libdap 3.14.0 issues

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Orion Poplawski

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Apr 16, 2015, 2:30:15 PM4/16/15

to sup...@opendap.org, Andrey Ponomarenko

Building libdap 3.14.0 on Fedora I ran into a couple issues:

- flex issues:

libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../d4_ce -I.
-I/usr/include/libxml2 -I.. -I../d4_ce -I. -I/usr/include/libxml2 -O2 -g
-pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches
-specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -c
d4_ce_parser.tab.cc -fPIC -DPIC -o
.libs/libd4_ce_parser_la-d4_ce_parser.tab.o
lex.d4_ce.cc: In member function 'virtual int libdap::D4CEScanner::yylex()':
lex.d4_ce.cc:864:35: warning: comparison between signed and unsigned
integer expressions [-Wsign-compare]
for ( yyl = (yy_more_len); yyl < yyleng; ++yyl )
^
lex.d4_ce.cc: At global scope:
lex.d4_ce.cc:31:25: error: prototype for 'size_t
d4_ceFlexLexer::LexerInput(char*, size_t)' does not match any in class
'd4_ceFlexLexer'
#define yyFlexLexer d4_ceFlexLexer
^
lex.d4_ce.cc:1281:8: note: in expansion of macro 'yyFlexLexer'
size_t yyFlexLexer::LexerInput( char* buf, size_t max_size )
^
In file included from lex.d4_ce.cc:395:0:
/usr/include/FlexLexer.h:133:14: error: candidate is: virtual int
d4_ceFlexLexer::LexerInput(char*, int)
virtual int LexerInput( char* buf, int max_size );
^
lex.d4_ce.cc:31:25: error: prototype for 'void
d4_ceFlexLexer::LexerOutput(const char*, size_t)' does not match any in
class 'd4_ceFlexLexer'
#define yyFlexLexer d4_ceFlexLexer
^
lex.d4_ce.cc:1308:6: note: in expansion of macro 'yyFlexLexer'
void yyFlexLexer::LexerOutput( const char* buf, size_t size )
^
In file included from lex.d4_ce.cc:395:0:
/usr/include/FlexLexer.h:134:15: error: candidate is: virtual void
d4_ceFlexLexer::LexerOutput(const char*, int)
virtual void LexerOutput( const char* buf, int size );
^
Makefile:997: recipe for target 'libd4_ce_parser_la-lex.d4_ce.lo' failed
make[3]: *** [libd4_ce_parser_la-lex.d4_ce.lo] Error 1

fixed with attached patch.

- --enable-valgrind fails with:

make[5]: Entering directory
'/export/home/orion/fedora/libdap/libdap-3.14.0/unit-tests'
==26177== FATAL: can't open suppressions file "valgrind_suppressions.txt"
Makefile:1881: recipe for target 'marshT.log' failed
make[5]: *** [marshT.log] Error 1

- --enable-coverage fails with:

libtool: link: g++ -fPIC -DPIC -shared -nostdlib
/usr/lib/gcc/x86_64-redhat-linux/4.9.2/../../../../lib64/crti.o
/usr/lib/gcc/x86_64-redhat-linux/4.9.2/crtbeginS.o
.libs/libdap_la-AttrTable.o .libs/libdap_la-DAS.o .libs/libdap_la-DDS.o
.libs/libdap_la-DataDDS.o .libs/libdap_la-DDXParserSAX2.o
.libs/libdap_la-BaseType.o .libs/libdap_la-Byte.o
.libs/libdap_la-Int32.o .libs/libdap_la-Float64.o .libs/libdap_la-Str.o
.libs/libdap_la-Url.o .libs/libdap_la-Vector.o .libs/libdap_la-Array.o
.libs/libdap_la-Structure.o .libs/libdap_la-Sequence.o
.libs/libdap_la-Grid.o .libs/libdap_la-UInt32.o .libs/libdap_la-Int16.o
.libs/libdap_la-UInt16.o .libs/libdap_la-Float32.o
.libs/libdap_la-Constructor.o .libs/libdap_la-BaseTypeFactory.o
.libs/libdap_la-SignalHandler.o .libs/libdap_la-Error.o
.libs/libdap_la-InternalErr.o .libs/libdap_la-util.o
.libs/libdap_la-xdrutil_ppc.o .libs/libdap_la-parser-util.o
.libs/libdap_la-escaping.o .libs/libdap_la-Clause.o
.libs/libdap_la-RValue.o .libs/libdap_la-ConstraintEvaluator.o
.libs/libdap_la-DapIndent.o .libs/libdap_la-XDRUtils.o
.libs/libdap_la-XDRFileMarshaller.o
.libs/libdap_la-XDRStreamMarshaller.o
.libs/libdap_la-XDRFileUnMarshaller.o
.libs/libdap_la-XDRStreamUnMarshaller.o .libs/libdap_la-mime_util.o
.libs/libdap_la-Keywords2.o .libs/libdap_la-XMLWriter.o
.libs/libdap_la-ServerFunctionsList.o .libs/libdap_la-ServerFunction.o
.libs/libdap_la-DapXmlNamespaces.o GNU/.libs/libdap_la-GetOpt.o
GNU/.libs/libdap_la-GNURegex.o .libs/libdap_la-D4StreamMarshaller.o
.libs/libdap_la-D4StreamUnMarshaller.o .libs/libdap_la-Int64.o
.libs/libdap_la-UInt64.o .libs/libdap_la-Int8.o
.libs/libdap_la-D4ParserSax2.o .libs/libdap_la-D4BaseTypeFactory.o
.libs/libdap_la-D4Dimensions.o .libs/libdap_la-D4EnumDefs.o
.libs/libdap_la-D4Group.o .libs/libdap_la-DMR.o
.libs/libdap_la-D4Attributes.o .libs/libdap_la-D4Enum.o
.libs/libdap_la-chunked_ostream.o .libs/libdap_la-chunked_istream.o
.libs/libdap_la-D4Sequence.o .libs/libdap_la-D4Maps.o
.libs/libdap_la-D4Opaque.o .libs/libdap_la-D4AsyncUtil.o
.libs/libdap_la-D4RValue.o -Wl,--whole-archive gl/.libs/libgnu.a
d4_ce/.libs/libd4_ce_parser.a ./.libs/libparsers.a
-Wl,--no-whole-archive -lpthread -lxml2 -lcrypto
-L/usr/lib/gcc/x86_64-redhat-linux/4.9.2
-L/usr/lib/gcc/x86_64-redhat-linux/4.9.2/../../../../lib64
-L/lib/../lib64 -L/usr/lib/../lib64
-L/usr/lib/gcc/x86_64-redhat-linux/4.9.2/../../.. -lstdc++ -lm -lc
-lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.9.2/crtendS.o
/usr/lib/gcc/x86_64-redhat-linux/4.9.2/../../../../lib64/crtn.o -Wl,-z
-Wl,relro -Wl,-soname -Wl,libdap.so.17 -o .libs/libdap.so.17.1.0

libtool: link: g++ -Wall -W -Wcast-align -Wl,-z -Wl,relro -o
.libs/getdap getdap-getdap.o ./.libs/libdapclient.so -lcurl
/export/home/orion/fedora/libdap/libdap-3.14.0/.libs/libdap.so
./.libs/libdap.so -lpthread -lxml2 -lcrypto
libtool: link: g++ -Wall -W -Wcast-align -Wl,-z -Wl,relro -o
.libs/getdap4 getdap4-getdap4.o ./.libs/libdapclient.so -lcurl
/export/home/orion/fedora/libdap/libdap-3.14.0/.libs/libdap.so
./.libs/libdap.so -lpthread -lxml2 -lcrypto
/export/home/orion/fedora/libdap/libdap-3.14.0/.libs/libdap.so:
undefined reference to `__gcov_init'
/export/home/orion/fedora/libdap/libdap-3.14.0/.libs/libdap.so:
undefined reference to `__gcov_merge_add'
collect2: error: ld returned 1 exit status

I suspect we're not passing needed flags to the link step.

