Leaving directory Error

Shell Programming and Scripting
1

Hi, i have a question, when I install any software it give error message like as follow :

 sudo make
[sudo] password for csm: 
make  all-recursive
make[1]: Entering directory `/home/csm/Desktop/miRanda-3.3a'
Making all in man
make[2]: Entering directory `/home/csm/Desktop/miRanda-3.3a/man'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/man'
Making all in RNAlib
make[2]: Entering directory `/home/csm/Desktop/miRanda-3.3a/RNAlib'
Making all in H
make[3]: Entering directory `/home/csm/Desktop/miRanda-3.3a/RNAlib/H'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/RNAlib/H'
make[3]: Entering directory `/home/csm/Desktop/miRanda-3.3a/RNAlib'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/RNAlib'
make[2]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/RNAlib'
Making all in src
make[2]: Entering directory `/home/csm/Desktop/miRanda-3.3a/src'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/src'
make[2]: Entering directory `/home/csm/Desktop/miRanda-3.3a'
make[2]: Leaving directory `/home/csm/Desktop/miRanda-3.3a'
make[1]: Leaving directory `/home/csm/Desktop/miRanda-3.3a'
csm@csm-HP-Z420:~/Desktop/miRanda-3.3a$ make install
Making install in man
make[1]: Entering directory `/home/csm/Desktop/miRanda-3.3a/man'
make[2]: Entering directory `/home/csm/Desktop/miRanda-3.3a/man'
make[2]: Nothing to be done for `install-exec-am'.
test -z "/usr/local/share/man/man1" || mkdir -p -- "/usr/local/share/man/man1"
 /usr/bin/install -c -m 644 './miranda.1' '/usr/local/share/man/man1/miranda.1'
/usr/bin/install: cannot remove �/usr/local/share/man/man1/miranda.1': Permission denied
make[2]: *** [install-man1] Error 1
make[2]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/man'
make[1]: *** [install-am] Error 2
make[1]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/man'
make: *** [install-recursive] Error 1
csm@csm-HP-Z420:~/Desktop/miRanda-3.3a$

how can i solve this problem?

2

I think, you should execute sudo make install , not just make install .

3

I have tried this also.... problem remains same...

4

OK, please post the output of

ls -ld /usr/local/share/man/man1
ls -l /usr/local/share/man/man1/miranda.1
5 
csm@csm-HP-Z420:~/Desktop/miRanda-3.3a$ ls -ld /usr/local/share/man/man1
drwxr-xr-x 2 root root 4096 Oct  1 12:14 /usr/local/share/man/man1
csm@csm-HP-Z420:~/Desktop/miRanda-3.3a$ ls -l /usr/local/share/man/man1/miranda.1
-rw-r--r-- 1 root root 6268 Oct  1 12:14 /usr/local/share/man/man1/miranda.1
6

Usualy it is:

./configure --prefix=/usr
make
sudo make install

Just so all 3 commands are there for completness.

Likewise for deinstall, just change the last command to:

sudo make uninstall

Hope this helps

7

Hmm, looks good. Is this on a NFS mounted filesystem?

