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INSTALL report for PICS on malbec2

This page was generated on 2019-10-16 11:58:27 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL PICS
StartedAt: 2019-10-15 18:49:04 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 18:49:36 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 31.4 seconds
RetCode: 0
Status:  OK 

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL PICS
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘PICS’ ...
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -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;
                  ^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -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]