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CHECK report for snapCGH on tokay2

This page was generated on 2019-10-16 12:20:22 -0400 (Wed, 16 Oct 2019).

Package 1547/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
snapCGH 1.54.0
John Marioni
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/snapCGH
Branch: RELEASE_3_9
Last Commit: 41a38a1
Last Changed Date: 2019-05-02 11:53:05 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: snapCGH
Version: 1.54.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:snapCGH.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings snapCGH_1.54.0.tar.gz
StartedAt: 2019-10-16 07:13:32 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:16:54 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 201.7 seconds
RetCode: 0
Status:  OK  
CheckDir: snapCGH.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:snapCGH.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings snapCGH_1.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/snapCGH.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.54.0'
* 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 ... NOTE
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'DNAcopy' 'limma' 'methods'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  cbind.SegList dim.SegList dimnames.SegList length.SegList
  rbind.SegList
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
MergeLevels.new: warning in matrix(1:ncol(dst), nrow = nrow(dst), ncol
  = ncol(dst), b = TRUE): partial argument match of 'b' to 'byrow'
Viterbi.five: warning in matrix(nrow = K, ncol = n, b = TRUE): partial
  argument match of 'b' to 'byrow'
Viterbi.four: warning in matrix(nrow = K, ncol = n, b = TRUE): partial
  argument match of 'b' to 'byrow'
Viterbi.three: warning in matrix(nrow = K, ncol = n, b = TRUE): partial
  argument match of 'b' to 'byrow'
Viterbi.two: warning in matrix(nrow = K, ncol = n, b = TRUE): partial
  argument match of 'b' to 'byrow'
find.param.five: warning in matrix(c(1 - p1 - p2 - p3 - p4, p1, p2, p3,
  p4, p5, 1 - p5 - p6 - p7 - p8, p6, p7, p8, p9, p10, 1 - p9 - p10 -
  p11 - p12, p11, p12, p13, p14, p15, 1 - p13 - p14 - p15 - p16, p16,
  p17, p18, p19, p20, 1 - p17 - p18 - p19 - p20), ncol = 5, b = TRUE):
  partial argument match of 'b' to 'byrow'
find.param.five: warning in matrix(c(p1 + p2 + p3 + p4, -p1, -p2, -p3,
  -p4, -p5, p5 + p6 + p7 + p8, -p6, -p7, -p8, -p9, -p10, p9 + p10 + p11
  + p12, -p11, -p12, -p13, -p14, -p15, p13 + p14 + p15 + p16, -p16,
  -p17, -p18, -p19, -p20, p17 + p18 + p19 + p20), ncol = 5, b = TRUE):
  partial argument match of 'b' to 'byrow'
find.param.four: warning in matrix(c(abs(1 - p1 - p2 - p3), p1, p2, p3,
  p4, abs(1 - p4 - p5 - p6), p5, p6, p7, p8, abs(1 - p7 - p8 - p9), p9,
  p10, p11, p12, abs(1 - p10 - p11 - p12)), ncol = 4, b = TRUE):
  partial argument match of 'b' to 'byrow'
find.param.four: warning in matrix(c(p1 + p2 + p3, -p1, -p2, -p3, -p4,
  p4 + p5 + p6, -p5, -p6, -p7, -p8, p7 + p8 + p9, -p9, -p10, -p11,
  -p12, p10 + p11 + p12), ncol = 4, b = TRUE): partial argument match
  of 'b' to 'byrow'
find.param.three: warning in matrix(c(abs(1 - p1 - p2), p1, p2, p3,
  abs(1 - p3 - p4), p4, p5, p6, abs(1 - p5 - p6)), ncol = 3, b = TRUE):
  partial argument match of 'b' to 'byrow'
find.param.three: warning in matrix(c(p1 + p2, -p1, -p2, -p3, p3 + p4,
  -p4, -p5, -p6, p5 + p6), ncol = 3, b = TRUE): partial argument match
  of 'b' to 'byrow'
find.param.two: warning in matrix(c(1 - p1, p1, p2, 1 - p2), ncol = 2,
  b = TRUE): partial argument match of 'b' to 'byrow'
find.param.two: warning in matrix(c(p1, -p1, -p2, p2), ncol = 2, b =
  TRUE): partial argument match of 'b' to 'byrow'
genomePlot: warning in matrix(data[ord, ], nrow =
  nrow(as.matrix(data[ord, ])), ncol = ncol(data), b = FALSE, dimnames
  = dimnames(data)): partial argument match of 'b' to 'byrow'
genomePlot: warning in matrix(data[chrom == nchr, ], nrow =
  nrow(as.matrix(data[chrom == nchr, ])), ncol = ncol(data), b = FALSE,
  dimnames = dimnames(data[chrom == nchr, ])): partial argument match
  of 'b' to 'byrow'
simulateData: warning in generate.data(mid.point.short[[i]],
  short.tiled[i], length.short.tiled[i], end.pos.short[[i]],
  start.short.tiled[i], length.chrom.short[i],
  zero.length.distr.non.tiled = zero.length.distr.non.tiled,
  non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
  zero.length.distr.tiled = zero.length.distr.tiled,
  non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
  argument match of 'zero.length.distr.non.tiled' to
  'zero.length.distr.non.tiled.'
simulateData: warning in generate.data(mid.point.short[[i]],
  short.tiled[i], length.short.tiled[i], end.pos.short[[i]],
  start.short.tiled[i], length.chrom.short[i],
