I recently upgraded my Ubuntu installation from 18.04 to 20.04. This upgraded my pandoc to version 2.5. This brought some incompatibilities like --smart not being supported anymore, and one more that I haven't been able to fix.
I'm trying to convert .tex files to .md. Suddenly pandoc is choking on underscores that were just fine before:
Error at "source" (line 281, column 50):
unexpected _
We can set the initial value of \texttt{recursion_depth} to a sensible value such as 3, as discussed previously.
^
I haven't been able to find anything in the documentation saying that underscore handling has changed in recent versions. I thought that maybe I'm missing some extension for the input or output format, but I haven't found anything either.
Any suggestions?
I guess this was a bug in 2.5 - upgrading to the latest version (2.14 at this time) made the error go away.
Related
I am attempting to install the Biomethyl package as part of a Bioinformatics internship I am working on. However I cannot seem to install the package properly. Having looked for answers over the last few days and failed, I turn to you guys.
Overall, the error I cannot seem to fix is the untar2 error (shown below)
I tried a wide variety of solutions, none of which worked.
Non-coding solutions that were attempted are the following:
i) Changing the directory of the package, locations ranged from desktop, to documents, and in the R folder itself
ii) Completely uninstalling R and RStudio as well as re-downloading the package
iii)Manually extract components of the package (failed miserably)
iv)Contacting the creator, this led me to see that my version of R (3.6) is not the issue. However this problem seems to be isolated to myself as he has not heard of similar problems from other users. Through this interaction, I also believe that there is no issue with the downloaded file.
v)Disabling all other computer functions that may have interfered with files being created or added, basically disabled my BitDefender, even if all proper authorizations were given to R and Rstudio.
As for the code, this is the code that should work as provided by the creator's github ( https://github.com/yuewangpanda/BioMethyl )
> install.packages("C:/Users/yohan/OneDrive/Documents/R/BioMethyl-master/BioMethyl_1.1.tar.gz", repos = NULL)
Which resulted in the following error
> install.packages("C:/Users/yohan/OneDrive/Documents/R/BioMethyl-master/BioMethyl_1.1.tar.gz", repos = NULL)
Installing package into ‘C:/Users/yohan/OneDrive/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Error in untar2(tarfile, files, list, exdir, restore_times) :
incomplete block on file
Warning in install.packages :
installation of package ‘C:/Users/yohan/OneDrive/Documents/R/BioMethyl-master/BioMethyl_1.1.tar.gz’ had non-zero exit status
Along with this, I tried swapping around the slashes, doubling them up, inverting their orientation (front slash instead of backslash).
I also tried adding type="source" which resulted in the same error.
Additionally, I tried to run the code directly into the console, again, it did not work.
Lastly, I tried installing it directly from the github repo and not from the downloaded file, but this was not possible due to privacy limitations on the github repo.
I thank you in advance for your help, also, if there are any issues with the question format please let me know and I will edit them accordingly.
Additional information:
OS: Windows 10
R Version:
> version
_
platform x86_64-w64-mingw32
arch x86_64
os mingw32
system x86_64, mingw32
status
major 3
minor 6.0
year 2019
month 04
day 26
svn rev 76424
language R
version.string R version 3.6.0 (2019-04-26)
nickname Planting of a Tree
I ended up figuring it out, i'll leave the answer here in case anyone else encounters this problem.
The issue seems to be downloading the repository as a whole, if you download the .tar.gz file in its unzipped format, it will work (at least it did for me)
This is the exact link from which I downloaded my copy of the file that worked for me.
https://github.com/yuewangpanda/BioMethyl/blob/ffcba473a3b12a159ce2dfdaf63c4f63d84b40ef/BioMethyl_1.1.tar.gz
Best of Luck
Y.Lefol
I am trying to run an example from the plexe-veins folder on my Mac OS High Sierra system, to my knowledge I have installed all necessary libs.
The only problem I have is with installing the omnetpp__0.7-1.tar.gz file. Some research online leads me to believe the version of R on my computer is unable to compile the file since the file is an older version. I have tried installing older versions but failed because of compatibility issues with my OS. I am at a complete dead-end with regards to that.
When I run the platooning example, the GUI opens up of and I am able to run the simulation for a few seconds until I get the error:
(omnetpp::cDoubleParImpl)simulationDuration: Cannot cast from type
double to integer -- in module (SimplePlatooningApp)
scenario.node[0].appl (id=11), at t=1.01s, event #204 TRAPPING on the
exception above, due to a debug-on-errors=true configuration option.
Is your debugger ready? ./run: line 2: 90810 Trace/BPT trap: 5
../../run "$#"
The version of omnet I installed is omnet++-5.4 and I also followed the procedure from the manual which includes the "./configure" and "make" commands. I run the example by entering the dir in question and run:
./run -u Cmdenv -c Sinusoidal -r 2
It appears my problem was multi-pronged. These are the steps I took to solve the problem:
I followed the suggestions offered by Julian with regards to the version of Omnet++ I installed, I downgraded to Omnet++ 5.0
I also noticed that I had a previously installed sumo (not plexe-sumo) on my system and thus it seemed to be running the simulation instead of plex-sumo. So I uninstalled it.
