I am a beginner in bash programming. I recently learn how to install some tools using wget and make but I have been advised to use brew to install futur tools as it is installing all the dependencies required to use tool (if I have well understood).
For some tools, I could use it without any problems. But when I am trying to use it to instal bwa it is not working and I get this following message.
(base) ML21-0036:~ akurtis$ brew install bwa
Running `brew update --preinstall`...
==> Auto-updated Homebrew!
Updated 1 tap (homebrew/core).
==> Updated Formulae
Updated 10 formulae.
Error: bwa: no bottle available!
You can try to install from source with:
brew install --build-from-source bwa
Please note building from source is unsupported. You will encounter build
failures with some formulae. If you experience any issues please create pull
requests instead of asking for help on Homebrew's GitHub, Twitter or any other
official channels.
I tried also to install it from source but it was not working too.
How should I use brew to install bwa on my computer.
I am running under BigSur
Related
I would like to upgrade my PCL to a newer version to fix a problem I have with QHull related to this issue.
I'm on ubuntu so I installed PCL with sudo apt install libpcl-dev but I can only get the version 1.10.1. How can I install a newer version ?
The problem is apparently fixed by this commit. It's in the tag 1.12.1.
I know that in theory I can use cmake and build my own PCL but from what I saw with the apt install, there is a huge amount of dependencies + I will also need this particular Qhull version that they mention in the issue and commit... I'm not sure I can make this work without the package manager. Any leads on this problem ?
Thanks !
In its simplest form, building and installing PCL goes likes this:
Clone the GitHub repo and cd inside it
Optionally checkout a git tag or stay on the master branch (default)
mkdir build && cd build
Run cmake with cmake ..
Build and install with make -j2 && sudo make install
For more information, see here: https://pcl.readthedocs.io/projects/tutorials/en/master/compiling_pcl_posix.html
When you previously had libpcl-dev installed, you can remove that package without (auto-)removing the dependencies, then you should have most if not all dependencies required for building from source already installed.
You didn't say which Ubuntu version you use, but judging from the version of libpcl-dev, I assume it is focal (20.04). The Qhull version installed there is fine, it already has a reentrant interface.
We need to install R-base version 3.5+ on an offline machine running SLES12.3
We have downloaded all the packages from the the SUSE r repo
http://download.opensuse.org/repositories/devel:/languages:/R:/released/openSUSE_12.3/x86_64/
while running zypper install on the packages there are additional dependencies that we are not able to find the relevant packages to download.
These include:
libtcl8.5.so()(64bit)
libgomp.so.l()(64bit)
But we are not able to find the dependency package that include these libraries.
What should be the correct approach for installing these libraries offline? where can we find these libraries?
Is there a better way for offline installing R-base ? we tried to follow the instructions on the cran rstudio page
The files you downloaded don't match the distribution you're running. SUSE Linux Enterprise (SLE) and openSUSE are similar in some ways, but these are really two separate distributions and you can not always mix binaries between the two. To install R on SLE Server 12.3, you should use the repository https://download.opensuse.org/repositories/devel:/languages:/R:/released/SLE_12/.
You can find out these URLs by looking at the right hand-side column at https://build.opensuse.org/project/show/devel:languages:R:released. Look for things called "SLE" there.
Install the Development Tools, according to this answer
zypper install --type pattern Basis-Devel
Download R source and install it
wget http://cran.univ-paris1.fr/src/base/R-3/R-3.5.0.tar.gz
tar zxf R-3.5.0.tar.gz
cd R-3.5.0
./configure --enable-R-shlib
make
make check
make install
Maybe there are still dependencies missing, which need to be installed with zypper (I don't have any Suse to try myself). With this method you have an "empty" R and you will install R packages one by one (with R CMD INSTALL). Maybe not the best answer for your need, but an answer.
I am trying to install two packages in R (3.3.2): devtools and git2r. They are depending on the existence of zlib. This comes with macOS Sierra (10.12.3) and it's version 1.2.8 by default.
When I'm trying to install these packages I get the error below.