8 
csm@csm-HP-Z420:~/Desktop/miRanda-3.3a$ ./configure --prefix=/usr
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 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 ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for a BSD-compatible install... /usr/bin/install -c
checking for ranlib... ranlib
checking for main in -lm... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/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 float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for size_t... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for working strtod... yes
checking for memset... yes
checking for sqrt... yes
checking for strchr... yes
checking for strdup... yes
checking for strrchr... yes
checking for strstr... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating RNAlib/H/Makefile
config.status: creating RNAlib/Makefile
config.status: creating man/Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
csm@csm-HP-Z420:~/Desktop/miRanda-3.3a$ make
make  all-recursive
make[1]: Entering directory `/home/csm/Desktop/miRanda-3.3a'
Making all in man
make[2]: Entering directory `/home/csm/Desktop/miRanda-3.3a/man'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/man'
Making all in RNAlib
make[2]: Entering directory `/home/csm/Desktop/miRanda-3.3a/RNAlib'
Making all in H
make[3]: Entering directory `/home/csm/Desktop/miRanda-3.3a/RNAlib/H'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/RNAlib/H'
make[3]: Entering directory `/home/csm/Desktop/miRanda-3.3a/RNAlib'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/RNAlib'
make[2]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/RNAlib'
Making all in src
make[2]: Entering directory `/home/csm/Desktop/miRanda-3.3a/src'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/src'
make[2]: Entering directory `/home/csm/Desktop/miRanda-3.3a'
make[2]: Leaving directory `/home/csm/Desktop/miRanda-3.3a'
make[1]: Leaving directory `/home/csm/Desktop/miRanda-3.3a'
csm@csm-HP-Z420:~/Desktop/miRanda-3.3a$ sudo make install
Making install in man
make[1]: Entering directory `/home/csm/Desktop/miRanda-3.3a/man'
make[2]: Entering directory `/home/csm/Desktop/miRanda-3.3a/man'
make[2]: Nothing to be done for `install-exec-am'.
test -z "/usr/share/man/man1" || mkdir -p -- "/usr/share/man/man1"
 /usr/bin/install -c -m 644 './miranda.1' '/usr/share/man/man1/miranda.1'
make[2]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/man'
make[1]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/man'
Making install in RNAlib
make[1]: Entering directory `/home/csm/Desktop/miRanda-3.3a/RNAlib'
Making install in H
make[2]: Entering directory `/home/csm/Desktop/miRanda-3.3a/RNAlib/H'
make[3]: Entering directory `/home/csm/Desktop/miRanda-3.3a/RNAlib/H'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/RNAlib/H'
make[2]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/RNAlib/H'
make[2]: Entering directory `/home/csm/Desktop/miRanda-3.3a/RNAlib'
make[3]: Entering directory `/home/csm/Desktop/miRanda-3.3a/RNAlib'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/RNAlib'
make[2]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/RNAlib'
make[1]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/RNAlib'
Making install in src
make[1]: Entering directory `/home/csm/Desktop/miRanda-3.3a/src'
make[2]: Entering directory `/home/csm/Desktop/miRanda-3.3a/src'
test -z "/usr/bin" || mkdir -p -- "/usr/bin"
  /usr/bin/install -c 'miranda' '/usr/bin/miranda'
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/src'
make[1]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/src'
make[1]: Entering directory `/home/csm/Desktop/miRanda-3.3a'
make[2]: Entering directory `/home/csm/Desktop/miRanda-3.3a'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/csm/Desktop/miRanda-3.3a'
make[1]: Leaving directory `/home/csm/Desktop/miRanda-3.3a'
csm@csm-HP-Z420:~/Desktop/miRanda-3.3a$

problem is same :frowning:

9

Looks good to my eyes.

What is the output of:

ls /usr/share/mi[rR]*
11

how can i check it sir? i am using ubuntu 14.0

12

Justvtype that onstead of 'make'.

13 
csm@csm-HP-Z420:~/Desktop/miRanda-3.3a$ ls /usr/share/mi[rR]*
ls: cannot access /usr/share/mi[rR]*: No such file or directory
csm@csm-HP-Z420:~/Desktop/miRanda-3.3a$
14

What is the content of:

cat configure.log
15 
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by miRanda configure 3.3a, which was
generated by GNU Autoconf 2.60.  Invocation command line was

  $ ./configure 

## --------- ##
## Platform. ##
## --------- ##

hostname = csm-HP-Z420
uname -m = x86_64
uname -r = 3.13.0-24-generic
uname -s = Linux
uname -v = #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014

/usr/bin/uname -p = unknown
/bin/uname -X     = unknown

/bin/arch              = unknown
/usr/bin/arch -k       = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo      = unknown
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown

PATH: /usr/local/sbin
PATH: /usr/local/bin
PATH: /usr/sbin
PATH: /usr/bin
PATH: /sbin
PATH: /bin
PATH: /usr/games
PATH: /usr/local/games
PATH: /home/csm/bin
PATH: /usr/local/java/jre1.8.0_25/bin


