Using Ubuntu, how do I install DBD::Sybase from CPAN? - sql-server

Whenever I try to build DBD::Sybase to connect to MSSQL I get an error,
$ sudo cpanp install DBD::Sybase
Installing DBD::Sybase (1.15)
Running [/usr/bin/perl /usr/bin/cpanp-run-perl /home/ecarroll/.cpanplus/5.14.2/build/DBD-Sybase-1.15/Makefile.PL INSTALLDIRS=site]...
Can't find any Sybase libraries in /etc/lib or /etc/lib64 at /home/ecarroll/.cpanplus/5.14.2/build/DBD-Sybase-1.15/Makefile.PL line 155, <IN> line 44.
BEGIN failed--compilation aborted at /usr/bin/cpanp-run-perl line 11, <IN> line 44.
[ERROR] Could not run '/usr/bin/perl Makefile.PL': Can't find any Sybase libraries in /etc/lib or /etc/lib64 at /home/ecarroll/.cpanplus/5.14.2/build/DBD-Sybase-1.15/Makefile.PL line 155, <IN> line 44.
BEGIN failed--compilation aborted at /usr/bin/cpanp-run-perl line 11, <IN> line 44.
-- cannot continue
[ERROR] Unable to create a new distribution object for 'DBD::Sybase' -- cannot continue
*** Install log written to:
/home/ecarroll/.cpanplus/install-logs/DBD-Sybase-1.15-1374605483.log
Error installing 'DBD::Sybase'
Problem installing one or more modules
I've also gotten this error on other Debian systems.

There are two ways to do that,
(a) with the freetds that the distro provides
or, (b) installing the vanilla freetds upstream and building against that.
The second option (b) is always possible, but then your system may have two different versions of freetds.
The first option can not be done without some hacking and the author will not fix it. He is simply hard headed and wants to fix internal structures to match the OS he uses rather than making it accepting of other configurations.
Internally DBD::Sybase expects there to be a directory, and a $libdir (a subdirectory with lib or lib64). The directories DBD::Sybase requires to build properly are not provided by the Debian package freetds-dev; the Debian package installs to /usr/include which doesn't have a lib or a lib64 subdirectory. You can get around this by fooling make and recreating that structure, first make sure you have freetds-dev installed,
sudo apt-get install freetds-dev
Then link it to create a pseudo-package. On my 64 bit machine, it looks something like this.
mkdir /tmp/freetds
ln -s /usr/lib/x86_64-linux-gnu/ /tmp/freetds/lib64
ln -s /usr/include /tmp/freetds/include/freetds
Now, it should work and you can build DBD::Sybase against system libraries.
sudo SYBASE=/tmp/freetds cpanp install DBD::Sybase
Viola.

To install modules for the system perl, you can install the packages from the Ubuntu repositories. While these may be out of date, library dependencies are resolved aoutomatically. In this case, a
$ sudo apt-get install libdbd-sybase-perl
should do the trick.

I believe you have to make the include subdirectory, otherwise the second ln will fail:
mkdir /tmp/freetds/include

Related

Installing TinyTeX in a Singularity container

I'm writing a paper in RMarkdown and for better reproducibility, I want to containerize all required software in a singularity container. Unfortunately, when I try to install TinyTeX (which is recommended for Rmarkdown and I would prefer over TeXLive to not inflate the container more than needed), it fails with the following error message (the full build log is pasted here):
Can't locate TeXLive/TLConfig.pm in #INC (you may need to install the TeXLive::TLConfig module) (#INC contains: /~/.TinyTeX/texmf-dist/scripts/texlive /~/.TinyTeX/tlpkg /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at ~/.TinyTeX/bin/x86_64-linux/tlmgr line 100.
BEGIN failed--compilation aborted at ~/.TinyTeX/bin/x86_64-linux/tlmgr line 100.
This is the build definition file, basically it uses a very slimmed down ubuntu 18.04 and then executes the %post section to install software
BootStrap: library
From: ubuntu:18.04
%post
# Add universe repository
echo "deb http://us.archive.ubuntu.com/ubuntu bionic universe" >> /etc/apt/sources.list
apt -y update
# Install utilites
apt install -y wget
# Install R
apt install -y r-base-core
## Install RMarkdown and TinyTeX
R --slave -e 'install.packages(c("rmarkdown","tinytex")); tinytex::install_tinytex()'
# Clean
apt-get clean
%environment
export LC_ALL="en_US.UTF-8"
%labels
Author DP
I have also tried tinytex::install_tinytex(dir="/opt/tinytex") but that didn't seem to change anything. Does anyone have an idea what's wrong?
That error message is complaining that your image (or, more likely, your path) is missing the TeXLive::TLConfig perl module.
My guess is that the path contents are not being rehashed with the installed modules after the install. The simplest solution is to break it into two commands:
R --slave -e 'install.packages(c("rmarkdown","tinytex"))'
R --slave -e 'tinytex::install_tinytex()'
Installation succeeds when I try that locally.
A potentially useful alternative, if the image is just for document generation, could be converting a docker image with rmarkdown and tex (e.g. https://hub.docker.com/r/rocker/verse) to a singularity one.
With singularity pull docker://rocker/verse you can do that for the latest version, or for a specific version with verse:version_number.