- Link is currently failing on Fedora Rawhide due to hardened build:

libtool: link: g++ -Wall -W -Wcast-align -Wl,-z -Wl,relro
-specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/getdap
getdap-getdap.o ./.libs/libdapclient.so -lcurl
/builddir/build/BUILD/libdap-3.14.0/.libs/libdap.so ./.libs/libdap.so
-lpthread -lxml2 -lcrypto
libtool: link: g++ -Wall -W -Wcast-align -Wl,-z -Wl,relro
-specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/getdap4
getdap4-getdap4.o ./.libs/libdapclient.so -lcurl
/builddir/build/BUILD/libdap-3.14.0/.libs/libdap.so ./.libs/libdap.so
-lpthread -lxml2 -lcrypto
/usr/bin/ld: getdap-getdap.o: relocation R_X86_64_32 against `.rodata'
can not be used when making a shared object; recompile with -fPIC
getdap-getdap.o: error adding symbols: Bad value
collect2: error: ld returned 1 exit status
/usr/bin/ld: getdap4-getdap4.o: relocation R_X86_64_32 against `.rodata'
can not be used when making a shared object; recompile with -fPIC
getdap4-getdap4.o: error adding symbols: Bad value
collect2: error: ld returned 1 exit status

--
Orion Poplawski
Technical Manager 303-415-9701 x222
NWRA/CoRA Division FAX: 303-415-9702
3380 Mitchell Lane or...@cora.nwra.com
Boulder, CO 80301 http://www.cora.nwra.com

libdap-flex.patch

Orion Poplawski

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Apr 16, 2015, 4:17:43 PM4/16/15

to sup...@opendap.org

On 04/16/2015 12:30 PM, Orion Poplawski wrote:
>
> - Link is currently failing on Fedora Rawhide due to hardened build:
>
> libtool: link: g++ -Wall -W -Wcast-align -Wl,-z -Wl,relro
> -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/getdap
> getdap-getdap.o ./.libs/libdapclient.so -lcurl
> /builddir/build/BUILD/libdap-3.14.0/.libs/libdap.so ./.libs/libdap.so
> -lpthread -lxml2 -lcrypto
> libtool: link: g++ -Wall -W -Wcast-align -Wl,-z -Wl,relro
> -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/getdap4
> getdap4-getdap4.o ./.libs/libdapclient.so -lcurl
> /builddir/build/BUILD/libdap-3.14.0/.libs/libdap.so ./.libs/libdap.so
> -lpthread -lxml2 -lcrypto
> /usr/bin/ld: getdap-getdap.o: relocation R_X86_64_32 against `.rodata'
> can not be used when making a shared object; recompile with -fPIC
> getdap-getdap.o: error adding symbols: Bad value
> collect2: error: ld returned 1 exit status
> /usr/bin/ld: getdap4-getdap4.o: relocation R_X86_64_32 against `.rodata'
> can not be used when making a shared object; recompile with -fPIC
> getdap4-getdap4.o: error adding symbols: Bad value
> collect2: error: ld returned 1 exit status
>

This is caused by the various Makefile.am files setting:

CXXFLAGS =

removing that fixes this.

James Gallagher

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Apr 17, 2015, 12:21:59 AM4/17/15

to Orion Poplawski, James Gallagher, sup...@opendap.org

> On Apr 16, 2015, at 2:17 PM, Orion Poplawski <or...@cora.nwra.com> wrote:
>
> On 04/16/2015 12:30 PM, Orion Poplawski wrote:
>>
>> - Link is currently failing on Fedora Rawhide due to hardened build:
>>
>> libtool: link: g++ -Wall -W -Wcast-align -Wl,-z -Wl,relro
>> -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/getdap
>> getdap-getdap.o ./.libs/libdapclient.so -lcurl
>> /builddir/build/BUILD/libdap-3.14.0/.libs/libdap.so ./.libs/libdap.so
>> -lpthread -lxml2 -lcrypto
>> libtool: link: g++ -Wall -W -Wcast-align -Wl,-z -Wl,relro
>> -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/getdap4
>> getdap4-getdap4.o ./.libs/libdapclient.so -lcurl
>> /builddir/build/BUILD/libdap-3.14.0/.libs/libdap.so ./.libs/libdap.so
>> -lpthread -lxml2 -lcrypto
>> /usr/bin/ld: getdap-getdap.o: relocation R_X86_64_32 against `.rodata'
>> can not be used when making a shared object; recompile with -fPIC
>> getdap-getdap.o: error adding symbols: Bad value
>> collect2: error: ld returned 1 exit status
>> /usr/bin/ld: getdap4-getdap4.o: relocation R_X86_64_32 against `.rodata'
>> can not be used when making a shared object; recompile with -fPIC
>> getdap4-getdap4.o: error adding symbols: Bad value
>> collect2: error: ld returned 1 exit status
>>
>
> This is caused by the various Makefile.am files setting:
>
> CXXFLAGS =
>
> removing that fixes this.

Thanks for the info - this and the previous messages. I'll put them in Jira for the next release, but I won't be able to do much until the middle of next week.

What version of Fedora are you using?

Thanks!

James

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Orion Poplawski

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Apr 17, 2015, 12:34:52 AM4/17/15

to James Gallagher, sup...@opendap.org

Fedora 21 and Rawhide. I'm also seeing a test hang on arm - but haven't
been able to debug that yet.

James Gallagher

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May 11, 2015, 7:17:00 PM5/11/15

to Orion Poplawski, James Gallagher, sup...@opendap.org, Andrey Ponomarenko

Applied

>
> - --enable-valgrind fails with:
>
> make[5]: Entering directory '/export/home/orion/fedora/libdap/libdap-3.14.0/unit-tests'
> ==26177== FATAL: can't open suppressions file "valgrind_suppressions.txt"
> Makefile:1881: recipe for target 'marshT.log' failed
> make[5]: *** [marshT.log] Error 1

valgrind_suppressions.txt was missing from EXTRA_DIST int eh unit-tests/Makefile.am. Added.

I’m looking at these now, but something’s just come up so it may have to wait until tomorrow before I can test my fixes.

