Thanks for the question. The problem is that libxml2 version 2.9.4 introduced a new format code for the xmlStrPrintf command, which wn_matrix and libnucnet use in NucNet Tools. This makes old versions of these codes fail to compile for libxml2 versions 2.9.4 or greater. To check your libxml2 version, type
xml2-config --version
I have fixed that for wn_matrix 0.17 and libnucnet 0.27. Be sure to update your NucNet Tools and clean your previous downloads. You can type, for example,
cd nucnet-tools-code svn up cd examples/network make clean_all make all_network
Or, more simply, you can type
cd nucnet-tools-code/examples/network ./examples_make
Let me know if that doesn't work. Best wishes.
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Here is the original posed question, which seems to have gotten lost:
When I compile NucNet Tools, I get the following error:
/opt/local/include/libxml2/libxml/xmlstring.h:98:17: note: candidate function
not viable: no known conversion from 'const xmlChar *' (aka
'const unsigned char *') to 'const char *' for 3rd argument
xmlStrPrintf (xmlChar *buf,
How do I fix that? Thanks.
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As a further follow up, despite the update, there may still be confilicts depending on how your libxml got patched. If you get xmlStrPrintf errors, you should be able to do the following (in bash):
cd nucnet-tools-code/examples/network/
export WN_XML_CHAR=xmlChar
make clean
make run_entropy
The environment variable WN_XML_CHAR sets the format string. The possible values are char and xmlChar, and the code usually chooses between them correctly depending on the version of libxml it detects. Sometimes, however, there's a mismatch and you have to set by hand as above. If the above doesn't work, try
export WN_XML_CHAR=char
make clean
make run_entropy
If one of these works, you can set WN_XML_CHAR in your .bashrc file.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Thanks for the question. The problem is that libxml2 version 2.9.4 introduced a new format code for the xmlStrPrintf command, which wn_matrix and libnucnet use in NucNet Tools. This makes old versions of these codes fail to compile for libxml2 versions 2.9.4 or greater. To check your libxml2 version, type
xml2-config --version
I have fixed that for wn_matrix 0.17 and libnucnet 0.27. Be sure to update your NucNet Tools and clean your previous downloads. You can type, for example,
cd nucnet-tools-code
svn up
cd examples/network
make clean_all
make all_network
Or, more simply, you can type
cd nucnet-tools-code/examples/network
./examples_make
Let me know if that doesn't work. Best wishes.
Here is the original posed question, which seems to have gotten lost:
When I compile NucNet Tools, I get the following error:
/opt/local/include/libxml2/libxml/xmlstring.h:98:17: note: candidate function not viable: no known conversion from 'const xmlChar *' (aka 'const unsigned char *') to 'const char *' for 3rd argument xmlStrPrintf (xmlChar *buf,How do I fix that? Thanks.
As a further follow up, despite the update, there may still be confilicts depending on how your libxml got patched. If you get xmlStrPrintf errors, you should be able to do the following (in bash):
cd nucnet-tools-code/examples/network/
export WN_XML_CHAR=xmlChar
make clean
make run_entropy
The environment variable WN_XML_CHAR sets the format string. The possible values are char and xmlChar, and the code usually chooses between them correctly depending on the version of libxml it detects. Sometimes, however, there's a mismatch and you have to set by hand as above. If the above doesn't work, try
export WN_XML_CHAR=char
make clean
make run_entropy
If one of these works, you can set WN_XML_CHAR in your .bashrc file.
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Hi Brad
I checked that we have xml2-config 2.7.6 vesion.
So I followed the commands you gave me. When I run: make all_network, it gives the following error
tar xz -C ../../vendor -f ../../vendor/wn_matrix.tar.gz
g++ -Werror -Wall -Wpointer-arith -Wwrite-strings -fshort-enums -fno-common -g -O0 -fopenmp -Wno-deprecated -DHYDRO_EXP_EXPANSION
xml2-config --cflagsgsl-config --cflags-I../../vendor/libnucnet/0.29/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.10/src -I../../vendor/libnuceq/0.7/src -I../.. -I ../../vendor/wn_sparse_solve/0.6/src -c ../../vendor/wn_matrix/0.18/src/WnMatrix.c -o ../../obj/WnMatrix.o../../vendor/wn_matrix/0.18/src/WnMatrix.c: In function ‘int WnMatrixassignElement(WnMatrix, size_t, size_t, double)’:
../../vendor/wn_matrix/0.18/src/WnMatrix.c:130: error: invalid conversion from ‘const WnChar’ to ‘const char’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:130: error: initializing argument 3 of ‘int xmlStrPrintf(xmlChar, int, const char, ...)’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:131: error: invalid conversion from ‘const WnChar’ to ‘const char’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:131: error: initializing argument 3 of ‘int xmlStrPrintf(xmlChar, int, const char*, ...)’
../../vendor/wn_matrix/0.18/src/WnMatrix.c: In function ‘int WnMatrixupdateElement(WnMatrix, size_t, size_t, double)’:
../../vendor/wn_matrix/0.18/src/WnMatrix.c:244: error: invalid conversion from ‘const WnChar’ to ‘const char’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:244: error: initializing argument 3 of ‘int xmlStrPrintf(xmlChar, int, const char, ...)’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:245: error: invalid conversion from ‘const WnChar’ to ‘const char’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:245: error: initializing argument 3 of ‘int xmlStrPrintf(xmlChar, int, const char, ...)’