## ----------- ##
## Core tests. ##
## ----------- ##

configure:1775: checking for a BSD-compatible install
configure:1831: result: /usr/bin/install -c
configure:1842: checking whether build environment is sane
configure:1885: result: yes
configure:1950: checking for gawk
configure:1966: found /usr/bin/gawk
configure:1977: result: gawk
configure:1988: checking whether make sets $(MAKE)
configure:2009: result: yes
configure:2199: checking build system type
configure:2217: result: x86_64-unknown-linux-gnu
configure:2239: checking host system type
configure:2254: result: x86_64-unknown-linux-gnu
configure:2326: checking for gcc
configure:2342: found /usr/bin/gcc
configure:2353: result: gcc
configure:2591: checking for C compiler version
configure:2598: gcc --version >&5
gcc (Ubuntu 4.9.2-0ubuntu1~14.04) 4.9.2
Copyright (C) 2014 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:2601: $? = 0
configure:2608: gcc -v >&5
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.9/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.9.2-0ubuntu1~14.04' --with-bugurl=file:///usr/share/doc/gcc-4.9/README.Bugs --enable-languages=c,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.9 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.9 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.9-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-4.9-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-4.9-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.9.2 (Ubuntu 4.9.2-0ubuntu1~14.04) 
configure:2611: $? = 0
configure:2618: gcc -V >&5
gcc: error: unrecognized command line option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:2621: $? = 4
configure:2644: checking for C compiler default output file name
configure:2671: gcc    conftest.c  >&5
configure:2674: $? = 0
configure:2720: result: a.out
configure:2725: checking whether the C compiler works
configure:2735: ./a.out
configure:2738: $? = 0
configure:2755: result: yes
configure:2762: checking whether we are cross compiling
configure:2764: result: no
configure:2767: checking for suffix of executables
configure:2774: gcc -o conftest    conftest.c  >&5
configure:2777: $? = 0
configure:2801: result: 
configure:2807: checking for suffix of object files
configure:2833: gcc -c   conftest.c >&5
configure:2836: $? = 0
configure:2859: result: o
configure:2863: checking whether we are using the GNU C compiler
configure:2892: gcc -c   conftest.c >&5
configure:2898: $? = 0
configure:2905: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:2908: $? = 0
configure:2915: test -s conftest.o
configure:2918: $? = 0
configure:2932: result: yes
configure:2937: checking whether gcc accepts -g
configure:2967: gcc -c -g  conftest.c >&5
configure:2973: $? = 0
configure:2980: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:2983: $? = 0
configure:2990: test -s conftest.o
configure:2993: $? = 0
configure:3123: result: yes
configure:3140: checking for gcc option to accept ISO C89
configure:3214: gcc  -c -g -O2  conftest.c >&5
configure:3220: $? = 0
configure:3227: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:3230: $? = 0
configure:3237: test -s conftest.o
configure:3240: $? = 0
configure:3260: result: none needed
configure:3289: checking for style of include used by make
configure:3317: result: GNU
configure:3345: checking dependency style of gcc
configure:3435: result: gcc3
configure:3478: checking for a BSD-compatible install
configure:3534: result: /usr/bin/install -c
configure:3588: checking for ranlib
configure:3604: found /usr/bin/ranlib
configure:3615: result: ranlib
configure:3646: checking for main in -lm
configure:3675: gcc -o conftest -g -O2   conftest.c -lm   >&5
configure:3681: $? = 0
configure:3688: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:3691: $? = 0
configure:3698: test -s conftest
configure:3701: $? = 0
configure:3715: result: yes
configure:3733: checking how to run the C preprocessor
configure:3773: gcc -E  conftest.c
configure:3779: $? = 0
configure:3817: gcc -E  conftest.c
conftest.c:12:28: fatal error: ac_nonexistent.h: No such file or directory
 #include <ac_nonexistent.h>
                            ^
compilation terminated.
configure:3823: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "miRanda"
| #define PACKAGE_TARNAME "miranda"
| #define PACKAGE_VERSION "3.3a"
| #define PACKAGE_STRING "miRanda 3.3a"
| #define PACKAGE_BUGREPORT "miranda {at} cbio.mskcc.org"
| #define PACKAGE "miranda"
| #define VERSION "3.3a"
| #define UNUSED __attribute__ ((unused))
| #define HAVE_LIBM 1
