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ACRMGroup / bioptools

Tools making use of BiopLib
http://www.bioinf.org.uk/software/bioptools/
GNU General Public License v3.0
17 stars 7 forks source link

installation problem #14

Closed Mar-Gra-creator closed 1 year ago

Mar-Gra-creator commented 3 years ago

hi have this error when im run make (following the installation instructions) :(

(base) marcin@marcin-Lenovo-ideapad-Y700-15ISK:~/bioptools-1.9/src$ makeenter code here
(cd libsrc/bioplib/src; make)
make[1]: enter the catalogue '/home/marcin/bioptools-1.9/src/libsrc/bioplib/src'

[...]

gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o AddNTerHs.o -c AddNTerHs.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o ApMatPDB.o -c ApMatPDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o AppendPDB.o -c AppendPDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o AtomNameMatch.o -c AtomNameMatch.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o CalcCellTrans.o -c CalcCellTrans.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o CalcChiPDB.o -c CalcChiPDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o CalcCterCoords.o -c CalcCterCoords.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o CalcRMSPDB.o -c CalcRMSPDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o CalcTetraHCoords.o -c CalcTetraHCoords.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o CopyPDB.o -c CopyPDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o CopyPDBCoords.o -c CopyPDBCoords.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o DNAtoAA.o -c DNAtoAA.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o DupePDB.o -c DupePDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o ExtractZonePDB.o -c ExtractZonePDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o FNam2PDB.o -c FNam2PDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o FindAtomInRes.o -c FindAtomInRes.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o FindNextChainPDB.o -c FindNextChainPDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o FindNextResidue.o -c FindNextResidue.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o FindResidue.o -c FindResidue.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o FindResidueSpec.o -c FindResidueSpec.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o FindZonePDB.o -c FindZonePDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o FitCaCbPDB.o -c FitCaCbPDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o FitCaPDB.o -c FitCaPDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o FitPDB.o -c FitPDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o FixCterPDB.o -c FixCterPDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o GetCGPDB.o -c GetCGPDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o GetCofGPDBRange.o -c GetCofGPDBRange.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o GetCofGPDBSCRange.o -c GetCofGPDBSCRange.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o GetCrystPDB.o -c GetCrystPDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o GetPDBByN.o -c GetPDBByN.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o GetPDBChainLabels.o -c GetPDBChainLabels.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o GetPDBCoor.o -c GetPDBCoor.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o HAddPDB.o -c HAddPDB.c
HAddPDB.c: In function ‘blOpenPGPFile’:
HAddPDB.c:1388:31: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
 1388 |          sprintf(buffer,"%s/%s",datadir,basename);
      |                               ^
HAddPDB.c:1388:10: note: ‘sprintf’ output 2 or more bytes (assuming 161) into a destination of size 160
 1388 |          sprintf(buffer,"%s/%s",datadir,basename);