../../vendor/wn_matrix/0.18/src/WnMatrix.c: In function ‘int WnMatrixremoveElement(WnMatrix, size_t, size_t)’:
../../vendor/wn_matrix/0.18/src/WnMatrix.c:282: error: invalid conversion from ‘const WnChar’ to ‘const char’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:282: error: initializing argument 3 of ‘int xmlStrPrintf(xmlChar, int, const char, ...)’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:283: error: invalid conversion from ‘const WnChar’ to ‘const char’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:283: error: initializing argument 3 of ‘int xmlStrPrintf(xmlChar, int, const char*, ...)’
../../vendor/wn_matrix/0.18/src/WnMatrix.c: In function ‘double WnMatrixgetElement(WnMatrix, size_t, size_t)’:
../../vendor/wn_matrix/0.18/src/WnMatrix.c:322: error: invalid conversion from ‘const WnChar’ to ‘const char’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:322: error: initializing argument 3 of ‘int xmlStrPrintf(xmlChar, int, const char, ...)’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:323: error: invalid conversion from ‘const WnChar’ to ‘const char’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:323: error: initializing argument 3 of ‘int xmlStrPrintf(xmlChar, int, const char, ...)’
../../vendor/wn_matrix/0.18/src/WnMatrix.c: In function ‘WnMatrixLine* WnMatrixgetRow(WnMatrix, size_t)’:
../../vendor/wn_matrix/0.18/src/WnMatrix.c:1044: error: invalid conversion from ‘const WnChar’ to ‘const char’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:1044: error: initializing argument 3 of ‘int xmlStrPrintf(xmlChar, int, const char, ...)’
../../vendor/wn_matrix/0.18/src/WnMatrix.c: In function ‘WnMatrixLine* WnMatrixgetColumn(WnMatrix, size_t)’:
../../vendor/wn_matrix/0.18/src/WnMatrix.c:1108: error: invalid conversion from ‘const WnChar’ to ‘const char’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:1108: error: initializing argument 3 of ‘int xmlStrPrintf(xmlChar, int, const char, ...)’
../../vendor/wn_matrix/0.18/src/WnMatrix.c: In function ‘xmlDoc WnMatrixCoomakeXmlDocument(WnMatrixCoo, const WnChar)’:
../../vendor/wn_matrix/0.18/src/WnMatrix.c:1903: error: invalid conversion from ‘const WnChar’ to ‘const char’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:1903: error: initializing argument 3 of ‘int xmlStrPrintf(xmlChar, int, const char, ...)’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:1920: error: invalid conversion from ‘const WnChar’ to ‘const char’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:1920: error: initializing argument 3 of ‘int xmlStrPrintf(xmlChar, int, const char, ...)’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:1937: error: invalid conversion from ‘const WnChar’ to ‘const char’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:1937: error: initializing argument 3 of ‘int xmlStrPrintf(xmlChar, int, const char, ...)’
../../vendor/wn_matrix/0.18/src/WnMatrix.c: In function ‘xmlDoc* WnMatrixCsrmakeXmlDocument(WnMatrixCsr, const WnChar)’:
../../vendor/wn_matrix/0.18/src/WnMatrix.c:2095: error: invalid conversion from ‘const WnChar’ to ‘const char’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:2095: error: initializing argument 3 of ‘int xmlStrPrintf(xmlChar, int, const char, ...)’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:2140: error: invalid conversion from ‘const WnChar’ to ‘const char’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:2140: error: initializing argument 3 of ‘int xmlStrPrintf(xmlChar, int, const char, ...)’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:2157: error: invalid conversion from ‘const WnChar’ to ‘const char’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:2157: error: initializing argument 3 of ‘int xmlStrPrintf(xmlChar, int, const char, ...)’
../../vendor/wn_matrix/0.18/src/WnMatrix.c: In function ‘xmlDoc WnMatrixYalemakeXmlDocument(WnMatrixYale, const WnChar)’:
../../vendor/wn_matrix/0.18/src/WnMatrix.c:2320: error: invalid conversion from ‘const WnChar’ to ‘const char’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:2320: error: initializing argument 3 of ‘int xmlStrPrintf(xmlChar, int, const char, ...)’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:2337: error: invalid conversion from ‘const WnChar’ to ‘const char’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:2337: error: initializing argument 3 of ‘int xmlStrPrintf(xmlChar, int, const char, ...)’
../../vendor/wn_matrix/0.18/src/WnMatrix.c: In function ‘xmlDoc* WnMatrixmake_gsl_vector_xml_document(gsl_vector, const WnChar)’:
../../vendor/wn_matrix/0.18/src/WnMatrix.c:2899: error: invalid conversion from ‘const WnChar’ to ‘const char’
../../vendor/wn_matrix/0.18/src/WnMatrix.c:2899: error: initializing argument 3 of ‘int xmlStrPrintf(xmlChar, int, const char, ...)’
make: *** [../../obj/WnMatrix.o] Error 1
Did you try
export WN_XML_CHAR=xmlChar
make clean
make run_entropy
Let me know. Best wishes.