pandoc: Undefined control sequence \colorbox - pdf

Problem
I have a file with a combination of Markdown and LaTex that I would like to convert into PDF. Pandoc seems to work in Ubuntu 20.04 but not in Debian 10.
My Installation
# Installing Pandoc and dependencies
apt-get install pandoc texlive-xetex texlive-latex-recommended
My Markdown
I have the following text in a file called test.md:
\centerline{\Large{\textbf{Test 1}}}
\colorbox{blue!25}{\Large{\textbf{Test 2}}}
**This is a test**
Convertion
# Conversion
pandoc -V geometry:margin=0.7in -s test.md -o output.pdf
In Ubuntu 20.04 a beautiful PDF i generated.
In Debian 10 (Docker) I get the following error:
! Undefined control sequence.
l.62 \colorbox
Am I missing some dependencies in Debian 10? Is there a way to see what Pandoc engine that is used by default? What am I doing wrong?
When running verbose mode it seems the installations are using different engines, however, when I specify the geometry driver such that they are the same, the problem remains.
# Debian 10
*geometry* driver: auto-detecting
*geometry* detected driver: xetex
# Ubuntu 20.04
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
Update: Workaround
Reading several posts on similar problems, I first tried to add \usepackage{xcolor} to the start of the document, but that didn't work. Then I found out that you have to add a YAML-header and then it works. The original problem however still puzzles me.
# Adding this to the start of the document fixed the problem
---
header-includes:
- \usepackage{xcolor}
output:
pdf_document
---

Debian 10 (buster) ships with pandoc 2.2.1, while Ubuntu 20.04 (focal) comes with pandoc 2.5. It seems that you hit a bug which was fixed in the later version.
However, this is curious. The changelog mentions that a bug like this was fixed in version 2.6, which is newer than either of your versions. So I'm honestly a bit puzzled about the exact nature of the bug you triggered.

Related

screen fails on NetBSD, reporting "poll: Invalid argument"

I have installed and used screen many times on several different operating systems. Recently I installed it on a NetBSD-8.0 virtual machine.
$ sudo pkgin install screen
calculating dependencies...done.
1 package to install:
screen-4.8.0nb1
0 to refresh, 0 to upgrade, 1 to install
0B to download, 1098K to install
proceed ? [Y/n] Y
installing screen-4.8.0nb1...
screen-4.8.0nb1: setting permissions on /usr/pkg/bin/screen-4.8.0 (o=root, g=wheel, m=4511)
screen-4.8.0nb1: adding /usr/pkg/bin/screen to /etc/shells
screen-4.8.0nb1: registering info file /usr/pkg/info/screen.info
===========================================================================
$NetBSD: MESSAGE,v 1.5 2005/12/28 17:53:24 reed Exp $
[snip]
===========================================================================
pkg_install warnings: 0, errors: 0
reading local summary...
processing local summary...
marking screen-4.8.0nb1 as non auto-removable
However, when I went to use it, I got an immediate failure.
$ uname -mrs
NetBSD 8.0 amd64
$ ls -l /usr/pkg/bin/screen
lrwxr-xr-x 1 root wheel 12 Apr 6 02:50 /usr/pkg/bin/screen -> screen-4.8.0
$ groups
users wheel
$ screen
poll: Invalid argument
This problem persists even when I first remove, then reinstall the screen package. Any suggestions as to what's wrong?
My guess is that the system used to build binary packages for 8.0 (as of the 8.0_2020Q1 pkgsrc release) is no longer quite compatible with the NetBSD-8.0 release. It is likely running on a newer release, inside a chroot(8) sandbox.
I would recommend using NetBSD-9.0 instead, as that is the latest NetBSD release, or NetBSD-8.2, as that is the latest release in the netbsd-8 branch. Using the latest NetBSD and pkgsrc releases provides better coverage against unpatched vulnerabilities.
However, if you want to keep using NetBSD-8.0, you can get a working screen(1) from the 8.0_2019Q4 pkgsrc release. To have pkgin(1) pull from that release, edit the /usr/pkg/etc/pkgin/repositories.conf file to use this repository URL:
http://ftp.NetBSD.org/pub/pkgsrc/packages/NetBSD/amd64/8.0_2019Q4/All
There is currently likely just one line in the file that is not commented out, and it points to a URL with just 8.0 in it (which on the server is a symbolic link to the latest pkgsrc release). Just replace that line, or comment it out and add the above line.
Then remove and re-install screen:
sudo pkgin remove screen && sudo pkgin install screen

