UNIX for Dummies Questions & Answers

csm@csm-HP-Z420:~$ cd Desktop/
csm@csm-HP-Z420:~/Desktop$ 
csm@csm-HP-Z420:~/Desktop$ cd microtar-0.9.6/
csm@csm-HP-Z420:~/Desktop/microtar-0.9.6$ ./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking whether make sets $(MAKE)... (cached) yes
checking for a BSD-compatible install... /usr/bin/install -c
checking for log in -lm... yes
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
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 for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for strchr... yes
checking for C compiler vendor... gnu
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking whether C compiler accepts -malign-double... yes
checking whether C compiler accepts -fstrict-aliasing... yes
checking whether C compiler accepts -ffast-math... yes
checking for gcc architecture flag... 
checking for x86 cpuid 0 output... d:756e6547:6c65746e:49656e69
checking for x86 cpuid 1 output... 306e4:b200800:7fbee3ff:bfebfbff
checking whether C compiler accepts -march=pentiumpro... no
checking whether C compiler accepts -mcpu=pentiumpro... no
checking whether C compiler accepts -mpentiumpro... no
checking for gcc architecture flag... unknown
checking whether C compiler accepts -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -ffast-math... yes
checking for OpenMP flag of C compiler... -fopenmp
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure: configuring in ViennaRNA-1.7.2
configure: running /bin/bash './configure' --prefix=/usr/local  --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking if malloc debugging is wanted... no
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking whether gcc accepts -fpic... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking for ranlib... ranlib
checking whether gcc and cc understand -c and -o together... yes
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
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 malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking for inline... inline
checking for strdup... yes
checking for strstr... yes
checking for strchr... yes
checking for erand48... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating ViennaRNA.spec
config.status: creating lib/Makefile
config.status: creating H/Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure:
Configure successful with the following options:

  Perl Extension:      yes
  Analyse{Dists,Seqs}: no
  Kinfold:             yes
  RNAforester:         yes

configure:
Finished configuring ViennaRNA and MicroTar.

csm@csm-HP-Z420:~/Desktop/microtar-0.9.6$ make
make  all-recursive
make[1]: Entering directory `/home/csm/Desktop/microtar-0.9.6'
Making all in ViennaRNA-1.7.2
make[2]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2'
make  all-recursive
make[3]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2'
Making all in lib
make[4]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/lib'
source='dist_vars.c' object='libRNA_a-dist_vars.o' libtool=no \
	depfile='.deps/libRNA_a-dist_vars.Po' tmpdepfile='.deps/libRNA_a-dist_vars.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-dist_vars.o `test -f 'dist_vars.c' || echo './'`dist_vars.c
source='fold_vars.c' object='libRNA_a-fold_vars.o' libtool=no \
	depfile='.deps/libRNA_a-fold_vars.Po' tmpdepfile='.deps/libRNA_a-fold_vars.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-fold_vars.o `test -f 'fold_vars.c' || echo './'`fold_vars.c
source='part_func.c' object='libRNA_a-part_func.o' libtool=no \
	depfile='.deps/libRNA_a-part_func.Po' tmpdepfile='.deps/libRNA_a-part_func.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-part_func.o `test -f 'part_func.c' || echo './'`part_func.c
source='read_epars.c' object='libRNA_a-read_epars.o' libtool=no \
	depfile='.deps/libRNA_a-read_epars.Po' tmpdepfile='.deps/libRNA_a-read_epars.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-read_epars.o `test -f 'read_epars.c' || echo './'`read_epars.c
source='treedist.c' object='libRNA_a-treedist.o' libtool=no \
