Installing Circos: Problems installing GD module on Mac OS - homebrew

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.

Related

Could not find HDF5 installation for PyTables on M1 Mac

Running on M1 Mac, macOS Monterey 12.4, Python 3.10.3
pip install tables
Collecting tables
Using cached tables-3.7.0.tar.gz (8.2 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... error
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [12 lines of output]
/var/folders/6g/9c7g_2tx2sb7lp8ttwtfky640000gn/T/H5closew_79lujq.c:2:5: error: implicit declaration of function 'H5close' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
H5close();
^
1 error generated.
cpuinfo failed, assuming no CPU features: No module named 'cpuinfo'
* Using Python 3.10.3 (v3.10.3:a342a49189, Mar 16 2022, 09:34:18) [Clang 13.0.0 (clang-1300.0.29.30)]
* Found cython 0.29.30
* USE_PKGCONFIG: False
.. ERROR:: Could not find a local HDF5 installation.
You may need to explicitly state where your local HDF5 headers and
library can be found by setting the ``HDF5_DIR`` environment
variable or by using the ``--hdf5`` command-line option.
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
I tried the following from this GitHub Issue:
pip install cython
brew install hdf5
brew install c-blosc
export HDF5_DIR=/usr/local/
export BLOSC_DIR=/usr/local/
pip install tables
But still getting the same error. Not sure if it's due to Homebrew using a different path on M1 Macs?
The issue is that Homebrew puts the files in opt/homebrew/opt/
This fixed it for me:
export HDF5_DIR=/opt/homebrew/opt/hdf5
export BLOSC_DIR=/opt/homebrew/opt/c-blosc
Again in completion to remove confusion. Running the following in terminal on Mac M1 should work.
pip install cython
brew install hdf5
brew install c-blosc
export HDF5_DIR=/opt/homebrew/opt/hdf5
export BLOSC_DIR=/opt/homebrew/opt/c-blosc
pip install tables
A solution from here solved the issue for me:
https://github.com/freqtrade/freqtrade/issues/4162
Scroll down and see "solution" provided by camxus

note: /usr/bin/ld: cannot find -lpq Rust

il" "-ldl" "-lutil" "-ldl" "-lrt" "-lpthread" "-lgcc_s" "-lc" "-lm" "-lrt" "-lpthread" "-lutil" "-lutil"
= note: /usr/bin/ld: cannot find -lpq
collect2: error: ld returned 1 exit status
error: aborting due to previous error
error: could not compile actix-todo.
To learn more, run the command again with --verbose.
It looks like you are missing the postgresql-libs package. Install it using your systems package manager.
For me I needed to install libpq-dev. You can install it on linux like this:
sudo apt install libpq-dev

Cannot compile Open CV on Ubuntu 18.04 because of jasper.h not found

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++'

openEmbedded sdk installation

I am trying to install openEmbedded sdk for arm with libxml2 and freetype packages.
I hope that somebody here can give me good advice.
Question is about deploying sdk and giving include paths to the makefile.
To deploy sdk, I use /home/vincent/oe_dir3/setup-scripts/build/tmp-defaultsetup-eglibc-eglibc/deploy/sdk/oecore-i686-armv5te-toolchain-oe-core.0.sh and chose /home/vincent/oe_dir3/oecore-i686/ directory.
First I am surprise I have no freetype or libxml2 include in the install directory.
vincent#electronic:~$ find /home/vincent/oe_dir3 -name "freetype" | grep "include/freetype"
/home/vincent/oe_dir3/setup-scripts/build/tmp-defaultsetup-eglibc-eglibc/sysroots/eukrea-cpuimx25/usr/include/freetype2/freetype
I continue to do the make with above path as include.
I meet following error :
Linking... /home/vincent/eclipseProjects/sensigom/obj/parcoursMusical.o
/home/vincent/oe_dir3/oecore-i686/sysroots/i686-oesdk-linux/usr/bin/armv5te-oe-linux-gnueabi/../../libexec/armv5te-oe-linux-gnueabi/gcc/arm-oe-linux-gnueabi/4.7.2/ld: cannot find crt1.o: No such file or directory
/home/vincent/oe_dir3/oecore-i686/sysroots/i686-oesdk-linux/usr/bin/armv5te-oe-linux-gnueabi/../../libexec/armv5te-oe-linux-gnueabi/gcc/arm-oe-linux-gnueabi/4.7.2/ld: cannot find crti.o: No such file or directory
/home/vincent/oe_dir3/oecore-i686/sysroots/i686-oesdk-linux/usr/bin/armv5te-oe-linux-gnueabi/../../libexec/armv5te-oe-linux-gnueabi/gcc/arm-oe-linux-gnueabi/4.7.2/ld: cannot find crtbegin.o: No such file or directory
/home/vincent/oe_dir3/oecore-i686/sysroots/i686-oesdk-linux/usr/bin/armv5te-oe-linux-gnueabi/../../libexec/armv5te-oe-linux-gnueabi/gcc/arm-oe-linux-gnueabi/4.7.2/ld: cannot find -lstdc++
/home/vincent/oe_dir3/oecore-i686/sysroots/i686-oesdk-linux/usr/bin/armv5te-oe-linux-gnueabi/../../libexec/armv5te-oe-linux-gnueabi/gcc/arm-oe-linux-gnueabi/4.7.2/ld: cannot find -lm
collect2: error: ld returned 1 exit status
I don't know where and also in which documentation to search. If you have any idea I would be happy.
Regards
Freetype and libxml2 have to be added to your rootfs befor you generate the sdk.
IMAGE_INSTALL += "freetype libxml2"
They mustthen appear in your sysroot