James

>
> - --enable-coverage fails with:
>
> libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/4.9.2/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.9.2/crtbeginS.o .libs/libdap_la-AttrTable.o .libs/libdap_la-DAS.o .libs/libdap_la-DDS.o .libs/libdap_la-DataDDS.o .libs/libdap_la-DDXParserSAX2.o .libs/libdap_la-BaseType.o .libs/libdap_la-Byte.o .libs/libdap_la-Int32.o .libs/libdap_la-Float64.o .libs/libdap_la-Str.o .libs/libdap_la-Url.o .libs/libdap_la-Vector.o .libs/libdap_la-Array.o .libs/libdap_la-Structure.o .libs/libdap_la-Sequence.o .libs/libdap_la-Grid.o .libs/libdap_la-UInt32.o .libs/libdap_la-Int16.o .libs/libdap_la-UInt16.o .libs/libdap_la-Float32.o .libs/libdap_la-Constructor.o .libs/libdap_la-BaseTypeFactory.o .libs/libdap_la-SignalHandler.o .libs/libdap_la-Error.o .libs/libdap_la-InternalErr.o .libs/libdap_la-util.o .libs/libdap_la-xdrutil_ppc.o .libs/libdap_la-parser-util.o .libs/libdap_la-escaping.o .libs/libdap_la-Clause.o .libs/libdap_la-RValue.o .libs/libdap_la-ConstraintEvaluator.o .libs/libdap_la-DapIndent.o .libs/libdap_la-XDRUtils.o .libs/libdap_la-XDRFileMarshaller.o .libs/libdap_la-XDRStreamMarshaller.o .libs/libdap_la-XDRFileUnMarshaller.o .libs/libdap_la-XDRStreamUnMarshaller.o .libs/libdap_la-mime_util.o .libs/libdap_la-Keywords2.o .libs/libdap_la-XMLWriter.o .libs/libdap_la-ServerFunctionsList.o .libs/libdap_la-ServerFunction.o .libs/libdap_la-DapXmlNamespaces.o GNU/.libs/libdap_la-GetOpt.o GNU/.libs/libdap_la-GNURegex.o .libs/libdap_la-D4StreamMarshaller.o .libs/libdap_la-D4StreamUnMarshaller.o .libs/libdap_la-Int64.o .libs/libdap_la-UInt64.o .libs/libdap_la-Int8.o .libs/libdap_la-D4ParserSax2.o .libs/libdap_la-D4BaseTypeFactory.o .libs/libdap_la-D4Dimensions.o .libs/libdap_la-D4EnumDefs.o .libs/libdap_la-D4Group.o .libs/libdap_la-DMR.o .libs/libdap_la-D4Attributes.o .libs/libdap_la-D4Enum.o .libs/libdap_la-chunked_ostream.o .libs/libdap_la-chunked_istream.o .libs/libdap_la-D4Sequence.o .libs/libdap_la-D4Maps.o .libs/libdap_la-D4Opaque.o .libs/libdap_la-D4AsyncUtil.o .libs/libdap_la-D4RValue.o -Wl,--whole-archive gl/.libs/libgnu.a d4_ce/.libs/libd4_ce_parser.a ./.libs/libparsers.a -Wl,--no-whole-archive -lpthread -lxml2 -lcrypto -L/usr/lib/gcc/x86_64-redhat-linux/4.9.2 -L/usr/lib/gcc/x86_64-redhat-linux/4.9.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.9.2/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.9.2/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.9.2/../../../../lib64/crtn.o -Wl,-z -Wl,relro -Wl,-soname -Wl,libdap.so.17 -o .libs/libdap.so.17.1.0
>
>
> libtool: link: g++ -Wall -W -Wcast-align -Wl,-z -Wl,relro -o .libs/getdap getdap-getdap.o ./.libs/libdapclient.so -lcurl /export/home/orion/fedora/libdap/libdap-3.14.0/.libs/libdap.so ./.libs/libdap.so -lpthread -lxml2 -lcrypto
> libtool: link: g++ -Wall -W -Wcast-align -Wl,-z -Wl,relro -o .libs/getdap4 getdap4-getdap4.o ./.libs/libdapclient.so -lcurl /export/home/orion/fedora/libdap/libdap-3.14.0/.libs/libdap.so ./.libs/libdap.so -lpthread -lxml2 -lcrypto
> /export/home/orion/fedora/libdap/libdap-3.14.0/.libs/libdap.so: undefined reference to `__gcov_init'
> /export/home/orion/fedora/libdap/libdap-3.14.0/.libs/libdap.so: undefined reference to `__gcov_merge_add'
> collect2: error: ld returned 1 exit status
>
>
> I suspect we're not passing needed flags to the link step.
>
> - Link is currently failing on Fedora Rawhide due to hardened build:
>
> libtool: link: g++ -Wall -W -Wcast-align -Wl,-z -Wl,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/getdap getdap-getdap.o ./.libs/libdapclient.so -lcurl /builddir/build/BUILD/libdap-3.14.0/.libs/libdap.so ./.libs/libdap.so -lpthread -lxml2 -lcrypto
> libtool: link: g++ -Wall -W -Wcast-align -Wl,-z -Wl,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/getdap4 getdap4-getdap4.o ./.libs/libdapclient.so -lcurl /builddir/build/BUILD/libdap-3.14.0/.libs/libdap.so ./.libs/libdap.so -lpthread -lxml2 -lcrypto
> /usr/bin/ld: getdap-getdap.o: relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
> getdap-getdap.o: error adding symbols: Bad value
> collect2: error: ld returned 1 exit status
> /usr/bin/ld: getdap4-getdap4.o: relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
> getdap4-getdap4.o: error adding symbols: Bad value
> collect2: error: ld returned 1 exit status
>
> --
> Orion Poplawski
> Technical Manager 303-415-9701 x222
> NWRA/CoRA Division FAX: 303-415-9702
> 3380 Mitchell Lane or...@cora.nwra.com
> Boulder, CO 80301 http://www.cora.nwra.com

> <libdap-flex.patch>

--
James Gallagher
jgallagher at opendap.org
406.723.8663

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James Gallagher

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May 12, 2015, 12:28:22 PM5/12/15

to Orion Poplawski, James Gallagher, sup...@opendap.org

Fixed. I added this because I thought it was needed to get distcheck to work. It’s not…

James

>
> --
> Orion Poplawski
> Technical Manager 303-415-9701 x222
> NWRA/CoRA Division FAX: 303-415-9702
> 3380 Mitchell Lane or...@cora.nwra.com
> Boulder, CO 80301 http://www.cora.nwra.com

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metall...@gmail.com

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Jul 6, 2015, 2:21:47 PM7/6/15

to sup...@opendap.org, aponom...@rosalab.ru, or...@cora.nwra.com

Jim,

I also got the following error when made libdap 3.14.0
lex.d4_ce.cc:1281: error: prototype for 'size_t d4_ceFlexLexer::LexerInput(char*, size_t)' does not match any in class 'd4_ceFlexLexer'
/usr/include/FlexLexer.h:133: error: candidate is: virtual int d4_ceFlexLexer::LexerInput(char*, int)
lex.d4_ce.cc:1308: error: prototype for 'void d4_ceFlexLexer::LexerOutput(const char*, size_t)' does not match any in class 'd4_ceFlexLexer'
/usr/include/FlexLexer.h:134: error: candidate is: virtual void d4_ceFlexLexer::LexerOutput(const char*, int)

make[3]: *** [libd4_ce_parser_la-lex.d4_ce.lo] Error 1

make[3]: Leaving directory `/export/00/src/libdap-3.14.0/d4_ce'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/export/00/src/libdap-3.14.0/d4_ce'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/export/00/src/libdap-3.14.0'
make: *** [all] Error 2

Thanks.

