LibStatGen Troubleshooting - Revision history

Mktrost: /* Possible Compile Errors */

2017-11-13T04:20:15Z

Possible Compile Errors

← Older revision		Revision as of 00:20, 13 November 2017
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	= Possible Compile Errors =		= Possible Compile Errors =

			'''If compilation fails due to warnings being treated as errors, please contact us so we can fix the warnings. As a work-around to get it to compile, you can disable the treatment of warnings as errors by editing libStatGen/general/Makefile to remove -Werror.'''

	The following are a list of compile errors that have been encountered with recommendations on what they mean and how to fix them.		The following are a list of compile errors that have been encountered with recommendations on what they mean and how to fix them.

Mktrost: /* Possible Compile Errors */

2015-02-19T20:20:49Z

Possible Compile Errors

← Older revision		Revision as of 16:20, 19 February 2015
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	The following are a list of compile errors that have been encountered with recommendations on what they mean and how to fix them.		The following are a list of compile errors that have been encountered with recommendations on what they mean and how to fix them.

	==== GenomeSequence.h:30:57: error: ~~openssl~~/~~md5.h~~: ~~No such file or directory~~ ====		== GenomeSequence.cpp:161: error: explicit instantiation... ==
			If you are compiling on OSX and encounter this error:
			;GenomeSequence.cpp<nowiki>:</nowiki> In instantiation of ‘std<nowiki>::</nowiki>basic_ostream<_CharT, _Traits>& std<nowiki>::</nowiki>operator<<(std<nowiki>::</nowiki>basic_ostream<_CharT, _Traits>&, const std<nowiki>::</nowiki>basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std<nowiki>::</nowiki>char_traits<char>, _Alloc = std<nowiki>::</nowiki>allocator<char>]’<nowiki>:</nowiki><br />GenomeSequence.cpp<nowiki>:</nowiki>161<nowiki>:</nowiki> instantiated from here<br />GenomeSequence.cpp<nowiki>:</nowiki>161<nowiki>:</nowiki> error<nowiki>:</nowiki> explicit instantiation of ‘std<nowiki>::</nowiki>basic_ostream<_CharT, _Traits>& std<nowiki>::</nowiki>operator<<(std<nowiki>::</nowiki>basic_ostream<_CharT, _Traits>&, const std<nowiki>::</nowiki>basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std<nowiki>::</nowiki>char_traits<char>, _Alloc = std<nowiki>::</nowiki>allocator<char>]’ but no definition available
			: Try compiling with:
			make USER_COMPILE_VARS=-mmacosx-version-min=10.8

	~~GenomeSequence requires md5 logic and makes calls to methods defined in md5.h which is found in the openssl library.~~

	~~The header files are included in the development version of the package.~~		== error: Sam[filename].h: No such file or directory or "'Sam[classname]' has not been declared" ==

	~~The package may be called something like: openssl-devel or libssl-dev (on ubuntu).~~


	==== error: Sam[filename].h: No such file or directory or "'Sam[classname]' has not been declared" ====
	This error and other, similar errors with "Sam....h: No such file or directory" or "'Sam...' has not been declared" typically means that the library build failed. Check for a previous error in your compile.		This error and other, similar errors with "Sam....h: No such file or directory" or "'Sam...' has not been declared" typically means that the library build failed. Check for a previous error in your compile.

	A successful compile of the library will publish SamFile.h and all the other header files from the library into ~~samtools/lib~~/include. If one of the programs within the statgen repository fails to compile with one of these errors, then the library did not successfully publish the header files and did not successfully ~~byild.~~		A successful compile of the library will publish SamFile.h and all the other header files from the library into libStatGen/include. If one of the programs within the statgen repository fails to compile with one of these errors, then the library did not successfully publish the header files and did not successfully build.


	~~==== GenomeSequence.cpp:552: warning: converting to `int' from `double' ====~~
	~~This has been fixed in versions after 3/1/11.~~

	~~Update statgen/lib/general/GenomeSequence.cpp line 552 to the following:~~
	~~<pre>~~
	~~newPercent = (int) (1~~.~~0 * fastaIndex / fastaDataSize) * 100;~~
	~~</pre>~~


	~~==== Complaints about unknown -Wno-unused-result option in lib/general/Makefile ====~~		== InputFile.h (or any other library file): No such file or directory ==
	~~This has been fixed in versions after 3/1/11.~~

