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BUILD BIN report for gaga on merida1

This page was generated on 2019-04-16 11:54:46 -0400 (Tue, 16 Apr 2019).

Package 567/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gaga 2.28.1
David Rossell
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/gaga
Branch: RELEASE_3_8
Last Commit: 884f515
Last Changed Date: 2019-01-04 13:33:31 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK 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: gaga
Version: 2.28.1
Command: rm -rf gaga.buildbin-libdir && mkdir gaga.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gaga_2.28.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R gaga.buildbin-libdir
StartedAt: 2019-04-16 04:05:03 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 04:05:48 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 44.9 seconds
RetCode: 0
Status:  OK 
PackageFile: gaga_2.28.1.tgz
PackageFileSize: 592.6 KiB

Command output

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###
### Running command:
###
###   rm -rf gaga.buildbin-libdir && mkdir gaga.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gaga_2.28.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R gaga.buildbin-libdir
###
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##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=gaga.buildbin-libdir gaga_2.28.1.tar.gz'
>>>>>>> 

* installing *source* package ‘gaga’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c cseqdesma.c -o cseqdesma.o
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
            ^˜
            =
4 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c cstat.c -o cstat.o
cstat.c:1838:6: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  if(abs(ndf - 2.0) < eps) {   /* df ˜= 2 */
     ^
cstat.c:1838:6: note: use function 'fabs' instead
  if(abs(ndf - 2.0) < eps) {   /* df ˜= 2 */
     ^˜˜
     fabs
cstat.c:18:19: warning: unused variable 'interface_c_sccs_id' [-Wunused-const-variable]
static const char interface_c_sccs_id[] = "%W%";
                  ^
cstat.c:19:19: warning: unused variable 'mess_c_sccs_id' [-Wunused-const-variable]
static const char mess_c_sccs_id[] = "%W%";
                  ^
cstat.c:20:19: warning: unused variable 'nrutil_c_sccs_id' [-Wunused-const-variable]
static const char nrutil_c_sccs_id[] = "%W%"; 
                  ^
cstat.c:21:19: warning: unused variable 'vector_c_sccs_id' [-Wunused-const-variable]
static const char vector_c_sccs_id[] = "%W%";
                  ^
cstat.c:22:19: warning: unused variable 'css_c_sccs_id' [-Wunused-const-variable]
static const char css_c_sccs_id[] = "@(#)$Workfile: rand.c$ $Revision: 5$";
                  ^
6 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 gaga.so cseqdesma.o cstat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.8-bioc/meat/gaga.buildbin-libdir/gaga/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 (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/3.5/Resources/lib/libgcc_s.1.dylib" "gaga.buildbin-libdir/gaga/libs//gaga.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "gaga.buildbin-libdir/gaga/libs//gaga.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/lib/libreadline.dylib" "gaga.buildbin-libdir/gaga/libs//gaga.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "gaga.buildbin-libdir/gaga/libs//gaga.so"