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o InPDBZone.o -c InPDBZone.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o InPDBZoneSpec.o -c InPDBZoneSpec.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o IndexPDB.o -c IndexPDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o KillPDB.o -c KillPDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o KillSidechain.o -c KillSidechain.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o KnownSeqLen.o -c KnownSeqLen.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o LegalAtomSpec.o -c LegalAtomSpec.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o MovePDB.o -c MovePDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o NumericAlign.o -c NumericAlign.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o OrderPDB.o -c OrderPDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o OriginPDB.o -c OriginPDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o PDB2Seq.o -c PDB2Seq.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o ParseRes.o -c ParseRes.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o RdSSPDB.o -c RdSSPDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o RdSecPDB.o -c RdSecPDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o RdSeqPDB.o -c RdSeqPDB.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o ReadCSSR.o -c ReadCSSR.c
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/home/marcin/anaconda3/include/libxml2 -I/home/marcin/anaconda3/include -o ReadPDB.o -c ReadPDB.c
In file included from /home/marcin/anaconda3/include/libxml2/libxml/encoding.h:31,
                 from /home/marcin/anaconda3/include/libxml2/libxml/parser.h:810,
                 from ReadPDB.c:324:
/home/marcin/anaconda3/include/unicode/ucnv.h:1:1: error: C++ style comments are not allowed in ISO C90
    1 | // Copyright (C) 2016 and later: Unicode, Inc. and others.
      | ^
/home/marcin/anaconda3/include/unicode/ucnv.h:1:1: note: (this will be reported only once per input file)
In file included from /home/marcin/anaconda3/include/unicode/ucnv.h:52,
                 from /home/marcin/anaconda3/include/libxml2/libxml/encoding.h:31,
                 from /home/marcin/anaconda3/include/libxml2/libxml/parser.h:810,
                 from ReadPDB.c:324:
/home/marcin/anaconda3/include/unicode/ucnv_err.h:1:1: error: C++ style comments are not allowed in ISO C90
    1 | // Copyright (C) 2016 and later: Unicode, Inc. and others.
      | ^
/home/marcin/anaconda3/include/unicode/ucnv_err.h:1:1: note: (this will be reported only once per input file)
In file included from /home/marcin/anaconda3/include/unicode/ucnv_err.h:88,
                 from /home/marcin/anaconda3/include/unicode/ucnv.h:52,
                 from /home/marcin/anaconda3/include/libxml2/libxml/encoding.h:31,
                 from /home/marcin/anaconda3/include/libxml2/libxml/parser.h:810,
                 from ReadPDB.c:324:
/home/marcin/anaconda3/include/unicode/utypes.h:1:1: error: C++ style comments are not allowed in ISO C90
    1 | // Copyright (C) 2016 and later: Unicode, Inc. and others.
      | ^
/home/marcin/anaconda3/include/unicode/utypes.h:1:1: note: (this will be reported only once per input file)
In file included from /home/marcin/anaconda3/include/unicode/utypes.h:38,
                 from /home/marcin/anaconda3/include/unicode/ucnv_err.h:88,
                 from /home/marcin/anaconda3/include/unicode/ucnv.h:52,
                 from /home/marcin/anaconda3/include/libxml2/libxml/encoding.h:31,
                 from /home/marcin/anaconda3/include/libxml2/libxml/parser.h:810,
                 from ReadPDB.c:324:
/home/marcin/anaconda3/include/unicode/umachine.h:1:1: error: C++ style comments are not allowed in ISO C90
    1 | // Copyright (C) 2016 and later: Unicode, Inc. and others.
      | ^
/home/marcin/anaconda3/include/unicode/umachine.h:1:1: note: (this will be reported only once per input file)
In file included from /home/marcin/anaconda3/include/unicode/umachine.h:46,
                 from /home/marcin/anaconda3/include/unicode/utypes.h:38,
                 from /home/marcin/anaconda3/include/unicode/ucnv_err.h:88,
                 from /home/marcin/anaconda3/include/unicode/ucnv.h:52,
                 from /home/marcin/anaconda3/include/libxml2/libxml/encoding.h:31,
                 from /home/marcin/anaconda3/include/libxml2/libxml/parser.h:810,
                 from ReadPDB.c:324:
/home/marcin/anaconda3/include/unicode/ptypes.h:1:1: error: C++ style comments are not allowed in ISO C90
    1 | // Copyright (C) 2016 and later: Unicode, Inc. and others.
