CGEN 2.2.0
William Wheeler
| 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/CGEN | | 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 | WARNINGS | |
| 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 | WARNINGS | OK |
| pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | WARNINGS | [ OK ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CGEN.buildbin-libdir CGEN_2.2.0.tar.gz'
>>>>>>>
* installing *source* package 'CGEN' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c Additive.c -o Additive.o
Additive.c:515:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
m = (double **) malloc(n*sizeof(double *));
^˜
Additive.c:517:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
m[i] = (double *) malloc((i + 1)*sizeof(double));
˜˜^˜˜ ˜
Additive.c:543:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
l = (int *) R_alloc(n0, sizeof(int));
˜˜˜˜˜˜˜ ^˜
Additive.c:547:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
g = (double *) R_alloc(n0, sizeof(double));
˜˜˜˜˜˜˜ ^˜
Additive.c:548:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
t = (double *) R_alloc(n, sizeof(double));
˜˜˜˜˜˜˜ ^
Additive.c:549:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
X = (double *) R_alloc(n, sizeof(double));
˜˜˜˜˜˜˜ ^
Additive.c:550:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
c = (double *) R_alloc(n, sizeof(double));
˜˜˜˜˜˜˜ ^
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c CML.c -o CML.o
CML.c:562:22: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
temp = 3* *D + 1 + value;
˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
CML.c:680:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
m = (double **) malloc(n*sizeof(double *));
^˜
CML.c:682:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
m[i] = (double *) malloc((i + 1)*sizeof(double));
˜˜^˜˜ ˜
CML.c:708:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
l = (int *) R_alloc(n0, sizeof(int));
˜˜˜˜˜˜˜ ^˜
CML.c:712:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
g = (double *) R_alloc(n0, sizeof(double));
˜˜˜˜˜˜˜ ^˜
CML.c:713:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
t = (double *) R_alloc(n, sizeof(double));
˜˜˜˜˜˜˜ ^
CML.c:714:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
X = (double *) R_alloc(n, sizeof(double));
˜˜˜˜˜˜˜ ^
CML.c:715:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
c = (double *) R_alloc(n, sizeof(double));
˜˜˜˜˜˜˜ ^
CML.c:1198:13: warning: unused function 'print_dVec' [-Wunused-function]
static void print_dVec(vec, n, name)
^
9 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ccl.c -o ccl.o
ccl.c:134:10: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
*CONV = conv ;
˜ ^˜˜˜
ccl.c:413:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
new -> g = j ; new -> h = k ;
˜ ^
ccl.c:413:30: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
new -> g = j ; new -> h = k ;
˜ ^
ccl.c:386:13: warning: function 'tree_print' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static void tree_print(tnode *node, int is_root)
^
4 warnings generated.
gfortran-4.2 -arch x86_64 -fPIC -g -O2 -Wall -pedantic -c csclust.f -o csclust.o
Warning: Nonconforming tab character in column 1 of line 46
Warning: Nonconforming tab character in column 1 of line 83
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csclust.f:222.3:
650 RETURN
1
Warning: Label 650 at (1) defined but not used
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c fsclust.c -o fsclust.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c hcl.c -o hcl.o
hcl.c:128:10: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
*CONV = conv ;
˜ ^˜˜˜
hcl.c:402:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
new -> g = j ; new -> h = k ;
˜ ^
hcl.c:402:30: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
new -> g = j ; new -> h = k ;
˜ ^
hcl.c:375:13: warning: function 'tree_print' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static void tree_print(tnode *node, int is_root)
^
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c pmatch.c -o pmatch.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o CGEN.so Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/CGEN.buildbin-libdir/CGEN/libs
** R
** data
** exec
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CGEN)
>>>>>>>
>>>>>>> FIXING LINKS FOR CGEN.buildbin-libdir/CGEN/libs//CGEN.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" "CGEN.buildbin-libdir/CGEN/libs//CGEN.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "CGEN.buildbin-libdir/CGEN/libs//CGEN.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" "CGEN.buildbin-libdir/CGEN/libs//CGEN.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "CGEN.buildbin-libdir/CGEN/libs//CGEN.so"