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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL PING
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘PING’ ...
** 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 init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -L/usr/local/lib -o PING.so init.o ping.o -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-PING/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PING)
