I am trying to install a program in Opensuse linux and while issuing the 'make' command, its showing me an error /bin/sh: C: command not found
Kindly help me to troubleshoot the problem.
I have gcc, c++ all install in the linux machine.
Thanks
Where does that error appear? Did it print anything else? What is the exact error message, word for word, letter for letter, keystroke for keystroke? I'd be surprised if that's actually what it said, there is no 'C' program that I know of.
and am trying to install on OpenSuse linux (Linux 3.11.10-21-desktop x86_64).
The install file mentions the following steps to install:
Code:
M. Zuker, March 2013.
INSTALLATION of mfold 3.5
mfold version 3.5 uses a configure script.
Some non-interactive mfold_util programs, in particular, sir_graph and
boxplot_ng, are included so that structure and dot plots can be
created. It is preferable to have the mfold_util-4.6 versions of these
programs.
With this version, no environment variables are required. Energy and
related files will be read from the installation data directory,
usually /usr/local/share/mfold (or $prefix/share/mfold, where $prefix
is specified by using --prefix= when running ./configure).
After running ./configure (or the more convenient ./Configure.bash
script),
make
compiles the Fortran, C and C++ programs and creates the mfold and
mfold_quik scripts.
make install
places the binaries and scripts into $prefix/bin and data files into
$prefix/share/mfold. These directories are created if they do not
already exist.
As in earlier versions, the current working directory will be searched
first for energy files when the folding program is run.
Please report bugs, other problems or suggestions to zukerm@rpi.edu
Look at the files in the "doc" directory, especially the manual, which
is in PostScript, pdf and HTML form.
I have already downloaded the program in /usr/local/mfold-3.6 folder.
This is the output of my ./Confiugre_bash:
Code:
linux-oc9r:/usr/local/mfold-3.6 # ./Configure.bash
configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-unknown-linux-gnu
checking for gawk... (cached) gawk
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether c++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of c++... gcc3
checking for gcc... cc
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking dependency style of cc... gcc3
checking whether ln -s works... yes
checking for g77... no
checking for xlf... no
checking for f77... no
checking for frt... no
checking for pgf77... no
checking for cf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for xlf90... no
checking for f90... no
checking for pgf90... no
checking for pghpf... no
checking for epcf90... no
checking for gfortran... no
checking for g95... no
checking for xlf95... no
checking for f95... no
checking for fort... no
checking for ifort... no
checking for ifc... no
checking for efc... no
checking for pgfortran... no
checking for pgf95... no
checking for lf95... no
checking for ftn... no
checking for nagfor... no
checking whether we are using the GNU Fortran 77 compiler... no
checking whether accepts -g... no
checking for ranlib... ranlib
checking how to run the C preprocessor... cc -E
checking whether cc understands -c and -o together... yes
checking for sqrt in -lm... yes
checking for gdImageCreate in -lgd... no
checking for jpeg_CreateCompress in -ljpeg... no
checking for png_init_io in -lpng... yes
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/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 gd.h usability... no
checking gd.h presence... no
checking for gd.h... no
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 stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking whether struct tm is in sys/time.h or time.h... time.h
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for error_at_line... yes
checking for bzero... yes
checking for floor... yes
checking for sqrt... yes
checking for strchr... yes
checking for strspn... yes
checking for strstr... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating c++/Makefile
config.status: creating src/Makefile
config.status: creating dat/Makefile
config.status: creating scripts/Makefile
config.status: creating scripts/filter-sort
config.status: creating scripts/h-num
config.status: creating scripts/reformat-seq.sh
config.status: creating scripts/mfold
config.status: creating scripts/mfold_quik
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
After that I issue "make" command which gives me huge compilation output, the first few lines I am pasting here:
Code:
linux-oc9r:/usr/local/mfold-3.6 # make
make all-recursive
make[1]: Entering directory `/usr/local/mfold-3.6'
Making all in src
make[2]: Entering directory `/usr/local/mfold-3.6/src'
C -O3 -Wall -fno-automatic -ffixed-line-length-none -c -o distance-distance.o `test -f 'distance.f' || echo './'`distance.f
/bin/sh: C: command not found
make[2]: [distance-distance.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none -o distance distance-distance.o distance-bpin.o distance-bpsrch.o -lpng -lm
make[2]: C: Command not found
make[2]: [distance] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none -c -o ct2bp-ct2bp.o `test -f 'ct2bp.f' || echo './'`ct2bp.f
/bin/sh: C: command not found
Here in the output you can see the error: "/bin/sh: C: command not found"
When I try to execute the program, it dies with an "auxgen" error, see below:
Code:
mfold version 3.6
REUSE= NO
auxgen failed
Job Aborted
I don't recognize that error at all. I certainly have no 'C' program on my system or see anything in my makefiles that would provoke such a message.
Code:
$ mfold SEQ='M23263_rna_300-1.txt' RUN_TYPE=text NA=RNA MA
mfold version 3.6
Invalid entry: MA on command line.
$
Actually -- I just noticed one big difference between what I did and what you did! Out of habit, I ran ./configure and not./Configure.bash.
To be precise, I ran ./configure --prefix=/home/username/archive/mfold. The prefix is where it installs -- I put it in my home directory. /usr/local/ would be a decent choice if you needed it to be global to the machine. You'd need to add it to your path to use it, PATH="${PATH}:/usr/local/bin" but it'd be separate from your system utilities and easy to remove if needed.
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