Jerry

James Gallagher

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Jul 6, 2015, 2:28:46 PM7/6/15

to metall...@gmail.com, James Gallagher, sup...@opendap.org, aponom...@rosalab.ru, or...@cora.nwra.com

On Jul 6, 2015, at 12:21 PM, metall...@gmail.com wrote:

Jim,

I also got the following error when made libdap 3.14.0
lex.d4_ce.cc:1281: error: prototype for 'size_t d4_ceFlexLexer::LexerInput(char*, size_t)' does not match any in class 'd4_ceFlexLexer'
/usr/include/FlexLexer.h:133: error: candidate is: virtual int d4_ceFlexLexer::LexerInput(char*, int)

The problem is that bison produces two different type signatures for FlexLexer and I’d, at one point, tried to bundle the generated source in the tar ball. This lead to the type conflict you’re seeing, so I backed away from that. I will check on the libdap source tar ball and see if making a new one will address this issue.

James

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James Gallagher

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Jul 6, 2015, 5:36:47 PM7/6/15

to metall...@gmail.com, James Gallagher, sup...@opendap.org, aponom...@rosalab.ru, or...@cora.nwra.com

On Jul 6, 2015, at 12:28 PM, James Gallagher <jgall...@opendap.org> wrote:

On Jul 6, 2015, at 12:21 PM, metall...@gmail.com wrote:

Jim,

I also got the following error when made libdap 3.14.0
lex.d4_ce.cc:1281: error: prototype for 'size_t d4_ceFlexLexer::LexerInput(char*, size_t)' does not match any in class 'd4_ceFlexLexer'
/usr/include/FlexLexer.h:133: error: candidate is: virtual int d4_ceFlexLexer::LexerInput(char*, int)

The problem is that bison produces two different type signatures for FlexLexer and I’d, at one point, tried to bundle the generated source in the tar ball. This lead to the type conflict you’re seeing, so I backed away from that. I will check on the libdap source tar ball and see if making a new one will address this issue.

Try this source dist: http://www.opendap.org/pub/source/libdap-3.14.1.tar.gz There is a gpg sig there too; same URL plus .sig. This version of the source fixes the issue with bison 3 I hope, but it’s very hard for me to test with lots of different bison versions, so your help would be great. By listing the generated cc and hh files as BUILT_SOURCES ‘make dist’ includes them. This may be a help or it may be a hinderance…

Thanks,

James

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metall...@gmail.com

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Jul 7, 2015, 1:27:44 PM7/7/15

to sup...@opendap.org, or...@cora.nwra.com, aponom...@rosalab.ru

Hi, Jim,

Thx for the revised version.

I am using bison 3.0.4. (On RH 6)

Here is the new errors:

libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../d4_ce -I. -I/usr/include/libxml2 -I.. -I../d4_ce -I. -I/usr/include/libxml2 -g -O2 -MT libd4_ce_parser_la-lex.d4_ce.lo -MD -MP -MF .deps/libd4_ce_parser_la-lex.d4_ce.Tpo -c lex.d4_ce.cc -fPIC -DPIC -o .libs/libd4_ce_parser_la-lex.d4_ce.o
lex.d4_ce.cc:1281: error: prototype for 'size_t d4_ceFlexLexer::LexerInput(char*, size_t)' does not match any in class 'd4_ceFlexLexer'
/usr/include/FlexLexer.h:133: error: candidate is: virtual int d4_ceFlexLexer::LexerInput(char*, int)
lex.d4_ce.cc:1308: error: prototype for 'void d4_ceFlexLexer::LexerOutput(const char*, size_t)' does not match any in class 'd4_ceFlexLexer'
/usr/include/FlexLexer.h:134: error: candidate is: virtual void d4_ceFlexLexer::LexerOutput(const char*, int)

make[3]: *** [libd4_ce_parser_la-lex.d4_ce.lo] Error 1

make[3]: Leaving directory `/export/00/src/libdap-3.14.1/d4_ce'

make[2]: *** [all] Error 2

make[2]: Leaving directory `/export/00/src/libdap-3.14.1/d4_ce'

make[1]: *** [all-recursive] Error 1

make[1]: Leaving directory `/export/00/src/libdap-3.14.1'

make: *** [all] Error 2

I did the 'make dist' and generated the libdap-3.14.1.tar.gz.
( You can email me how I can deliver it to you. )

Jerry Wang from JPL

On Thursday, April 16, 2015 at 11:30:15 AM UTC-7, Orion Poplawski wrote:

Orion Poplawski

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Jul 7, 2015, 2:06:27 PM7/7/15

to James Gallagher, metall...@gmail.com, sup...@opendap.org, aponom...@rosalab.ru

On 07/06/2015 03:36 PM, James Gallagher wrote:
>
>> On Jul 6, 2015, at 12:28 PM, James Gallagher <jgall...@opendap.org

>> <mailto:jgall...@opendap.org>> wrote:
>>
>>
>>> On Jul 6, 2015, at 12:21 PM, metall...@gmail.com

>>> <mailto:metall...@gmail.com> wrote:
>>>
>>> Jim,
>>>
>>> I also got the following error when made libdap 3.14.0
>>> lex.d4_ce.cc:1281: error: prototype for 'size_t
>>> d4_ceFlexLexer::LexerInput(char*, size_t)' does not match any in class
>>> 'd4_ceFlexLexer'
>>> /usr/include/FlexLexer.h:133: error: candidate is: virtual int
>>> d4_ceFlexLexer::LexerInput(char*, int)
>>
>> The problem is that bison produces two different type signatures for
>> FlexLexer and I’d, at one point, tried to bundle the generated source in the
>> tar ball. This lead to the type conflict you’re seeing, so I backed away
>> from that. I will check on the libdap source tar ball and see if making a
>> new one will address this issue.
>
> Try this source
> dist: http://www.opendap.org/pub/source/libdap-3.14.1.tar.gz There is a gpg
> sig there too; same URL plus .sig. This version of the source fixes the issue
> with bison 3 I hope, but it’s very hard for me to test with lots of different
> bison versions, so your help would be great. By listing the generated cc and
> hh files as BUILT_SOURCES ‘make dist’ includes them. This may be a help or it
> may be a hinderance…
>
> Thanks,
> James

