My ultimate goal is to run a twiki website for my research group.
I have space on RedHat server that is running Apache, etc., but upon which I do not have root access. Since I cannot install perl modules with the current permissions, I've decided to manually install a local version of perl. Got that working no problem. The following modules are required to get twiki to work:
FreezeThaw - http://search.cpan.org/~ilyaz/FreezeThaw
CGI::Session - http://search.cpan.org/~markstos/CGI-Session
Error - http://search.cpan.org/~shlomif/Error
GD - http://search.cpan.org/~lds/GD
HTML::Tree - http://search.cpan.org/~petek/HTML-Tree
Time-modules - http://search.cpan.org/~muir/Time-modules
I have installed FreezeThaw, CGI, Error, and it fails on GD with the following error:
UNRECOVERABLE ERROR Could not find gdlib-config in the search path.
Please install libgd 2.0.28 or higher. If you want to try to
compile anyway, please rerun this script with the option --ignore_missing_gd.
In searching for how to get around this newest obstacle, I found a previous SO question: How to install GD library with Strawberry Perl asked about installing this and the top answer suggested manually compiling gdlib. You'll note, however, that that link is broken. The base site: http://www.libgd.org/ is basically down saying to go to the project's bitbucket page.
So I got the tarball from that page and am trying to install it. The following problems occur when I follow the instructions included. README.TXT says: "If the sources have been fetched from CVS, run bootstrap.sh [options]."
Running bootstrap.sh yields:
configure.ac:64: warning: macro `AM_ICONV' not found in library
configure.ac:10: required directory ./config does not exist cp: cannot
create regular file `config/config.guess': No such file or directory
configure.ac:11: installing `config/config.guess' configure.ac:11:
error while copying cp: cannot create regular file
`config/config.sub': No such file or directory configure.ac:11:
installing `config/config.sub' configure.ac:11: error while
copying cp: cannot create regular file `config/install-sh': No such
file or directory configure.ac:28: installing `config/install-sh'
configure.ac:28: error while copying cp: cannot create regular
file `config/missing': No such file or directory configure.ac:28:
installing `config/missing' configure.ac:28: error while copying
configure.ac:577: required file `config/Makefile.in' not found
configure.ac:577: required file `config/gdlib-config.in' not found
configure.ac:577: required file `test/Makefile.in' not found
Makefile.am:14: Libtool library used but `LIBTOOL' is undefined
Makefile.am:14: The usual way to define `LIBTOOL' is to add
AC_PROG_LIBTOOL' Makefile.am:14: to configure.ac' and run
aclocal' and autoconf' again. Makefile.am:14: If `AC_PROG_LIBTOOL'
is in `configure.ac', make sure Makefile.am:14: its definition is in
aclocal's search path. cp: cannot create regular file
`config/depcomp': No such file or directory Makefile.am: installing
`config/depcomp' Makefile.am: error while copying Failed
And it says I should also install the following 3rd party libraries:
zlib, available from http://www.gzip.org/zlib/
Data compression library
libpng, available from http://www.libpng.org/pub/png/
Portable Network Graphics library; requires zlib
FreeType 2.x, available from http://www.freetype.org/
Free, high-quality, and portable font engine
JPEG library, available from http://www.ijg.org/
Portable JPEG compression/decompression library
XPM, available from http://koala.ilog.fr/lehors/xpm.html
X Pixmap library
Which I am ignoring for now.
Switching to the generic instructions it says follow the advice in the INSTALL file; which says: "cd to the directory containing the package's source code and type ./configure to configure the package for your system." Which flat does not work: I've cd'ed into every directory of the tarball and running that command does nothing.
So, trying to install twiki required me to install perl, which required me to install the perl modules: FreezeThaw, CGI, Error, HTML, Time-modules, and GD -- which itself required me to install gdlib -- which further suggested I install zlib, libpng, FreeType 2.x, JPEG library, and XPM. And of course, I'm stuck at the installing gdlib stage.
My question is: what other process can possibly demean humanity to such a level? I cannot fathom the depths of cruelty that lay ahead of me as I dive ever deeper into this misery onion. Should I just end it all? Can meaning be brought from this madness? Will the sun come up tomorrow, and if so, does it even matter?
But seriously, any suggestions on what to do differently/better would be much appreciated -- I can't remember what a child's laughter sounds like anymore.
Install the package gd-devel, it contains /usr/bin/gdlib-config.
This should work:
sudo apt-get -y install libgd2-xpm-dev build-essential
Related
I am running a toolkit named RNA Framework that requires ViennaRNA to be installed.
I have installed the ViennaRNA 2.4.14 to run a function named rf-fold, However, I constantly receive this error:
[!] Error: ViennaRNA package's Perl module RNA.pm is required.