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:3863: result: gcc -E
configure:3892: gcc -E  conftest.c
configure:3898: $? = 0
configure:3936: gcc -E  conftest.c
conftest.c:12:28: fatal error: ac_nonexistent.h: No such file or directory
 #include <ac_nonexistent.h>
                            ^
compilation terminated.
configure:3942: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "miRanda"
| #define PACKAGE_TARNAME "miranda"
| #define PACKAGE_VERSION "3.3a"
| #define PACKAGE_STRING "miRanda 3.3a"
| #define PACKAGE_BUGREPORT "miranda {at} cbio.mskcc.org"
| #define PACKAGE "miranda"
| #define VERSION "3.3a"
| #define UNUSED __attribute__ ((unused))
| #define HAVE_LIBM 1
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:3987: checking for grep that handles long lines and -e
configure:4061: result: /bin/grep
configure:4066: checking for egrep
configure:4144: result: /bin/grep -E
configure:4149: checking for ANSI C header files
configure:4179: gcc -c -g -O2  conftest.c >&5
configure:4185: $? = 0
configure:4192: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:4195: $? = 0
configure:4202: test -s conftest.o
configure:4205: $? = 0
configure:4301: gcc -o conftest -g -O2   conftest.c -lm  >&5
configure:4304: $? = 0
configure:4310: ./conftest
configure:4313: $? = 0
configure:4330: result: yes
configure:4354: checking for sys/types.h
configure:4375: gcc -c -g -O2  conftest.c >&5
configure:4381: $? = 0
configure:4388: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:4391: $? = 0
configure:4398: test -s conftest.o
configure:4401: $? = 0
configure:4414: result: yes
configure:4354: checking for sys/stat.h
configure:4375: gcc -c -g -O2  conftest.c >&5
configure:4381: $? = 0
configure:4388: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:4391: $? = 0
configure:4398: test -s conftest.o
configure:4401: $? = 0
configure:4414: result: yes
configure:4354: checking for stdlib.h
configure:4375: gcc -c -g -O2  conftest.c >&5
configure:4381: $? = 0
configure:4388: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:4391: $? = 0
configure:4398: test -s conftest.o
configure:4401: $? = 0
configure:4414: result: yes
configure:4354: checking for string.h
configure:4375: gcc -c -g -O2  conftest.c >&5
configure:4381: $? = 0
configure:4388: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:4391: $? = 0
configure:4398: test -s conftest.o
configure:4401: $? = 0
configure:4414: result: yes
configure:4354: checking for memory.h
configure:4375: gcc -c -g -O2  conftest.c >&5
configure:4381: $? = 0
configure:4388: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:4391: $? = 0
configure:4398: test -s conftest.o
configure:4401: $? = 0
configure:4414: result: yes
configure:4354: checking for strings.h
configure:4375: gcc -c -g -O2  conftest.c >&5
configure:4381: $? = 0
configure:4388: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:4391: $? = 0
configure:4398: test -s conftest.o
configure:4401: $? = 0
configure:4414: result: yes
configure:4354: checking for inttypes.h
configure:4375: gcc -c -g -O2  conftest.c >&5
configure:4381: $? = 0
configure:4388: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:4391: $? = 0
configure:4398: test -s conftest.o
configure:4401: $? = 0
configure:4414: result: yes
configure:4354: checking for stdint.h
configure:4375: gcc -c -g -O2  conftest.c >&5
configure:4381: $? = 0
configure:4388: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:4391: $? = 0
configure:4398: test -s conftest.o
configure:4401: $? = 0
configure:4414: result: yes
configure:4354: checking for unistd.h
configure:4375: gcc -c -g -O2  conftest.c >&5
configure:4381: $? = 0
configure:4388: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:4391: $? = 0
configure:4398: test -s conftest.o
configure:4401: $? = 0
configure:4414: result: yes
configure:4444: checking float.h usability
configure:4461: gcc -c -g -O2  conftest.c >&5
configure:4467: $? = 0
configure:4474: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:4477: $? = 0
configure:4484: test -s conftest.o
configure:4487: $? = 0
configure:4498: result: yes
configure:4502: checking float.h presence
configure:4517: gcc -E  conftest.c
configure:4523: $? = 0
configure:4544: result: yes
configure:4577: checking for float.h
configure:4585: result: yes
configure:4444: checking limits.h usability
configure:4461: gcc -c -g -O2  conftest.c >&5
configure:4467: $? = 0
configure:4474: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:4477: $? = 0
configure:4484: test -s conftest.o
configure:4487: $? = 0
configure:4498: result: yes
configure:4502: checking limits.h presence
