BioC 3.1: CHECK report for snapCGH on moscato2

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### Running command:
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###   rm -rf snapCGH.buildbin-libdir snapCGH.Rcheck && mkdir snapCGH.buildbin-libdir snapCGH.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=snapCGH.buildbin-libdir snapCGH_1.38.0.tar.gz >snapCGH.Rcheck\00install.out 2>&1 && cp snapCGH.Rcheck\00install.out snapCGH-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=snapCGH.buildbin-libdir --install="check:snapCGH-install.out" --force-multiarch --no-vignettes --timings snapCGH_1.38.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/snapCGH.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.38.0'
* 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 '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 ... OK
* 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'
* 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 'E:/biocbld/bbs-3.1-bioc/meat/snapCGH.buildbin-libdir/snapCGH/libs/i386/snapCGH.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-3.1-bioc/meat/snapCGH.buildbin-libdir/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 the system RNG.
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 ...
** running examples for arch 'i386' ... [5s] OK
** running examples for arch 'x64' ... [6s] 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
  'E:/biocbld/bbs-3.1-bioc/meat/snapCGH.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'snapCGH' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c optimizer.c -o optimizer.o
optimizer.c: In function 'fr_two':
optimizer.c:26:30: warning: unused variable 'temp3' [-Wunused-variable]
optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable]
optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable]
optimizer.c: In function 'fr_three':
optimizer.c:195:30: warning: unused variable 'temp3' [-Wunused-variable]
optimizer.c:195:23: warning: unused variable 'temp2' [-Wunused-variable]
optimizer.c:195:10: warning: unused variable 'denom' [-Wunused-variable]
optimizer.c:194:69: warning: unused variable 'alphahat' [-Wunused-variable]
optimizer.c: In function 'fr_four':
optimizer.c:413:30: warning: unused variable 'temp3' [-Wunused-variable]
optimizer.c:413:23: warning: unused variable 'temp2' [-Wunused-variable]
optimizer.c:413:10: warning: unused variable 'denom' [-Wunused-variable]
optimizer.c:412:69: warning: unused variable 'alphahat' [-Wunused-variable]
optimizer.c: In function 'fr_five':
optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable]
optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable]
optimizer.c:687:10: warning: unused variable 'denom' [-Wunused-variable]
optimizer.c:686:69: warning: unused variable 'alphahat' [-Wunused-variable]
optimizer.c:997:58: warning: 'gammaC[4][4]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[4][3]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[4][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[4][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[4][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[3][4]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[3][3]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[3][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[3][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[3][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[2][4]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[2][3]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[2][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[2][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[2][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[1][4]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[1][3]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[1][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[1][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[1][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[0][4]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[0][3]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[0][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[0][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[0][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:943:4: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
optimizer.c: In function 'fr_four':
optimizer.c:641:58: warning: 'gammaC[3][3]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[3][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[3][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[3][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[2][3]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[2][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[2][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[2][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[1][3]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[1][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[1][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[1][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[0][3]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[0][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[0][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[0][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:585:1: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
optimizer.c: In function 'fr_three':
optimizer.c:366:58: warning: 'gammaC[2][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:366:58: warning: 'gammaC[2][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:366:58: warning: 'gammaC[2][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:366:58: warning: 'gammaC[1][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:366:58: warning: 'gammaC[1][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:366:58: warning: 'gammaC[1][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:366:58: warning: 'gammaC[0][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:366:58: warning: 'gammaC[0][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:366:58: warning: 'gammaC[0][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c: In function 'fr_two':
optimizer.c:150:58: warning: 'gammaC[1][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:150:58: warning: 'gammaC[1][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:150:58: warning: 'gammaC[0][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:150:58: warning: 'gammaC[0][0]' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.o -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/snapCGH.buildbin-libdir/snapCGH/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc,  :
  No generic function found corresponding to requested imported methods for "as.list" from package "multtest" (malformed exports?)
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc,  :
  No generic function found corresponding to requested imported methods for "as.list" from package "multtest" (malformed exports?)
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'snapCGH' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c optimizer.c -o optimizer.o
optimizer.c: In function 'fr_two':
optimizer.c:26:30: warning: unused variable 'temp3' [-Wunused-variable]
optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable]
optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable]
optimizer.c: In function 'fr_three':
optimizer.c:195:30: warning: unused variable 'temp3' [-Wunused-variable]
optimizer.c:195:23: warning: unused variable 'temp2' [-Wunused-variable]
optimizer.c:195:10: warning: unused variable 'denom' [-Wunused-variable]
optimizer.c:194:69: warning: unused variable 'alphahat' [-Wunused-variable]
optimizer.c: In function 'fr_four':
optimizer.c:413:30: warning: unused variable 'temp3' [-Wunused-variable]
optimizer.c:413:23: warning: unused variable 'temp2' [-Wunused-variable]
optimizer.c:413:10: warning: unused variable 'denom' [-Wunused-variable]
optimizer.c:412:69: warning: unused variable 'alphahat' [-Wunused-variable]
optimizer.c: In function 'fr_five':
optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable]
optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable]
optimizer.c:687:10: warning: unused variable 'denom' [-Wunused-variable]
optimizer.c:686:69: warning: unused variable 'alphahat' [-Wunused-variable]
optimizer.c:943:4: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
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]
gcc -m64 -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.o -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/snapCGH.buildbin-libdir/snapCGH/libs/x64
** testing if installed package can be loaded
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc,  :
  No generic function found corresponding to requested imported methods for "as.list" from package "multtest" (malformed exports?)
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'snapCGH' as snapCGH_1.38.0.zip
* DONE (snapCGH)

name	user	system	elapsed
LargeDataObject	0	0	0
convert.output	0.02	0.00	0.01
dim	0.01	0.00	0.02

name	user	system	elapsed
LargeDataObject	0	0	0
convert.output	0	0	0
dim	0.02	0.00	0.02

BioC 3.1: CHECK report for snapCGH on moscato2

Summary

Command output