      | ^
/home/marcin/anaconda3/include/unicode/ptypes.h:1:1: note: (this will be reported only once per input file)
In file included from /home/marcin/anaconda3/include/unicode/ptypes.h:52,
                 from /home/marcin/anaconda3/include/unicode/umachine.h:46,
                 from /home/marcin/anaconda3/include/unicode/utypes.h:38,
                 from /home/marcin/anaconda3/include/unicode/ucnv_err.h:88,
                 from /home/marcin/anaconda3/include/unicode/ucnv.h:52,
                 from /home/marcin/anaconda3/include/libxml2/libxml/encoding.h:31,
                 from /home/marcin/anaconda3/include/libxml2/libxml/parser.h:810,
                 from ReadPDB.c:324:
/home/marcin/anaconda3/include/unicode/platform.h:1:1: error: C++ style comments are not allowed in ISO C90
    1 | // Copyright (C) 2016 and later: Unicode, Inc. and others.
      | ^
/home/marcin/anaconda3/include/unicode/platform.h:1:1: note: (this will be reported only once per input file)
In file included from /home/marcin/anaconda3/include/unicode/platform.h:24,
                 from /home/marcin/anaconda3/include/unicode/ptypes.h:52,
                 from /home/marcin/anaconda3/include/unicode/umachine.h:46,
                 from /home/marcin/anaconda3/include/unicode/utypes.h:38,
                 from /home/marcin/anaconda3/include/unicode/ucnv_err.h:88,
                 from /home/marcin/anaconda3/include/unicode/ucnv.h:52,
                 from /home/marcin/anaconda3/include/libxml2/libxml/encoding.h:31,
                 from /home/marcin/anaconda3/include/libxml2/libxml/parser.h:810,
                 from ReadPDB.c:324:
/home/marcin/anaconda3/include/unicode/uconfig.h:1:1: error: C++ style comments are not allowed in ISO C90
    1 | // Copyright (C) 2016 and later: Unicode, Inc. and others.
      | ^
/home/marcin/anaconda3/include/unicode/uconfig.h:1:1: note: (this will be reported only once per input file)
In file included from /home/marcin/anaconda3/include/unicode/platform.h:25,
                 from /home/marcin/anaconda3/include/unicode/ptypes.h:52,
                 from /home/marcin/anaconda3/include/unicode/umachine.h:46,
                 from /home/marcin/anaconda3/include/unicode/utypes.h:38,
                 from /home/marcin/anaconda3/include/unicode/ucnv_err.h:88,
                 from /home/marcin/anaconda3/include/unicode/ucnv.h:52,
                 from /home/marcin/anaconda3/include/libxml2/libxml/encoding.h:31,
                 from /home/marcin/anaconda3/include/libxml2/libxml/parser.h:810,
                 from ReadPDB.c:324:
/home/marcin/anaconda3/include/unicode/uvernum.h:1:1: error: C++ style comments are not allowed in ISO C90
    1 | // Copyright (C) 2016 and later: Unicode, Inc. and others.
      | ^
/home/marcin/anaconda3/include/unicode/uvernum.h:1:1: note: (this will be reported only once per input file)
In file included from /home/marcin/anaconda3/include/unicode/umachine.h:379,
                 from /home/marcin/anaconda3/include/unicode/utypes.h:38,
                 from /home/marcin/anaconda3/include/unicode/ucnv_err.h:88,
                 from /home/marcin/anaconda3/include/unicode/ucnv.h:52,
                 from /home/marcin/anaconda3/include/libxml2/libxml/encoding.h:31,
                 from /home/marcin/anaconda3/include/libxml2/libxml/parser.h:810,
                 from ReadPDB.c:324:
/home/marcin/anaconda3/include/unicode/urename.h:1:1: error: C++ style comments are not allowed in ISO C90
    1 | // Copyright (C) 2016 and later: Unicode, Inc. and others.
      | ^
/home/marcin/anaconda3/include/unicode/urename.h:1:1: note: (this will be reported only once per input file)
In file included from /home/marcin/anaconda3/include/unicode/utypes.h:39,
                 from /home/marcin/anaconda3/include/unicode/ucnv_err.h:88,
                 from /home/marcin/anaconda3/include/unicode/ucnv.h:52,
                 from /home/marcin/anaconda3/include/libxml2/libxml/encoding.h:31,
                 from /home/marcin/anaconda3/include/libxml2/libxml/parser.h:810,
                 from ReadPDB.c:324:
/home/marcin/anaconda3/include/unicode/uversion.h:1:1: error: C++ style comments are not allowed in ISO C90
    1 | // Copyright (C) 2016 and later: Unicode, Inc. and others.
      | ^
/home/marcin/anaconda3/include/unicode/uversion.h:1:1: note: (this will be reported only once per input file)
In file included from /home/marcin/anaconda3/include/unicode/utypes.h:44,
                 from /home/marcin/anaconda3/include/unicode/ucnv_err.h:88,
                 from /home/marcin/anaconda3/include/unicode/ucnv.h:52,
                 from /home/marcin/anaconda3/include/libxml2/libxml/encoding.h:31,
                 from /home/marcin/anaconda3/include/libxml2/libxml/parser.h:810,
                 from ReadPDB.c:324:
/home/marcin/anaconda3/include/unicode/utf.h:1:1: error: C++ style comments are not allowed in ISO C90
    1 | // Copyright (C) 2016 and later: Unicode, Inc. and others.
      | ^
/home/marcin/anaconda3/include/unicode/utf.h:1:1: note: (this will be reported only once per input file)
In file included from /home/marcin/anaconda3/include/unicode/utf.h:217,
                 from /home/marcin/anaconda3/include/unicode/utypes.h:44,
                 from /home/marcin/anaconda3/include/unicode/ucnv_err.h:88,
                 from /home/marcin/anaconda3/include/unicode/ucnv.h:52,
                 from /home/marcin/anaconda3/include/libxml2/libxml/encoding.h:31,
                 from /home/marcin/anaconda3/include/libxml2/libxml/parser.h:810,
                 from ReadPDB.c:324:
/home/marcin/anaconda3/include/unicode/utf8.h:1:1: error: C++ style comments are not allowed in ISO C90
    1 | // Copyright (C) 2016 and later: Unicode, Inc. and others.
      | ^
/home/marcin/anaconda3/include/unicode/utf8.h:1:1: note: (this will be reported only once per input file)
In file included from /home/marcin/anaconda3/include/unicode/utf.h:218,
                 from /home/marcin/anaconda3/include/unicode/utypes.h:44,
                 from /home/marcin/anaconda3/include/unicode/ucnv_err.h:88,
                 from /home/marcin/anaconda3/include/unicode/ucnv.h:52,
                 from /home/marcin/anaconda3/include/libxml2/libxml/encoding.h:31,
                 from /home/marcin/anaconda3/include/libxml2/libxml/parser.h:810,
                 from ReadPDB.c:324:
/home/marcin/anaconda3/include/unicode/utf16.h:1:1: error: C++ style comments are not allowed in ISO C90
    1 | // Copyright (C) 2016 and later: Unicode, Inc. and others.
      | ^
/home/marcin/anaconda3/include/unicode/utf16.h:1:1: note: (this will be reported only once per input file)
In file included from /home/marcin/anaconda3/include/unicode/utf.h:221,
                 from /home/marcin/anaconda3/include/unicode/utypes.h:44,
                 from /home/marcin/anaconda3/include/unicode/ucnv_err.h:88,
                 from /home/marcin/anaconda3/include/unicode/ucnv.h:52,
                 from /home/marcin/anaconda3/include/libxml2/libxml/encoding.h:31,
                 from /home/marcin/anaconda3/include/libxml2/libxml/parser.h:810,
                 from ReadPDB.c:324:
/home/marcin/anaconda3/include/unicode/utf_old.h:1:1: error: C++ style comments are not allowed in ISO C90
    1 | // Copyright (C) 2016 and later: Unicode, Inc. and others.
      | ^
/home/marcin/anaconda3/include/unicode/utf_old.h:1:1: note: (this will be reported only once per input file)
In file included from /home/marcin/anaconda3/include/unicode/utf_old.h:150,
                 from /home/marcin/anaconda3/include/unicode/utf.h:221,
                 from /home/marcin/anaconda3/include/unicode/utypes.h:44,
                 from /home/marcin/anaconda3/include/unicode/ucnv_err.h:88,
                 from /home/marcin/anaconda3/include/unicode/ucnv.h:52,
                 from /home/marcin/anaconda3/include/libxml2/libxml/encoding.h:31,
                 from /home/marcin/anaconda3/include/libxml2/libxml/parser.h:810,
                 from ReadPDB.c:324:
/home/marcin/anaconda3/include/unicode/utf.h:1:1: error: C++ style comments are not allowed in ISO C90
    1 | // Copyright (C) 2016 and later: Unicode, Inc. and others.
      | ^
/home/marcin/anaconda3/include/unicode/utf.h:1:1: note: (this will be reported only once per input file)
