I am currently having problems using TinyTeX in a conda environment with Snakemake. I have to install TinyTeX installation files using the command tinytex::install_tinytex() before running the pipeline. This installs TinyTeX outside of the created environment (which isn't that big of a problem... but not preferred either) . The main problem is that every time I execute my Snakemake pipeline it will try to reinstall this installation which I don't want. Could anyone tell me what the easiest way is for me to check whether it's installed already? Should I be using the command Rscript -e \"tinytex:::is_tinytex()\" with an if-statement? And what is the best way to write that if-statement by calling Rscript -e in Snakemake? Or should I just write a boolean text-file on first run which specifies whether TinyTeX has been installed before?
It kinda sucks that the TinyTeX conda dependency doesn't work on its own without additional installation...
Snakemake rule (ignore input/output):
rule assembly_report_rmarkdown:
input:
rules.assembly_graph2image_bandage.output,
rules.assembly_assessment_quast.output,
rules.coverage_calculator_shortreads.output,
rules.coverage_calculator_longreads.output
output:
config["outdir"] + "Hybrid_assembly_report.pdf"
conda:
"envs/r-rmarkdown.yaml"
shell:
"""
cp report/RMarkdown/Hybrid_assembly_report.Rmd {config[outdir]}Hybrid_assembly_report.Rmd
Rscript -e \"tinytex::install_tinytex()\"
Rscript -e \"rmarkdown::render('{config[outdir]}Hybrid_assembly_report.Rmd')\"
rm -f {config[outdir]}Hybrid_assembly_report.Rmd {config[outdir]}Hybrid_assembly_report.tex
"""
Conda YAML:
name: r-rmarkdown
channels:
- conda-forge
- bioconda
dependencies:
- r-base=4.0.3
- r-rmarkdown=2.5
- r-tinytex=0.27
Thanks in advance.
I think I've solved the issue. Instead of calling Rscript -e, I have put the following if-statement in the setup chunk in R Markdown (Which runs before running any other code if i'm correct). I then proceeded to uninstall TinyTeX to see whether it will install for once only which it did.
knitr::opts_chunk$set(echo = TRUE)
library(knitr)
if (!tinytex:::is_tinytex()){
tinytex::install_tinytex()
}
I am running the golang command "go get -t github.com/otiai10/gosseract" , causing the error tessbridge.cpp:5:10: fatal error: leptonica/allheaders.h: No such file or directory, #include <leptonica/allheaders.h>. That library is https://github.com/DanBloomberg/leptonica. How do I install it from source so that the gcc command will work.
Before that command was producing the error "gcc not found", but then I followed https://superuser.com/questions/1294343/install-gcc-in-git-for-windows-bash-environment to setup gcc on windows.
I have not been able to find any references for what gcc expects when it encounters an include<>, and where those files should be located on the file system for it to link properly. Is it possible to install this library manually?
Here is much simpler solution for you. There was no need to install gcc on git-bash.
Install MSYS2. Follow complete installation guide.
On MSYS2 console enter the following commands :
pacman -S mingw-w64-x86_64-gcc
pacman -S mingw-w64-x86_64-leptonica
Add C:\msys64\mingw64\bin to PATH.
First step can be further simplified if you use Chocolatey. Just run these commands in elevated powershell : (Ignore first command if choco is already installed.)
Set-ExecutionPolicy Bypass -Scope Process -Force; [System.Net.ServicePointManager]::SecurityProtocol = [System.Net.ServicePointManager]::SecurityProtocol -bor 3072; iex ((New-Object System.Net.WebClient).DownloadString('https://chocolatey.org/install.ps1'))
Reopen elevated powershell and run these:
choco install -y msys2 --params="/InstallDir:C:\msys64"
refreshenv
$env:Path += ";C:\msys64\usr\bin"
pacman -S mingw-w64-x86_64-gcc
pacman -S mingw-w64-x86_64-leptonica
[Environment]::SetEnvironmentVariable("Path", "C:\msys64\mingw64\bin;" + $env:Path, "User")
As the title said I can't install that specific version of g++ in my current ubuntu (20.04).
I have been trying the usual things as: sudo apt install g++- (and displaying all posibilities but there where only versions from 8 to 10). Same happend looking for gcc possibilities.