A hindrance I think. On Fedora 21 with flex 2.5.37 (source of
/usr/include/FlexLexer.h) and bison 3.0.2 I get:

lex.d4_ce.cc: In member function 'virtual int libdap::D4CEScanner::yylex()':
lex.d4_ce.cc:864:35: warning: comparison between signed and unsigned integer
expressions [-Wsign-compare]
for ( yyl = (yy_more_len); yyl < yyleng; ++yyl )
^
lex.d4_ce.cc: At global scope:

lex.d4_ce.cc:1281:8: error: prototype for 'size_t

d4_ceFlexLexer::LexerInput(char*, size_t)' does not match any in class
'd4_ceFlexLexer'

size_t yyFlexLexer::LexerInput( char* buf, size_t max_size )
^
In file included from lex.d4_ce.cc:395:0:
/usr/include/FlexLexer.h:133:14: error: candidate is: virtual int
d4_ceFlexLexer::LexerInput(char*, int)
virtual int LexerInput( char* buf, int max_size );
^

lex.d4_ce.cc:1308:6: error: prototype for 'void

d4_ceFlexLexer::LexerOutput(const char*, size_t)' does not match any in class
'd4_ceFlexLexer'

void yyFlexLexer::LexerOutput( const char* buf, size_t size )
^
In file included from lex.d4_ce.cc:395:0:
/usr/include/FlexLexer.h:134:15: error: candidate is: virtual void
d4_ceFlexLexer::LexerOutput(const char*, int)
virtual void LexerOutput( const char* buf, int size );
^

Makefile:946: recipe for target 'libd4_ce_parser_la-lex.d4_ce.lo' failed

If I remove the lex.*.cc files it compiles fine.

--
Orion Poplawski
Technical Manager 303-415-9701 x222

NWRA, Boulder/CoRA Office FAX: 303-415-9702
3380 Mitchell Lane or...@nwra.com
Boulder, CO 80301 http://www.nwra.com

James Gallagher

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Jul 7, 2015, 7:03:44 PM7/7/15

to Orion Poplawski, James Gallagher, metall...@gmail.com, sup...@opendap.org, aponom...@rosalab.ru

Yeah. As I was pressing send I thought that might be the case - more of a hindrance. I’ll fix this.

Thanks for the feedback.

James

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metall...@gmail.com

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Jul 21, 2015, 10:20:15 AM7/21/15

to sup...@opendap.org, aponom...@rosalab.ru, or...@cora.nwra.com

Still got the following errors trying to compile libdap:

lex.d4_ce.cc:1281: error: prototype for 'size_t d4_ceFlexLexer::LexerInput(char*, size_t)' does not match any in class 'd4_ceFlexLexer'

/usr/include/FlexLexer.h:133: error: candidate is: virtual int d4_ceFlexLexer::LexerInput(char*, int)
lex.d4_ce.cc:1308: error: prototype for 'void d4_ceFlexLexer::LexerOutput(const char*, size_t)' does not match any in class 'd4_ceFlexLexer'
/usr/include/FlexLexer.h:134: error: candidate is: virtual void d4_ceFlexLexer::LexerOutput(const char*, int)

make[3]: *** [libd4_ce_parser_la-lex.d4_ce.lo] Error 1

make[3]: Leaving directory `/export/00/src/libdap-3.14.1/d4_ce'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/export/00/src/libdap-3.14.1/d4_ce'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/export/00/src/libdap-3.14.1'
make: *** [all] Error 2

On Thursday, April 16, 2015 at 11:30:15 AM UTC-7, Orion Poplawski wrote:

Message has been deleted

aleksan...@gmail.com

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Sep 14, 2015, 11:40:18 AM9/14/15

to User Support, aponom...@rosalab.ru, or...@cora.nwra.com

Any news on this issue? I'm having quite similar issues when trying to create binaries for anaconda:

Removing old build environment

Removing old work directory

BUILD START: libdap-3.14.0-0

Fetching package metadata: ........

Solving package specifications: .

The following packages will be downloaded:

package | build

---------------------------|-----------------

bison-3.0.4 | 0 1021 KB

The following NEW packages will be INSTALLED:

autoconf: 2.69-1

automake: 1.14-pl5.18.2_2

bison: 3.0.4-0

cloog: 0.18.0-0

flex: 2.5.39-0

gmp: 5.1.2-2

isl: 0.12.2-0

libgcc: 4.8.4-1

libtool: 2.4.2-1

libxml2: 2.9.2-0

m4: 1.4.17-0

mpc: 1.0.1-0

mpfr: 3.1.2-0

perl: 5.18.2-1

zlib: 1.2.8-0

Fetching packages ...

bison-3.0.4-0. 100% |###########################################################################################################| Time: 0:00:00 113.28 MB/s

Extracting packages ...

[ COMPLETE ]|##############################################################################################################################| 100%

Linking packages ...

[ COMPLETE ]|##############################################################################################################################| 100%

Removing old work directory

Source cache directory is: /root/anaconda/conda-bld/src_cache

Found source in cache: libdap-3.14.0.tar.gz

Extracting download

Package: libdap-3.14.0-0

source tree in: /root/anaconda/conda-bld/work/libdap-3.14.0

+ export CFLAGS=-I/root/anaconda/envs/_build/include

+ CFLAGS=-I/root/anaconda/envs/_build/include

+ export CPPFLAGS=-I/root/anaconda/envs/_build/include

+ CPPFLAGS=-I/root/anaconda/envs/_build/include

+ printenv

CPU_COUNT=4

PYTHONNOUSERSITE=1

CPPFLAGS=-I/root/anaconda/envs/_build/include

PERL_VER=5.18.2

R=/root/anaconda/envs/_build/bin/R

PY_VER=2.7

NPY_VER=N.o.n.e

PKG_BUILDNUM=0

CONDA_BUILD=1

PATH=/root/anaconda/envs/_build/bin:/root/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games

SRC_DIR=/root/anaconda/conda-bld/work/libdap-3.14.0

LD_RUN_PATH=/root/anaconda/envs/_build/lib

PWD=/root/anaconda/conda-bld/work/libdap-3.14.0

PY3K=0

PKG_VERSION=3.14.0

STDLIB_DIR=/root/anaconda/envs/_build/lib/python2.7

LANG=en_US.UTF-8

SHLVL=1

HOME=/root

CFLAGS=-I/root/anaconda/envs/_build/include

SP_DIR=/root/anaconda/envs/_build/lib/python2.7/site-packages

SYS_PREFIX=/root/anaconda

PREFIX=/root/anaconda/envs/_build

RECIPE_DIR=/media/sf_Documents/conda/nansat/libdap

PKG_CONFIG_PATH=/root/anaconda/envs/_build/lib/pkgconfig

CONDA_DEFAULT_ENV=/root/anaconda/envs/_build

ARCH=64

SYS_PYTHON=/root/anaconda/bin/python

PKG_NAME=libdap

PYTHON=/root/anaconda/envs/_build/bin/python

_=/usr/bin/printenv

+ sed -i 's/\/bin\/sh/\/bin\/bash/g' ./aclocal.m4 ./conf/compile ./conf/config.guess ./conf/config.rpath ./conf/config.sub ./conf/depcomp ./conf/install-sh ./conf/libtool.m4 ./conf/ltmain.sh ./conf/missing ./configure ./dap-config-pkgconfig ./dap-config.in ./gl/config.charset ./gl/m4/lib-ld.m4 ./gl/m4/lib-link.m4 ./OSX_Resources/InstallationCheck ./tests/atconfig ./tests/DMRTest ./tests/DDSTest ./tests/DASTest ./tests/EXPRTest ./tests/getdapTest ./unit-tests/cache-testsuite/cleanup.sh.in

