https://bioinformaticsonline.com/snippets/view/37942/installing-nupack306? https://bioinformaticsonline.com/snippets/view/37942/installing-nupack306 Thu, 18 Oct 2018 04:06:28 -0500 https://bioinformaticsonline.com/snippets/view/37942/installing-nupack306 #http://www.nupack.org/downloads/source ➜ tools git:(master) ✗ cd nupack3.0.6 ➜ nupack3.0.6 git:(master) ✗ make make -C src/ make[1]: Entering directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src' make -C shared/rng make[2]: Entering directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/shared/rng' cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -c -o mt19937ar.o mt19937ar.c mkdir -p ../../../lib ar rcs ../../../lib/libmt19937.a mt19937ar.o make[2]: Leaving directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/shared/rng' make -C shared make[2]: Entering directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/shared' mkdir -p ../../lib touch ../../lib/.exist cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -Iconstants -c -o utils.o utils.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -Iconstants -c -o hash.o hash.c ar rcs ../../lib/libutils.a utils.o hash.o make[2]: Leaving directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/shared' make -C thermo/utils make[2]: Entering directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/thermo/utils' cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o backtrack.o backtrack.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o CalculateEnergy.o CalculateEnergy.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o ene.o ene.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o GetEnergy.o GetEnergy.c GetEnergy.c: In function ‘EnergyPk’: GetEnergy.c:304:7: warning: variable ‘leftSingle’ set but not used [-Wunused-but-set-variable] int leftSingle; ^~~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o init.o init.c init.c: In function ‘LoadEnergies’: init.c:633:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:635:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:661:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:666:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:692:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:698:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:721:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:723:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:755:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:760:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:791:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:795:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:819:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:823:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:847:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:851:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:876:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:880:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:903:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:907:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:932:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:934:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:946:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:948:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:953:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); //read in label ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:975:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:981:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:986:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); //read in label ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1012:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1017:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1022:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); //read in label ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1046:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1051:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1075:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1077:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1103:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1105:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1204:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1206:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1231:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1236:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1265:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1269:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1298:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1300:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1338:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1343:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1383:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1387:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1414:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1418:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1445:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1449:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1476:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1480:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1509:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1513:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1544:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1546:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1561:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1563:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1568:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); //read in label ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1594:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1600:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1605:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); //read in label ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1635:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1640:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1645:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); //read in label ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1673:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1678:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1709:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1711:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1747:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1749:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o mfeUtils.o mfeUtils.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o min.o min.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o nsStar.o nsStar.c nsStar.c: In function ‘nsStarPairsOrParensFull’: nsStar.c:30:12: warning: variable ‘pf’ set but not used [-Wunused-but-set-variable] DBL_TYPE pf; ^~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o pairsPr.o pairsPr.c pairsPr.c: In function ‘prFastILoops’: pairsPr.c:262:12: warning: variable ‘oldValue’ set but not used [-Wunused-but-set-variable] DBL_TYPE oldValue; ^~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o pf.o pf.c pf.c: In function ‘pfuncFullWithSymHelper’: pf.c:108:7: warning: variable ‘pair_flag’ set but not used [-Wunused-but-set-variable] int pair_flag; ^~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o pfuncUtils.o pfuncUtils.c pfuncUtils.c: In function ‘PrintStructure’: pfuncUtils.c:950:7: warning: variable ‘lastL’ set but not used [-Wunused-but-set-variable] int lastL, lastR; ^~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o pknots.o pknots.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o sumexp.o sumexp.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o sumexp_pk.o sumexp_pk.c sumexp_pk.c: In function ‘makeNewQgIx’: sumexp_pk.c:791:6: warning: variable ‘asymmetry’ set but not used [-Wunused-but-set-variable] int asymmetry; ^~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o ReadCommandLineNPK.o ReadCommandLineNPK.c ReadCommandLineNPK.c: In function ‘getUserInput’: ReadCommandLineNPK.c:651:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf( "%s", theseq); ^~~~~~~~~~~~~~~~~~~~ ReadCommandLineNPK.c:656:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf( "%d", &nStrands); ^~~~~~~~~~~~~~~~~~~~~~~ ReadCommandLineNPK.c:664:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf( "%s", line); ^~~~~~~~~~~~~~~~~~ ReadCommandLineNPK.c:674:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, stdin); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadCommandLineNPK.c:676:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, stdin); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadCommandLineNPK.c:716:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf("%s", structure); ^~~~~~~~~~~~~~~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o DNAGlobals.o DNAGlobals.c mkdir -p ../../../lib ar rcs ../../../lib/libpfunc.a backtrack.o CalculateEnergy.o ene.o GetEnergy.o init.o mfeUtils.o min.o nsStar.o pairsPr.o pf.o pfuncUtils.o pknots.o sumexp.o sumexp_pk.o ReadCommandLineNPK.o DNAGlobals.o ../../../src/shared/utils.o make[2]: Leaving directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/thermo/utils' make -C thermo/complexes make[2]: Entering directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/thermo/complexes' cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../utils -I../../../src/shared -I../../../src/shared/constants -c -o complexes.o complexes.c complexes.c: In function ‘main’: complexes.c:110:16: warning: variable ‘tmpPerm’ set but not used [-Wunused-but-set-variable] permutation *tmpPerm; ^~~~~~~ complexes.c:199:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf("%s", filePrefix); ^~~~~~~~~~~~~~~~~~~~~~~ complexes.c:284:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf("%d", &nStrands); ^~~~~~~~~~~~~~~~~~~~~~ complexes.c:293:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf("%s", line); ^~~~~~~~~~~~~~~~~ complexes.c:302:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf("%d", &maxComplexSize); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../utils -I../../../src/shared -I../../../src/shared/constants -c -o complexesUtils.o complexesUtils.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../utils -I../../../src/shared -I../../../src/shared/constants -c -o permBG.o permBG.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../utils -I../../../src/shared -I../../../src/shared/constants -c -o ReadCommandLine.o ReadCommandLine.c ReadCommandLine.c: In function ‘ReadInputFileComplexes’: ReadCommandLine.c:401:7: warning: the address of ‘line’ will always evaluate as ‘true’ [-Waddress] if( !line) { ^ ReadCommandLine.c:405:10: warning: the address of ‘line’ will always evaluate as ‘true’ [-Waddress] while( line && (line[0] == '%' || line[0] == '>') ) { ^~~~ ReadCommandLine.c:408:8: warning: the address of ‘line’ will always evaluate as ‘true’ [-Waddress] if ( !line) { ^ ReadCommandLine.c:346:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, F_inp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadCommandLine.c:348:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, F_inp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadCommandLine.c:366:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, F_inp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadCommandLine.c:368:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, F_inp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadCommandLine.c:387:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, F_inp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadCommandLine.c:389:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, F_inp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadCommandLine.c:400:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, F_inp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadCommandLine.c:406:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, F_inp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p ../../../bin cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../utils -I../../../src/shared -I../../../src/shared/constants complexes.o complexesUtils.o permBG.o \ ReadCommandLine.o -o ../../../bin/complexes -L../../../lib -lpfunc -lutils -lmt19937 -lm make[2]: Leaving directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/thermo/complexes' make -C thermo/distributions make[2]: Entering directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/thermo/distributions' mkdir -p ../../../bin touch ../../../bin/.exist cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -c -o distributions.o distributions.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -c -o ReadCommandLine.o ReadCommandLine.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -c -o InputFileReader.o InputFileReader.c InputFileReader.c: In function ‘getSize’: InputFileReader.c:162:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); ^~~~~~~~~~~~~~~~~~~~~~ InputFileReader.c: In function ‘ReadInputFiles’: InputFileReader.c:339:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); ^~~~~~~~~~~~~~~~~~~~~~ InputFileReader.c: In function ‘ReadInputFilesPerm’: InputFileReader.c:736:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); ^~~~~~~~~~~~~~~~~~~~~~ InputFileReader.c:751:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); ^~~~~~~~~~~~~~~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -c -o OutputWriter.o OutputWriter.c OutputWriter.c: In function ‘WriteOutput’: OutputWriter.c:91:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); ^~~~~~~~~~~~~~~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -c -o CalcDist.o CalcDist.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants distributions.o ReadCommandLine.o InputFileReader.o \ OutputWriter.o CalcDist.o -o ../../../bin/distributions -lm \ ../../../lib/libutils.a make[2]: Leaving directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/thermo/distributions' make -C thermo/concentrations make[2]: Entering directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/thermo/concentrations' cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/shared -c -o concentrations.o concentrations.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/shared -c -o ReadCommandLine.o ReadCommandLine.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/shared -c -o InputFileReader.o InputFileReader.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/shared -c -o OutputWriter.o OutputWriter.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/shared -c -o CalcConc.o CalcConc.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/shared -c -o FracPair.o FracPair.c FracPair.c: In function ‘FracPair’: FracPair.c:88:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); ^~~~~~~~~~~~~~~~~~~~~~ FracPair.c:115:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fpeq); ^~~~~~~~~~~~~~~~~~~~~~~~ FracPair.c:174:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fpeq); ^~~~~~~~~~~~~~~~~~~~~~~~ FracPair.c:231:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); ^~~~~~~~~~~~~~~~~~~~~~ FracPair.c:234:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); // This is the first base-pair and pair prob ^~~~~~~~~~~~~~~~~~~~~~ FracPair.c:242:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); ^~~~~~~~~~~~~~~~~~~~~~ mkdir -p ../../../bin cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/shared concentrations.o ReadCommandLine.o InputFileReader.o \ OutputWriter.o CalcConc.o FracPair.o \ -o ../../../bin/concentrations -L../../../lib -lm ../../../lib/libutils.a ../../../lib/libmt19937.a mkdir -p ../../../lib ar rcs ../../../lib/libpfunc.a CalcConc.o make[2]: Leaving directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/thermo/concentrations' make -C thermo/basics make[2]: Entering directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/thermo/basics' cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng -c -o count.o count.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng count.o -o ../../../bin/count -L../../../lib -lpfunc -lutils -lmt19937 -lm cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng -c -o energy.o energy.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng energy.o -o ../../../bin/energy -L../../../lib -lpfunc -lutils -lmt19937 -lm cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng -c -o mfe.o mfe.c mfe.c: In function ‘main’: mfe.c:40:12: warning: variable ‘mfe’ set but not used [-Wunused-but-set-variable] DBL_TYPE mfe; ^~~ mfe.c:66:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf("%s", inputFile); ^~~~~~~~~~~~~~~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng mfe.o -o ../../../bin/mfe -L../../../lib -lpfunc -lutils -lmt19937 -lm cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng -c -o defect.o defect.c defect.c: In function ‘main’: defect.c:37:12: warning: variable ‘mfe’ set but not used [-Wunused-but-set-variable] DBL_TYPE mfe; // Minimum free energy (not really used) ^~~ defect.c:155:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); // Free energy of MFE ^~~~~~~~~~~~~~~~~~~~~~ defect.c:157:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); // Possibly secondary structure in dot-parens ^~~~~~~~~~~~~~~~~~~~~~ defect.c:159:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); ^~~~~~~~~~~~~~~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng defect.o -o ../../../bin/defect -L../../../lib -lpfunc -lutils -lmt19937 -lm cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng -c -o pfunc.o pfunc.