	depfile='.deps/libRNA_a-treedist.Po' tmpdepfile='.deps/libRNA_a-treedist.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-treedist.o `test -f 'treedist.c' || echo './'`treedist.c
source='energy_par.c' object='libRNA_a-energy_par.o' libtool=no \
	depfile='.deps/libRNA_a-energy_par.Po' tmpdepfile='.deps/libRNA_a-energy_par.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-energy_par.o `test -f 'energy_par.c' || echo './'`energy_par.c
source='inverse.c' object='libRNA_a-inverse.o' libtool=no \
	depfile='.deps/libRNA_a-inverse.Po' tmpdepfile='.deps/libRNA_a-inverse.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-inverse.o `test -f 'inverse.c' || echo './'`inverse.c
inverse.c: In function ‘pf_cost':
inverse.c:484:16: warning: passing argument 1 of ‘pf_fold' discards ‘const' qualifier from pointer target type
    f = pf_fold(string, structure);
                ^
In file included from inverse.c:20:0:
./../H/part_func.h:6:15: note: expected ‘char *' but argument is of type ‘const char *'
 extern float  pf_fold(char *sequence, char *structure);
               ^
source='ProfileDist.c' object='libRNA_a-ProfileDist.o' libtool=no \
	depfile='.deps/libRNA_a-ProfileDist.Po' tmpdepfile='.deps/libRNA_a-ProfileDist.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-ProfileDist.o `test -f 'ProfileDist.c' || echo './'`ProfileDist.c
source='RNAstruct.c' object='libRNA_a-RNAstruct.o' libtool=no \
	depfile='.deps/libRNA_a-RNAstruct.Po' tmpdepfile='.deps/libRNA_a-RNAstruct.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-RNAstruct.o `test -f 'RNAstruct.c' || echo './'`RNAstruct.c
source='utils.c' object='libRNA_a-utils.o' libtool=no \
	depfile='.deps/libRNA_a-utils.Po' tmpdepfile='.deps/libRNA_a-utils.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-utils.o `test -f 'utils.c' || echo './'`utils.c
source='fold.c' object='libRNA_a-fold.o' libtool=no \
	depfile='.deps/libRNA_a-fold.Po' tmpdepfile='.deps/libRNA_a-fold.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-fold.o `test -f 'fold.c' || echo './'`fold.c
source='naview.c' object='libRNA_a-naview.o' libtool=no \
	depfile='.deps/libRNA_a-naview.Po' tmpdepfile='.deps/libRNA_a-naview.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-naview.o `test -f 'naview.c' || echo './'`naview.c
naview.c: In function ‘dump_loops':
naview.c:334:3: warning: format ‘%d' expects argument of type ‘int', but argument 2 has type ‘long int' [-Wformat=]
   printf("\nRoot loop is #%d\n",(root-loops)+1);
   ^
source='PS_dot.c' object='libRNA_a-PS_dot.o' libtool=no \
	depfile='.deps/libRNA_a-PS_dot.Po' tmpdepfile='.deps/libRNA_a-PS_dot.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-PS_dot.o `test -f 'PS_dot.c' || echo './'`PS_dot.c
source='stringdist.c' object='libRNA_a-stringdist.o' libtool=no \
	depfile='.deps/libRNA_a-stringdist.Po' tmpdepfile='.deps/libRNA_a-stringdist.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-stringdist.o `test -f 'stringdist.c' || echo './'`stringdist.c
stringdist.c:24:0: warning: "INFINITY" redefined
 #define INFINITY       10000
 ^
In file included from /usr/include/math.h:38:0,
                 from stringdist.c:12:
/usr/include/x86_64-linux-gnu/bits/inf.h:26:0: note: this is the location of the previous definition
 # define INFINITY (__builtin_inff())
 ^
source='params.c' object='libRNA_a-params.o' libtool=no \
	depfile='.deps/libRNA_a-params.Po' tmpdepfile='.deps/libRNA_a-params.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-params.o `test -f 'params.c' || echo './'`params.c
source='subopt.c' object='libRNA_a-subopt.o' libtool=no \
	depfile='.deps/libRNA_a-subopt.Po' tmpdepfile='.deps/libRNA_a-subopt.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-subopt.o `test -f 'subopt.c' || echo './'`subopt.c
source='list.c' object='libRNA_a-list.o' libtool=no \
	depfile='.deps/libRNA_a-list.Po' tmpdepfile='.deps/libRNA_a-list.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-list.o `test -f 'list.c' || echo './'`list.c
source='Lfold.c' object='libRNA_a-Lfold.o' libtool=no \
	depfile='.deps/libRNA_a-Lfold.Po' tmpdepfile='.deps/libRNA_a-Lfold.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-Lfold.o `test -f 'Lfold.c' || echo './'`Lfold.c