There also seemed to be a problem with a static declaration of 'abs'followed by a non-static declaration which caused omnetpp_0.7.1.tar.gz to fail while compiling. I solved this issue by locating the stdlib.h file in xcode.app/Contents/Developer/Toolchains/usr/include/v1 and commented out "inline _LIBCPP_INLINE_VISIBILITY" (there should be a better fix).
I appreciate the help!!!
The part of OMNeT is a casting error. This is due to OMNeT++ 5.4 which changed some internals on parameters and therefore is simply to new for Plexe 2.0. You have to use an older version like OMNeT 5.0 or 5.1 as this is what Plexe 2.0 was built upon.
Also see these posts:
Error in Veins tutorial simulation
Error while running example of the veins in the last step of the installation
Is casting possible in parameter expressions in OMNET++?
so I am trying to compile openjdk8 from sources, but I am stuck at missing files problem in the end of compilation process...
Here is the software that I use:
Windows 7 SP1 x64
Windows SDK for Windows 7.1
Microsoft .NET Framework 4
Visual Studio 2010 Express Edition
GNU make 3.82 (compiled by myself)
Freetype 2.3 (compiled by myself)
Oracle JDK 1.7 update 71
Direct X 9.0 (August 2009)
Cygwin
Here are the manuals which I was reading from:
Official README
Royvanrijn's build guide
Some other build guide
Build guide using MSYS
With all these guides I am able to let it compile, however during the Building Images - step , I get an error that some files are missing ( and they are indeed missing ) , which makes me think that something has gone wrong during the build...
There are several points where I afraid I might be doing something wrong...
Cygwin
Right now I use cygwin version 2.8. The openjdk configure script requires cygwin version >1.7 but fails to recognize that 2.8 is greater than 1.7 and throws me an error, so i've tweaked the script (made build work like 2 months ago)...
./configure
My configure command looks as follows:
./configure --disable-ccache --with-freetype=/cygdrive/c/freetype
Maybe I need more arguments here to make it work ( note that i've copied self compiled make executable to cygwin bin folder, so that i dont need to provide its location )
Visual Studio C++ 2010 Express
I would rather try Professional Trial version, but it cannot be found anywhere anymore... (except torrents...) I have a strong feeling that Express version is not suitable for openjdk build. I also get that error with missing ammintrin.h file, but it is easily resolved by creating the empty header file in the include folder of Visual Studio installation.
My basic procedure of building is:
Install all the software above
hg clone http://hg.openjdk.java.net/jdk8/jdk8
./get_source.sh
./configure --disable-ccache --with-freetype=/cygdrive/c/freetype`
make clean images
However, here how it ends :
Does anyone have any clue of how to solve this?
I found the proper fix: using the Cygwin installer, downgrade Grep to 2.27, which properly ignores CRLF line endings.
Run the Cygwin setup (e.g. setup-x86_64.exe)
Advance through the setup wizard until you get to the package selection
Choose "Full" from the View drop-down menu
Type "grep" into the search field
Click the icon in the New column until it shows a 2.x version (2.27 as of this writing)
Click Next and then Finish.
I found myself in the same position as you, except in my case I need OpenJDK build to be repeatable, so "run make repeatedly until it finishes" wasn't an acceptable solution.
Through some experimenting, I found the root cause:
grep was failing because the file being processed had Windows line endings (CRLF)
The Windows line endings were due to the fact that the file is generated by a Java app (fixpaths) which emits platform-native line endings
Identifying fixpaths led me to an old OpenJDK e-mail thread, which reported that some users were having the same problem and fixed it by downgrading.
This gave me the idea to try downgrading grep. I did so, and it worked.
So, after couple of days at this task my only approach was to ignore the errors with the missing files and continue extracting files... This resulted in still working jdk image, which i currently use. My guess is that the errors come frome Oracle boot jdk. Since i am compiling an openjdk, it cannot find oracleJDK files in its headers and thus produces errors.
So, if anyone also gets same errors a me, try to ignore the missing files error and continue the images build.
Error: Due to incompatibility with several Python libraries, path cannot contain non-ascii characters (special characters or diacritics). Please choose a different path
path is set from browse in installer and has no special characters ?
Found that this is an Anaconda 4.3.0/4.3.0.1 bug caused by the NSIS installer. You can find the bug description posted begin February 2017 here. In that post mingwandroid proposed also a fix proposal that could be integrated in the 4.3.12 release.
I've been spending a couple of days trying to set up my project in Code::Blocks on a Macbook pro (2006) with OSX 10.8.1 (I got it for free!).
After installing Xcode, command line tools, and then restarting I got the basic gcc support (will uninstall Xcode and then just use cmd line tools when I get things working). Then I proceeded to cmake and make install GLEW, GLFW3 and GLM (GLM only needed make install). I then rebootet once more to get things mostly working, I'm down to four errors, and these come from the func_trigonometric.inl file that GLM uses. The build message is as follows:
/usr/local/includ... 165 current parser token 'if'
/usr/local/includ... 37 parsing namespace 'glm'
/usr/local/includ... 160 parsing function body 'tanh'
/usr/local/includ... 160 in compound statement ('{}')
note: diagnostic msg: Error generating preprocessed source(s).
I'm not sure where to go from here.
EDIT:
I tried to install GLM the normal way with just dragging the folder to the location it should be in (include), the error still persists, I really need help with getting rid of this error.
I found out what was causing the errors, the version of GLM I was using was too new for OSX 8.1.1
Changing out GLM from version 9.6 to version 9.4 fixed the errors.