configure:4517: gcc -E  conftest.c
configure:4523: $? = 0
configure:4544: result: yes
configure:4577: checking for limits.h
configure:4585: result: yes
configure:4434: checking for stdlib.h
configure:4440: result: yes
configure:4434: checking for string.h
configure:4440: result: yes
configure:4600: checking for an ANSI C-conforming const
configure:4675: gcc -c -g -O2  conftest.c >&5
configure:4681: $? = 0
configure:4688: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:4691: $? = 0
configure:4698: test -s conftest.o
configure:4701: $? = 0
configure:4713: result: yes
configure:4723: checking for stdbool.h that conforms to C99
configure:4816: gcc -c -g -O2  conftest.c >&5
configure:4822: $? = 0
configure:4829: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:4832: $? = 0
configure:4839: test -s conftest.o
configure:4842: $? = 0
configure:4854: result: yes
configure:4856: checking for _Bool
configure:4886: gcc -c -g -O2  conftest.c >&5
configure:4892: $? = 0
configure:4899: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:4902: $? = 0
configure:4909: test -s conftest.o
configure:4912: $? = 0
configure:4924: result: yes
configure:4943: checking for size_t
configure:4973: gcc -c -g -O2  conftest.c >&5
configure:4979: $? = 0
configure:4986: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:4989: $? = 0
configure:4996: test -s conftest.o
configure:4999: $? = 0
configure:5011: result: yes
configure:5030: checking for stdlib.h
configure:5036: result: yes
configure:5194: checking for GNU libc compatible malloc
configure:5228: gcc -o conftest -g -O2   conftest.c -lm  >&5
configure:5231: $? = 0
configure:5237: ./conftest
configure:5240: $? = 0
configure:5256: result: yes
configure:5289: checking for stdlib.h
configure:5295: result: yes
configure:5453: checking for GNU libc compatible realloc
configure:5487: gcc -o conftest -g -O2   conftest.c -lm  >&5
configure:5490: $? = 0
configure:5496: ./conftest
configure:5499: $? = 0
configure:5515: result: yes
configure:5543: checking for working strtod
configure:5594: gcc -o conftest -g -O2   conftest.c -lm  >&5
configure:5597: $? = 0
configure:5603: ./conftest
configure:5606: $? = 0
configure:5622: result: yes
configure:5827: checking for memset
configure:5883: gcc -o conftest -g -O2   conftest.c -lm  >&5
conftest.c:55:6: warning: conflicting types for built-in function 'memset'
 char memset ();
      ^
configure:5889: $? = 0
configure:5896: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:5899: $? = 0
configure:5906: test -s conftest
configure:5909: $? = 0
configure:5923: result: yes
configure:5827: checking for sqrt
configure:5883: gcc -o conftest -g -O2   conftest.c -lm  >&5
conftest.c:56:6: warning: conflicting types for built-in function 'sqrt'
 char sqrt ();
      ^
configure:5889: $? = 0
configure:5896: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:5899: $? = 0
configure:5906: test -s conftest
configure:5909: $? = 0
configure:5923: result: yes
configure:5827: checking for strchr
configure:5883: gcc -o conftest -g -O2   conftest.c -lm  >&5
conftest.c:57:6: warning: conflicting types for built-in function 'strchr'
 char strchr ();
      ^
configure:5889: $? = 0
configure:5896: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:5899: $? = 0
configure:5906: test -s conftest
configure:5909: $? = 0
configure:5923: result: yes
configure:5827: checking for strdup
configure:5883: gcc -o conftest -g -O2   conftest.c -lm  >&5
conftest.c:58:6: warning: conflicting types for built-in function 'strdup'
 char strdup ();
      ^
configure:5889: $? = 0
configure:5896: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:5899: $? = 0
configure:5906: test -s conftest
configure:5909: $? = 0
configure:5923: result: yes
configure:5827: checking for strrchr
configure:5883: gcc -o conftest -g -O2   conftest.c -lm  >&5
conftest.c:59:6: warning: conflicting types for built-in function 'strrchr'
 char strrchr ();
      ^
configure:5889: $? = 0
configure:5896: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:5899: $? = 0
configure:5906: test -s conftest
configure:5909: $? = 0
configure:5923: result: yes
configure:5827: checking for strstr
configure:5883: gcc -o conftest -g -O2   conftest.c -lm  >&5
conftest.c:60:6: warning: conflicting types for built-in function 'strstr'
 char strstr ();
      ^
configure:5889: $? = 0
configure:5896: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:5899: $? = 0
configure:5906: test -s conftest
configure:5909: $? = 0
configure:5923: result: yes
configure:6050: creating ./config.status