source='cofold.c' object='libRNA_a-cofold.o' libtool=no \
	depfile='.deps/libRNA_a-cofold.Po' tmpdepfile='.deps/libRNA_a-cofold.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-cofold.o `test -f 'cofold.c' || echo './'`cofold.c
source='part_func_co.c' object='libRNA_a-part_func_co.o' libtool=no \
	depfile='.deps/libRNA_a-part_func_co.Po' tmpdepfile='.deps/libRNA_a-part_func_co.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-part_func_co.o `test -f 'part_func_co.c' || echo './'`part_func_co.c
source='ProfileAln.c' object='libRNA_a-ProfileAln.o' libtool=no \
	depfile='.deps/libRNA_a-ProfileAln.Po' tmpdepfile='.deps/libRNA_a-ProfileAln.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-ProfileAln.o `test -f 'ProfileAln.c' || echo './'`ProfileAln.c
source='duplex.c' object='libRNA_a-duplex.o' libtool=no \
	depfile='.deps/libRNA_a-duplex.Po' tmpdepfile='.deps/libRNA_a-duplex.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-duplex.o `test -f 'duplex.c' || echo './'`duplex.c
duplex.c: In function ‘aliduplexfold':
duplex.c:385:38: warning: passing argument 3 of ‘alibacktrack' from incompatible pointer type
   struc = alibacktrack(i_min, j_min, S1, S2);
                                      ^
duplex.c:37:16: note: expected ‘const short int **' but argument is of type ‘short int **'
 PRIVATE char * alibacktrack(int i, int j, const short *S1[], const short *S2[]);
                ^
duplex.c:385:42: warning: passing argument 4 of ‘alibacktrack' from incompatible pointer type
   struc = alibacktrack(i_min, j_min, S1, S2);
                                          ^
duplex.c:37:16: note: expected ‘const short int **' but argument is of type ‘short int **'
 PRIVATE char * alibacktrack(int i, int j, const short *S1[], const short *S2[]);
                ^
duplex.c: In function ‘aliduplex_subopt':
duplex.c:462:32: warning: passing argument 3 of ‘alibacktrack' from incompatible pointer type
       struc = alibacktrack(i,j,S1,S2);
                                ^
duplex.c:37:16: note: expected ‘const short int **' but argument is of type ‘short int **'
 PRIVATE char * alibacktrack(int i, int j, const short *S1[], const short *S2[]);
                ^
duplex.c:462:35: warning: passing argument 4 of ‘alibacktrack' from incompatible pointer type
       struc = alibacktrack(i,j,S1,S2);
                                   ^
duplex.c:37:16: note: expected ‘const short int **' but argument is of type ‘short int **'
 PRIVATE char * alibacktrack(int i, int j, const short *S1[], const short *S2[]);
                ^
source='alifold.c' object='libRNA_a-alifold.o' libtool=no \
	depfile='.deps/libRNA_a-alifold.Po' tmpdepfile='.deps/libRNA_a-alifold.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-alifold.o `test -f 'alifold.c' || echo './'`alifold.c
source='alipfold.c' object='libRNA_a-alipfold.o' libtool=no \
	depfile='.deps/libRNA_a-alipfold.Po' tmpdepfile='.deps/libRNA_a-alipfold.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-alipfold.o `test -f 'alipfold.c' || echo './'`alipfold.c
alipfold.c: In function ‘alipf_fold':
alipfold.c:107:40: warning: passing argument 2 of ‘make_pscores' from incompatible pointer type
   make_pscores((const short *const*)S, sequences, n_seq, structure);
                                        ^
alipfold.c:42:14: note: expected ‘const char * const*' but argument is of type ‘char **'
 PRIVATE void make_pscores(const short *const *S, const char *const* AS,
              ^
alipfold.c: In function ‘alipf_circ_fold':
alipfold.c:150:40: warning: passing argument 2 of ‘make_pscores' from incompatible pointer type
   make_pscores((const short *const*)S, sequences, n_seq, structure);
                                        ^
alipfold.c:42:14: note: expected ‘const char * const*' but argument is of type ‘char **'
 PRIVATE void make_pscores(const short *const *S, const char *const* AS,
              ^
source='aln_util.c' object='libRNA_a-aln_util.o' libtool=no \
	depfile='.deps/libRNA_a-aln_util.Po' tmpdepfile='.deps/libRNA_a-aln_util.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-aln_util.o `test -f 'aln_util.c' || echo './'`aln_util.c