Please ensure that `ViennaRNA package v2.2.0` (or greater) is installed and try again
When I check the missing RNA.pm module, I can see it is in this path:
/home/user/ViennaRNA/lib/site_perl/5.28.0/
when I check which Perl I am using (type: which Perl) it gives me:
/home/user/perl5/perlbrew/perls/perl-5.28.0/bin/perl
I tried different ways to install the ViennaRNA, including conda install -c bioconda viennarna, compile and make install from ViennaRNA-2.4.14.tar.gz file from the official website. But I cannot get over this error.
I saw a similar issue here and there is a solution (https://www.perlmonks.org/?node_id=1052814), but I don't fully understand the content. Thanks in advance for any help and sorry if it is a basic question!
I think the RNA.pm come with the package, when you download ViennaRNA-2.4.14.tar.gz and install following this link.
So I found my RNA.pm is in the directory:
/share/apps/ViennaRNA-2.1.7/compile-install/lib/site_perl/5.14.2/x86_64-linux-thread-multi/RNA.pm
And I modified the PERL5LIB environment variable by :
export PERL5LIB=/share/apps/ViennaRNA-2.1.7/compile-install/lib/
Problem solved!
As the title says, the library libpq.so is not in the path given by pg_config --libdir. I install postgresql posqtgresql-devel which provides the package libpq5 which in turn installs the libpq.so.
$ pg_config --libdir
/usr/lib/postgresql10/lib64
$ find /usr/ -name libpq.so
/usr/lib64/libpq.so
Our applications rely on the path given by pg_config --libdir to look for libpq.so but it fails. Is this some problem with OpenSUSE package management or is it that we shouldn't be using pg_config for this purpose?
pg_config provides information about how PostgreSQL was built.
It is usually used to build server extensions, but it should also work with client code like you are trying to do.
Since your PostgreSQL is installed in a path that contains the version, but your libpq.so is not, I'd assume that the latter is a symbolic link rather than being part of the installation package.
If there is no libpq.so in your PostgreSQL lib directory, I'd call that a packaging error. You should discuss that with the packagers.
I'm trying to run this script on my computer (MAC)
http://mkweb.bcgsc.ca/color-summarizer/?download
It's the first time in my life touching the terminal... so you understand that I ask very basic questions. please do forgive me...
basically when i execute the script, I would always get this kind of message :
Can't locate Imager/File/GIF.pm in #INC (you may need to install the
Imager::File::GIF module) (#INC contains:
/Applications/colorsummarizer/colorsummarizer-0.77/bin/lib
/Applications/colorsummarizer/colorsummarizer-0.77/bin/../lib
/Applications/colorsummarizer/colorsummarizer-0.77/bin
/Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18
/Network/Library/Perl/5.18/darwin-thread-multi-2level
/Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2/darwin-thread-
multi-2level /Library/Perl/Updates/5.18.2
/System/Library/Perl/5.18/darwin-thread-multi-2level
/System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-
thread-multi-2level /System/Library/Perl/Extras/5.18) at
/Library/Perl/5.18/darwin-thread-multi-2level/Imager.pm line 1677.
And so I use :
sudo cpan install Imager::File::GIF
for example. But the I get this :
Warning (mostly harmless): No library found for -lgif
GIF: Test code failed: Can't link/include 'gif_lib.h', 'stdio.h',
'errno.h', 'string.h', 'gif'
OS unsupported: GIF libraries or headers not found
Warning: No success on command[/usr/bin/perl Makefile.PL]
TONYC/Imager-File-GIF-0.91.tar.gz
/usr/bin/perl Makefile.PL -- NOT OK
Running make test
Make had some problems, won't test
Running make install
Make had some problems, won't install
Could not read metadata file. Falling back to other methods to determine prerequisites
And ! it seems like even when I appear to install something successfully, The system ask me to re-install them again and again and again...
Maybe I did some very fundamental mistakes ?
Thanks a lot for your attention
The issue identified by the following message is not harmless at all, actually:
Warning (mostly harmless): No library found for -lgif
GIF: Test code failed: Can't link/include 'gif_lib.h', 'stdio.h',
'errno.h', 'string.h', 'gif'
The module uses libgif to do all the heavy work, but it's not installed. Furthermore, the installation procedure needs the library's header files.
Imager::File::GIF provides GIF file format support for Imager.
It requires libgif to be installed, including development headers.
For Linux distributions this typically requires installation of the
associated -dev or -devel package.
Installing the required library and header files might be as simple as asking your OS's package manager to install libgif-dev or libgif-devel.
Try to just install Imager like this, it might be all you need:
sudo cpan Imager
After that it could open gifs for me.
I'm trying to install Math::Pari module but getting error.
I'm installing on Windows Server 2012R2, I've Strawberry perl v5.18.4.1 32-bit currently installed on it.
Actually Math::Pari is dependency for Net::SSH::W32Perl and I want to install that module.
Following is the error log. Please Give me step by step installation procedure.
cpanm (App::cpanminus) 1.7039 on perl 5.018004 built for MSWin32-x64-multi-thread
Work directory is C:\Users\script/.cpanm/work/1438929213.2276
You have make C:\strawberry\c\bin\dmake.exe
You have LWP 6.08
Falling back to Archive::Tar 2.02
Searching Math::Pari () on cpanmetadb ...