python tensorflow module dependency on glibc

I successfully build bazel and tensorflow from the source code, but when using the tensorflow module I am getting the following error:
./new_python/bin/python
>>>import tensorflow as tf
Error MSG: File "/home/niraj/Ansible/new_python/lib/python2.7/site-packages/‌​tensorflow/python/py‌​wrap_tensorflow.py", line 28, in <module> _pywrap_tensorflow = swig_import_helper()
ImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/niraj/Ansible/new_python/lib/python2.7/site-packages/t‌​ensorflow/python/_py‌​wrap_tensorflow.so)
I am using RHEL6 machine. Any idea how to fix this ?
I found two bug reports on github regarding this very problem
https://github.com/tensorflow/tensorflow/issues/110
https://github.com/bazelbuild/bazel/issues/760
At least I get the impression that getting tensorflow to work on RHEL 6 is at least 'difficult' - as some claim in those two bugreports that they got it to work, with some limitations - if not, at least for now, impossible.
At least for Ubuntu 12.04 and CentOS 6.7 there are solutions. The 2nd answer (mentions CentOS) should work on RHEL 6 as well.
Old/First answer:
According to the link I gathered from this answer, RHEL 6 ships with libc 2.12, not 2.14.
You would have to compile the tensorflow stuff again and link it to an existing libc 2.14 on your system. I'm not quite sure how you were able to compile it without already having libc 2.14 somewhere on your system.
What made the trick for me was updating glibc (in my case to 2.17 version) by:
wget http://copr-be.cloud.fedoraproject.org/results/mosquito/myrepo-el6/epel-6-x86_64/glibc-2.17-55.fc20/glibc-2.17-55.el6.x86_64.rpm
wget http://copr-be.cloud.fedoraproject.org/results/mosquito/myrepo-el6/epel-6-x86_64/glibc-2.17-55.fc20/glibc-common-2.17-55.el6.x86_64.rpm
wget http://copr-be.cloud.fedoraproject.org/results/mosquito/myrepo-el6/epel-6-x86_64/glibc-2.17-55.fc20/glibc-devel-2.17-55.el6.x86_64.rpm
wget http://copr-be.cloud.fedoraproject.org/results/mosquito/myrepo-el6/epel-6-x86_64/glibc-2.17-55.fc20/glibc-headers-2.17-55.el6.x86_64.rpm
sudo rpm -Uvh glibc-2.17-55.el6.x86_64.rpm \
glibc-common-2.17-55.el6.x86_64.rpm \
glibc-devel-2.17-55.el6.x86_64.rpm \
glibc-headers-2.17-55.el6.x86_64.rpm --force --nodeps
I link original answer

Raspberry Pi -fatal error: sys/cdefs.h: No such file or directory

I'm trying to compile gcc5.3.0 on my Raspberry Pi with latest Raspbian system image.
$ ./configure --enbale-checking=release --enable-languages=c,c++,fortran --host=arm-cortexa7_neon-linux-gnueabihf --build=arm-cortexa7_neon-linux-gnueabihf --target=arm-cortexa7_neon-linux-gnueabihf
$ make
However, the original compiler (gcc4.9) complains about not founding sys/cdefs.h when compiling libgcc.
I checked I have libc6-dev and build-essential installed.
So I used grep -R 'cdefs' /usr/include/ to search it and I found it at /usr/include/bsd/. I created the sys directory and made hard links to these headers under /usr/include/bsd/sys.
This time it gave me a more weird error,
/usr/include/stdio.h:312:8: error: unknown type name 'FILE'.
I searched this on stackoverflow, and there's a similar question, https://stackoverflow.com/a/21047237/5691005. But when I removed /usr/include/sys and /usr/include/bsd, then reinstalled libc6-dev, I cannot find sys/cdefs.h under /usr/include, and the compiler gave errors still.
I'm now totally lost. Any suggestion will be appreciated.
I had similar problem with compiling gcc-8.2. I tried to do as described here with reinstalling:
sudo apt-get --reinstall install libc6 libc6-dev
After that I was locating all missing headers:
find / -name cdefs.h
and copying them to /usr/include:
those steps allowed only to move forward but I still didn't manage to completely build gcc.
The best solution I found is to download compiled version of gcc-8.1 from:
https://solarianprogrammer.com/2017/12/07/raspberry-pi-raspbian-compiling-gcc/
I also ran into this problem when creating a containerized build environment for cross-compiled Qt applications for raspberry pi 4.
I found I needed to edit the mkspec for the linux-rasp-pi4-v3d device and add another cflag so that gcc could find the header from my Raspi sysroot that was used to cross-compile Qt.
Specifically under qtbase/mkspecs/devices/linux-rasp-pi4-v3d-g++/qmake.conf:
QMAKE_CFLAGS = -march=armv8-a -mtune=cortex-a72 -mfpu=crypto-neon-fp-armv8 -I$$[QT_SYSROOT]/usr/include/arm-linux-gnueabihf

Unable to import matplotlib._png (pylab)