## ---------------------- ##
## Running config.status. ##
## ---------------------- ##

This file was extended by miRanda config.status 3.3a, which was
generated by GNU Autoconf 2.60.  Invocation command line was

  CONFIG_FILES    = 
  CONFIG_HEADERS  = 
  CONFIG_LINKS    = 
  CONFIG_COMMANDS = 
  $ ./config.status 

on csm-HP-Z420

config.status:635: creating Makefile
config.status:635: creating RNAlib/H/Makefile
config.status:635: creating RNAlib/Makefile
config.status:635: creating man/Makefile
config.status:635: creating src/Makefile
config.status:635: creating config.h
config.status:873: config.h is unchanged
config.status:919: executing depfiles commands

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_build=x86_64-unknown-linux-gnu
ac_cv_c_compiler_gnu=yes
ac_cv_c_const=yes
ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_func_malloc_0_nonnull=yes
ac_cv_func_memset=yes
ac_cv_func_realloc_0_nonnull=yes
ac_cv_func_sqrt=yes
ac_cv_func_strchr=yes
ac_cv_func_strdup=yes
ac_cv_func_strrchr=yes
ac_cv_func_strstr=yes
ac_cv_func_strtod=yes
ac_cv_header_float_h=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_limits_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_stdbool_h=yes
ac_cv_header_stdc=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_unistd_h=yes
ac_cv_host=x86_64-unknown-linux-gnu
ac_cv_lib_m_main=yes
ac_cv_objext=o
ac_cv_path_EGREP='/bin/grep -E'
ac_cv_path_GREP=/bin/grep
ac_cv_path_install='/usr/bin/install -c'
ac_cv_prog_AWK=gawk
ac_cv_prog_CPP='gcc -E'
ac_cv_prog_ac_ct_CC=gcc
ac_cv_prog_ac_ct_RANLIB=ranlib
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
ac_cv_prog_make_make_set=yes
ac_cv_type__Bool=yes
ac_cv_type_size_t=yes
am_cv_CC_dependencies_compiler_type=gcc3

