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BUILD BIN report for PICS on tokay2

This page was generated on 2019-10-16 12:23:46 -0400 (Wed, 16 Oct 2019).

Package 1213/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PICS 2.28.0
Renan Sauteraud
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/PICS
Branch: RELEASE_3_9
Last Commit: 8cf1a4a
Last Changed Date: 2019-05-02 11:53:14 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: PICS
Version: 2.28.0
Command: rm -rf PICS.buildbin-libdir && mkdir PICS.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PICS.buildbin-libdir PICS_2.28.0.tar.gz
StartedAt: 2019-10-16 09:54:05 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 09:54:51 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 46.5 seconds
RetCode: 0
Status:  OK  
PackageFile: PICS_2.28.0.zip
PackageFileSize: 1.824 MiB

Command output

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###
### Running command:
###
###   rm -rf PICS.buildbin-libdir && mkdir PICS.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PICS.buildbin-libdir PICS_2.28.0.tar.gz
###
##############################################################################
##############################################################################



install for i386

* installing *source* package 'PICS' ...
** using staged installation

   **********************************************
   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-3~1.9-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-3~1.9-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]sFFilter[0] & sF[k]sRFilter[0] & sR[k]seFilter[0] & se[k]seFilterF[0] & se[k]seFilterR[0] & se[k]scoreFilter[0] & score[k]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]sFFilter[0] & sF[k]sRFilter[0] & sR[k]seFilter[0] & se[k]seFilterF[0] & se[k]seFilterR[0] & se[k]scoreFilter[0] & score[k]