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INSTALL report for PING on malbec1

This page was generated on 2019-04-16 11:49:31 -0400 (Tue, 16 Apr 2019).

Package 1161/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PING 2.26.0
Renan Sauteraud
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/PING
Branch: RELEASE_3_8
Last Commit: 5b0be17
Last Changed Date: 2018-10-30 11:41:48 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64 [ OK ] OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: PING
Version: 2.26.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL PING
StartedAt: 2019-04-15 18:29:43 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 18:30:28 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 45.4 seconds
RetCode: 0
Status:  OK 

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL PING
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘PING’ ...
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-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c ping.c -o ping.o
ping.c: In function ‘fitModelAllk’:
ping.c:145:40: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
   if( REAL(VECTOR_ELT(paraPrior, 5))[0]>0 & REAL(VECTOR_ELT(paraEM, 0))[0]==0) // automatically decide minK and maxKK for histone data, when minK=0
                                        ^
ping.c: In function ‘iterEM’:
ping.c:659:25: warning: unused variable ‘mu’ [-Wunused-variable]
  double oldMu[p], w[p], mu[p], delta[p], sF[p], sR[p], sumDiff=0.0;
                         ^
ping.c: In function ‘ECM1’:
ping.c:912:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
   if(status1==0 & status2==0)
             ^
ping.c:1072:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
   if(status1==0 & status2==0)
             ^
ping.c:760:15: 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);
               ^
ping.c: In function ‘ECM1PE’:
ping.c:1320:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
   if(status1==0 & status2==0)
             ^
ping.c:1473:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
   if(status1==0 & status2==0)
             ^
ping.c:1108:15: warning: unused variable ‘k’ [-Wunused-variable]
  int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NFR=length(F);
               ^
ping.c: In function ‘ECM2’:
ping.c:1536:66: warning: unused variable ‘ee’ [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                                  ^
ping.c:1536:57: warning: unused variable ‘ggR’ [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                         ^
ping.c:1536:52: warning: unused variable ‘ggF’ [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                    ^
ping.c:1536:47: warning: unused variable ‘aaR’ [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                               ^
ping.c:1536:42: warning: unused variable ‘aaF’ [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                          ^
ping.c:1536:29: warning: unused variable ‘etaDiff’ [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                             ^
ping.c:1536:9: warning: variable ‘chiSum’ set but not used [-Wunused-but-set-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
         ^
ping.c:1527:15: 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);
               ^
ping.c: In function ‘ECM2PE’:
ping.c:1743:66: warning: unused variable ‘ee’ [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                                  ^
ping.c:1743:57: warning: unused variable ‘ggR’ [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                         ^
ping.c:1743:52: warning: unused variable ‘ggF’ [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                                    ^
ping.c:1743:47: warning: unused variable ‘aaR’ [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                               ^
ping.c:1743:42: warning: unused variable ‘aaF’ [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                                          ^
ping.c:1743:29: warning: unused variable ‘etaDiff’ [-Wunused-variable]
  double chiSum, etaF, etaR, etaDiff, dd, aaF, aaR, ggF, ggR, cc, ee;
                             ^
ping.c:1734:15: warning: unused variable ‘k’ [-Wunused-variable]
  int i=0,j=0, k=0, K=length(VECTOR_ELT(para, 0)), NFR=length(F);
               ^
ping.c: In function ‘getInfMat’:
ping.c:2590:80: warning: unused variable ‘PhiRw’ [-Wunused-variable]
    double aNormF, aNormR, bNormF, bNormR, P0F=1.0, P0R=1.0, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR; 
                                                                                ^
ping.c:2590:73: warning: unused variable ‘PhiFw’ [-Wunused-variable]
    double aNormF, aNormR, bNormF, bNormR, P0F=1.0, P0R=1.0, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR; 
                                                                         ^
ping.c: In function ‘getInfMatPE’:
ping.c:3040:59: warning: unused variable ‘PhiFRw’ [-Wunused-variable]
   double aNormF, aNormR, bNormF, bNormR, P0FR=1.0, PhiFR, PhiFRw, wPjFR; 
                                                           ^
ping.c: In function ‘mergePeak’:
ping.c:3312:20: warning: variable ‘tstatMax’ set but not used [-Wunused-but-set-variable]
   double tstat=0.0,tstatMax=0.0;
                    ^
ping.c:3301:11: warning: unused variable ‘j’ [-Wunused-variable]
   int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
           ^
ping.c:3301:7: warning: unused variable ‘i’ [-Wunused-variable]
   int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
       ^
ping.c: In function ‘BIC’:
ping.c:2101:6: 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;
      ^
ping.c: In function ‘BICPE’:
ping.c:2208:6: warning: ‘penalty’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  bic = logDensityMixPE(yF, yR, w, muF, muR, sigmaSqF, sigmaSqR, K, NFR) - penalty;
      ^
ping.c: In function ‘fitModelK’:
ping.c:477:18: warning: ‘firstFit’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  SEXP ans, temp, firstFit;
                  ^
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o PING.so init.o ping.o -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/PING/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PING)