+ bash configure --enable-threads=pth --prefix=/root/anaconda/envs/_build

checking for a BSD-compatible install... /usr/bin/install -c

checking whether build environment is sane... yes

checking for a thread-safe mkdir -p... /bin/mkdir -p

checking for gawk... gawk

checking whether make sets $(MAKE)... yes

configure: Package Major Version: 3

configure: Package Minor Version: 14

configure: Package SubMinor Version: 0

checking build system type... x86_64-unknown-linux-gnu

checking host system type... x86_64-unknown-linux-gnu

checking for gawk... (cached) gawk

checking for g++... g++

checking whether the C++ compiler works... yes

checking for C++ compiler default output file name... a.out

checking for suffix of executables...

checking whether we are cross compiling... no

checking for suffix of object files... o

checking whether we are using the GNU C++ compiler... yes

checking whether g++ accepts -g... yes

checking for style of include used by make... GNU

checking dependency style of g++... gcc3

checking for gcc... gcc

checking whether we are using the GNU C compiler... yes

checking whether gcc accepts -g... yes

checking for gcc option to accept ISO C89... none needed

checking dependency style of gcc... gcc3

checking how to run the C preprocessor... gcc -E

checking for grep that handles long lines and -e... /bin/grep

checking for egrep... /bin/grep -E

checking for Minix Amsterdam compiler... no

checking for ar... ar

checking for ranlib... ranlib

checking whether gcc and cc understand -c and -o together... yes

checking for ANSI C header files... yes

checking for sys/types.h... yes

checking for sys/stat.h... yes

checking for stdlib.h... yes

checking for string.h... yes

checking for memory.h... yes

checking for strings.h... yes

checking for inttypes.h... yes

checking for stdint.h... yes

checking for unistd.h... yes

checking minix/config.h usability... no

checking minix/config.h presence... no

checking for minix/config.h... no

checking whether it is safe to define __EXTENSIONS__... yes

checking whether _XOPEN_SOURCE should be defined... no

checking for flex... flex

checking lex output file root... lex.yy

checking lex library... none needed

checking whether yytext is a pointer... no

checking whether ln -s works... yes

checking whether make sets $(MAKE)... (cached) yes

checking how to print strings... printf

checking for a sed that does not truncate output... /bin/sed

checking for fgrep... /bin/grep -F

checking for ld used by gcc... /usr/bin/ld

checking if the linker (/usr/bin/ld) is GNU ld... yes

checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B

checking the name lister (/usr/bin/nm -B) interface... BSD nm

checking the maximum length of command line arguments... 1572864

checking whether the shell understands some XSI constructs... yes

checking whether the shell understands "+="... yes

checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop

checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop

checking for /usr/bin/ld option to reload object files... -r

checking for objdump... objdump

checking how to recognize dependent libraries... pass_all

checking for dlltool... no

checking how to associate runtime and link libraries... printf %s\n

checking for archiver @FILE support... @

checking for strip... strip

checking for ranlib... (cached) ranlib

checking command to parse /usr/bin/nm -B output from gcc object... ok

checking for sysroot... no

checking for mt... mt

checking if mt is a manifest tool... no

checking for dlfcn.h... yes

checking for objdir... .libs

checking if gcc supports -fno-rtti -fno-exceptions... no

checking for gcc option to produce PIC... -fPIC -DPIC

checking if gcc PIC flag -fPIC -DPIC works... yes

checking if gcc static flag -static works... yes

checking if gcc supports -c -o file.o... yes

checking if gcc supports -c -o file.o... (cached) yes

checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes

checking whether -lc should be explicitly linked in... no

checking dynamic linker characteristics... GNU/Linux ld.so

checking how to hardcode library paths into programs... immediate

checking whether stripping libraries is possible... yes

checking if libtool supports shared libraries... yes

checking whether to build shared libraries... yes

checking whether to build static libraries... yes

checking how to run the C++ preprocessor... g++ -E

checking for ld used by g++... /usr/bin/ld -m elf_x86_64

checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes

checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes

checking for g++ option to produce PIC... -fPIC -DPIC

checking if g++ PIC flag -fPIC -DPIC works... yes

checking if g++ static flag -static works... yes

checking if g++ supports -c -o file.o... yes

checking if g++ supports -c -o file.o... (cached) yes

checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes

checking dynamic linker characteristics... (cached) GNU/Linux ld.so

checking how to hardcode library paths into programs... immediate

checking for bison... bison

checking for bison 3.0... found vesion 3.0.4

checking for dirent.h that defines DIR... yes

checking for library containing opendir... none required

checking for ANSI C header files... (cached) yes

checking for sys/wait.h that is POSIX.1 compatible... yes

checking fcntl.h usability... yes

checking fcntl.h presence... yes

checking for fcntl.h... yes

checking malloc.h usability... yes

checking malloc.h presence... yes

checking for malloc.h... yes

checking for memory.h... (cached) yes

checking netinet/in.h usability... yes

checking netinet/in.h presence... yes

checking for netinet/in.h... yes

checking stddef.h usability... yes

checking stddef.h presence... yes

checking for stddef.h... yes

checking for stdlib.h... (cached) yes

checking for string.h... (cached) yes

checking for strings.h... (cached) yes

checking sys/param.h usability... yes

checking sys/param.h presence... yes

checking for sys/param.h... yes

checking sys/time.h usability... yes

checking sys/time.h presence... yes

checking for sys/time.h... yes

checking for unistd.h... (cached) yes

checking uuid/uuid.h usability... no

checking uuid/uuid.h presence... no

checking for uuid/uuid.h... no

checking for an ANSI C-conforming const... yes

checking for inline... inline

checking for size_t... yes

checking for struct stat.st_blksize... yes

checking whether time.h and sys/time.h may both be included... yes

checking whether struct tm is in sys/time.h or time.h... time.h

checking for working volatile... yes

checking whether byte ordering is bigendian... no

checking size of int... 4

checking size of long... 8

checking size of char... 1

checking size of double... 8

checking size of float... 4

checking for inttypes.h... (cached) yes

checking size of int32_t... 4

checking size of uint32_t... 4

checking size of int16_t... 2

checking size of uint16_t... 2

checking size of uint8_t... 1

checking for library containing xdr_void... none required

checking for xdr_uint32_t in -lc... yes

checking for alarm... yes

checking for atexit... yes

checking for bzero... yes

checking for dup2... yes

checking for getcwd... yes

checking for getpagesize... yes

checking for localtime_r... yes

checking for memmove... yes

checking for memset... yes

checking for pow... no

checking for putenv... yes

checking for setenv... yes

checking for strchr... yes

checking for strerror... yes

checking for strtol... yes

checking for strtoul... yes

checking for timegm... yes

checking for mktime... yes

checking for working alloca.h... yes

checking for alloca... yes

checking whether <wchar.h> uses 'inline' correctly... yes

checking for btowc... yes

checking for symlink... yes

checking for mbsinit... yes

checking for mbrtowc... yes

checking for nl_langinfo... yes

checking for isblank... yes

checking for iswctype... yes

checking for wcscoll... yes

checking for wcrtomb... yes

checking for iswcntrl... yes

checking for nl_langinfo and CODESET... yes

checking for a traditional french locale... none

checking whether the preprocessor supports include_next... yes

