Package: tweeDEseq

Version: 1.6.1

Command: rm -rf tweeDEseq.buildbin-libdir && mkdir tweeDEseq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh tweeDEseq_1.6.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R tweeDEseq.buildbin-libdir

StartedAt: 2013-05-01 12:59:14 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 12:59:25 -0700 (Wed, 01 May 2013)

EllapsedTime: 10.9 seconds

RetCode: 0

Status:  OK

PackageFile: tweeDEseq_1.6.1.tgz

PackageFileSize: 415.4 KiB

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=tweeDEseq.buildbin-libdir tweeDEseq_1.6.1.tar.gz'
>>>>>>> 

* installing *source* package 'tweeDEseq' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c cov_wt_C.c -o cov_wt_C.o
cov_wt_C.c:6:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  res = (double *)malloc(n*sizeof(double));
                         ^˜
cov_wt_C.c:35:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  xc = (double *)malloc((n)*sizeof(double));
                         ^ ˜
cov_wt_C.c:52:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  y = (double *)malloc((*n)*sizeof(double));
                        ^˜ ˜
cov_wt_C.c:53:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  res = (double *)malloc((*p*2)*sizeof(double));
                          ˜˜^˜ ˜
cov_wt_C.c:88:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  resk3 = (double *)malloc(n*sizeof(double));
                           ^˜
cov_wt_C.c:119:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  y = (double *)malloc((*n)*sizeof(double));
                        ^˜ ˜
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c init_tweeDEseq.c -o init_tweeDEseq.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c loglikGlm.c -o loglikGlm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c logprobs.c -o logprobs.o
logprobs.c:28:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      newC = (double*)realloc(newC, k*sizeof(double));
                                    ^˜
logprobs.c:54:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    oldC = (double*)realloc(oldC, (k+1)*sizeof(double));
                                   ˜^˜ ˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c permtest.c -o permtest.o
permtest.c:43:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
permtest.c:53:11: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    rnd = floor(runif(0,n-i));
        ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
permtest.c:65:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  x1 = (double *)malloc(n1*sizeof(double));
                        ^˜˜
permtest.c:66:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  x2 = (double *)malloc(n2*sizeof(double));
                        ^˜˜
permtest.c:101:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  pvalreals = (double *)malloc((*n)*sizeof(double));
                                ^˜ ˜
permtest.c:102:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  pvalperms = (double **)malloc((*nperm)*sizeof(double *));
                                 ^˜˜˜˜˜ ˜
permtest.c:104:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    pvalperms[i] = (double *)malloc((*n)*sizeof(double));
                                     ^˜ ˜
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c probs.c -o probs.o
probs.c:7:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  C = (double **)malloc(n*sizeof(double *));
                        ^˜
probs.c:9:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    C[i] = (double *)malloc((i+1)*sizeof(double));
                             ˜^˜ ˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c zhu2.c -o zhu2.o
zhu2.c:18:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    r = (double *)malloc((*n)*sizeof(double));
                          ^˜ ˜
zhu2.c:30:14: warning: ordered comparison between pointer and zero ('double *' and 'int') is an extension [-Wpedantic]
      if((tol>0)&&(res[i+1]<=*tol)&&(res[i+1]<res[i])){
          ˜˜˜^˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c zhu3.c -o zhu3.o
zhu3.c:7:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  res = (double *)malloc((n+1)*sizeof(double));
                          ˜^˜ ˜
zhu3.c:16:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    r = (double *)malloc((n)*sizeof(double));
                          ^ ˜
2 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o tweeDEseq.so cov_wt_C.o init_tweeDEseq.o loglikGlm.o logprobs.o permtest.o probs.o zhu2.o zhu3.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/tweeDEseq.buildbin-libdir/tweeDEseq/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (tweeDEseq)


>>>>>>> 
>>>>>>> FIXING LINKS FOR tweeDEseq.buildbin-libdir/tweeDEseq/libs//tweeDEseq.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "tweeDEseq.buildbin-libdir/tweeDEseq/libs//tweeDEseq.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "tweeDEseq.buildbin-libdir/tweeDEseq/libs//tweeDEseq.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "tweeDEseq.buildbin-libdir/tweeDEseq/libs//tweeDEseq.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "tweeDEseq.buildbin-libdir/tweeDEseq/libs//tweeDEseq.so"