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CHECK report for PICS on tokay2

This page was generated on 2018-10-17 08:34:45 -0400 (Wed, 17 Oct 2018).

Package 1096/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PICS 2.24.0
Renan Sauteraud
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/PICS
Branch: RELEASE_3_7
Last Commit: 3620173
Last Changed Date: 2018-04-30 10:35:13 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: PICS
Version: 2.24.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PICS.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings PICS_2.24.0.tar.gz
StartedAt: 2018-10-17 03:58:48 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:02:17 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 208.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: PICS.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PICS.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings PICS_2.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/PICS.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PICS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PICS' version '2.24.0'
* 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 'PICS' can be installed ... WARNING
Found the following significant warnings:
  pics.c:803:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  pics.c:963:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  segment.c:123:19: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  segment.c:1543:21: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  segment.c:1544:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  segment.c:1545:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  segment.c:1546:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  segment.c:1547:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  segment.c:1548:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  segment.c:1549:20: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/PICS.Rcheck/00install.out' for details.
* 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
* 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 ... NOTE
':::' calls which should be '::':
  'parallel:::detectCores' 'parallel:::makeCluster'
  'parallel:::parLapply' 'parallel:::stopCluster'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot,pics-segReads: warning in symbols((map[, 1] + map[, 2])/2,
  rep(0.35, nMap), rectangle = cbind(map[, 2] - map[, 1], rep(0.6,
  nMap)), inches = FALSE, bg = grey(0.6), fg = 0, add = TRUE, xlim =
  c(m, M), ylim = c(0, 1)): partial argument match of 'rectangle' to
  'rectangles'
plot,pics-segReads: warning in symbols(x@estimates$mu, rep(0.5, K), rec
  = matrix(rep(c(147, 0.8), K), ncol = 2, byrow = TRUE), inches =
  FALSE, bg = grey(0.5 * pmin(se(x)/50, 1)), fg = 0, add = TRUE, xlim =
  c(m, M), ylim = c(0, 1)): partial argument match of 'rec' to
  'rectangles'
plot,pics-segReads: warning in symbols(x@estimates$mu, rep(0.5, K), rec
  = matrix(rep(c(147, 0.8), K), ncol = 2, byrow = TRUE), inches =
  FALSE, fg = 0, bg = 1, add = TRUE, xlim = c(m, M), ylim = c(0, 1)):
  partial argument match of 'rec' to 'rectangles'
bam2gr: no visible global function definition for 'reshape'
Undefined global functions or variables:
  reshape
Consider adding
  importFrom("stats", "reshape")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'picsList,ANY,ANY,ANY'
  generic '[' and siglist 'segReadsList,ANY,ANY,ANY'
  generic '[' and siglist 'segReadsListPE,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both 'src/Makevars.in' and 'src/Makevars'.
Installation with --no-configure' is unlikely to work.  If you intended
'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win'
otherwise remove it.  If 'configure' created 'src/Makevars', you need a
'cleanup' script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* 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: 2 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/PICS.Rcheck/00check.log'
for details.

Installation output

PICS.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/PICS_2.24.0.tar.gz && rm -rf PICS.buildbin-libdir && mkdir PICS.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PICS.buildbin-libdir PICS_2.24.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL PICS_2.24.0.zip && rm PICS_2.24.0.tar.gz PICS_2.24.0.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  813k  100  813k    0     0  11.9M      0 --:--:-- --:--:-- --:--:-- 13.4M

install for i386

* installing *source* package 'PICS' ...

