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###
### Running command:
###
### rm -rf netresponse.buildbin-libdir && mkdir netresponse.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh netresponse_1.62.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R netresponse.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=netresponse.buildbin-libdir netresponse_1.62.0.tar.gz'
>>>>>>>
* installing *source* package ‘netresponse’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c netresponse.c -o netresponse.o
netresponse.c:264:15: warning: unused variable 'prior_fields' [-Wunused-variable]
const char *prior_fields[]={"Mumu","S2mu",
^
netresponse.c:686:6: warning: variable 'Mumu' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if(dim1) {
^~~~
netresponse.c:713:21: note: uninitialized use occurs here
vdp_mk_log_lambda(Mumu, S2mu, Mubar, Mutilde,
^~~~
netresponse.c:686:3: note: remove the 'if' if its condition is always true
if(dim1) {
^~~~~~~~~
netresponse.c:655:15: note: initialize the variable 'Mumu' to silence this warning
double *Mumu, *S2mu, *Mubar, *Mutilde,
^
= NULL
netresponse.c:686:6: warning: variable 'S2mu' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if(dim1) {
^~~~
netresponse.c:713:27: note: uninitialized use occurs here
vdp_mk_log_lambda(Mumu, S2mu, Mubar, Mutilde,
^~~~
netresponse.c:686:3: note: remove the 'if' if its condition is always true
if(dim1) {
^~~~~~~~~
netresponse.c:655:22: note: initialize the variable 'S2mu' to silence this warning
double *Mumu, *S2mu, *Mubar, *Mutilde,
^
= NULL
netresponse.c:686:6: warning: variable 'Mubar' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if(dim1) {
^~~~
netresponse.c:713:33: note: uninitialized use occurs here
vdp_mk_log_lambda(Mumu, S2mu, Mubar, Mutilde,
^~~~~
netresponse.c:686:3: note: remove the 'if' if its condition is always true
if(dim1) {
^~~~~~~~~
netresponse.c:655:30: note: initialize the variable 'Mubar' to silence this warning
double *Mumu, *S2mu, *Mubar, *Mutilde,
^
= NULL
netresponse.c:686:6: warning: variable 'Mutilde' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if(dim1) {
^~~~
netresponse.c:713:40: note: uninitialized use occurs here
vdp_mk_log_lambda(Mumu, S2mu, Mubar, Mutilde,
^~~~~~~
netresponse.c:686:3: note: remove the 'if' if its condition is always true
if(dim1) {
^~~~~~~~~
netresponse.c:655:40: note: initialize the variable 'Mutilde' to silence this warning
double *Mumu, *S2mu, *Mubar, *Mutilde,
^
= NULL
netresponse.c:686:6: warning: variable 'AlphaKsi' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if(dim1) {
^~~~
netresponse.c:714:7: note: uninitialized use occurs here
AlphaKsi, BetaKsi, KsiAlpha, KsiBeta,
^~~~~~~~
netresponse.c:686:3: note: remove the 'if' if its condition is always true
if(dim1) {
^~~~~~~~~
netresponse.c:656:14: note: initialize the variable 'AlphaKsi' to silence this warning
*AlphaKsi, *BetaKsi, *KsiAlpha, *KsiBeta, *U_p, *prior_alpha,
^
= NULL
netresponse.c:686:6: warning: variable 'BetaKsi' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if(dim1) {
^~~~
netresponse.c:714:17: note: uninitialized use occurs here
AlphaKsi, BetaKsi, KsiAlpha, KsiBeta,
^~~~~~~
netresponse.c:686:3: note: remove the 'if' if its condition is always true
if(dim1) {
^~~~~~~~~
netresponse.c:656:24: note: initialize the variable 'BetaKsi' to silence this warning
*AlphaKsi, *BetaKsi, *KsiAlpha, *KsiBeta, *U_p, *prior_alpha,
^
= NULL
netresponse.c:686:6: warning: variable 'KsiAlpha' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if(dim1) {
^~~~
netresponse.c:714:26: note: uninitialized use occurs here
AlphaKsi, BetaKsi, KsiAlpha, KsiBeta,
^~~~~~~~
netresponse.c:686:3: note: remove the 'if' if its condition is always true
if(dim1) {
^~~~~~~~~
netresponse.c:656:35: note: initialize the variable 'KsiAlpha' to silence this warning
*AlphaKsi, *BetaKsi, *KsiAlpha, *KsiBeta, *U_p, *prior_alpha,
^
= NULL
netresponse.c:686:6: warning: variable 'KsiBeta' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if(dim1) {
^~~~
netresponse.c:714:36: note: uninitialized use occurs here
AlphaKsi, BetaKsi, KsiAlpha, KsiBeta,
^~~~~~~
netresponse.c:686:3: note: remove the 'if' if its condition is always true
if(dim1) {
^~~~~~~~~
netresponse.c:656:45: note: initialize the variable 'KsiBeta' to silence this warning
*AlphaKsi, *BetaKsi, *KsiAlpha, *KsiBeta, *U_p, *prior_alpha,
^
= NULL
netresponse.c:696:6: warning: variable 'U_p' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if(dim2) {
^~~~
netresponse.c:716:7: note: uninitialized use occurs here
U_p, U_hat,
^~~
netresponse.c:696:3: note: remove the 'if' if its condition is always true
if(dim2) {
^~~~~~~~~
netresponse.c:656:51: note: initialize the variable 'U_p' to silence this warning
*AlphaKsi, *BetaKsi, *KsiAlpha, *KsiBeta, *U_p, *prior_alpha,
^
= NULL
netresponse.c:696:6: warning: variable 'U_hat' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if(dim2) {
^~~~
netresponse.c:716:12: note: uninitialized use occurs here
U_p, U_hat,
^~~~~
netresponse.c:696:3: note: remove the 'if' if its condition is always true
if(dim2) {
^~~~~~~~~
netresponse.c:661:14: note: initialize the variable 'U_hat' to silence this warning
SEXP* U_hat;
^
= NULL
11 warnings generated.
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o netresponse.so netresponse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.18-bioc/meat/netresponse.buildbin-libdir/00LOCK-netresponse/00new/netresponse/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 (netresponse)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR netresponse.buildbin-libdir/netresponse/libs/netresponse.so
>>>>>>>
>>>>>>> Paths before fix:
netresponse.buildbin-libdir/netresponse/libs/netresponse.so:
netresponse.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.3-x86_64/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-x86_64/Resources/lib/libgcc_s.1.1.dylib" "netresponse.buildbin-libdir/netresponse/libs/netresponse.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "netresponse.buildbin-libdir/netresponse/libs/netresponse.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "netresponse.buildbin-libdir/netresponse/libs/netresponse.so"
>>>>>>> Paths after fix:
netresponse.buildbin-libdir/netresponse/libs/netresponse.so:
netresponse.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.3-x86_64/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)
