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BioC 2.14: BUILD BIN report for CGEN on morelia

This page was generated on 2014-10-08 09:04:23 -0700 (Wed, 08 Oct 2014).

Package 129/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CGEN 2.6.1
William Wheeler
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/CGEN
Last Changed Rev: 90176 / Revision: 95116
Last Changed Date: 2014-05-09 15:54:26 -0700 (Fri, 09 May 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK [ OK ]

Summary

Package: CGEN
Version: 2.6.1
Command: rm -rf CGEN.buildbin-libdir && mkdir CGEN.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CGEN_2.6.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CGEN.buildbin-libdir
StartedAt: 2014-10-08 02:49:04 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 02:49:10 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 6.2 seconds
RetCode: 0
Status:  OK 
PackageFile: CGEN_2.6.1.tgz
PackageFileSize: 735.3 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CGEN.buildbin-libdir && mkdir CGEN.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CGEN_2.6.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CGEN.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CGEN.buildbin-libdir CGEN_2.6.1.tar.gz'
>>>>>>> 

* installing *source* package ‘CGEN’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c Additive.c -o Additive.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c CML.c -o CML.o
CML.c:1198:13: warning: unused function 'print_dVec' [-Wunused-function]
static void print_dVec(vec, n, name)
            ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c ccl.c -o ccl.o
ccl.c:78:79: warning: incompatible integer to pointer conversion passing 'int' to parameter of type 'const char *' [-Wint-conversion]
        if(S > 8) { Rprintf("Maximum matched set size > 8 not supported.\n") ; error(1) ; }
                                                                                     ^
/Library/Frameworks/R.framework/Resources/include/R_ext/Error.h:33:27: note: passing argument to parameter here
void Rf_error(const char *, ...) __attribute__((noreturn));
                          ^
ccl.c:478:86: warning: incompatible integer to pointer conversion passing 'int' to parameter of type 'const char *' [-Wint-conversion]
        if (n < 0) { Rprintf("\nError: factorial of negative integer not defined\n"); error(1); }
                                                                                            ^
/Library/Frameworks/R.framework/Resources/include/R_ext/Error.h:33:27: note: passing argument to parameter here
void Rf_error(const char *, ...) __attribute__((noreturn));
                          ^
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)
            ^
3 warnings generated.
gfortran-4.8   -fPIC  -g -O2 -Wall  -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
Warning: Nonconforming tab character in column 2 of line 190
Warning: Nonconforming tab character in column 1 of line 203
Warning: Nonconforming tab character in column 1 of line 205
Warning: Nonconforming tab character in column 1 of line 207
Warning: Nonconforming tab character in column 1 of line 270
Warning: Nonconforming tab character in column 1 of line 271
Warning: Nonconforming tab character in column 1 of line 275
Warning: Nonconforming tab character in column 1 of line 276
Warning: Nonconforming tab character in column 1 of line 277
Warning: Nonconforming tab character in column 1 of line 278
Warning: Nonconforming tab character in column 1 of line 282
Warning: Nonconforming tab character in column 1 of line 283
Warning: Nonconforming tab character in column 1 of line 286
Warning: Nonconforming tab character in column 1 of line 287
Warning: Nonconforming tab character in column 1 of line 288
Warning: Nonconforming tab character in column 1 of line 289
Warning: Nonconforming tab character in column 1 of line 290
Warning: Nonconforming tab character in column 1 of line 291
Warning: Nonconforming tab character in column 1 of line 292
Warning: Nonconforming tab character in column 1 of line 293
Warning: Nonconforming tab character in column 1 of line 294
Warning: Nonconforming tab character in column 1 of line 295
Warning: Nonconforming tab character in column 1 of line 296
Warning: Nonconforming tab character in column 1 of line 306
Warning: Nonconforming tab character in column 1 of line 307
Warning: Nonconforming tab character in column 1 of line 309
Warning: Nonconforming tab character in column 1 of line 310
Warning: Nonconforming tab character in column 1 of line 311
Warning: Nonconforming tab character in column 1 of line 312
Warning: Nonconforming tab character in column 1 of line 313
Warning: Nonconforming tab character in column 1 of line 314
Warning: Nonconforming tab character in column 1 of line 315
Warning: Nonconforming tab character in column 1 of line 316
Warning: Nonconforming tab character in column 1 of line 317
Warning: Nonconforming tab character in column 1 of line 319
Warning: Nonconforming tab character in column 1 of line 320
Warning: Nonconforming tab character in column 1 of line 321
Warning: Nonconforming tab character in column 1 of line 329
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 -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c fsclust.c -o fsclust.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c hcl.c -o hcl.o
hcl.c:72:79: warning: incompatible integer to pointer conversion passing 'int' to parameter of type 'const char *' [-Wint-conversion]
        if(S > 8) { Rprintf("Maximum matched set size > 8 not supported.\n") ; error(1) ; }
                                                                                     ^
/Library/Frameworks/R.framework/Resources/include/R_ext/Error.h:33:27: note: passing argument to parameter here
void Rf_error(const char *, ...) __attribute__((noreturn));
                          ^
hcl.c:467:86: warning: incompatible integer to pointer conversion passing 'int' to parameter of type 'const char *' [-Wint-conversion]
        if (n < 0) { Rprintf("\nError: factorial of negative integer not defined\n"); error(1); }
                                                                                            ^
/Library/Frameworks/R.framework/Resources/include/R_ext/Error.h:33:27: note: passing argument to parameter here
void Rf_error(const char *, ...) __attribute__((noreturn));
                          ^
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)
            ^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -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 -o CGEN.so Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-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/3.1/Resources/lib/libgcc_s.1.dylib" "CGEN.buildbin-libdir/CGEN/libs//CGEN.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.3.dylib" "CGEN.buildbin-libdir/CGEN/libs//CGEN.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/lib/libreadline.dylib" "CGEN.buildbin-libdir/CGEN/libs//CGEN.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libquadmath.0.dylib" "CGEN.buildbin-libdir/CGEN/libs//CGEN.so"