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


** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c pics.c -o pics.o
pics.c: In function 'iterEM':
pics.c:581:25: warning: unused variable 'mu' [-Wunused-variable]
  double oldMu[p], w[p], mu[p], delta[p], sF[p], sR[p], sumDiff=0;
                         ^
pics.c: In function 'ECM1':
pics.c:803:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   if(status1==0 & status2==0)
             ^
pics.c:963:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   if(status1==0 & status2==0)
             ^
pics.c:651:15: warning: unused variable 'k' [-Wunused-variable]
  int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NF=length(F), NR=length(R);
               ^
pics.c: In function 'ECM2':
pics.c:1009:66: warning: unused variable 'ee' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                                  ^
pics.c:1009:57: warning: unused variable 'ggR' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                         ^
pics.c:1009:52: warning: unused variable 'ggF' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                    ^
pics.c:1009:47: warning: unused variable 'aaR' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                               ^
pics.c:1009:42: warning: unused variable 'aaF' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                          ^
pics.c:1009:29: warning: unused variable 'etaDiff' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                             ^
pics.c:1009:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
         ^
pics.c:1000:15: warning: unused variable 'k' [-Wunused-variable]
  int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NF=length(F), NR=length(R);
               ^
pics.c: In function 'BIC':
pics.c:1272:96: warning: unused variable 'k' [-Wunused-variable]
  int  nu=INTEGER(nuC)[0], K=length(VECTOR_ELT(para, 0)), NF=length(F), NR=length(R), i=0, j=0, k=0, N, type=INTEGER(mselect)[0];
                                                                                                ^
pics.c: In function 'getInfMat':
pics.c:1633:76: warning: unused variable 'PhiRw' [-Wunused-variable]
    double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR; 
                                                                            ^
pics.c:1633:69: warning: unused variable 'PhiFw' [-Wunused-variable]
    double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR; 
                                                                     ^
pics.c: In function 'mergePeak':
pics.c:1889:11: warning: unused variable 'j' [-Wunused-variable]
   int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
           ^
pics.c:1889:7: warning: unused variable 'i' [-Wunused-variable]
   int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
       ^
pics.c: In function 'BIC':
pics.c:1307:6: warning: 'penalty' may be used uninitialized in this function [-Wmaybe-uninitialized]
  bic = logDensityMix(yF, w, muF, sigmaSqF, K, NF) + logDensityMix(yR, w, muR, sigmaSqR, K,NR) - penalty;
      ^
pics.c: In function 'fitModelK':
pics.c:421:18: warning: 'firstFit' may be used uninitialized in this function [-Wmaybe-uninitialized]
  SEXP ans, temp, firstFit;
                  ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c segment.c -o segment.o
segment.c: In function 'segReads':
segment.c:123:19: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   if(length(contF)>0 & length(contR)>0)
                   ^
segment.c:114:45: warning: unused variable 'count' [-Wunused-variable]
   int i=0,nR=length(dataR),nF=length(dataF),count=0,lengthCenter=0;
                                             ^
segment.c: In function 'callRegions':
segment.c:308:7: warning: unused variable 'i' [-Wunused-variable]
   int i=0,p=0;
       ^
segment.c: In function 'getSegL':
segment.c:1364:11: warning: unused variable 'j' [-Wunused-variable]
  int i=0, j=0, n=length(list), nF, nR, nProtect=0;
           ^
segment.c: In function 'getDensity':
segment.c:1543:21: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
         if((delta[k]>deltaFilter[0] & delta[k]<deltaFilter[1]) & 
                     ^
segment.c:1544:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
           (sF[k]>sFFilter[0] & sF[k]<sFFilter[1]) & 
                 ^
segment.c:1545:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
           (sR[k]>sRFilter[0] & sR[k]<sRFilter[1]) & 
                 ^
segment.c:1546:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
           (se[k]>seFilter[0] & se[k]<seFilter[1]) &
                 ^
segment.c:1547:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
           (se[k]>seFilterF[0] & se[k]<seFilterF[1]) &
                 ^
segment.c:1548:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
           (se[k]>seFilterR[0] & se[k]<seFilterR[1]) &          
                 ^
segment.c:1549:20: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
           (score[k]>scoreFilter[0] & score[k]<scoreFilter[1]))
                    ^
segment.c:1494:19: warning: variable 'chr' set but not used [-Wunused-but-set-variable]
   SEXP ans, x, y, chr, names;
                   ^
segment.c:1490:8: warning: unused variable 'filter1' [-Wunused-variable]
   SEXP filter1;
        ^
segment.c:1489:11: warning: unused variable 'muFilter' [-Wunused-variable]
   double *muFilter, *deltaFilter, *sFFilter, *sRFilter, *seFilter, *seFilterF, *seFilterR, *scoreFilter, *score;
           ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o PICS.dll tmp.def pics.o segment.o -lws2_32 -L/i386/lib -lgsl -lgslcblas -lm -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/PICS.buildbin-libdir/PICS/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PICS'
    finding HTML links ... done
    PICS                                    html  
    SegReadsList                            html  
    bam2gr                                  html  
    makeRangedDataOutput                    html  
    pics-class                              html  
    picsError-class                         html  
    picsFDR                                 html  
    picsList-class                          html  
    plot-FDR                                html  
    segChrRead                              html  
    segReads                                html  
    segReadsListPE                          html  
    segReadsPE                              html  
    segmentPICS                             html  
    setParaEM                               html  
    setParaPrior                            html  
    show                                    html  
    summary                                 html  
    summarySeg                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'PICS' ...

