[Debian-med-packaging] Bug#792434: OSX Compile Errors

[Ted Toal]

Package: ncbi-epcr
Version: 2.3.12

When I try to build the e-PCR program, a variety of errors occur.  The build command I use is:

make LF64LDFLAGS= LF64CCFLAGS=-DNATIVE_LARGEFILES

I am using OSX Yosemite V10.10.3, with Xcode 5.02 and Xcode command line tools installed. 

I was able to fix the errors with these code changes:

1. Uncomment '#include <sstream>' in mmap.cpp

2. Add these includes to epcr/minilcs.hpp:

#include <cstdlib>
#include <sstream>

With these changes the build succeeds but several warnings are issued.  Some include a description of how these warnings can be eliminated with code changes (that seem like reasonable changes).  I was able to eliminate the warnings with this command line:

make LF64LDFLAGS= LF64CCFLAGS=-DNATIVE_LARGEFILES COMMON_CC_FLAGS=-w

I suggest that the above command line be included in the BUILD.html and BUILD.txt files under the OSX section.  The warnings are:

stsfilter.cpp:47:49: warning: '&&' within '||' [-Wlogical-op-parentheses]
    return (o1.pos2<o2.pos2 || o1.pos2==o2.pos2 && o1.pos1<o2.pos1);
                            ~~ ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
stsfilter.cpp:47:49: note: place parentheses around the '&&' expression to silence this warning

fahash_lookup.cpp:343:38: warning: '&&' within '||' [-Wlogical-op-parentheses]
                return sid < s.sid || sid == s.sid && pos < s.pos;
                                   ~~ ~~~~~~~~~~~~~^~~~~~~~~~~~~~
fahash_lookup.cpp:343:38: note: place parentheses around the '&&' expression to silence this warning

fahash_lookup.cpp:385:60: warning: '&&' within '||' [-Wlogical-op-parentheses]
                 ( gaps() < h.gaps() || gaps() == h.gaps() &&
                                     ~~ ~~~~~~~~~~~~~~~~~~~^~
fahash_lookup.cpp:385:60: note: place parentheses around the '&&' expression to silence this warning
                                                           ^
fahash_lookup.cpp:384:52: warning: '&&' within '||' [-Wlogical-op-parentheses]
                 ( pos2 < h.pos2 || pos2 == h.pos2 &&
                                 ~~ ~~~~~~~~~~~~~~~^~
fahash_lookup.cpp:384:52: note: place parentheses around the '&&' expression to silence this warning
                                                   ^
fahash_lookup.cpp:383:52: warning: '&&' within '||' [-Wlogical-op-parentheses]
            return pos1 < h.pos1 || pos1 == h.pos1 && 
                                 ~~ ~~~~~~~~~~~~~~~^~
fahash_lookup.cpp:383:52: note: place parentheses around the '&&' expression to silence this warning
                                                   ^
fahash_lookup.cpp:435:54: warning: '&&' within '||' [-Wlogical-op-parentheses]
    return ( o1.pos2 < o2.pos2 || o1.pos2 == o2.pos2 && o1.pos1 < o2.pos1 );
                               ~~ ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
fahash_lookup.cpp:435:54: note: place parentheses around the '&&' expression to silence this warning

fahash_main.cpp:257:9: warning: enumeration value 'eNone' not handled in switch [-Wswitch]
        switch(command) {
               ^

fahash_main.cpp:261:1: warning: control may reach end of non-void function [-Wreturn-type]
}
^

re-PCR_main.cpp:345:9: warning: enumeration value 'eNone' not handled in switch [-Wswitch]
        switch(command) {
               ^

re-PCR_main.cpp:349:1: warning: control may reach end of non-void function [-Wreturn-type]
}
^

re-PCR_main.cpp:488:46: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long' [-Wformat]
                            argv[i],fcount+1,fcount+stslist.size());
                                             ^~~~~~~~~~~~~~~~~~~~~

re-PCR_main.cpp:502:38: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long' [-Wformat]
                    argv[i],fcount+1,fcount+stslist.size());
                                     ^~~~~~~~~~~~~~~~~~~~~



--
Ted Toal, Graduate Student, twtoal at ucdavis.edu <mailto:twtoal at ucdavis.edu>
Brady Lab, UC Davis, Life Sciences 2243
One Shields Ave., Davis, CA  95616, ph: (530) 752-2537

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