source='LPfold.c' object='libRNA_a-LPfold.o' libtool=no \
	depfile='.deps/libRNA_a-LPfold.Po' tmpdepfile='.deps/libRNA_a-LPfold.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-LPfold.o `test -f 'LPfold.c' || echo './'`LPfold.c
source='part_func_up.c' object='libRNA_a-part_func_up.o' libtool=no \
	depfile='.deps/libRNA_a-part_func_up.Po' tmpdepfile='.deps/libRNA_a-part_func_up.TPo' \
	depmode=gcc3 /bin/bash ../depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./../H    -fpic -g -O2 -c -o libRNA_a-part_func_up.o `test -f 'part_func_up.c' || echo './'`part_func_up.c
rm -f libRNA.a
ar cru libRNA.a libRNA_a-dist_vars.o libRNA_a-fold_vars.o libRNA_a-part_func.o libRNA_a-read_epars.o libRNA_a-treedist.o libRNA_a-energy_par.o libRNA_a-inverse.o libRNA_a-ProfileDist.o libRNA_a-RNAstruct.o libRNA_a-utils.o libRNA_a-fold.o libRNA_a-naview.o libRNA_a-PS_dot.o libRNA_a-stringdist.o libRNA_a-params.o libRNA_a-subopt.o libRNA_a-list.o libRNA_a-Lfold.o libRNA_a-cofold.o libRNA_a-part_func_co.o libRNA_a-ProfileAln.o libRNA_a-duplex.o libRNA_a-alifold.o libRNA_a-alipfold.o libRNA_a-aln_util.o libRNA_a-LPfold.o libRNA_a-part_func_up.o 
ranlib libRNA.a
make[4]: Leaving directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/lib'
Making all in H
make[4]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/H'
make[4]: Nothing to be done for `all'.
make[4]: Leaving directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/H'
make[4]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2'
make[4]: Leaving directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2'
make[3]: Leaving directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2'
make[2]: Leaving directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2'
make[2]: Entering directory `/home/csm/Desktop/microtar-0.9.6'
source='microtar.c' object='microtar.o' libtool=no \
	depfile='.deps/microtar.Po' tmpdepfile='.deps/microtar.TPo' \
	depmode=gcc3 /bin/bash ./depcomp \
	gcc -DHAVE_CONFIG_H -I. -I. -I.  -I./ViennaRNA-1.7.2/H   -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -ffast-math -c `test -f 'microtar.c' || echo './'`microtar.c
gcc  -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -ffast-math   -o microtar  microtar.o ViennaRNA-1.7.2/lib/libRNA.a -lm 
make[2]: Leaving directory `/home/csm/Desktop/microtar-0.9.6'
make[1]: Leaving directory `/home/csm/Desktop/microtar-0.9.6'
csm@csm-HP-Z420:~/Desktop/microtar-0.9.6$ make install
Making install in ViennaRNA-1.7.2
make[1]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2'
Making install in lib
make[2]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/lib'
make[3]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/lib'
/bin/bash ../mkinstalldirs /usr/local/lib
 /usr/bin/install -c -m 644 libRNA.a /usr/local/lib/libRNA.a
/usr/bin/install: cannot remove ‘/usr/local/lib/libRNA.a': Permission denied
make[3]: *** [install-libLIBRARIES] Error 1
make[3]: Leaving directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/lib'
make[2]: *** [install-am] Error 2
make[2]: Leaving directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/lib'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2'
make: *** [install-recursive] Error 1
csm@csm-HP-Z420:~/Desktop/microtar-0.9.6$ sudo make install
[sudo] password for csm: 
Making install in ViennaRNA-1.7.2
make[1]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2'
Making install in lib
make[2]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/lib'
make[3]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/lib'
/bin/bash ../mkinstalldirs /usr/local/lib
 /usr/bin/install -c -m 644 libRNA.a /usr/local/lib/libRNA.a
 ranlib /usr/local/lib/libRNA.a
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/lib'
make[2]: Leaving directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/lib'
Making install in H
make[2]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/H'
make[3]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/H'
make[3]: Nothing to be done for `install-exec-am'.
