For jbrowse I use fink to install libpng, but I still can't get it working. It spits out this error message:
configure: error: libpng not found. Please install libpng and try
again. Or if it is already installed (e.g. in /usr/X11), pass the
include and link paths to configure like so: ./configure
CXXFLAGS=-I/usr/X11/include LDFLAGS=-L/usr/X11/lib
+ cd ../..
+ set -x
+ bin/wig-to-json.pl --key 'Image - volvox_microarray.wig' --wig docs/tutorial/data_files/volvox_microarray.wig --category
'Pre-generated images' --out sample_data/json/volvox
I don't really know what this error message means and when I type in the terminal
./configure CXXFLAGS=-I/usr/X11/include LDFLAGS=-L/usr/X11/lib
It gives me an error that ./configure: No such file or directory.
I am a Novice at command line. Someone please help!
Related
I am trying to compile Opencv on Ubuntu 18.04. I installed many dependencies packages but when I run make I get the error:
grfmt_jpeg2000.cpp:59:10: fatal error: jasper/jasper.h: No such file or directory
#include <jasper/jasper.h>
^~~~~~~~~~~~~~~~~
compilation terminated.
I had already jasper installed and installed libjasperreports-java. However the file jasper.h cannot still be found in my system. Is there any library I can install with apt install to get that file? Or am I missing any other library?
EDIT 1
I tried also downloading the opencv_contrib to install extra moduels of openCV but first of all jaspar is not present and secondly setting the build with
cmake -D CMAKE_INSTALL_PREFIX=./ -D CMAKE_BUILD_TYPE=Debug -D OPENCV_EXTRA_MODULES_PATH=../opencv_contrib/modules ../openCV
returns the error:
Make Error at cmake/OpenCVModule.cmake:352 (message):
Duplicated modules NAMES has been found
while CMakeError.log contains many errors of the type:
Build output check failed:
Regex: 'command line option .* is valid for .* but not for C\+\+'
Output line: 'cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++'
Getting this error during "make" in mpich
GEN lib/libmpi.la
libtool: error: only absolute run-paths are allowed
Compiler being used is clang (the code builds fine with gcc). Any idea what this error could be due to?
Here is the configure command:
./configure '--prefix=$PWD/BIN' '--with-device=ch3:nemesis:mxm' '--with-mxm=/home/xyz/software/hpcx-v1.9.5-gcc-inbox-redhat7.3-x86_64/mxm' '--disable-spawn' '--disable-ft-tests' '--enable-g=all' '--enable-nemesis-dbg-localoddeven' '--enable-large-tests' '--disable-perftest' 'CC=clang' 'CXX=clang++' 'FC=gfortran' 'F77=gfortran' --cache-file=/dev/null --disable-fortran
I think the issue is the evaluation of $PWD within the quotes. If you replace
./configure '--prefix=$PWD/BIN' ...
with
./configure --prefix=$PWD/BIN ...
you should be good.
I ran into this error as well when building a different piece of software. The solution for me was to enclose the shell variable in --prefix= with {}:
./configure --prefix=${PWD}/BIN
I would like to install Circos. I followed the instructions on Circos website. In particular, I checked for missing perl modules. I'm missing several of them:
missing Font::TTF::Font
missing GD
missing GD::Polyline
missing SVG
missing Statistics::Basic
missing Text::Format
So I followed again the instructions about Installing Perl Modules on Mac OS X on Circos website. Specifically, I followed the detailed instructions in Paulo Nuin's blog post. Freetype and Fontconfig were missing and I installed them.
Now, when I run the configuration for libgd-2.2.1, I get this configuration summary:
Support for Zlib: yes
Support for PNG library: yes
Support for JPEG library: yes
Support for WebP library: no
Support for TIFF library: no
Support for Freetype 2.x library: yes
Support for Fontconfig library: yes
Support for Xpm library: no
Support for liq library: no
Support for pthreads: yes
It looks good enough to me. But when I run the make, I get errors:
clang: warning: argument unused during compilation: '-pthread'
ld: malformed 64-bit a.b.c.d.e version number: 4.20201
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [libgd.la] Error 1
make[1]: *** [all] Error 2
make: *** [all-recursive] Error 1
Since it was not working, I followed this recommendation on Stackoverflow and I ran
brew install gd
(I had to update brew by doing
cd /usr/local/Library
git pull origin master
following this answer on Stackoverflow.)
But I get an error:
Error: You must `brew link libpng freetype` before gd can be installed
And when I run 'brew link libpng freetype', I get another error:
Linking /usr/local/Cellar/libpng/1.6.21...
Error: Could not symlink bin/libpng-config
Target /usr/local/bin/libpng-config
already exists. You may want to remove it:
rm '/usr/local/bin/libpng-config'
To force the link and overwrite all conflicting files:
brew link --overwrite libpng
To list all files that would be deleted:
brew link --overwrite --dry-run libpng
Any solution to finally be able to run Circos?
Thanks in advance for your help!
Finally, I solved the problem by changing the permissions in /usr/local:
sudo chown -R $(whoami) /usr/local
Following the recommendations on brew webpage.
Once this was solved, I just installed GD in Perl, as described in the last step in Paulo Nuin's post.
I'm working with Tmote-sky nodes. I have installed instant-contiki as a virtual machine using VMware player. Now I can't compile any .c file on the nodes. I have always this error message:
make: msp430-gcc: Command not found
CC ../../core/net/rime/rimeaddr.c
make: msp430-gcc: Command not found
make: *** [obj_sky/rimeaddr.o] Error 127
I thought that it was because of msp430-gcc toolchain. I've installed this toolchain which normally exists with instant-contiki but I still have this problem.
Can some one help me please?
You have to install gcc-msp430 with the following command:
sudo apt-get install gcc-msp430
Try this :
the problem causes with little switch. remove it you're good to go.
open this file in note pad and goto line 132
contiki/cpu/msp40/Makefile.msp430
remove -g switch from the following line:
CFLAGSNO = -Wall -mmcu=$(CC_MCU) -g $(CFLAGSWERROR)
the line will be:
CFLAGSNO = -Wall -mmcu=$(CC_MCU) $(CFLAGSWERROR)
just clean up and recompile.
it should work.... :)
I am attempting to make a project and have run into this error when trying to issue an install command on a handful of executables. Looks something like this:
(in highest level dir:)
DIRS = \
dir1 \
dir2 \
... \
lastDir \
all clean release:
for x in $(DIRS); do cd $$x; make $#; cd ..; done
Then in dir1, for example:
all: $(PROG)
install $(PROG) ../../bin
and the same for each directory. Log looks like this:
[exec] install my_prog_name ../../bin
[exec] install: my_prog_name was not found anywhere!
[exec] make[1]: Leaving dir1
Neither makefile (in upper or lower directory) has been changed since the last successful build, same with the build file (using ant).
Kind of looks like either a pathing issue or a permissions issue. Permissions on destination directory are 777, though. Issuing the install command manually in dir1 works fine...
Thanks for the help!
Are you running this on Solaris? It seems the Solaris version of the install command is prone to generate this error.
I'm not sure what the root cause is, but you could try using /usr/ucb/install, plain cp or the GNU ginstall.