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Package 136/671HostnameOS / ArchBUILDCHECKBUILD BIN
CNORdt 1.2.0
A. MacNamara
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/CNORdt
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: CNORdt
Version: 1.2.0
Command: rm -rf CNORdt.buildbin-libdir && mkdir CNORdt.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNORdt_1.2.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CNORdt.buildbin-libdir
StartedAt: 2013-05-01 12:16:01 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 12:16:11 -0700 (Wed, 01 May 2013)
EllapsedTime: 10.1 seconds
RetCode: 0
Status:  OK 
PackageFile: CNORdt_1.2.0.tgz
PackageFileSize: 275.1 KiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CNORdt.buildbin-libdir CNORdt_1.2.0.tar.gz'
>>>>>>> 

* installing *source* package 'CNORdt' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c simulatorDT.c -o simulatorDT.o
simulatorDT.c:63:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        maxIx = (int*) malloc(nReacs * sizeof(int));
                              ^˜˜˜˜˜ ˜
simulatorDT.c:70:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        indexStimuli = (int*) malloc(nStimuli * sizeof(int));
                                     ^˜˜˜˜˜˜˜ ˜
simulatorDT.c:77:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        indexInhibitors = (int*) malloc(nInhibitors * sizeof(int));
                                        ^˜˜˜˜˜˜˜˜˜˜ ˜
simulatorDT.c:84:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        finalCube = (int**) malloc(nReacs * sizeof(int*));
                                   ^˜˜˜˜˜ ˜
simulatorDT.c:86:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            finalCube[i] = (int*) malloc(nMaxInputs * sizeof(int));
                                         ^˜˜˜˜˜˜˜˜˜ ˜
simulatorDT.c:94:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        ixNeg = (int**) malloc(nReacs * sizeof(int*));
                               ^˜˜˜˜˜ ˜
simulatorDT.c:96:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            ixNeg[i] = (int*) malloc(nMaxInputs * sizeof(int));
                                     ^˜˜˜˜˜˜˜˜˜ ˜
simulatorDT.c:104:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        ignoreCube = (int**) malloc(nReacs * sizeof(int*));
                                    ^˜˜˜˜˜ ˜
simulatorDT.c:106:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            ignoreCube[i] = (int*) malloc(nMaxInputs * sizeof(int));
                                          ^˜˜˜˜˜˜˜˜˜ ˜
simulatorDT.c:114:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        valueInhibitors = (int**) malloc(nCond * sizeof(int*));
                                         ^˜˜˜˜ ˜
simulatorDT.c:116:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            valueInhibitors[i] = (int*) malloc(nInhibitors * sizeof(int));
                                               ^˜˜˜˜˜˜˜˜˜˜ ˜
simulatorDT.c:124:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        valueStimuli = (int**) malloc(nCond * sizeof(int*));
                                      ^˜˜˜˜ ˜
simulatorDT.c:126:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            valueStimuli[i] = (int*) malloc(nStimuli * sizeof(int));
                                            ^˜˜˜˜˜˜˜ ˜
simulatorDT.c:134:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        prevSim = (int**) malloc(nCond * sizeof(int*));
                                 ^˜˜˜˜ ˜
simulatorDT.c:136:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            prevSim[i] = (int*) malloc(nSpecies * sizeof(int));
                                       ^˜˜˜˜˜˜˜ ˜
simulatorDT.c:243:19: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
                        if((track_cond == nCond)) {
                            ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
simulatorDT.c:243:19: note: remove extraneous parentheses around the comparison to silence this warning
                        if((track_cond == nCond)) {
                           ˜           ^       ˜
simulatorDT.c:243:19: note: use '=' to turn this equality comparison into an assignment
                        if((track_cond == nCond)) {
                                       ^˜
                                       =
simulatorDT.c:55:6: warning: unused variable 'nTimes' [-Wunused-variable]
        int nTimes = INTEGER(nTimes_in)[0];
            ^
simulatorDT.c:53:6: warning: unused variable 'nSignals' [-Wunused-variable]
        int nSignals = INTEGER(nSignals_in)[0];
            ^
18 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 CNORdt.so simulatorDT.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/CNORdt.buildbin-libdir/CNORdt/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNORdt)


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