  zero.length.distr.non.tiled = zero.length.distr.non.tiled,
  non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
  zero.length.distr.tiled = zero.length.distr.tiled,
  non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
  argument match of 'non.zero.length.distr.non.tiled' to
  'non.zero.length.distr.non.tiled.'
simulateData: warning in generate.data(mid.point.short[[i]],
  short.tiled[i], length.short.tiled[i], end.pos.short[[i]],
  start.short.tiled[i], length.chrom.short[i],
  zero.length.distr.non.tiled = zero.length.distr.non.tiled,
  non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
  zero.length.distr.tiled = zero.length.distr.tiled,
  non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
  argument match of 'zero.length.distr.tiled' to
  'zero.length.distr.tiled.'
simulateData: warning in generate.data(mid.point.short[[i]],
  short.tiled[i], length.short.tiled[i], end.pos.short[[i]],
  start.short.tiled[i], length.chrom.short[i],
  zero.length.distr.non.tiled = zero.length.distr.non.tiled,
  non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
  zero.length.distr.tiled = zero.length.distr.tiled,
  non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
  argument match of 'non.zero.length.distr.tiled' to
  'non.zero.length.distr.tiled.'
simulateData: warning in generate.data(mid.point.long[[i]],
  long.tiled[i], length.long.tiled[i], end.pos.long[[i]],
  start.long.tiled[i], length.chrom.long[i],
  zero.length.distr.non.tiled = zero.length.distr.non.tiled,
  non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
  zero.length.distr.tiled = zero.length.distr.tiled,
  non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
  argument match of 'zero.length.distr.non.tiled' to
  'zero.length.distr.non.tiled.'
simulateData: warning in generate.data(mid.point.long[[i]],
  long.tiled[i], length.long.tiled[i], end.pos.long[[i]],
  start.long.tiled[i], length.chrom.long[i],
  zero.length.distr.non.tiled = zero.length.distr.non.tiled,
  non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
  zero.length.distr.tiled = zero.length.distr.tiled,
  non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
  argument match of 'non.zero.length.distr.non.tiled' to
  'non.zero.length.distr.non.tiled.'
simulateData: warning in generate.data(mid.point.long[[i]],
  long.tiled[i], length.long.tiled[i], end.pos.long[[i]],
  start.long.tiled[i], length.chrom.long[i],
  zero.length.distr.non.tiled = zero.length.distr.non.tiled,
  non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
  zero.length.distr.tiled = zero.length.distr.tiled,
  non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
  argument match of 'zero.length.distr.tiled' to
  'zero.length.distr.tiled.'
simulateData: warning in generate.data(mid.point.long[[i]],
  long.tiled[i], length.long.tiled[i], end.pos.long[[i]],
  start.long.tiled[i], length.chrom.long[i],
  zero.length.distr.non.tiled = zero.length.distr.non.tiled,
  non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
  zero.length.distr.tiled = zero.length.distr.tiled,
  non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
  argument match of 'non.zero.length.distr.tiled' to
  'non.zero.length.distr.tiled.'
generate.data: no visible binding for global variable
  'zero.length.distr.non.tiled'
generate.data: no visible binding for global variable
  'non.zero.length.distr.non.tiled'
generate.data: no visible binding for global variable
  'zero.length.distr.tiled'
generate.data: no visible binding for global variable
  'non.zero.length.distr.tiled'
heatmapGenome: no visible binding for global variable 'floor.func'
readPositionalInfo: no visible binding for global variable 'RGList'
simulateData: no visible binding for global variable
  'zero.length.distr.non.tiled'
simulateData: no visible binding for global variable
  'zero.length.distr.tiled'
simulateData: no visible binding for global variable
  'non.zero.length.distr.non.tiled'
simulateData: no visible binding for global variable
  'non.zero.length.distr.tiled'
Undefined global functions or variables:
  RGList floor.func non.zero.length.distr.non.tiled
  non.zero.length.distr.tiled zero.length.distr.non.tiled
  zero.length.distr.tiled
* checking Rd files ... NOTE
prepare_Rd: genomePlot.Rd:51-57: Dropping empty section \examples
prepare_Rd: heatmapGenome.Rd:76-77: Dropping empty section \examples
prepare_Rd: plotSegmentedGenome.Rd:52-58: Dropping empty section \examples
prepare_Rd: sim.structure.Rd:57-58: Dropping empty section \examples
* 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 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/snapCGH/libs/i386/snapCGH.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/snapCGH.Rcheck/00check.log'
for details.