	~~Update stagen/lib/general/Makefile line 17 to the following:~~
	~~<pre>~~
	~~WARNINGS+=$(shell if [ X$(CCVERSION) \> X4.2.0 ] ; then echo " -Wno-unused-result" ; fi)~~
	~~</pre>~~


	==== InputFile.h (or any other library file): No such file or directory ====
	Errors like the following:		Errors like the following:
	<pre>		<pre>
Line 43:		Line 23:
	FastQFile.h:23:26: StringBasics.h: No such file or directory		FastQFile.h:23:26: StringBasics.h: No such file or directory
	</pre>		</pre>
	Tend to occur if the library directory containing the file has not yet been compiled. ~~Either compile~~ the entire library by typing make in ~~statgen/ or statgen/lib or compile the subdirectories in the correct order. lib/general is required for most other library directories~~.		Tend to occur if the library directory containing the file has not yet been compiled. Try recompiling the entire library by typing make in libStatGen.


	~~=== Old Errors That Should No Longer Exist ===~~		== Compile Error on first time building ==
	==== Compile Error on first time building ====
	Record the error.		Record the error.

	Try to recompile and see if that fixes the problem. If it does fix the compile error, let me know what the original error was so I can fix the dependency so it compiles in the correct order.		Try to recompile and see if that fixes the problem. If it does fix the compile error, let me know what the original error was so I can fix the dependency so it compiles in the correct order.

	'''NOTE: In the latest version ~~(in development~~, ~~after 0.1.4), I think I have~~ this fixed.'''		'''NOTE: In the latest version, this should be fixed.'''


	~~==== make test produces messages like "ERROR: Missing required tag: LN." and "Can't modify the key tag, ID from pid to pid1" ====~~
	These messages are currently expected. Some of the tests run by 'make test' test error conditions to make sure they are handled properly. These error conditions print messages to the screen about the errors. These messages are expected and are not a failure of 'make test'.

Mktrost at 18:42, 23 August 2011

2011-08-23T18:42:41Z

@@ Line 2: / Line 2: @@
 The following are a list of compile errors that have been encountered with recommendations on what they mean and how to fix them.
 ==== GenomeSequence.h:30:57: error: openssl/md5.h: No such file or directory ====
@@ Line 25: / Line 16: @@
 A successful compile of the library will publish SamFile.h and all the other header files from the library into samtools/lib/include.  If one of the programs within the statgen repository fails to compile with one of these errors, then the library did not successfully publish the header files and did not successfully byild.
@@ Line 57: / Line 44: @@
 </pre>
 Tend to occur if the library directory containing the file has not yet been compiled.  Either compile the entire library by typing make in statgen/ or statgen/lib or compile the subdirectories in the correct order.  lib/general is required for most other library directories.

Mktrost: moved StatGen Troubleshooting to LibStatGen Troubleshooting

2011-08-23T18:40:33Z

moved StatGen Troubleshooting to LibStatGen Troubleshooting

← Older revision	Revision as of 14:40, 23 August 2011
(No difference)

Mktrost at 20:30, 24 March 2011

2011-03-24T20:30:54Z

← Older revision		Revision as of 16:30, 24 March 2011
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	=== Possible Compile Errors ===		= Possible Compile Errors =

	The following are a list of compile errors that have been encountered with recommendations on what they mean and how to fix them.		The following are a list of compile errors that have been encountered with recommendations on what they mean and how to fix them.

Mktrost at 13:48, 15 March 2011

2011-03-15T13:48:38Z

← Older revision		Revision as of 09:48, 15 March 2011
Line 47:		Line 47:
	WARNINGS+=$(shell if [ X$(CCVERSION) \> X4.2.0 ] ; then echo " -Wno-unused-result" ; fi)		WARNINGS+=$(shell if [ X$(CCVERSION) \> X4.2.0 ] ; then echo " -Wno-unused-result" ; fi)
	</pre>		</pre>


			==== InputFile.h (or any other library file): No such file or directory ====
			Errors like the following:
			<pre>
			FastQFile.cpp:20:23: InputFile.h: No such file or directory
			In file included from FastQFile.cpp:21:
			FastQFile.h:23:26: StringBasics.h: No such file or directory
			</pre>
			Tend to occur if the library directory containing the file has not yet been compiled. Either compile the entire library by typing make in statgen/ or statgen/lib or compile the subdirectories in the correct order. lib/general is required for most other library directories.