I am unable to import matplotlib._png:
import matplotlib._png as _png ImportError:
/home/james/opt/python/virtualenvs/work/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/_png.so:
undefined symbol: png_set_longjmp_fn
This error prevents me from running import pylab (sincce this ultimately imports matplotlib._png).
I installed matplotlib from source, and made sure to add the path with local installations (/home/james/local) to basedir in setupext.py before running python setup.py install.
REQUIRED DEPENDENCIES AND EXTENSIONS
numpy: yes [version 1.7.1]
dateutil: yes [using dateutil version 2.1]
tornado: yes [using tornado version 3.0.1]
pyparsing: yes [using pyparsing version 1.5.7]
pycxx: yes [Couldn't import. Using local copy.]
libagg: yes [pkg-config information for 'libagg' could not
be found Using local copy.]
freetype: yes [version 16.0.10]
png: yes [version 1.2.10]
My research so far:
As can be seen above, matplotlib seems to find version 1.2.10 even though the version that I have under /home/james/local is 1.6.2:
$ find . -iname '*libpng*'
./libpng16.so.16.1.0
./libpng16.so
./libpng16.so.16
./libpng16.a
./libpng.a
./libpng.so
./libpng16.la
./pkgconfig/libpng.pc
./pkgconfig/libpng16.pc
./libpng.la
More specifically, I modified the following line in setupext.py with:
return basedir_map.get(sys.platform, ['/home/james/local', '/usr/local', '/usr'])
but matplotlib seems to have found the system version:
$ locate libpng
/usr/lib/libpng.so
/usr/lib/libpng.so.3
/usr/lib/libpng.so.3.10.0
/usr/lib/libpng12.a
/usr/lib/libpng12.so
/usr/lib/libpng12.so.0
/usr/lib/libpng12.so.0.10.0
Could this be the problem? Why am I unable to import matplotlib._png?
Update:
Looking at setupext.py, it looks like python setup install queries pkg-config through the SetupPackage method _check_for_pkg_config to determine the version of libpng I have installed. It turns out that pkg-config is returning the system installation:
$ pkg-config --libs libpng
-lpng12
even though I have updated basedir in matplotlib's setupext.py, and LD_LIBRARY_PATH to make them point to the the more recent version of libpng that I have locally installed.
Any ideas on how to have pkg-config return the right version?
It's a pkg-config issue; matplotlib's installation is (unfortunately, or perhaps not) relying too much on pkg-config's output.
Assuming you have build libpng the normal way, there should be a pkgconfig subdirectory in your /home/james/local/lib, which contains libpng.pc (and libpng16.pc). When setupext.py runs pkg-config, the latter should of course try and pick up the correct .pc file for libpng. For that, use the PKG_CONFIG_PATH variable and point it to the pkgconfig subdirectory:
$ export PKG_CONFIG_PATH=/home/james/local/lib/pkgconfig
Then, install matplotlib again, and see that it now finds the correct libpng version:
$ python setup.py build
basedirlist is: ['/usr/local', '/usr']
============================================================================
BUILDING MATPLOTLIB
matplotlib: 1.1.0
python: 2.7.4 (default, Apr 8 2013, 16:36:47) [GCC 4.4.5]
platform: linux2
REQUIRED DEPENDENCIES
numpy: 1.7.0
freetype2: 12.0.6
OPTIONAL BACKEND DEPENDENCIES
libpng: 1.6.1
Tkinter: Tkinter: 81008, Tk: 8.4, Tcl: 8.4
(For me, with a different PKG_CONFIG_PATH of course. Yes, I may want to upgrade some dependencies.)
Note that I didn't even alter basedirlist; it's just at its default.
In case pkg-config fails to now pick up some other package, just add more directories to PKG_CONFIG_PATH with colons in between. But I guess this should be enough.
Try
export LD_LIBRARY_PATH=/home/james/local/lib
and then execute Matplotlib... that would point matplotlib to your local version.

Install apache module X-Sendfile on MAMP

How can I install X-Sendfile apache module so that MAMP can use it?
I have followed these instructions to install X-Sendfile, but it didn't work (it seems like it just installed it for the default apache installation). I also tried to manually copy /usr/libexec/apache2/mod_xsendfile.so to /Applications/MAMP/Library/modules/, but that produced the following error when restarting Apache:
Cannot load /Applications/MAMP/Library/modules/mod_xsendfile.so into server: cannot create object file image or add library
naabster's answer is correct if your MAMP binary is built for the same architecture as your kernel. The problem you're having might be that MAMP is not built using the same architecture -- I have Lion running here (10.7.3) with XAMPP 1.7.3 and I just ran across the same issue you were having.
Here's how I figured out what was wrong on my system, and how I fixed it. If your issue is the same as mine, then you should be able to follow along and verify as you go.
First, here's the output of 'uname -a' to show you that what I'm running:
Darwin Tads-Mac-Pro.local 11.3.0 Darwin Kernel Version 11.3.0:
Thu Jan 12 18:47:41 PST 2012; root:xnu-1699.24.23~1/RELEASE_X86_64 x86_64
Here are the steps I took to track down the problem and fix it:
Figure out what attributes the other (working) modules had that my freshly-built xsendfile module was missing. I picked mod_headers.so as an example. The command to find that info is 'file [filename]'. I'm running this from a terminal cd'd to the /Applications/XAMPP/xamppfiles/modules directory:
file mod_headers.so
mod_headers.so: Mach-O universal binary with 2 architectures
mod_headers.so (for architecture i386): Mach-O bundle i386
mod_headers.so (for architecture ppc): Mach-O bundle ppc
As you can see, XAMPP kindly provides a universal binary that supports i386 and ppc architectures. However, because the Lion kernel is running x86_64, everything I build using apxs unless I tell it to otherwise will be x86_64.
Check the mach-o bundle type and architecture(s) supported by the module that was built with the recommended apxs build command ('sudo apxs -cia mod_xsendfile.c'). Because we're passing '-i' the apxs will install the .so into the default apache modules dir ... /usr/libexec/apache2...
file /usr/libexec/apache2/mod_xsendfile.so
/usr/libexec/apache2/mod_xsendfile.so: Mach-O 64-bit bundle x86_64
Just to double-check that this is the problem you can also look at the httpd (apache) binary:
file /Applications/XAMPP/xamppfiles/bin/httpd
/Applications/XAMPP/xamppfiles/bin/httpd: Mach-O universal binary with 2 architectures
/Applications/XAMPP/xamppfiles/bin/httpd (for architecture i386): Mach-O executable i386
/Applications/XAMPP/xamppfiles/bin/httpd (for architecture ppc): Mach-O executable ppc
Well now, that certainly will not work with an apache instance built without an x86_64 image. Trust, but verify, eh!
Now that I'm certain I understand the issue, let's re-build the .so with the proper architecture forced on the apxs command line. To do that I'm just adding two new params, Wl (linker flags) and Wc (compiler flags). The -i means 'install' (move .so into the modules directory) and the -a means 'activate' (add or re-enable LoadModule line in the httpd.conf)
sudo apxs -cia -Wl,"-arch i386" -Wc,"-arch i386" mod_xsendfile.c
re-check that our new .so supports an architecture that matches the Apache installed (i386, not x86_64)
file /Applications/XAMPP/xamppfiles/modules/mod_xsendfile.so
/Applications/XAMPP/xamppfiles/modules/mod_xsendfile.so: Mach-O bundle i386
Awesome. Now then, copy this turkey into the XAMPP install dir:
sudo cp /usr/libexec/apache2/mod_xsendfile.so /Applications/XAMPP/xamppfiles/modules/
And add the LoadModule line to the /Applications/XAMPP/xamppfiles/etc/httpd.conf.
LoadModule xsendfile_module modules/mod_xsendfile.so
You should be able to fire up the server using either the UI or the apachectl script found in the xamppfiles/bin directory.
Hope that helps you.
Also, I did a pretty decent due-diligence search and found just about squat looking for 'XAMPP X-SendFile cannot create object' in the Goog. What I did find was your question here, once I eliminated the 'XAMPP' since I was searching for 'XAMPP', not 'MAMP'
I started out with the 'x'AMP stack something like 10 years back using LAMPP, then WAMPP but the ApacheFriends guys call theirs XAMPP now for all of the platforms they support. I prefer using theirs since I know if I have to set up on a Windows server I can just download the same package that I use now but for Windows and I can expect to find all of the same servers installed without (too many) surprises.
So, just to be (very) thorough, the other way to discover these types of problems more easily is via Console.app. Open that up, filter on org.apache.httpd and you should see something similar to this:
httpd: Syntax error on line 117 of /private/etc/apache2/httpd.conf: Cannot load
/usr/libexec/apache2/mod_xsendfile.so into server:
dlopen(/usr/libexec/apache2/mod_xsendfile.so, 10): no suitable image found.
Did find:\n\t/usr/libexec/apache2/mod_xsendfile.so: mach-o, but wrong architecture
You can also get that from a command line when you start the apache server manually:
sudo apachectl -E /tmp/foo.txt -k start; tail -f /tmp/foo.txt
This worked for me:
Install mod_xsendfile according to this for the default OsX Apache server.
copy /usr/libexec/apache2/mod_xsendfile.so to /Applications/MAMP/Library/modules/
Edit the Mamp httpd.conf file and add this line: LoadModule xsendfile_module modules/mod_xsendfile.so
Restart Mamp