npm / yeoman install generator-angular without sudo

I tried to install generator-angularjs using Yo (Yoeman) without sudo:
npm install -g generator-angular
I get:
Error: EACCES, mkdir '/usr/lib/node_modules/generator-angular'
When I type in sudo yo, yo tells me that I should not use sudo (which is perfectly understandable).
I have a ~/node_modules directory - why doesn't yo install its packages there?
Generators are designed to be installed globally. Otherwise, you always have to install the generator you're about to use in each project, which is unnecessarily painful. Also, you don't get to see the lovely yo menu which lists you all the available generators (unless of course, you install them all locally):
Setting up npm for global installation
So, how do we get npm to install packages globally? As you correctly said, you should never, ever run yo with sudo. There are lots of different solutions to this problem and you can spend hours discussing their pros and cons religiously.
I personally dislike installing my user packages into the global /usr/ folder. /usr/ is for software that is shared across all users on the computer. Even if it's only using the machine, there are still good reasons to respect the way the Unix file system hierarchy is designed. For example if you decide at one point to wipe your whole node installation.
My preferred way of enabling npm to install packages globally without breaking out of $HOME is to set a local node prefix. This is as easy as running
echo 'prefix = ~/.node' >> ~/.npmrc
in your local shell. After that, you want to adjust your $PATH, to point to the new installation destination for global node executables by adjusting your favorite shell's config. E.g. by adding
export PATH="$PATH:$HOME/.node/bin"
to your ~/.bashrc. After that, you can happily run npm install -g generator-angular without sudo, without running into permission conflicts and if something is completely broken and you want to start from scratch, all you need to do is remove your ~/.node directory.
Thanks to #passy I managed to finally get this working on ubuntu 13.04 (in case anyone is having similar set up issues) with the following :
sudo apt-get update
sudo apt-get install python-software-properties python g++ make
sudo add-apt-repository ppa:chris-lea/node.js
sudo apt-get update
sudo apt-get install nodejs
trying to run:
npm install -g yo
resulted in
Error: EACCES, mkdir '/usr/lib/node_modules/yo'
Fixed using:
echo prefix = ~/.node >> ~/.npmrc
echo 'export PATH=$HOME/.node/bin:$PATH' >> ~/.bashrc
. ~/.bashrc
Running:
yo webapp
resulted in:
Error: EACCES, permission denied '/home/username/.config/configstore/update-notifier-yo.yml'
Fixed using:
sudo chown yourusername:yourusername /home/yourusername/.config/configstore/update-notifier-yo.yml
hi in my case (on ubuntu 12.04), the prefix addition in ~/.npmrc did not changed anything.
if so, build the node package by yourself and install it in /opt/node or /home/user/.node.
I had an almost identical error involving a rogue .yo-rc.json file in my root directory from a project I installed earlier. Yeoman was switching cwd from the installation dir to root dir half way through the installation, but was only outputting the EACCESS permissions error without any details that the installation directory was /. It took ages to figure out why this was, and involved debugging through the Yeoman source, but I eventually learned that Yeoman will look up through the directory tree until it finds a .yo-rc.json, and generate the code there by calling chdir to the new location.
Yeoman should maybe check that the user has write permissions for the directory. Alternatively, it could mention in the output either that the cwd has changed, or print the name of the installation directory if where it finds .yo-rc.json is different than cwd.
The command for finding rogue .yo-rc.json files
sudo find / -name .yo-rc.json
From yoeman getting started page appears the command:
yo doctor
In my case, $NODE_PATH (which in my case, Ubuntu 14.04, is defined in /etc/profile.d) isn't the same than npm root. Adding in npm root in $NODE_PATH solve the problem.
I have been trying to get yeoman to play nice with my vagrant box and this is what I had to do to install npm packages globally without sudo on ubuntu:
1. Create the directory to store global packages
$ mkdir "${HOME}/.npm-packages"
2. Tell npm where to put any packages installed globally
Insert this snippet into your ~/.npmrc file:
prefix=${HOME}/.npm-packages
3. Make sure that npm can locate installed binaries et cetera
Insert this snippet into your .bashrc/.zshrc:
NPM_PACKAGES="${HOME}/.npm-packages"
PATH="$NPM_PACKAGES/bin:$PATH"
// `unset` `manpath` to allow inheritance from `/etc/manpath` with
// the `manpath` command
unset MANPATH // remove this line if you have previously modified `manpath`
export MANPATH="$NPM_PACKAGES/share/man:$(manpath)"
4. Run the following or restart terminal
$ source ~/.bashrc
Hope this helps anyone who finds themselves in a similar situation.

Lost ability to run as sudo following MacPorts upgrade

I recently updgraded MacPorts from 1.9.2 to 2.0.3. Since then, I've lost the ability to run as sudo.
sudo: can't stat /opt/local/etc/sudoers: No such file or directory
sudo: no valid sudoers sources found, quitting
Unsure if these are related, but I'm wondering what the best course of action is at this point.
port installed returns
sudo #1.7.4p2_0
sudo #1.7.7_0 (active)
Further investigation suggests I've installed MacPorts' sudo without an accompanying /opt/local/etc/sudoers file. I've managed to create such a file using visudo, copying the content of /etc/sudoers, chmod to 0440 and ownership to root:wheel.
I guess the question now is whether I should use MacPorts' sudo or uninstall it? And how did I end up with installing the MacPorts' sudo?
Not a Mac man myself, but have a look at this page:
http://developer.apple.com/library/mac/#documentation/Darwin/Reference/ManPages/man5/sudoers.5.html
...and also a look at the man page for visudo, which is used to edit the sudoers file:
http://developer.apple.com/library/mac/#documentation/Darwin/Reference/ManPages/man8/visudo.8.html#//apple_ref/doc/man/8/visudo

macports repair/replace command?

I accidentally removed /opt/local/bin/perl5.8.9 , which seems to be the main binary file for perl compiled by macports.
Now I have a lots of ports depending on perl5, but don't want to uninstall and reinstall all of them.
Is there a way to repair or reinstall and replace a port?
Or is /opt/local/bin/xx only a symlink? If so, where is the original binary?
I'd try this:
$ port -f uninstall perl5.8 # Force removal of perl5.8
$ port install perl5.8 # Install it again

Can deb packages from one machine be installed in another?

Install python-netinterfaces on machine1 using apt-get
Copy the python-interfaces deb package cached in /var/cache/apt/archive from machine to machine2
Change the /etc/apt/sources.list to point to the directory where the package is copied in machine2
Run teh following command
sudo apt-get install python-interfaces
It inturn tries to install python-chardet-whl
and I get the error
warning: the following packages cannot be authenticated!
If I install the python-chardlet-whl from command line it fails with the authentication error message. however, it passes with --force-yes message.
I searched in the web for solutions and tried some suggestions like apt-key update, but nothing worked.
Is it possible to install package installed from one machine in another?
note: Both have same hardware and OS/other-software is installed is same
Are you sure destination machine has same repository list as source machine?
apt-cache showpkg python-chardet-whl
After adding repository to destination machine it would show you repository that package belongs to
Then you need to run:
sudo apt-get update
To update the repository list, by doing this you problem should fix
Also make sure that package does not need any dependency that is not installed on the system.

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