checking whether system header files limit the line length... no

checking for langinfo.h... yes

checking for unistd.h... (cached) yes

checking for xlocale.h... yes

checking for wchar.h... yes

checking for stdint.h... (cached) yes

checking for features.h... yes

checking for wctype.h... yes

checking for working fcntl.h... yes

checking whether getc_unlocked is declared... yes

checking whether we are using the GNU C Library >= 2.1 or uClibc... yes

checking for wchar_t... yes

checking whether NULL can be used in arbitrary expressions... yes

checking for ld used by gcc... /usr/bin/ld -m elf_x86_64

checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes

checking for shared library run path origin... done

checking whether imported symbols can be declared weak... yes

checking how to link with libpth... -lpth

checking for multithread API to use... none

checking whether malloc, realloc, calloc are POSIX compliant... yes

checking for mbstate_t... yes

checking for a traditional japanese locale... none

checking for a transitional chinese locale... none

checking for a french Unicode locale... none

checking whether alarm is declared... yes

checking for C/C++ restrict keyword... __restrict

checking for stdlib.h... (cached) yes

checking for GNU libc compatible malloc... yes

checking for stdbool.h that conforms to C99... yes

checking for _Bool... yes

checking for unsigned long long int... yes

checking for long long int... yes

checking whether stdint.h conforms to C99... yes

checking for pid_t... yes

checking for mode_t... yes

checking for wint_t... yes

checking for alloca as a compiler built-in... yes

checking whether btowc(0) is correct... yes

checking whether btowc(EOF) is correct... guessing yes

checking byteswap.h usability... yes

checking byteswap.h presence... yes

checking for byteswap.h... yes

checking whether langinfo.h defines CODESET... yes

checking whether langinfo.h defines T_FMT_AMPM... yes

checking whether langinfo.h defines ERA... yes

checking whether langinfo.h defines YESEXPR... yes

checking whether nl_langinfo is declared without a macro... yes

checking whether locale.h conforms to POSIX:2001... yes

checking whether locale.h defines locale_t... yes

checking whether struct lconv is properly defined... yes

checking whether setlocale is declared without a macro... yes

checking whether duplocale is declared without a macro... yes

checking for stdlib.h... (cached) yes

checking for GNU libc compatible malloc... (cached) yes

checking whether mbrtowc handles incomplete characters... guessing yes

checking whether mbrtowc works as well as mbtowc... guessing yes

checking whether mbrtowc handles a NULL pwc argument... guessing yes

checking whether mbrtowc handles a NULL string argument... guessing yes

checking whether mbrtowc has a correct return value... guessing yes

checking whether mbrtowc returns 0 when parsing a NUL character... guessing yes

checking whether mbrtowc handles incomplete characters... (cached) guessing yes

checking whether mbrtowc works as well as mbtowc... (cached) guessing yes

checking whether YESEXPR works... yes

checking for working re_compile_pattern... yes

checking for ssize_t... yes

checking whether NULL can be used in arbitrary expressions... (cached) yes

checking whether _Exit is declared without a macro... yes

checking whether atoll is declared without a macro... yes

checking whether canonicalize_file_name is declared without a macro... yes

checking whether getloadavg is declared without a macro... yes

checking whether getsubopt is declared without a macro... yes

checking whether grantpt is declared without a macro... yes

checking whether initstate is declared without a macro... yes

checking whether initstate_r is declared without a macro... yes

checking whether mkdtemp is declared without a macro... yes

checking whether mkostemp is declared without a macro... yes

checking whether mkostemps is declared without a macro... yes

checking whether mkstemp is declared without a macro... yes

checking whether mkstemps is declared without a macro... yes

checking whether posix_openpt is declared without a macro... yes

checking whether ptsname is declared without a macro... yes

checking whether ptsname_r is declared without a macro... yes

checking whether random is declared without a macro... yes

checking whether random_r is declared without a macro... yes

checking whether realpath is declared without a macro... yes

checking whether rpmatch is declared without a macro... yes

checking whether secure_getenv is declared without a macro... yes

checking whether setenv is declared without a macro... yes

checking whether setstate is declared without a macro... yes

checking whether setstate_r is declared without a macro... yes

checking whether srandom is declared without a macro... yes

checking whether srandom_r is declared without a macro... yes

checking whether strtod is declared without a macro... yes

checking whether strtoll is declared without a macro... yes

checking whether strtoull is declared without a macro... yes

checking whether unlockpt is declared without a macro... yes

checking whether unsetenv is declared without a macro... yes

checking whether chdir is declared without a macro... yes

checking whether chown is declared without a macro... yes

checking whether dup is declared without a macro... yes

checking whether dup2 is declared without a macro... yes

checking whether dup3 is declared without a macro... yes

checking whether environ is declared without a macro... yes

checking whether euidaccess is declared without a macro... yes

checking whether faccessat is declared without a macro... yes

checking whether fchdir is declared without a macro... yes

checking whether fchownat is declared without a macro... yes

checking whether fdatasync is declared without a macro... yes

checking whether fsync is declared without a macro... yes

checking whether ftruncate is declared without a macro... yes

checking whether getcwd is declared without a macro... yes

checking whether getdomainname is declared without a macro... yes

checking whether getdtablesize is declared without a macro... yes

checking whether getgroups is declared without a macro... yes

checking whether gethostname is declared without a macro... yes

checking whether getlogin is declared without a macro... yes

checking whether getlogin_r is declared without a macro... yes

checking whether getpagesize is declared without a macro... yes

checking whether getusershell is declared without a macro... yes

checking whether setusershell is declared without a macro... yes

checking whether endusershell is declared without a macro... yes

checking whether group_member is declared without a macro... yes

checking whether isatty is declared without a macro... yes

checking whether lchown is declared without a macro... yes

checking whether link is declared without a macro... yes

checking whether linkat is declared without a macro... yes

checking whether lseek is declared without a macro... yes

checking whether pipe is declared without a macro... yes

checking whether pipe2 is declared without a macro... yes

checking whether pread is declared without a macro... yes

checking whether pwrite is declared without a macro... yes

checking whether readlink is declared without a macro... yes

checking whether readlinkat is declared without a macro... yes

checking whether rmdir is declared without a macro... yes

checking whether sethostname is declared without a macro... yes

checking whether sleep is declared without a macro... yes

checking whether symlink is declared without a macro... yes

checking whether symlinkat is declared without a macro... yes

checking whether ttyname_r is declared without a macro... yes

checking whether unlink is declared without a macro... yes

checking whether unlinkat is declared without a macro... yes

checking whether usleep is declared without a macro... yes

checking whether btowc is declared without a macro... yes

checking whether wctob is declared without a macro... yes

checking whether mbsinit is declared without a macro... yes

checking whether mbrtowc is declared without a macro... yes