## ----------------- ##
## Output variables. ##
## ----------------- ##

ACLOCAL='${SHELL} /home/csm/Desktop/miRanda-3.3a/missing --run aclocal-1.9'
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='${SHELL} /home/csm/Desktop/miRanda-3.3a/missing --run tar'
AUTOCONF='${SHELL} /home/csm/Desktop/miRanda-3.3a/missing --run autoconf'
AUTOHEADER='${SHELL} /home/csm/Desktop/miRanda-3.3a/missing --run autoheader'
AUTOMAKE='${SHELL} /home/csm/Desktop/miRanda-3.3a/missing --run automake-1.9'
AWK='gawk'
CC='gcc'
CCDEPMODE='depmode=gcc3'
CFLAGS='-g -O2'
CPP='gcc -E'
CPPFLAGS=''
CYGPATH_W='echo'
DEFS='-DHAVE_CONFIG_H'
DEPDIR='.deps'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/bin/grep -E'
EXEEXT=''
GREP='/bin/grep'
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='${SHELL} $(install_sh) -c -s'
ISODATE='2015-10-05'
LDFLAGS=''
LIBOBJS=''
LIBS='-lm '
LTLIBOBJS=''
MAKEINFO='${SHELL} /home/csm/Desktop/miRanda-3.3a/missing --run makeinfo'
OBJEXT='o'
PACKAGE='miranda'
PACKAGE_BUGREPORT='miranda {at} cbio.mskcc.org'
PACKAGE_NAME='miRanda'
PACKAGE_STRING='miRanda 3.3a'
PACKAGE_TARNAME='miranda'
PACKAGE_VERSION='3.3a'
PATH_SEPARATOR=':'
POW_LIB=''
RANLIB='ranlib'
SET_MAKE=''
SHELL='/bin/bash'
STRIP=''
VERSION='3.3a'
ac_ct_CC='gcc'
am__fastdepCC_FALSE='#'
am__fastdepCC_TRUE=''
am__include='include'
am__leading_dot='.'
am__quote=''
am__tar='${AMTAR} chof - "$$tardir"'
am__untar='${AMTAR} xf -'
bindir='${exec_prefix}/bin'
build='x86_64-unknown-linux-gnu'
build_alias=''
build_cpu='x86_64'
build_os='linux-gnu'
build_vendor='unknown'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='${prefix}'
host='x86_64-unknown-linux-gnu'
host_alias=''
host_cpu='x86_64'
host_os='linux-gnu'
host_vendor='unknown'
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
install_sh='/home/csm/Desktop/miRanda-3.3a/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
mkdir_p='mkdir -p --'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/usr/local'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

#define PACKAGE_NAME "miRanda"
#define PACKAGE_TARNAME "miranda"
#define PACKAGE_VERSION "3.3a"
#define PACKAGE_STRING "miRanda 3.3a"
#define PACKAGE_BUGREPORT "miranda {at} cbio.mskcc.org"
#define PACKAGE "miranda"
#define VERSION "3.3a"
#define UNUSED __attribute__ ((unused))
#define HAVE_LIBM 1
#define STDC_HEADERS 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STRINGS_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1
#define HAVE_FLOAT_H 1
#define HAVE_LIMITS_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE__BOOL 1
#define HAVE_STDBOOL_H 1
#define HAVE_STDLIB_H 1
#define HAVE_MALLOC 1
#define HAVE_STDLIB_H 1
#define HAVE_REALLOC 1
#define HAVE_MEMSET 1
#define HAVE_SQRT 1
#define HAVE_STRCHR 1
#define HAVE_STRDUP 1
#define HAVE_STRRCHR 1
#define HAVE_STRSTR 1

configure: exit 0
16

The first issues rises at:

| #include <ac_nonexistent.h>
configure:3863: result: gcc -E
configure:3892: gcc -E  conftest.c
configure:3898: $? = 0
configure:3936: gcc -E  conftest.c
conftest.c:12:28: fatal error: ac_nonexistent.h: No such file or directory
 #include <ac_nonexistent.h>
                            ^
compilation terminated.
configure:3942: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "miRanda"
| #define PACKAGE_TARNAME "miranda"
| #define PACKAGE_VERSION "3.3a"
| #define PACKAGE_STRING "miRanda 3.3a"
| #define PACKAGE_BUGREPORT "miranda {at} cbio.mskcc.org"
| #define PACKAGE "miranda"
| #define VERSION "3.3a"
| #define UNUSED __attribute__ ((unused))
| #define HAVE_LIBM 1
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>

There are multiple of this kind, i assume causes be the first issue:

conftest.c:55:6: warning: conflicting types for built-in function 'memset'
 char memset ();
      ^
configure:5889: $? = 0
configure:5896: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:5899: $? = 0
configure:5906: test -s conftest
configure:5909: $? = 0
configure:5923: result: yes
configure:5827: checking for sqrt
configure:5883: gcc -o conftest -g -O2   conftest.c -lm  >&5
conftest.c:56:6: warning: conflicting types for built-in function 'sqrt'
 char sqrt ();
      ^
configure:5889: $? = 0
configure:5896: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:5899: $? = 0
configure:5906: test -s conftest
configure:5909: $? = 0
configure:5923: result: yes
configure:5827: checking for strchr
configure:5883: gcc -o conftest -g -O2   conftest.c -lm  >&5
conftest.c:57:6: warning: conflicting types for built-in function 'strchr'
 char strchr ();
      ^

Are you packaging (as in writing the autotools/makefiles) this or just trying to compile it?
Because to me, experiences - but still novice, it looks like there is an issue with either the code or the makefiles, tending to blame the code.