I've been trying a lot of things.
directly installing via CRAN in RStudio: no effect.
trying to locate zlib on macOS: can't find zlib.
installing via R CMD INSTALL git2r: no effect.
I notice someone has a similar issue posted on GitHub: https://github.com/ropensci/git2r/issues. There is no solution yet.
Does anyone here have an idea?
Thanks!
Sander
ERROR MESSAGE BELOW
configure error in "/private/tmp/RtmpP6HZFx/R.INSTALLe73412909267/git2r"
configure error
The zlib library that is required to build git2r was not found.
Please install:
zlib1g-dev (package on e.g. Debian and Ubuntu)
zlib-devel (package on e.g. Fedora, CentOS and RHEL)
and try again.
If the zlib library is installed on your system but the git2r configuration is unable to find it, you can specify the include and lib path to zlib with:
"R CMD INSTALL --configure-args='--with-zlib-include=INCLUDE_PATH --with-zlib-lib=LIB_PATH' git2r"
See "config.log" for more details
ERROR: configuration failed for package "git2r"
*removing "/usr/local/lib/R/3.3/site-library/git2r"
UPDATE: the same issue persists on macOS X 10.12.5 in combination with R 3.4.0 - the latter I need for DESeq2.
Solution...Mmm. Not really. I simply uninstalled R and all the packages, and than I reinstalled everything again. I installed R and RStudio via homebrew, following the instructions here: https://rud.is/b/2015/10/22/installing-r-on-os-x-100-homebrew-edition/.
Oddly enough: all issues disappeared.
UPDATE #1: this solution does not - obviously - work for the combination R 3.4.0 and macOS X 10.12.5. We need a solution for this issue.
UPDATE #2: I have discovered what I believe was the issue: a wrong path to the xcode command line tools.
sudo xcode-select --reset did the trick and now xcode-select -p points to /Library/Developer/CommandLineTools. And which xcode-select points to /usr/bin/xcode-select. Googling I discovered that it is not needed to install Xcode through the App Store as it states on http://railsapps.github.io/xcode-command-line-tools.html:
"On earlier versions of macOS, it was more difficult to install Xcode Command Line Tools. It required a huge download of the full Xcode package from the Mac App Store or registration as an Apple developer for a smaller Command Line Tools package. Mac OS X Mavericks made installation of Xcode Command Line Tools much simpler.".
i was having the same problem. i have a note 8(samsung). just go to GitHub and install zlib from there.
I recently needed to install R 3.2 to get a package from Bioconductor working, but after I installed, I get the following error:
[16:16:11 20] $ r
dyld: Library not loaded: /usr/local/lib/gcc/4.9/libgfortran.3.dylib
Referenced from: /usr/local/Cellar/r/3.2.0/R.framework/Versions/3.2/Resources/lib/libR.dylib
Reason: image not found
Trace/BPT trap: 5
Sure enough, brew was set to use gcc 5, so I told brew to use the 4.9 version
brew switch gcc 4.9
which got R running, but then R would fail in the middle of a package install (specifically when I ran biocLite('DESeq2').
Since then, I have tried a number of things, including trying to install gcc 4.8 (but I can't seem to get R to use it, even via ~/.R/Makevars). Even if 4.9 is not installed, R insists on calling the path shown above.
The windows version of R seems to say 4.9 does not work with 3.2:
R-devel temporarily used a new toolchain based on 4.9.2 gcc, put together by Duncan Murdoch using build scripts written by a contractor. However, there were too many incompatibilities with existing code, and this toolchain will not be used for R 3.2.0. See notes for details on building and testing the new toolchain.
Any help would be greatly appreciated!
Edit:
I tried installing from source, as suggested by #lmw., but it fails:
[11:27:55 2] $ brew install r --build-from-source
==> Installing r from homebrew/homebrew-science
==> Installing r dependency: gcc
==> Downloading http://ftpmirror.gnu.org/gcc/gcc-5.1.0/gcc-5.1.0.tar.bz2
######################################################################## 100.0%
curl: (28) Resolving timed out after 5542 milliseconds
Trying a mirror...
==> Downloading https://ftp.gnu.org/gnu/gcc/gcc-5.1.0/gcc-5.1.0.tar.bz2
######################################################################## 100.0%
==> Patching
patching file gcc/jit/Make-lang.in
==> ../configure --build=x86_64-apple-darwin14.3.0 --prefix=/usr/local/Cellar/gcc/5.1.0 --libdir=/usr/local/Cellar/gc
==> make bootstrap
==> make install
==> Caveats
GCC has been built with multilib support. Notably, OpenMP may not work:
https://gcc.gnu.org/bugzilla/show_bug.cgi?id=60670
If you need OpenMP support you may want to
brew reinstall gcc --without-multilib
==> Summary
🍺 /usr/local/Cellar/gcc/5.1.0: 1351 files, 248M, built in 32.5 minutes
==> Installing r
==> Using Homebrew-provided fortran compiler.
This may be changed by setting the FC environment variable.
==> Downloading http://cran.rstudio.com/src/base/R-3/R-3.2.0.tar.gz
######################################################################## 100.0%
==> Patching
patching file src/modules/lapack/vecLibg95c.c
==> ./configure --prefix=/usr/local/Cellar/r/3.2.0_1 --with-libintl-prefix=/usr/local/opt/gettext --enable-memory-pro
==> make
** installing vignettes
** testing if installed package can be loaded
* DONE (survival)
make[1]: *** [recommended-packages] Error 2
make: *** [stamp-recommended] Error 2
READ THIS: https://git.io/brew-troubleshooting
If reporting this issue please do so at (not Homebrew/homebrew):
https://github.com/homebrew/homebrew-science/issues
Edit 2:
Just for the fun of it, I tried installing r without the --build-from-source option, and it worked. See my solution below. (I think building from source may have fixed the issue with the gcc 5 upgrade, which got things working. I am not going to try it (things are finally working again...why screw with it?), but I wonder if I could remove the variables I set in ~/.R/Makevars (again, see solution below).
Rebuilding R from source fixes the same problem for me.
brew reinstall r --build-from-source
This was resolved by this commit, with new bottles for R. Make sure you brew update and brew upgrade r.
This is not a complete fix (it uses an older gcc version), but it get's me running again:
brew tap homebrew/homebrew-versions
brew install gcc48
brew install r
NOTE: I ran brew install r --build-from-source (reinstall did not work), which rebuilt something, but not r (it failed). It may be partially responsible for this working. Please let me know if it is! I'd like to give #lmw credit if his answer is the reason this worked.
Edit ~/.R/Makevars and add the following lines (edit paths as necessary):
CC=/usr/local/Cellar/gcc48/4.8.4/bin/gcc-4.8
CXX=/usr/local/Cellar/gcc48/4.8.4/bin/g++-4.8
CFLAGS=-std=c99
Run r.
(If you're trying to install bioconductor)
source("http://bioconductor.org/biocLite.R")
biocLite()
I'm trying to install the BayesVarSel package on a ubuntu 12 box on AWS EC2. It works fine on my windows 7 machine (R 2.15.1).
I've attached a screenshot of the error message. It appears to be an issue with the GNU GSL library. I couldn't find a quick way to install GSL (ie sudo apt-get GSL, etc.) so I wanted to see if others have had a similar issue. I'm open to other packages with similar functionality.
EDIT:
A couple other things I've tried without luck :
I was able to recreate the error with Ubuntu 12.04.1 LTS (desktop) running in VirtualBox.
As #Dirk Eddelbuettel suggested, sudo apt-cache search libgsl produced a useful list of packages. It's not clear why that didn't work on your machine.
I installed libgsl with:
sudo apt-get install libgsl0ldbl
sudo apt-get install libgsl0-dev
Now BayesVarSel compiles and loads without error.
Do
apt-cache search libgsl
and everything should be a little clearer. Those packages have existed longer than either Ubuntu or Amazon EC2 so it really should not take superhuman effort to find them.
And if apt-cache search libgsl is too difficult, try packages.ubuntu.com
where you can search for the package containing the file in your error message (eg /usr/include/gsl/gsl_vector.h) and "Yes, Veronica" you can search for substrings too.
On Fedora the required package can be installed with dnf install gsl-devel.