Also tried this: gist.github.com/application2000/73fd6f4bf1be6600a2cf9f56315a2d91 (same problem)
And after looking for a while I gave up in my research and ended up here. Hope someone with more wisdom than me can give my a hand with this.
These steps should work:
sudo dpkg --add-architecture i386
sudo apt update
sudo apt upgrade
sudo apt-get install gcc-multilib libstdc++6:i386
wget https://ftp.gnu.org/gnu/gcc/gcc-4.8.5/gcc-4.8.5.tar.bz2 --no-check-certificate
tar xf gcc-4.8.5.tar.bz2
# cd gcc-4.8.5
# ./contrib/download_prerequisites
# cd ..
sed -i -e 's/__attribute__/\/\/__attribute__/g' gcc-4.8.5/gcc/cp/cfns.h
sed -i 's/struct ucontext/ucontext_t/g' gcc-4.8.5/libgcc/config/i386/linux-unwind.h
mkdir xgcc-4.8.5
pushd xgcc-4.8.5
$PWD/../gcc-4.8.5/configure --enable-languages=c,c++ --prefix=/usr --enable-shared --enable-plugin --program-suffix=-4.8.5
make MAKEINFO="makeinfo --force" -j
sudo make install -j
Note that you have to uncomment the .../download_prerequisites on some platform. For me it worked without on Centos 7 or Ubuntu 20 with the mandatory packages installed:
Ubuntu/Debian:
sudo apt install make wget git gcc g++ lhasa libgmp-dev libmpfr-dev libmpc-dev flex bison gettext texinfo ncurses-dev autoconf rsync
Centos:
sudo yum install wget gcc gcc-c++ python git perl-Pod-Simple gperf patch autoconf automake make makedepend bison flex ncurses-devel gmp-devel mpfr-devel libmpc-devel gettext-devel texinfo
Few seconds later (/giggles) gcc-4.8.5 is installed and available.
Notes:
if you don't have the resources to run make -j omit -j or use -j4 (or a different number which is adequate for your system)
your milage may vary and you may need to install further i386 packages
Since I can't comment I will add to #bebbo solution that on an Ubuntu 20.04 I had to add to his steps patching the following patches:
Add an include to signal.h to libsanitizer/asan/asan_linux.cc
https://patchwork.ozlabs.org/project/gcc/patch/6824253.3U2boEivI2#devpool21/
change a line in libsanitizer/tsan/tsan_platform_linux.cc
as shown. line number may not be the one stated in the patch so search for the line that was changed. There is no need to apply the patch to the other files
https://git.pantherx.org/mirror/guix/commit/0b93d04ac537d6413999349ebe7cdcb1e961700e
Adding to kpeace's answer...
sed -i '/#include <pthread.h>/a #include <signal.h>' path_to_gcc4.8.5src/libsanitizer/asan/asan_linux.cc
sed -i 's/__res_state \\*statp = (__res_state\\*)state\\;/struct __res_state \\*statp = (struct __res_state\\*)state\\;/g' path_to_gcc4.8.5src/libsanitizer/tsan/tsan_platform_linux.cc
Just adding a couple of sed lines to patch them inline.
Also, I've been writing some Ruby scripts to install some software (for fun of course.) I've recently successfully compiled gcc-4.8.5 under LinuxMint 20.1 (Ubuntu 20.04 based, compiler is the system gcc: 9.3.0, installed with sudo apt install build-essential) with this script. Also, I've installed all the packages that Bebbo suggested, including gcc-multilib and libstdc++6:i386 before running this script. Check up InstGcc4 class at the bottom of the code.
install_gcc.rb
They might end up to be 'un-installable' state a few months later. But at least gcc-4.8.5 works now.
ps. I've started to compile this old gcc due to CUDA... My hardware is a decade old GeForce 9600/9400 (yeah 2008 MBP) and CUDA 6.5 was the best option for that machine.
pps. Anyway, strange thing is, I had to give out '-std=gnu++11' for CXXFLAGS to avoid errors.
I am experiencing very annoying problems with the application apktool problem.
I do not understand what i am doing wrong, or what the problem is.
I tried this on debian , and on linux mint. I used different versions of apktool,
resulting in the same error:
I: Checking whether sources has changed...
I: Checking whether resources has changed...
I: Building resources...
Exception in thread "main" brut.androlib.AndrolibException: brut.common.BrutException: could not exec command: [aapt, p, -F, /tmp/APKTOOL3630495287059303807.tmp, -I, /home/awesomename/apktool/framework/1.apk, -S, /home/awesomename/out/./res, -M, /home/awesomename/out/./AndroidManifest.xml]
at brut.androlib.res.AndrolibResources.aaptPackage(Unknown Source)
at brut.androlib.Androlib.buildResourcesFull(Unknown Source)
at brut.androlib.Androlib.buildResources(Unknown Source)
at brut.androlib.Androlib.build(Unknown Source)
at brut.androlib.Androlib.build(Unknown Source)
at brut.apktool.Main.cmdBuild(Unknown Source)
at brut.apktool.Main.main(Unknown Source)
Caused by: brut.common.BrutException: could not exec command: [aapt, p, -F, /tmp/APKTOOL3630495287059303807.tmp, -I, /home/windows/apktool/framework/1.apk, -S, /home/windows/out/./res, -M, /home/windows/out/./AndroidManifest.xml]
at brut.util.OS.exec(Unknown Source)
... 7 more
Caused by: java.io.IOException: Cannot run program "aapt": error=2, No such file or directory
at java.lang.ProcessBuilder.start(ProcessBuilder.java:1041)
at java.lang.Runtime.exec(Runtime.java:617)
at java.lang.Runtime.exec(Runtime.java:485)
... 8 more
Caused by: java.io.IOException: error=2, No such file or directory
at java.lang.UNIXProcess.forkAndExec(Native Method)
at java.lang.UNIXProcess.<init>(UNIXProcess.java:135)
at java.lang.ProcessImpl.start(ProcessImpl.java:130)
at java.lang.ProcessBuilder.start(ProcessBuilder.java:1022)
... 10 more
It seems it can not use aapt , but i read about apktool.
And it seems that aapt is build inside apktool , why is it not working ?
It seems there's some problem in building the resources while recompiling the apk.
what you can do is, when you decompile your apk use this command
apktool d -f -r apkfilename.apk
here -f is to replace previous decompiled apk's code and -r is to ignore the decompiling of resources.
this would prevent the resources from being decompiled and will simply copy the same resources when you recompile the apk.
In case you've been using v1 and now upgraded to v2, try manually deleting the framework file.
On windows 8 it's normally at C:\Users\YourName\apktool\framework\1.apk.
The file should be regenerated once you try to build something.
My problem was solved by deleting the \framework\1.apk, making a backup on the files I modified, ereasing the dir and decompiling the *.apk again, etc... (on linux, the path is home/[user]/apktool/...). After the update, apktool always loaded the old resource table. N
For me, I solved this problem by first clearing apktool's framework directory by typing in the terminal.
$ apktool empty-framework-dir
Afterwards I uninstalled apktool and related files by typing
$ sudo apt purge apktool
Then i went to https://bitbucket.org/iBotPeaches/apktool/downloads/ to get the latest jar file for apktool(apktool_2.5.0.jar as at the time of writing this).
On first run
$ java -jar apktool_2.5.0.jar b <MyAPP.apk> #Without ><
it works.
since I work with apktool most of the times I needed a situation where I can run apktool from anywhere so I gave the jar file execute permissions by typing
$ sudo chmod +x apktool_2.5.0.jar
Afterwards I moved it /usr/bin/ by typing
$ sudo apktool_2.5.0.jar /usr/bin/
Definitely seems like the aapt PATH problem I had awhile back. Have you added aapt to PATH? If you still have problems, I have made a good apk kit in bash to avoid all these dependency problems. It supports apktool, signapk, zipalign,adb, fastboot, and heimdall. Check it out. All you need is a current java install.
http://forum.xda-developers.com/android/development/toolkit-apk-munky-rench-t3026757/post58747626#post58747626
There isn’t really enough information to give you a definite answer.
How ever you mentioned using different versions but the aapt issue was solved in version 2.4. Dependencies have been reduced to java version 1.8 or greater and the framework.
I use Debian and have the following:
Apktool 2.4
java version 11
Android framework
That’s all it took to get rid of the aapt path error.
The last error I came across was unrelated to aapt but was on the framework so I ran this command
apktool empty-framework-dir
And it solved it.
try to put the dir which include aapt file to your PATH. for example, export PATH=$PATH:./ ./apktool b
try to install ia32-libs and update latest version of apktool. (if possible restart)
apktool requires "ia32-libs" which is not available after Ubuntu 12.04. install ia32-libs
sudo apt-get install lib32z1 lib32ncurses5 lib32bz2-1.0 lib32stdc++6
Download latest version of apktools.jar - https://bitbucket.org/iBotPeaches/apktool/downloads
apktool complete installation guide - http://ibotpeaches.github.io/Apktool/install/
I just encounter same problem when run apktool d foo.apk(decompiled success) and then apktool b foo(recompile failed with similar error).
The apktool tool above was installed via sudo apt-get install apktool on Kali Linux.
So, the solution was visits apktool's official site, e.g. https://connortumbleson.com/2017/01/23/apktool-v2-2-2-released/ (it's latest version at this time of writing), download it, md5sum it, e.g. md5sum apktool_2.2.2.jar to verify, then rename that apktool_2.2.2.jar to apktool.jar.
Then do java -jar ./apktool.jar b foo to recompile, it success without error (the generated apk located at ./foo/dist/foo.apk).
The main issue is apktool version you need 2.4.0
You must manually install it from ibotpeaches git hub
here some good info
https://www.youtube.com/watch?v=kB6s10Uwpcs
and a automated script for kali
https://github.com/catenatedgoose?tab=repositories
In my mind the problem is how you install apktool...
I had the same problem and I did this and it worked very well:
For installation you first have to remove any installed apktool by the command:
sudo apt purge apktool
Then you'll have to install apktool but in a different way.
To continue save the link bellow as apktool in a directory.
[https://raw.githubusercontent.com/iBotPeaches/Apktool/master/scripts/linux/apktool]
Then open this link below and download the latest apktool.jar file: https://bitbucket.org/iBotPeaches/apktool/downloads/
Then rename the file as apktool.jar
After that give both files the permission by the command:
Sudo chmod -x apktool.jar
And for the saved script:
Sudo chmod -x apktool
At the end copy both files in the directory:
/usr/local/bin
By the command:
Sudo cp apktool.jar /usr/local/bin
And the script file:
Sudo cp apktool /usr/local/bin
After that try running apktoolin the terminal.
The solution is to include your apktool directory into your system PATH.
hope this is just a very simple question. Ok, here's what I've done: I wanted to install gmp under my Linux Ubuntu 11.10. I have both g++ and gcc on my system. So I downloaded the latest release from the gmp official site (gmp 5.0.2), extracted it and then, since I need the c++ gmp interface, I simply run:
./configure --enable-cxx
But it keeps working for a while and then prints out:
checking for suitable m4... configure: error: No usable m4 in $PATH or /usr/5bin (see config.log for reasons).
Did I do something wrong? Thank you very much!
Matteo
try sudo apt-get install m4 and rerun the ./configure
I know this was from 7 years ago, but Im looking at installing gmp5.1.3 from source on an older system right now. I noted the "funny output" checking for suitable m4... configure: error: No usable m4 in $PATH or /usr/5bin 5bin hunh? I though it was a typo, and it probably is. On line 27285 of configure script, there is ac_dummy="$PATH:/usr/5bin"
that is a shell variable that the script then looks for and doesn't find. in the *nix default FHS, /usr/5bin doesn't exist.
the problem with ac_dummy="$PATH:/usr/5bin" is that the next few lines are a for loop searching the $PATH variable + /usr/5bin for m4.
on my system, /usr/sbin is where the m4 files are located, and is not part of the default $PATH variable.
Fixes:
you could modify your $PATH variable to include /usr/sbin.
you could modify the configure script to say ac_dummy="$PATH:/usr/sbin"
you could wait 7 years for someone to file a bug report.
depending on age and support of your OS, sudo apt-get install m4 could also work.
I have the same error, sudo apt-get install m4 solve this problem.