If you just want to compile this, have you read the README and INSTALL files?
If you did, and followed each and every step, send the logfile to one of the devs.

If you're about to package this, you might have missed to addd the required files to the Makefile in that dir, and/or missed to add it in the makefile of the top-level-dir of the project.

hth

17

When you have

#include <somefile.h>
  1. somefile.h must exist as /usr/include/somefile.h

OR

  1. You must tell gcc to look for it elsewhere with an option like this:
    -I /path/to/more/include/files

OR

  1. The files exists in the current directory
    Change <somefile.h> to "somefile.h"

#3 is generally a bad idea for compiling externally created C file sets. Somebody else wrote it, so you do not change it. Except in really dire circumstances.

18

sir, this reply is quit confusing for me, is there any easy understandable way so that we can resolve this?

---------- Post updated 10-07-15 at 01:55 AM ---------- Previous update was 10-06-15 at 05:21 AM ----------

I run command as follow:
and get leaving directory error. kindly direct which file i should edit . step by step

csm@csm-HP-Z420:~/Desktop/miRanda-3.3a$ ./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 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 ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for a BSD-compatible install... /usr/bin/install -c
checking for ranlib... ranlib
checking for main in -lm... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/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 float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for size_t... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for working strtod... yes
checking for memset... yes
checking for sqrt... yes
checking for strchr... yes
checking for strdup... yes
checking for strrchr... yes
checking for strstr... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating RNAlib/H/Makefile
config.status: creating RNAlib/Makefile
config.status: creating man/Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
csm@csm-HP-Z420:~/Desktop/miRanda-3.3a$ sudo make
[sudo] password for csm: 
make  all-recursive
make[1]: Entering directory `/home/csm/Desktop/miRanda-3.3a'
Making all in man
make[2]: Entering directory `/home/csm/Desktop/miRanda-3.3a/man'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/man'
Making all in RNAlib
make[2]: Entering directory `/home/csm/Desktop/miRanda-3.3a/RNAlib'
Making all in H
make[3]: Entering directory `/home/csm/Desktop/miRanda-3.3a/RNAlib/H'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/RNAlib/H'
make[3]: Entering directory `/home/csm/Desktop/miRanda-3.3a/RNAlib'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/RNAlib'
make[2]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/RNAlib'
Making all in src
make[2]: Entering directory `/home/csm/Desktop/miRanda-3.3a/src'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/csm/Desktop/miRanda-3.3a/src'
make[2]: Entering directory `/home/csm/Desktop/miRanda-3.3a'
make[2]: Leaving directory `/home/csm/Desktop/miRanda-3.3a'
make[1]: Leaving directory `/home/csm/Desktop/miRanda-3.3a'
csm@csm-HP-Z420:~/Desktop/miRanda-3.3a$
19

What makes you think that:

make[1]: Leaving directory `/home/csm/Desktop/miRanda-3.3a'

indicates that there is an error? In earlier output, you showed us fatal errors like:

conftest.c:12:28: fatal error: ac_nonexistent.h: No such file or directory
 #include <ac_nonexistent.h>
                            ^
compilation terminated.

which clearly indicates an error that must be fixed before you can successfully make whatever you are trying to make. And you showed us warnings like:

conftest.c:55:6: warning: conflicting types for built-in function 'memset'
 char memset ();
      ^

which indicates a problem that might still produce code you're trying to produce, but should be fixed before you trying running the code it produced.

I don't see any warnings or errors in the output you presented in post #17 in this thread; it looks like make worked through several layers of makefiles and didn't find anything that needed to be built.

What were you trying to build that was not built?

20

i am just not able to install it because i am not able to pick out the problem.
i never ever face this type of proble before while installing any software :(:confused: