Your message dated Tue, 14 Jul 2015 22:08:48 +0200
with message-id <[email protected]>
and subject line Re: Bug#792434: OSX Compile Errors
has caused the Debian Bug report #792434,
regarding OSX Compile Errors
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
792434: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=792434
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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, [email protected] <mailto:[email protected]>
Brady Lab, UC Davis, Life Sciences 2243
One Shields Ave., Davis, CA 95616, ph: (530) 752-2537
--- End Message ---
--- Begin Message ---
Hi Ted,
I'm sorry but you are reporting the bug on the Debian bug tracker. OSX
is no supoprted Debian platform and thus I will close your bug report.
If you want to get e-PCR running on OSX you need to contact its authors.
For sure you are also welcome to install Debian on your machine and
we will be happy to solve any problem you might face.
Kind regards
Andreas.
On Tue, Jul 14, 2015 at 11:45:08AM -0700, Ted Toal wrote:
> 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, [email protected] <mailto:[email protected]>
> Brady Lab, UC Davis, Life Sciences 2243
> One Shields Ave., Davis, CA 95616, ph: (530) 752-2537
>
> _______________________________________________
> Debian-med-packaging mailing list
> [email protected]
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
--
http://fam-tille.de
--- End Message ---
