PICS 2.30.0
Renan Sauteraud
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/PICS |
| Branch: RELEASE_3_10 |
| Last Commit: a78c196 |
| Last Changed Date: 2019-10-29 13:08:15 -0400 (Tue, 29 Oct 2019) |
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | [ OK ] | |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf PICS.buildbin-libdir && mkdir PICS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh PICS_2.30.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R PICS.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=PICS.buildbin-libdir PICS_2.30.0.tar.gz'
>>>>>>>
* installing *source* package ‘PICS’ ...
** using staged installation
checking for pkg-config... /usr/local/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
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c pics.c -o pics.o
pics.c:288:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
if(abs(REAL(yF)[i]-mu[k]+delta[k]/2.)/sqrt(sF[k])<calpha)
^
pics.c:288:10: note: use function 'fabs' instead
if(abs(REAL(yF)[i]-mu[k]+delta[k]/2.)/sqrt(sF[k])<calpha)
^~~
fabs
pics.c:296:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
if(abs(REAL(yR)[i]-mu[k]-delta[k]/2.)/sqrt(sR[k])<calpha)
^
pics.c:296:10: note: use function 'fabs' instead
if(abs(REAL(yR)[i]-mu[k]-delta[k]/2.)/sqrt(sR[k])<calpha)
^~~
fabs
pics.c:309:12: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
if(abs(REAL(cF)[i]-mu[k]+delta[k]/2.)/sqrt(sF[k])<calpha)
^
pics.c:309:12: note: use function 'fabs' instead
if(abs(REAL(cF)[i]-mu[k]+delta[k]/2.)/sqrt(sF[k])<calpha)
^~~
fabs
pics.c:317:12: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
if(abs(REAL(cR)[i]-mu[k]-delta[k]/2.)/sqrt(sR[k])<calpha)
^
pics.c:317:12: note: use function 'fabs' instead
if(abs(REAL(cR)[i]-mu[k]-delta[k]/2.)/sqrt(sR[k])<calpha)
^~~
fabs
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: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: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: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:1009:29: warning: unused variable 'etaDiff' [-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: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:1301:3: warning: variable 'penalty' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
default:
^~~~~~~
pics.c:1307:97: note: uninitialized use occurs here
bic = logDensityMix(yF, w, muF, sigmaSqF, K, NF) + logDensityMix(yR, w, muR, sigmaSqR, K,NR) - penalty;
^~~~~~~
pics.c:1275:42: note: initialize the variable 'penalty' to silence this warning
double bic, tmp, muF[K], muR[K], penalty, distance;
^
= 0.0
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:1889:7: warning: unused variable 'i' [-Wunused-variable]
int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
^
pics.c:1889:11: warning: unused variable 'j' [-Wunused-variable]
int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
^
19 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c segment.c -o segment.o
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:308:7: warning: unused variable 'i' [-Wunused-variable]
int i=0,p=0;
^
segment.c:406:6: warning: variable 'pp' is incremented both in the loop header and in the loop body [-Wfor-loop-analysis]
pp++;
^
segment.c:395:27: note: incremented here
for (pp=start; pp<=p; pp++) {
^
segment.c:536:6: warning: variable 'pp' is incremented both in the loop header and in the loop body [-Wfor-loop-analysis]
pp++;
^
segment.c:525:27: note: incremented here
for (pp=start; pp<=p; pp++) {
^
segment.c:1364:11: warning: unused variable 'j' [-Wunused-variable]
int i=0, j=0, n=length(list), nF, nR, nProtect=0;
^
segment.c:1489:11: warning: unused variable 'muFilter' [-Wunused-variable]
double *muFilter, *deltaFilter, *sFFilter, *sRFilter, *seFilter, *seFilterF, *seFilterR, *scoreFilter, *score;
^
segment.c:1490:8: warning: unused variable 'filter1' [-Wunused-variable]
SEXP filter1;
^
7 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o PICS.so pics.o segment.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.10-bioc/meat/PICS.buildbin-libdir/00LOCK-PICS/00new/PICS/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 (PICS)
>>>>>>>
>>>>>>> FIXING LINKS FOR PICS.buildbin-libdir/PICS/libs//PICS.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "PICS.buildbin-libdir/PICS/libs//PICS.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "PICS.buildbin-libdir/PICS/libs//PICS.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "PICS.buildbin-libdir/PICS/libs//PICS.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "PICS.buildbin-libdir/PICS/libs//PICS.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "PICS.buildbin-libdir/PICS/libs//PICS.so"