/bin/bash ../mkinstalldirs /usr/local/include/ViennaRNA
 /usr/bin/install -c -m 644 energy_par.h /usr/local/include/ViennaRNA/energy_par.h
 /usr/bin/install -c -m 644 pair_mat.h /usr/local/include/ViennaRNA/pair_mat.h
 /usr/bin/install -c -m 644 RNAstruct.h /usr/local/include/ViennaRNA/RNAstruct.h
 /usr/bin/install -c -m 644 dist_vars.h /usr/local/include/ViennaRNA/dist_vars.h
 /usr/bin/install -c -m 644 fold.h /usr/local/include/ViennaRNA/fold.h
 /usr/bin/install -c -m 644 part_func.h /usr/local/include/ViennaRNA/part_func.h
 /usr/bin/install -c -m 644 stringdist.h /usr/local/include/ViennaRNA/stringdist.h
 /usr/bin/install -c -m 644 edit_cost.h /usr/local/include/ViennaRNA/edit_cost.h
 /usr/bin/install -c -m 644 fold_vars.h /usr/local/include/ViennaRNA/fold_vars.h
 /usr/bin/install -c -m 644 profiledist.h /usr/local/include/ViennaRNA/profiledist.h
 /usr/bin/install -c -m 644 treedist.h /usr/local/include/ViennaRNA/treedist.h
 /usr/bin/install -c -m 644 energy_const.h /usr/local/include/ViennaRNA/energy_const.h
 /usr/bin/install -c -m 644 inverse.h /usr/local/include/ViennaRNA/inverse.h
 /usr/bin/install -c -m 644 PS_dot.h /usr/local/include/ViennaRNA/PS_dot.h
 /usr/bin/install -c -m 644 utils.h /usr/local/include/ViennaRNA/utils.h
 /usr/bin/install -c -m 644 params.h /usr/local/include/ViennaRNA/params.h
 /usr/bin/install -c -m 644 subopt.h /usr/local/include/ViennaRNA/subopt.h
 /usr/bin/install -c -m 644 cofold.h /usr/local/include/ViennaRNA/cofold.h
 /usr/bin/install -c -m 644 duplex.h /usr/local/include/ViennaRNA/duplex.h
 /usr/bin/install -c -m 644 alifold.h /usr/local/include/ViennaRNA/alifold.h
 /usr/bin/install -c -m 644 aln_util.h /usr/local/include/ViennaRNA/aln_util.h
 /usr/bin/install -c -m 644 part_func_co.h /usr/local/include/ViennaRNA/part_func_co.h
 /usr/bin/install -c -m 644 ProfileAln.h /usr/local/include/ViennaRNA/ProfileAln.h
 /usr/bin/install -c -m 644 LPfold.h /usr/local/include/ViennaRNA/LPfold.h
 /usr/bin/install -c -m 644 Lfold.h /usr/local/include/ViennaRNA/Lfold.h
 /usr/bin/install -c -m 644 part_func_up.h /usr/local/include/ViennaRNA/part_func_up.h
make[3]: Leaving directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/H'
make[2]: Leaving directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/H'
make[2]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2'
make[3]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2'
make[3]: Nothing to be done for `install-exec-am'.
/bin/bash ./mkinstalldirs /usr/local/share/ViennaRNA
 /usr/bin/install -c -m 644 vienna13.par /usr/local/share/ViennaRNA/vienna13.par
 /usr/bin/install -c -m 644 default.par /usr/local/share/ViennaRNA/default.par
make[3]: Leaving directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2'
make[2]: Leaving directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2'
make[1]: Leaving directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2'
make[1]: Entering directory `/home/csm/Desktop/microtar-0.9.6'
make[2]: Entering directory `/home/csm/Desktop/microtar-0.9.6'
/bin/bash ./mkinstalldirs /usr/local/bin
  /usr/bin/install -c microtar /usr/local/bin/microtar
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/csm/Desktop/microtar-0.9.6'
make[1]: Leaving directory `/home/csm/Desktop/microtar-0.9.6'
csm@csm-HP-Z420:~/Desktop/microtar-0.9.6$

make[3]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/lib'
/bin/bash ../mkinstalldirs /usr/local/lib
 /usr/bin/install -c -m 644 libRNA.a /usr/local/lib/libRNA.a
/usr/bin/install: cannot remove ‘/usr/local/lib/libRNA.a': Permission denied
make[3]: *** [install-libLIBRARIES] Error 1

csm@csm-HP-Z420:~/Desktop/microtar-0.9.6$ sudo make install
Making install in ViennaRNA-1.7.2
make[1]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2'
Making install in lib
make[2]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/lib'
make[3]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/lib'
/bin/bash ../mkinstalldirs /usr/local/lib
 /usr/bin/install -c -m 644 libRNA.a /usr/local/lib/libRNA.a
 ranlib /usr/local/lib/libRNA.a
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/lib'
make[2]: Leaving directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/lib'
Making install in H
make[2]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/H'
make[3]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/H'
make[3]: Nothing to be done for `install-exec-am'.