checking whether mbrlen is declared without a macro... yes

checking whether mbsrtowcs is declared without a macro... yes

checking whether mbsnrtowcs is declared without a macro... yes

checking whether wcrtomb is declared without a macro... yes

checking whether wcsrtombs is declared without a macro... yes

checking whether wcsnrtombs is declared without a macro... yes

checking whether wcwidth is declared without a macro... yes

checking whether wmemchr is declared without a macro... yes

checking whether wmemcmp is declared without a macro... yes

checking whether wmemcpy is declared without a macro... yes

checking whether wmemmove is declared without a macro... yes

checking whether wmemset is declared without a macro... yes

checking whether wcslen is declared without a macro... yes

checking whether wcsnlen is declared without a macro... yes

checking whether wcscpy is declared without a macro... yes

checking whether wcpcpy is declared without a macro... yes

checking whether wcsncpy is declared without a macro... yes

checking whether wcpncpy is declared without a macro... yes

checking whether wcscat is declared without a macro... yes

checking whether wcsncat is declared without a macro... yes

checking whether wcscmp is declared without a macro... yes

checking whether wcsncmp is declared without a macro... yes

checking whether wcscasecmp is declared without a macro... yes

checking whether wcsncasecmp is declared without a macro... yes

checking whether wcscoll is declared without a macro... yes

checking whether wcsxfrm is declared without a macro... yes

checking whether wcsdup is declared without a macro... yes

checking whether wcschr is declared without a macro... yes

checking whether wcsrchr is declared without a macro... yes

checking whether wcscspn is declared without a macro... yes

checking whether wcsspn is declared without a macro... yes

checking whether wcspbrk is declared without a macro... yes

checking whether wcsstr is declared without a macro... yes

checking whether wcstok is declared without a macro... yes

checking whether wcswidth is declared without a macro... yes

checking whether mbrtowc handles incomplete characters... (cached) guessing yes

checking whether mbrtowc works as well as mbtowc... (cached) guessing yes

checking whether wcrtomb return value is correct... guessing yes

checking whether iswcntrl works... yes

checking for towlower... yes

checking for wctype_t... yes

checking for wctrans_t... yes

checking whether wctype is declared without a macro... yes

checking whether iswctype is declared without a macro... yes

checking whether wctrans is declared without a macro... yes

checking whether towctrans is declared without a macro... yes

checking for pkg-config... no

checking for CURL... checking for libcurl... yes; used curl-config and found version 7.43.0

checking for XML2... checking for libxml2... yes; used xml2-config and found version 2.9.2

checking for pthread_kill in -lpthread... yes

checking for uuid_generate in -luuid... no

checking for cppunit-config... no

checking for Cppunit - version >= 1.12.0... no

configure: "Not building developer version"

checking that generated files are newer than configure... done

configure: creating ./config.status

config.status: creating Makefile

config.status: creating libdap.pc

config.status: creating libdapclient.pc

config.status: creating libdapserver.pc

config.status: creating main_page.doxygen

config.status: creating doxy.conf

config.status: creating abi_checker.xml

config.status: creating gl/Makefile

config.status: creating d4_ce/Makefile

config.status: creating tests/Makefile

config.status: creating tests/atlocal

config.status: creating unit-tests/Makefile

config.status: creating unit-tests/cache-testsuite/Makefile

config.status: creating dap-config

config.status: creating config.h

config.status: creating dods-datatypes-config.h

config.status: creating xdr-datatypes-config.h

config.status: executing tests/atconfig commands

config.status: executing depfiles commands

config.status: executing libtool commands

+ sed -i 's/\/bin\/sh/\/bin\/bash/g' Makefile

+ make

CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /root/anaconda/conda-bld/work/libdap-3.14.0/conf/missing --run aclocal-1.12 -I conf -I gl/m4

/root/anaconda/conda-bld/work/libdap-3.14.0/conf/missing: line 51: aclocal-1.12: command not found

WARNING: 'aclocal-1.12' is missing on your system. You should only need it if

you modified 'acinclude.m4' or 'configure.ac'. You might want

to install the Automake and Perl packages. Grab them from

any GNU archive site.

cd . && /bin/bash /root/anaconda/conda-bld/work/libdap-3.14.0/conf/missing --run automake-1.12 --foreign

/root/anaconda/conda-bld/work/libdap-3.14.0/conf/missing: line 51: automake-1.12: command not found

WARNING: 'automake-1.12' is missing on your system. You should only need it if

you modified 'Makefile.am', 'acinclude.m4' or 'configure.ac'.

You might want to install the Automake and Perl packages.

Grab them from any GNU archive site.

CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /root/anaconda/conda-bld/work/libdap-3.14.0/conf/missing --run autoconf

/bin/bash ./config.status --recheck

running CONFIG_SHELL=/bin/bash /bin/bash configure --enable-threads=pth --prefix=/root/anaconda/envs/_build CPPFLAGS=-I/root/anaconda/envs/_build/include CFLAGS=-I/root/anaconda/envs/_build/include --no-create --no-recursion

checking for a BSD-compatible install... /usr/bin/install -c

checking whether build environment is sane... yes

checking for a thread-safe mkdir -p... /bin/mkdir -p

checking for gawk... gawk

checking whether make sets $(MAKE)... yes

configure: Package Major Version: 3

configure: Package Minor Version: 14

configure: Package SubMinor Version: 0

checking build system type... x86_64-unknown-linux-gnu

checking host system type... x86_64-unknown-linux-gnu

checking for gawk... (cached) gawk

checking for g++... g++

checking whether the C++ compiler works... yes

checking for C++ compiler default output file name... a.out

checking for suffix of executables...

checking whether we are cross compiling... no

checking for suffix of object files... o

checking whether we are using the GNU C++ compiler... yes

checking whether g++ accepts -g... yes

checking for style of include used by make... GNU

checking dependency style of g++... gcc3

checking for gcc... gcc

checking whether we are using the GNU C compiler... yes

checking whether gcc accepts -g... yes

checking for gcc option to accept ISO C89... none needed

checking dependency style of gcc... gcc3

checking how to run the C preprocessor... gcc -E

checking for grep that handles long lines and -e... /bin/grep

checking for egrep... /bin/grep -E

checking for Minix Amsterdam compiler... no

checking for ar... ar

checking for ranlib... ranlib

checking whether gcc and cc understand -c and -o together... yes

checking for ANSI C header files... yes

checking for sys/types.h... yes

checking for sys/stat.h... yes

checking for stdlib.h... yes

checking for string.h... yes

checking for memory.h... yes

checking for strings.h... yes

checking for inttypes.h... yes

checking for stdint.h... yes

checking for unistd.h... yes

checking minix/config.h usability... no

checking minix/config.h presence... no

checking for minix/config.h... no

checking whether it is safe to define __EXTENSIONS__... yes

checking whether _XOPEN_SOURCE should be defined... no

checking for flex... flex

checking lex output file root... lex.yy

checking lex library... none needed

checking whether yytext is a pointer... no

checking whether ln -s works... yes

checking whether make sets $(MAKE)... (cached) yes

checking how to print strings... printf

checking for a sed that does not truncate output... /bin/sed

checking for fgrep... /bin/grep -F

checking for ld used by gcc... /usr/bin/ld

checking if the linker (/usr/bin/ld) is GNU ld... yes

checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B

checking the name lister (/usr/bin/nm -B) interface... BSD nm

checking the maximum length of command line arguments... 3458764513820540925