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


** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c pics.c -o pics.o
pics.c: In function 'iterEM':
pics.c:581:25: warning: unused variable 'mu' [-Wunused-variable]
  double oldMu[p], w[p], mu[p], delta[p], sF[p], sR[p], sumDiff=0;
                         ^
pics.c: In function 'ECM1':
pics.c:803:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   if(status1==0 & status2==0)
             ^
pics.c:963:13: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   if(status1==0 & status2==0)
             ^
pics.c:651:15: warning: unused variable 'k' [-Wunused-variable]
  int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NF=length(F), NR=length(R);
               ^
pics.c: In function 'ECM2':
pics.c:1009:66: warning: unused variable 'ee' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                                  ^
pics.c:1009:57: warning: unused variable 'ggR' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                         ^
pics.c:1009:52: warning: unused variable 'ggF' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                    ^
pics.c:1009:47: warning: unused variable 'aaR' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                               ^
pics.c:1009:42: warning: unused variable 'aaF' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                          ^
pics.c:1009:29: warning: unused variable 'etaDiff' [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                             ^
pics.c:1009:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
         ^
pics.c:1000:15: warning: unused variable 'k' [-Wunused-variable]
  int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NF=length(F), NR=length(R);
               ^
pics.c: In function 'BIC':
pics.c:1272:96: warning: unused variable 'k' [-Wunused-variable]
  int  nu=INTEGER(nuC)[0], K=length(VECTOR_ELT(para, 0)), NF=length(F), NR=length(R), i=0, j=0, k=0, N, type=INTEGER(mselect)[0];
                                                                                                ^
pics.c: In function 'getInfMat':
pics.c:1633:76: warning: unused variable 'PhiRw' [-Wunused-variable]
    double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR; 
                                                                            ^
pics.c:1633:69: warning: unused variable 'PhiFw' [-Wunused-variable]
    double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR; 
                                                                     ^
pics.c: In function 'mergePeak':
pics.c:1889:11: warning: unused variable 'j' [-Wunused-variable]
   int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
           ^
pics.c:1889:7: warning: unused variable 'i' [-Wunused-variable]
   int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
       ^
pics.c: In function 'BIC':
pics.c:1307:6: warning: 'penalty' may be used uninitialized in this function [-Wmaybe-uninitialized]
  bic = logDensityMix(yF, w, muF, sigmaSqF, K, NF) + logDensityMix(yR, w, muR, sigmaSqR, K,NR) - penalty;
      ^
pics.c: In function 'fitModelK':
pics.c:421:18: warning: 'firstFit' may be used uninitialized in this function [-Wmaybe-uninitialized]
  SEXP ans, temp, firstFit;
                  ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c segment.c -o segment.o
segment.c: In function 'segReads':
segment.c:123:19: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   if(length(contF)>0 & length(contR)>0)
                   ^
segment.c:114:45: warning: unused variable 'count' [-Wunused-variable]
   int i=0,nR=length(dataR),nF=length(dataF),count=0,lengthCenter=0;
                                             ^
segment.c: In function 'callRegions':
segment.c:308:7: warning: unused variable 'i' [-Wunused-variable]
   int i=0,p=0;
       ^
segment.c: In function 'getSegL':
segment.c:1364:11: warning: unused variable 'j' [-Wunused-variable]
  int i=0, j=0, n=length(list), nF, nR, nProtect=0;
           ^
segment.c: In function 'getDensity':
segment.c:1543:21: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
         if((delta[k]>deltaFilter[0] & delta[k]<deltaFilter[1]) & 
                     ^
segment.c:1544:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
           (sF[k]>sFFilter[0] & sF[k]<sFFilter[1]) & 
                 ^
segment.c:1545:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
           (sR[k]>sRFilter[0] & sR[k]<sRFilter[1]) & 
                 ^
segment.c:1546:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
           (se[k]>seFilter[0] & se[k]<seFilter[1]) &
                 ^
segment.c:1547:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
           (se[k]>seFilterF[0] & se[k]<seFilterF[1]) &
                 ^
segment.c:1548:17: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
           (se[k]>seFilterR[0] & se[k]<seFilterR[1]) &          
                 ^
segment.c:1549:20: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
           (score[k]>scoreFilter[0] & score[k]<scoreFilter[1]))
                    ^
segment.c:1494:19: warning: variable 'chr' set but not used [-Wunused-but-set-variable]
   SEXP ans, x, y, chr, names;
                   ^
segment.c:1490:8: warning: unused variable 'filter1' [-Wunused-variable]
   SEXP filter1;
        ^
segment.c:1489:11: warning: unused variable 'muFilter' [-Wunused-variable]
   double *muFilter, *deltaFilter, *sFFilter, *sRFilter, *seFilter, *seFilterF, *seFilterR, *scoreFilter, *score;
           ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o PICS.dll tmp.def pics.o segment.o -lws2_32 -L/x64/lib -lgsl -lgslcblas -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/PICS.buildbin-libdir/PICS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PICS' as PICS_2.24.0.zip
* DONE (PICS)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'PICS' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Example timings

PICS.Rcheck/examples_i386/PICS-Ex.timings

nameusersystemelapsed
makeRangedDataOutput000
pics-class000
picsError-class000
picsList-class000
segmentPICS1.110.071.58
setParaPrior000

PICS.Rcheck/examples_x64/PICS-Ex.timings

nameusersystemelapsed
makeRangedDataOutput000
pics-class000
picsError-class000
picsList-class000
segmentPICS1.200.011.32
setParaPrior000