Installation output

snapCGH.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/snapCGH_1.54.0.tar.gz && rm -rf snapCGH.buildbin-libdir && mkdir snapCGH.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=snapCGH.buildbin-libdir snapCGH_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL snapCGH_1.54.0.zip && rm snapCGH_1.54.0.tar.gz snapCGH_1.54.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  620k  100  620k    0     0  8125k      0 --:--:-- --:--:-- --:--:-- 8867k

install for i386

* installing *source* package 'snapCGH' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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];
                                                                     ^
optimizer.c: In function 'fr_two':
optimizer.c:150:58: warning: 'gammaC[1][1]' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 alpha[k][t] = alpha[k][t] + alpha[d][t-1]*gammaC[d][k];
                                                          ^
optimizer.c:150:58: warning: 'gammaC[1][0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
optimizer.c:150:58: warning: 'gammaC[0][1]' may be used uninitialized in this function [-Wmaybe-uninitialized]
optimizer.c:150:58: warning: 'gammaC[0][0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/snapCGH.buildbin-libdir/00LOCK-snapCGH/00new/snapCGH/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: more than one default provided in switch() call 
** 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  
    non.zero.length.distr.non.tiled         html  
    non.zero.length.distr.tiled             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  
    zero.length.distr.non.tiled             html  
    zero.length.distr.tiled                 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

install for x64

* installing *source* package 'snapCGH' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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];
                                                                     ^
optimizer.c:943:4: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
    for(t = 1; t < nrow1; t++){
    ^
optimizer.c: In function 'fr_four':
optimizer.c:585:1: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
 for(t = 1; t < nrow1; t++){  
 ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/snapCGH.buildbin-libdir/snapCGH/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'snapCGH' as snapCGH_1.54.0.zip
* DONE (snapCGH)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'snapCGH' successfully unpacked and MD5 sums checked

Tests output


Example timings

snapCGH.Rcheck/examples_i386/snapCGH-Ex.timings

nameusersystemelapsed
LargeDataObject000
convert.output000
dim000

snapCGH.Rcheck/examples_x64/snapCGH-Ex.timings

nameusersystemelapsed
LargeDataObject000
convert.output000
dim000