/bin/bash ../mkinstalldirs /usr/local/include/ViennaRNA
 /usr/bin/install -c -m 644 energy_par.h /usr/local/include/ViennaRNA/energy_par.h
 /usr/bin/install -c -m 644 pair_mat.h /usr/local/include/ViennaRNA/pair_mat.h
 /usr/bin/install -c -m 644 RNAstruct.h /usr/local/include/ViennaRNA/RNAstruct.h
 /usr/bin/install -c -m 644 dist_vars.h /usr/local/include/ViennaRNA/dist_vars.h
 /usr/bin/install -c -m 644 fold.h /usr/local/include/ViennaRNA/fold.h
 /usr/bin/install -c -m 644 part_func.h /usr/local/include/ViennaRNA/part_func.h
 /usr/bin/install -c -m 644 stringdist.h /usr/local/include/ViennaRNA/stringdist.h
 /usr/bin/install -c -m 644 edit_cost.h /usr/local/include/ViennaRNA/edit_cost.h
 /usr/bin/install -c -m 644 fold_vars.h /usr/local/include/ViennaRNA/fold_vars.h
 /usr/bin/install -c -m 644 profiledist.h /usr/local/include/ViennaRNA/profiledist.h
 /usr/bin/install -c -m 644 treedist.h /usr/local/include/ViennaRNA/treedist.h
 /usr/bin/install -c -m 644 energy_const.h /usr/local/include/ViennaRNA/energy_const.h
 /usr/bin/install -c -m 644 inverse.h /usr/local/include/ViennaRNA/inverse.h
 /usr/bin/install -c -m 644 PS_dot.h /usr/local/include/ViennaRNA/PS_dot.h
 /usr/bin/install -c -m 644 utils.h /usr/local/include/ViennaRNA/utils.h
 /usr/bin/install -c -m 644 params.h /usr/local/include/ViennaRNA/params.h
 /usr/bin/install -c -m 644 subopt.h /usr/local/include/ViennaRNA/subopt.h
 /usr/bin/install -c -m 644 cofold.h /usr/local/include/ViennaRNA/cofold.h
 /usr/bin/install -c -m 644 duplex.h /usr/local/include/ViennaRNA/duplex.h
 /usr/bin/install -c -m 644 alifold.h /usr/local/include/ViennaRNA/alifold.h
 /usr/bin/install -c -m 644 aln_util.h /usr/local/include/ViennaRNA/aln_util.h
 /usr/bin/install -c -m 644 part_func_co.h /usr/local/include/ViennaRNA/part_func_co.h
 /usr/bin/install -c -m 644 ProfileAln.h /usr/local/include/ViennaRNA/ProfileAln.h
 /usr/bin/install -c -m 644 LPfold.h /usr/local/include/ViennaRNA/LPfold.h
 /usr/bin/install -c -m 644 Lfold.h /usr/local/include/ViennaRNA/Lfold.h
 /usr/bin/install -c -m 644 part_func_up.h /usr/local/include/ViennaRNA/part_func_up.h
make[3]: Leaving directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/H'
make[2]: Leaving directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2/H'
make[2]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2'
make[3]: Entering directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2'
make[3]: Nothing to be done for `install-exec-am'.
/bin/bash ./mkinstalldirs /usr/local/share/ViennaRNA
 /usr/bin/install -c -m 644 vienna13.par /usr/local/share/ViennaRNA/vienna13.par
 /usr/bin/install -c -m 644 default.par /usr/local/share/ViennaRNA/default.par
make[3]: Leaving directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2'
make[2]: Leaving directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2'
make[1]: Leaving directory `/home/csm/Desktop/microtar-0.9.6/ViennaRNA-1.7.2'
make[1]: Entering directory `/home/csm/Desktop/microtar-0.9.6'
make[2]: Entering directory `/home/csm/Desktop/microtar-0.9.6'
/bin/bash ./mkinstalldirs /usr/local/bin
  /usr/bin/install -c microtar /usr/local/bin/microtar
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/csm/Desktop/microtar-0.9.6'
make[1]: Leaving directory `/home/csm/Desktop/microtar-0.9.6'
csm@csm-HP-Z420:~/Desktop/microtar-0.9.6$