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###
### Running command:
###
### rm -rf SUITOR.buildbin-libdir && mkdir SUITOR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SUITOR_1.4.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SUITOR.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SUITOR.buildbin-libdir SUITOR_1.4.0.tar.gz'
>>>>>>>
* installing *source* package ‘SUITOR’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SUITOR_init.c -o SUITOR_init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c source.c -o source.o
source.c:166:17: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static double * dVec_alloc(n, initFlag, initVal)
^
source.c:185:14: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static int * iVec_alloc(n, initFlag, initVal)
^
source.c:203:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static char * cVec_alloc(n, initFlag, initVal)
^
source.c:222:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void copy_dVec(v, n, ret)
^
source.c:233:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void matrixMult(m1, m1_nr, m1_nc, m2, m2_nc, ret)
^
source.c:256:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static int which_max(v, n)
^
source.c:280:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void which_max_cols(mat, nr, nc, ret)
^
source.c:292:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static int update_cons(cons, cons_len, index, nc)
^
source.c:323:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static int myStopFun(cons, cons_len, inc, hMat, hnr, hnc, maxIndex)
^
source.c:348:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void get_runif_vec(v, n, a, b)
^
source.c:359:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static int get_idxMat0(idx, nr, nc, k, kfold)
^
source.c:385:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static double loglike(input, log_input, input_k_hat, idxMat, delta_denom, len, which_idx)
^
source.c:416:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void replaceZeroVal_dVec(v, n, minval)
^
source.c:428:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static double get_delta_denom(v, n)
^
source.c:444:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static double get_max(v, n)
^
source.c:460:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void my_update_H(pV, w, h, wnr, wnc, hnc)
^
source.c:539:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void my_update_W(pV, w, h, wnr, wnc, hnc)
^
source.c:611:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void my_update_brunet(i, x, w, h, str)
^
source.c:636:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void get_init_WH(runifVec, w, h, wlen, hlen, maxval)
^
source.c:655:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void call_nmf(mat, str)
^
source.c:714:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void update_x_k(x_k, x_k_hat, idxMat, n)
^
source.c:838:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static double get_median(v, n)
^
source.c:863:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void get_init_x_k(x, x_k, idxMat, nr, nc, tmpvec, minvalue)
^
source.c:916:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void get_colsums(x, nr, nc, ret)
^
source.c:934:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void transpose(v, nr, nc, ret)
^
source.c:949:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void ECM_update_h(h1, h0, w0, x_k, hnr, hnc, wnr, wnc, xnr, xnc, vM, vN, vN2)
^
source.c:983:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void ECM_update_w(w1, h1, w0, x_k, hnr, hnc, wnr, wnc, xnr, xnc, vM, vN, vN2)
^
source.c:1017:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static int ECM_alg(str)
^
source.c:1093:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void init_wh_rank(str, rank)
^
source.c:1119:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void suitor_main(str)
^
source.c:1203:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void init_logx(x, logx, n)
^
source.c:1221:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void NMFSTR_init(str, iargs, dargs, xmat)
^
source.c:1311:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void NMFSTR_free(str, EMflag)
^
source.c:1339:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void C_call_nmf(mat, iargs, dargs, retW, retH)
^
source.c:1361:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void C_call_suitor(mat, iargs, dargs, rankVec, kVec, ret_train, ret_test, ret_convVec, ret_EM_niterVec)
^
35 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o SUITOR.so SUITOR_init.o source.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/SUITOR.buildbin-libdir/00LOCK-SUITOR/00new/SUITOR/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 (SUITOR)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR SUITOR.buildbin-libdir/SUITOR/libs/SUITOR.so
>>>>>>>
>>>>>>> Paths before fix:
SUITOR.buildbin-libdir/SUITOR/libs/SUITOR.so:
SUITOR.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "SUITOR.buildbin-libdir/SUITOR/libs/SUITOR.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "SUITOR.buildbin-libdir/SUITOR/libs/SUITOR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "SUITOR.buildbin-libdir/SUITOR/libs/SUITOR.so"
>>>>>>> Paths after fix:
SUITOR.buildbin-libdir/SUITOR/libs/SUITOR.so:
SUITOR.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
