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Package 241/671HostnameOS / ArchBUILDCHECKBUILD BIN
gaga 2.6.0
David Rossell
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/gaga
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ]

Summary

Package: gaga
Version: 2.6.0
Command: rm -rf gaga.buildbin-libdir && mkdir gaga.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gaga_2.6.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R gaga.buildbin-libdir
StartedAt: 2013-05-01 12:24:03 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 12:24:21 -0700 (Wed, 01 May 2013)
EllapsedTime: 18.5 seconds
RetCode: 0
Status:  OK 
PackageFile: gaga_2.6.0.tgz
PackageFileSize: 480.3 KiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=gaga.buildbin-libdir gaga_2.6.0.tar.gz'
>>>>>>> 

* installing *source* package 'gaga' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c cseqdesma.c -o cseqdesma.o
cseqdesma.c:622:48: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  for (i=0; i<ncolxpred; i++) { groupspred[i]= floor(i/(*mpred)); }
                                             ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cseqdesma.c:918:48: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  for (i=0; i<ncolxpred; i++) { groupspred[i]= floor(i/(*mpred)); }
                                             ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cseqdesma.c:1926:17: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    Bburnin= 0.2*(*Bgibbs);   //Gibbs samples to exclude from training sample
           ˜ ˜˜˜^˜˜˜˜˜˜˜˜˜
cseqdesma.c:3654:47: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  for (i=0; i<ncolpred; i++) { groupspred[i]= floor(i / (*deltat)); }
                                            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cseqdesma.c:3838:47: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  for (i=0; i<ncolpred; i++) { groupspred[i]= floor(i / (*deltat)); }
                                            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cseqdesma.c:4038:47: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  for (i=0; i<ncolpred; i++) { groupspred[i]= floor(i / (*deltat)); }
                                            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cseqdesma.c:4524:14: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((*usesumx==0)) {                                               //if suff stat not pre-computed
     ˜˜˜˜˜˜˜˜^˜˜
cseqdesma.c:4524:14: note: remove extraneous parentheses around the comparison to silence this warning
if ((*usesumx==0)) {                                               //if suff stat not pre-computed
    ˜        ^  ˜
cseqdesma.c:4524:14: note: use '=' to turn this equality comparison into an assignment
if ((*usesumx==0)) {                                               //if suff stat not pre-computed
             ^˜
             =
cseqdesma.c:5836:13: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
  if ((*usel==0)) {
       ˜˜˜˜˜^˜˜
cseqdesma.c:5836:13: note: remove extraneous parentheses around the comparison to silence this warning
  if ((*usel==0)) {
      ˜     ^  ˜
cseqdesma.c:5836:13: note: use '=' to turn this equality comparison into an assignment
  if ((*usel==0)) {
            ^˜
            =
cseqdesma.c:6070:13: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
  if ((*usel==0)) {
       ˜˜˜˜˜^˜˜
cseqdesma.c:6070:13: note: remove extraneous parentheses around the comparison to silence this warning
  if ((*usel==0)) {
      ˜     ^  ˜
cseqdesma.c:6070:13: note: use '=' to turn this equality comparison into an assignment
  if ((*usel==0)) {
            ^˜
            =
cseqdesma.c:6340:13: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
  if ((*usel==0)) {                                           //If l values have to be generated
       ˜˜˜˜˜^˜˜
cseqdesma.c:6340:13: note: remove extraneous parentheses around the comparison to silence this warning
  if ((*usel==0)) {                                           //If l values have to be generated
      ˜     ^  ˜
cseqdesma.c:6340:13: note: use '=' to turn this equality comparison into an assignment
  if ((*usel==0)) {                                           //If l values have to be generated
            ^˜
            =
10 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c cstat.c -o cstat.o
cstat.c:571:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  a = (double ***) malloc(n1 * sizeof(double **));
                          ^˜ ˜
cstat.c:574:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  a[0] = (double **) malloc(n1 * n2 * sizeof(double *));
                            ˜˜˜^˜˜˜ ˜
cstat.c:578:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  a[0][0] = (double *) malloc(n1 * n2 * n3 * sizeof(double));
                              ˜˜˜˜˜˜˜˜^˜˜˜ ˜
cstat.c:648:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  a = (int ***) malloc(n1 * sizeof(int **));
                       ^˜ ˜
cstat.c:651:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  a[0] = (int **) malloc(n1 * n2 * sizeof(int *));
                         ˜˜˜^˜˜˜ ˜
cstat.c:655:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  a[0][0] = (int *) malloc(n1 * n2 * n3 * sizeof(int));
                           ˜˜˜˜˜˜˜˜^˜˜˜ ˜
cstat.c:1311:11: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
qsort (v, size, sizeof (double), dcompare);
˜˜˜˜˜     ^˜˜˜
cstat.c:1410:10: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    r= i + (popsize - i - 1)*runif();
     ˜ ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cstat.c:1421:10: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    r= i + (popsize - i - 1)*runif();
     ˜ ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cstat.c:1461:14: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  return(min + runif()*(max+1-min));
  ˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cstat.c:1838:14: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  if(abs(ndf - 2.0) < eps) {   /* df ˜= 2 */
     ˜˜˜ ˜˜˜˜^˜˜˜˜
cstat.c:2669:9: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    n = (long)(*a - 1.25e0);
      ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
12 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 gaga.so cseqdesma.o cstat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/gaga.buildbin-libdir/gaga/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gaga)


>>>>>>> 
>>>>>>> FIXING LINKS FOR gaga.buildbin-libdir/gaga/libs//gaga.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" "gaga.buildbin-libdir/gaga/libs//gaga.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "gaga.buildbin-libdir/gaga/libs//gaga.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" "gaga.buildbin-libdir/gaga/libs//gaga.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "gaga.buildbin-libdir/gaga/libs//gaga.so"