In file included from /home/marcin/anaconda3/include/unicode/ucnv_err.h:88,
                 from /home/marcin/anaconda3/include/unicode/ucnv.h:52,
                 from /home/marcin/anaconda3/include/libxml2/libxml/encoding.h:31,
                 from /home/marcin/anaconda3/include/libxml2/libxml/parser.h:810,
                 from ReadPDB.c:324:
/home/marcin/anaconda3/include/unicode/utypes.h:428:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
  428 | #endif  // U_HIDE_DEPRECATED_API
      |         ^
/home/marcin/anaconda3/include/unicode/utypes.h:470:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
  470 | #endif  // U_HIDE_DEPRECATED_API
      |         ^
/home/marcin/anaconda3/include/unicode/utypes.h:517:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
  517 | #endif  // U_HIDE_DEPRECATED_API
      |         ^
/home/marcin/anaconda3/include/unicode/utypes.h:548:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
  548 | #endif  // U_HIDE_DEPRECATED_API
      |         ^
/home/marcin/anaconda3/include/unicode/utypes.h:574:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
  574 | #endif  // U_HIDE_DEPRECATED_API
      |         ^
/home/marcin/anaconda3/include/unicode/utypes.h:610:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
  610 | #endif  // U_HIDE_DEPRECATED_API
      |         ^
/home/marcin/anaconda3/include/unicode/utypes.h:631:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
  631 | #endif  // U_HIDE_DEPRECATED_API
      |         ^
/home/marcin/anaconda3/include/unicode/utypes.h:651:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
  651 | #endif  // U_HIDE_DEPRECATED_API
      |         ^
/home/marcin/anaconda3/include/unicode/utypes.h:659:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
  659 | #endif  // U_HIDE_DEPRECATED_API
      |         ^
In file included from /home/marcin/anaconda3/include/unicode/ucnv.h:53,
                 from /home/marcin/anaconda3/include/libxml2/libxml/encoding.h:31,
                 from /home/marcin/anaconda3/include/libxml2/libxml/parser.h:810,
                 from ReadPDB.c:324:
/home/marcin/anaconda3/include/unicode/uenum.h:1:1: error: C++ style comments are not allowed in ISO C90
    1 | // Copyright (C) 2016 and later: Unicode, Inc. and others.
      | ^
/home/marcin/anaconda3/include/unicode/uenum.h:1:1: note: (this will be reported only once per input file)
In file included from /home/marcin/anaconda3/include/unicode/uenum.h:23,
                 from /home/marcin/anaconda3/include/unicode/ucnv.h:53,
                 from /home/marcin/anaconda3/include/libxml2/libxml/encoding.h:31,
                 from /home/marcin/anaconda3/include/libxml2/libxml/parser.h:810,
                 from ReadPDB.c:324:
/home/marcin/anaconda3/include/unicode/localpointer.h:1:1: error: C++ style comments are not allowed in ISO C90
    1 | // Copyright (C) 2016 and later: Unicode, Inc. and others.
      | ^
/home/marcin/anaconda3/include/unicode/localpointer.h:1:1: note: (this will be reported only once per input file)
In file included from /home/marcin/anaconda3/include/libxml2/libxml/encoding.h:31,
                 from /home/marcin/anaconda3/include/libxml2/libxml/parser.h:810,
                 from ReadPDB.c:324:
/home/marcin/anaconda3/include/unicode/ucnv.h:952:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
  952 | #endif  // U_HIDE_DEPRECATED_API
      |         ^
make[1]: *** [Makefile:125: ReadPDB.o] error 1
make[1]: exiting from catalogue '/home/marcin/bioptools-1.9/src/libsrc/bioplib/src'
make: *** [Makefile:16: bioplib] error 2
Mar-Gra-creator commented 3 years ago

solved - deactivate conda base environment 😑

AndrewCRMartin commented 3 years ago

I was about to reply saying that the problem is that you have your Anaconda installation include files in your path before the standard header files.

There are also some warnings there picked up by newer compilers and we will endeavour to fix all of those.

Andrew

On Thu, 2 Sept 2021 at 08:37, Mar-Gra-creator @.***> wrote:

solved - deactivate conda base environment 😑

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