Mktrost at 16:35, 3 March 2011

2011-03-03T16:35:54Z

@@ Line 2: / Line 2: @@
 The following are a list of compile errors that have been encountered with recommendations on what they mean and how to fix them.
 ==== Compile Error on first time building ====
@@ Line 7: / Line 8: @@
 Try to recompile and see if that fixes the problem.  If it does fix the compile error, let me know what the original error was so I can fix the dependency so it compiles in the correct order.
 ==== GenomeSequence.h:30:57: error: openssl/md5.h: No such file or directory ====
@@ Line 15: / Line 19: @@
 The package may be called something like: openssl-devel or libssl-dev (on ubuntu).
 ==== error: Sam[filename].h: No such file or directory or "'Sam[classname]' has not been declared" ====
@@ Line 20: / Line 25: @@
 A successful compile of the library will publish SamFile.h and all the other header files from the library into samtools/lib/include.  If one of the programs within the statgen repository fails to compile with one of these errors, then the library did not successfully publish the header files and did not successfully byild.
 ==== make test produces messages like "ERROR: Missing required tag: LN." and "Can't modify the key tag, ID from pid to pid1" ====
 These messages are currently expected.  Some of the tests run by 'make test' test error conditions to make sure they are handled properly.  These error conditions print messages to the screen about the errors.  These messages are expected and are not a failure of 'make test'.

Mktrost at 17:16, 22 February 2011

2011-02-22T17:16:01Z

← Older revision		Revision as of 13:16, 22 February 2011
Line 3:		Line 3:
	The following are a list of compile errors that have been encountered with recommendations on what they mean and how to fix them.		The following are a list of compile errors that have been encountered with recommendations on what they mean and how to fix them.

			==== Compile Error on first time building ====
			Record the error.

			Try to recompile and see if that fixes the problem. If it does fix the compile error, let me know what the original error was so I can fix the dependency so it compiles in the correct order.

	==== GenomeSequence.h:30:57: error: openssl/md5.h: No such file or directory ====		==== GenomeSequence.h:30:57: error: openssl/md5.h: No such file or directory ====

Mktrost at 22:00, 24 January 2011

2011-01-24T22:00:52Z

← Older revision		Revision as of 18:00, 24 January 2011
Line 12:		Line 12:
	The package may be called something like: openssl-devel or libssl-dev (on ubuntu).		The package may be called something like: openssl-devel or libssl-dev (on ubuntu).

	==== ~~Validate.cpp:22:21:~~ error: ~~SamFile~~.h: No such file or directory ====		==== error: Sam[filename].h: No such file or directory or "'Sam[classname]' has not been declared" ====
	This error and other, similar errors with "Sam....h: No such file or directory" or "'Sam...' has not been declared" typically means that the library build failed. Check for a previous error in your compile.		This error and other, similar errors with "Sam....h: No such file or directory" or "'Sam...' has not been declared" typically means that the library build failed. Check for a previous error in your compile.

	A successful compile of the library will publish SamFile.h and all the other header files from the library into samtools/lib/include. If one of the programs within the statgen repository fails to compile with one of these errors, then the library did not successfully publish the header files and did not successfully byild.		A successful compile of the library will publish SamFile.h and all the other header files from the library into samtools/lib/include. If one of the programs within the statgen repository fails to compile with one of these errors, then the library did not successfully publish the header files and did not successfully byild.

			==== make test produces messages like "ERROR: Missing required tag: LN." and "Can't modify the key tag, ID from pid to pid1" ====
			These messages are currently expected. Some of the tests run by 'make test' test error conditions to make sure they are handled properly. These error conditions print messages to the screen about the errors. These messages are expected and are not a failure of 'make test'.

Mktrost at 20:39, 24 January 2011

2011-01-24T20:39:57Z

← Older revision		Revision as of 16:39, 24 January 2011
Line 1:		Line 1:

	=== Possible Compile Errors ===		=== Possible Compile Errors ===

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	The package may be called something like: openssl-devel or libssl-dev (on ubuntu).		The package may be called something like: openssl-devel or libssl-dev (on ubuntu).

			==== Validate.cpp:22:21: error: SamFile.h: No such file or directory ====
			This error and other, similar errors with "Sam....h: No such file or directory" or "'Sam...' has not been declared" typically means that the library build failed. Check for a previous error in your compile.

			A successful compile of the library will publish SamFile.h and all the other header files from the library into samtools/lib/include. If one of the programs within the statgen repository fails to compile with one of these errors, then the library did not successfully publish the header files and did not successfully byild.