image::magick not installing with cpan in perl v5.14.2 from dwimperl

I am attempting to rebuild my development/test environment on a new laptop running windows7 32 bit. imageMagick is one of the modules I had installed in an (ancient) version on my old laptop. I have downloaded and installed perl from dwimperl, which is v5.14.2 and had a couple modules install, and several did not.
cpanm Image::Magick - failed
cpanm DB_File - failed
cpanm Time::HiRes - failed
I searched around and found a discussion on magick failing to install on v5.12, but couldn't tell if that was supposed to have been fixed, or if I need to attempt to recreate the fix discussed for 5.12
should I try installing perl from Strawberry? looks like it is a little newer v5.18 ?
is there something I can tweak and re-run cpan installs?
I installed the binaries from imagemagick, from Link first, then cpan again, and cpan still fails....
This is the top part of the build log down to where it really goes south and starts kicking out errors:
cpanm (App::cpanminus) 1.6941 on perl 5.014002 built for MSWin32-x86-multi-thread
Work directory is C:\Users\dtbaker/.cpanm/work/1377281741.8420
You have make C:\Dwimperl\c\bin\dmake.exe
You have LWP 6.03
Falling back to Archive::Tar 1.80
Searching Image::Magick on cpanmetadb ...
--> Working on Image::Magick
Fetching http://www.cpan.org/authors/id/J/JC/JCRISTY/PerlMagick-6.86.tar.gz
-> OK
Unpacking PerlMagick-6.86.tar.gz
Entering PerlMagick-6.86
META.yml/json not found. Creating skelton for it.
Configuring PerlMagick-6.86
Running Makefile.PL
################################### WARNING! ###################################
# It seems that you are trying to install Perl::Magick on a MS Windows box with
# perl + gcc compiler (e.g. strawberry perl), however we cannot find ImageMagick
# binaries installed on your system.
#
# Please check the following prerequisites:
#
# 1) You need to have installed ImageMagick Windows binaries from
# http://www.imagemagick.org/script/binary-releases.php#windows
#
# 2) We only support dynamic (DLL) ImageMagick binaries
# note: it is not possible to mix 32/64-bit binaries of perl and ImageMagick
#
# 3) During installation select that you want to install ImageMagick's
# development files (libraries+headers)
#
# 4) You also need to have ImageMagick's directory in your PATH
# note: we are checking the presence of convert.exe and/or identify.exe tools
#
# 5) You might need Visual C++ Redistributable Package installed on your system
# see instructions on ImageMagick's Binary Release webpage
#
# We are gonna continue, but chances for successful build are very low!
################################################################################
Checking if your kit is complete...
Looks good
Note (probably harmless): No library found for -lMagickCore-6.Q16
Writing Makefile for Image::Magick
Writing MYMETA.yml and MYMETA.json
-> OK
Checking dependencies from MYMETA.json ...
Checking if you have ExtUtils::MakeMaker 0 ... Yes (6.62)
Building and testing Image-Magick-6.86
cp Magick.pm blib\lib\Image\Magick.pm
AutoSplitting blib\lib\Image\Magick.pm (blib\lib\auto\Image\Magick)
C:\Dwimperl\perl\bin\perl.exe C:\Dwimperl\perl\lib\ExtUtils\xsubpp -typemap C:\Dwimperl\perl\lib\ExtUtils\typemap -typemap typemap Magick.xs > Magick.xsc && C:\Dwimperl\perl\bin\perl.exe -MExtUtils::Command -e mv -- Magick.xsc Magick.c
gcc -c -s -O2 -DWIN32 -DPERL_TEXTMODE_SCRIPTS -DUSE_SITECUSTOMIZE -DPERL_IMPLICIT_CONTEXT -DPERL_IMPLICIT_SYS -fno-strict-aliasing -mms-bitfields -s -O2 -DVERSION=\"6.86\" -DXS_VERSION=\"6.86\" "-IC:\Dwimperl\perl\lib\CORE" -D_LARGE_FILES=1 -DHAVE_CONFIG_H Magick.c
Magick.xs:60:31: error: magick/MagickCore.h: No such file or directory
Magick.xs:167: error: expected specifier-qualifier-list before 'MagickRealType'
Magick.xs:188: error: expected specifier-qualifier-list before 'ImageInfo'
Magick.xs:210: error: 'MagickNoiseOptions' undeclared here (not in a function)
however we cannot find ImageMagick binaries installed on your system.
Is ImageMagick is in your path, as recommanded in the 4) point? Open cmd.exe and type convert -v or convert.exe -v. If you don't see informations about Image Magick (Windows have a built-in convert command), it is very likely you have to add it to your path.
You also have to check points 1), 3), and 5). After that try again to run installation process through cpanm.
Trying to install for Citrus Perl, I discovered on debugging through the Perl part of the install that the mingw64 install had not included 'pexports.exe'. Downloading that from https://sourceforge.net/projects/mingw/files/MinGW/Extension/pexports/
and placing it in the mingw64 directory was necessary to solve the problem of a long list of library export symbols not found.
Prior to that I had also set the environment variables CPATH, C_INCLUDE_PATH, and CPLUS_INCLUDE_PATH to point to the "include" directory of the ImageMagick install include directory in C:\Program Files (x86). (When you install ImageMagick you should check the box to install also for Strawberry Perl.)

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