--> Working on Math::Pari
Fetching http://www.cpan.org/authors/id/I/IL/ILYAZ/modules/Math-Pari-2.010808.zip
-> OK
Unpacking Math-Pari-2.010808.zip
Entering Math-Pari-2.010808/
Checking configure dependencies from META.json
Checking if you have ExtUtils::MakeMaker 6.58 ... Yes (6.98)
Configuring Math-Pari-2.010808
Running Makefile.PL
Did not find GP/PARI build directory around.
Apparently, you are running a 64-bit Perl built with MicroSoft's compilers.
GP/PARI (at least the versions I know how to work with, 2.1.* and 2.3.*)
cannot be built in this environment. I won't auto-download GP/PARI.
If you believe that this message is printed erroneously, please report
(see files README and INSTALL), and put force_download on the command line:
perl Makefile.PL force_download
One can rerun Makefile.PL after fetching GP/PARI archive (e.g., pari-2.1.7.tgz,
or pari-2.3.4.tar.gz) manually to the current directory, or a (grand)parent
directory of the current directory.
[Keep in mind that the numbers "inside version" of Math::Pari module
correspond to the last versions of GP/PARI it was tested with (additionally,
2.0108* works best with the last 2.1.* version, 2.1.7).
As an alternative to having archive in CWD or its (grand)parent, specify
pari_tgz=PATH_TO_TAR_GZ
option to Makefile.PL.
There is no need to extract the archive, or build GP/PARI; but if you
have it extracted [and patched, if needed], you may specify
paridir=PATH_TO_DIST_DIR
option to Makefile.PL instead of `pari_tgz'. However, in this case
the files WON'T be auto-patched.
As a last-resort solution, there is also a possibility to use an already
compiled PARI library. See the documentation in README and INSTALL files.]
Could not find GP/PARI build directory, please run Makefile.PL
with paridir=/directory option.
-> N/A
-> FAIL Configure failed for Math-Pari-2.010808. See C:\Users\script\.cpanm\work\1438929213.2276\build.log for details.
I thought I'd add a note for anyone coming here as a result of a Google search after their own Math::Pari install fails under Strawberry Perl.
Here is what worked for me (Strawberry 5.22):
A. from the cpan shell, tried to install Math::Pari. this failed
B. Downloaded pari-2.1.7 and placed the extracted folder pari-2.1.7 in the cpan build folder that was created in (0). This is found, by default, in C:\Strawberry\cpan\build
C.perl Makefile.PL Configure machine=none
D. dmake
E. dmake install
It basically means that 64 bit versions of perl are not supported. It also means that if you're sure that you're running a 32 bit version incorrectly detected as 64 bit, you can try opening a command line and then doing
cd C:\Users\script\.cpanm\work\1438929213.2276\
perl Makefile.PL force_download
I am having an infuriating time trying to get an install of apache with perl. I am following the instructions on the mod_perl site located here: http://perl.apache.org/docs/2.0/user/install/install.html
I get as far as the part where it asks me to run this command, but I get an error:
$ perl Makefile.PL MP_APXS=/usr/local/httpd/prefork/bin/apxs
Reading Makefile.PL args from #ARGV
MP_APXS = /usr/local/httpd/prefork/bin/apxs
no conflicting prior mod_perl version found - good.
Configuring Apache/2.4.2 mod_perl/2.0.7 Perl/v5.12.3
[ error] Can't find apr include/ directory,
[ error] use MP_APR_CONFIG=/path/to/apr-config
I ran the commands they suggested for installing apache to install my apache:
$ ./configure --prefix=$HOME/httpd/prefork --with-mpm=prefork
$ make && make install
But I am not sure where this apr-config thing is supposed to be as it doesn't appear to be anywhere in my apache2 folder.
If it might be an issue, I am using Mac OS X 10.7.3. I know an apache server comes with Mac OS X, but I need to do this install on a different computer from the ground up, so I have to start this whole install from the ground up on my computer.
Thanks ahead of time for any help you can provide.
When mod_perl 2.0.8 comes out, I hope that it gets finally httpd 2.4 support, because the current versions surely don't have.
When you fix your initial problems, you will eventually get stuck at ‘conn_rec’ has no member named ‘remote_ip’. Delete httpd 2.4 and use 2.2 meanwhile.
You need to include the path to binary executable file apr-1-config. Run the below command
perl Makefile.PL MP_APXS=/usr/local/apache2/bin/apxs MP_APR_CONFIG=/usr/local/apr/bin/apr-1-config
It worked for me..Hope the same for you too.
On Lion here, my APR include directory seems to be /usr/include/apr-1, but it already came with mod_perl.
$ find / -name apr*
/usr/include/apr-1
...
$ find / -name mod_perl.so
/usr/libexec/apache2/mod_perl.so
If you have the .so already you should be able to just add in your config file:
LoadModule perl_module libexec/apache2/mod_perl.so