Package: ACME

Version: 2.43.0

Command: rm -rf ACME.buildbin-libdir && mkdir ACME.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ACME_2.43.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ACME.buildbin-libdir

StartedAt: 2020-01-16 10:23:31 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 10:24:00 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 28.4 seconds

RetCode: 0

Status:  OK

PackageFile: ACME_2.43.0.tgz

PackageFileSize: 9.632 MiB

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ACME.buildbin-libdir && mkdir ACME.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ACME_2.43.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ACME.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ACME.buildbin-libdir ACME_2.43.0.tar.gz'
>>>>>>> 

* installing *source* package ‘ACME’ ...
** using staged installation
** 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 windowChisq.c -o windowChisq.o
windowChisq.c:57:71: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses]
    while((xlocations[i]-xlocations[firstprobe-1] < (halfWindowSize)) &
                                                                      ^
windowChisq.c:57:71: note: place parentheses around the '>' expression to silence this warning
    while((xlocations[i]-xlocations[firstprobe-1] < (halfWindowSize)) &
                                                                      ^
windowChisq.c:57:71: note: place parentheses around the & expression to evaluate it first
    while((xlocations[i]-xlocations[firstprobe-1] < (halfWindowSize)) &
                                                                      ^
          (
windowChisq.c:62:70: warning: & has lower precedence than <; < will be evaluated first [-Wparentheses]
    while((xlocations[lastprobe+1]-xlocations[i] < (halfWindowSize)) &
                                                                     ^
windowChisq.c:62:70: note: place parentheses around the '<' expression to silence this warning
    while((xlocations[lastprobe+1]-xlocations[i] < (halfWindowSize)) &
                                                                     ^
windowChisq.c:62:70: note: place parentheses around the & expression to evaluate it first
    while((xlocations[lastprobe+1]-xlocations[i] < (halfWindowSize)) &
                                                                     ^
          (
windowChisq.c:21:11: warning: unused variable 'xa' [-Wunused-variable]
  double *xa,*xlocations,*xchivals;
          ^
windowChisq.c:86:20: warning: incompatible function pointer types initializing 'DL_FUNC' (aka 'void *(*)()') with an expression of type 'SEXP (*)(SEXP, SEXP, SEXP, SEXP, SEXP)' (aka 'struct SEXPREC *(*)(struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *)') [-Wincompatible-function-pointer-types]
    {"windowChisq",&windowChisq,5},
                   ^~~~~~~~~~~~
4 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 ACME.so windowChisq.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/ACME.buildbin-libdir/00LOCK-ACME/00new/ACME/libs
** R
** data
** 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 (ACME)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "ACME.buildbin-libdir/ACME/libs//ACME.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.3.dylib" "ACME.buildbin-libdir/ACME/libs//ACME.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.5.2.dylib" "ACME.buildbin-libdir/ACME/libs//ACME.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.dylib" "ACME.buildbin-libdir/ACME/libs//ACME.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "ACME.buildbin-libdir/ACME/libs//ACME.so"