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng pfunc.o -o ../../../bin/pfunc -L../../../lib -lpfunc -lutils -lmt19937 -lm cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng -c -o pairs.o pairs.c pairs.c: In function ‘main’: pairs.c:85:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf("%s", inputFile); ^~~~~~~~~~~~~~~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng pairs.o -o ../../../bin/pairs -L../../../lib -lpfunc -lutils -lmt19937 -lm cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng -c -o prob.o prob.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng prob.o -o ../../../bin/prob -L../../../lib -lpfunc -lutils -lmt19937 -lm cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng -c -o subopt.o subopt.c subopt.c: In function ‘main’: subopt.c:74:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf("%s", inputFile); ^~~~~~~~~~~~~~~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng subopt.o -o ../../../bin/subopt -L../../../lib -lpfunc -lutils -lmt19937 -lm cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng -c -o sample.o sample.c sample.c: In function ‘main’: sample.c:73:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf("%s", inputFile); ^~~~~~~~~~~~~~~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng sample.o -o ../../../bin/sample -L../../../lib -lpfunc -lutils -lmt19937 -lm make[2]: Leaving directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/thermo/basics' make -C design/design_pfunc_utils make[2]: Entering directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/design/design_pfunc_utils' cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../thermo/utils -I../../../src/shared/constants -I../../../src/shared -c -o nsStar_psStar.o nsStar_psStar.c nsStar_psStar.c: In function ‘nsStarFull’: nsStar_psStar.c:39:12: warning: variable ‘pf’ set but not used [-Wunused-but-set-variable] DBL_TYPE pf; ^~ nsStar_psStar.c: In function ‘nsStarPairsOrParensFull’: nsStar_psStar.c:83:12: warning: variable ‘pf’ set but not used [-Wunused-but-set-variable] DBL_TYPE pf; ^~ nsStar_psStar.c: In function ‘psStarFullWithSym’: nsStar_psStar.c:236:7: warning: variable ‘tmpLength’ set but not used [-Wunused-but-set-variable] int tmpLength; ^~~~~~~~~ nsStar_psStar.c: In function ‘psStarPairsOrParensFullWithSym’: nsStar_psStar.c:277:7: warning: variable ‘tmpLength’ set but not used [-Wunused-but-set-variable] int tmpLength; ^~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../thermo/utils -I../../../src/shared/constants -I../../../src/shared -c -o pairPrStruct.o pairPrStruct.c mkdir -p ../../../lib ar rcs ../../../lib/libdesign_pfunc_utils.a nsStar_psStar.o pairPrStruct.o make[2]: Leaving directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/design/design_pfunc_utils' make -C design/single-complex make[2]: Entering directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/design/single-complex' cc -DNUPACK_SAMPLE -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/thermo/utils -I../../../src/design/design_pfunc_utils -I../../../src/shared/rng -c -o design.o design.c design.c: In function ‘main’: design.c:81:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(seedFile, "%u\n", &rand_seed); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -DNUPACK_SAMPLE -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/thermo/utils -I../../../src/design/design_pfunc_utils -I../../../src/shared/rng -c -o design_utils.o design_utils.c design_utils.c: In function ‘loadBadStrings’: design_utils.c:135:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(in, "%s\n", tmp); ^~~~~~~~~~~~~~~~~~~~~~~ design_utils.c: In function ‘loadStringFromInitFile’: design_utils.c:243:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(initFile, "%s", tmpString); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -DNUPACK_SAMPLE -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/thermo/utils -I../../../src/design/design_pfunc_utils -I../../../src/shared/rng -c -o design_engine.o design_engine.c design_engine.c: In function ‘parseStructure’: design_engine.c:1257:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(in, "%s\n", buffer); ^~~~~~~~~~~~~~~~~~~~~~~~~~ design_engine.c:1302:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(in, "%s\n", buffer); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -DNUPACK_SAMPLE -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/thermo/utils -I../../../src/design/design_pfunc_utils -I../../../src/shared/rng -c -o design_test.o design_test.c cc -DNUPACK_SAMPLE -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/thermo/utils -I../../../src/design/design_pfunc_utils -I../../../src/shared/rng -c -o read_command_line.o read_command_line.c read_command_line.c: In function ‘readCommandLine’: read_command_line.c:137:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (options == -1) ^~ read_command_line.c:140:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ switch (options) { ^~~~~~ mkdir -p ../../../bin cc -DNUPACK_SAMPLE -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/thermo/utils -I../../../src/design/design_pfunc_utils -I../../../src/shared/rng design.o design_utils.o design_engine.o design_test.o \ read_command_line.o -o ../../../bin/design -lm \ ../../../lib/libdesign_pfunc_utils.a ../../../lib/libpfunc.a ../../../lib/libmt19937.a ../../../lib/libutils.a -L../../../lib make[2]: Leaving directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/design/single-complex' make[1]: Leaving directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src']]> Jit