Cloning the v 1.1.0 of pkgdown and trying to run pkgdown::build_site() gives me the following error:
> pkgdown::build_site()
══ Building pkgdown site ═══════════════════════════════════════════════════════
Reading from: '/home/farm/Documents/pkgdown-1.1.0'
Writing to: '/home/farm/Documents/pkgdown-1.1.0/docs'
── Initialising site ───────────────────────────────────────────────────────────
Writing 'sitemap.xml'
── Building home ───────────────────────────────────────────────────────────────
<ENOENT: [ENOENT] Failed to remove '/tmp/Rtmp0utBMA/file114d619b1b68.html': no such file or directory>
Error: [ENOENT] Failed to remove '/tmp/Rtmp0utBMA/file114d619b1b68.html': no such file or directory
Execution halted
Most likely is a problem with my Linux and R, not the package itself. That being said, this is the environment:
R: 3.5.1
Manjaro: 18.0.0-rc
How can I fix this? I'm trying to avoid using chmod -R 777 /tmp/
note: I also ran devtools::test() and devtools::check(), no errors or warnings.
After trying to build a package from scratch, I found my mistake... Pandoc was missing, installing it from AUR fixed it.
Related
I'm trying to install jupyter_nbextensions_configurator on windows10 for python3.7 using conda.
An error occurred while installing the package.
I have already tried to reinstall anaconda,but the problem still occurs.
ERROR conda.core.link:_execute(700): An error occurred while installing package 'conda-forge::jupyter_nbextensions_configurator-0.4.1-py37_0'.
Rolling back transaction: done
LinkError: post-link script failed for package conda-forge::jupyter_nbextensions_configurator-0.4.1-py37_0
location of failed script: C:\Users\Cesare\Anaconda3\Scripts\.jupyter_nbextensions_configurator-post-link.bat
I want to know how to install it successfully.
I too was facing the same problem. Here's the output when I tried cloning the base environment [Running as Administrator]:
(base) PS C:\WINDOWS\system32> conda create --name django --clone base
WARNING: A conda environment already exists at 'C:\Users\Tanishk\anaconda3\envs\django'
Remove existing environment (y/[n])? y
Source: C:\Users\Tanishk\anaconda3
Destination: C:\Users\Tanishk\anaconda3\envs\django
The following packages cannot be cloned out of the root environment:
- conda-forge/win-64::conda-4.9.2-py38haa244fe_0
- defaults/win-64::conda-build-3.20.5-py38_1
- defaults/win-64::conda-env-2.6.0-1
Packages: 305
Files: 2077
Preparing transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(698): An error occurred while installing package 'defaults::openssl-1.1.1h-he774522_0'.
Rolling back transaction: done
CondaError: Cannot link a source that does not exist. C:\Users\Tanishk\anaconda3\pkgs\openssl-1.1.1h-he774522_0\Library\bin\openssl.exe
Running `conda clean --packages` may resolve your problem.
()
You will notice the package giving me problem is different than yours, but the ERROR remains the same (ERROR conda.core.link).
Here's how I solved it:
Google the package mentioned in the ERROR. In my case it was openssl-1.1.1h-he774522_0
Open the result from Anaconda Files (should likely be the first search result):
anaconda / packages / openssl 1 - Files :: Anaconda Cloud
Ctrl+F to find the package in the list.
Download the compressed package to your local Downloads folder.
Backup the contents of the installed erroneous package *C:\Users\Tanishk\anaconda3\pkgs\openssl-1.1.1h-he774522_0* somewhere.
Copy the contents of the de-compressed downloaded package into the *C:\Users\Tanishk\anaconda3\pkgs\openssl-1.1.1h-he774522_0* folder.
Re-try in Anaconda prompt with whatever you got stuck at.
Note:
After step 7, I got another same error but for a different package this time (vs2015_runtime-14.16.27012-hf0eaf9b_3). I performed the same steps for this package too --> Google -- Download -- Replace old content. And I was able to run things successfully after that.
I suggest to google the package because if you search for the package name on Anaconda itself, it will ask you to login first.
I am writing an R package that depends on Stan and Rstan. I run the installation on an Azure machine Standard_D64_v3 and install r-base and r-cran-stan with sudo apt-get and rstan and Rcpp with R's install.packages()(among others, see shell setup script and R setup script).
This process worked OK last month. Today I was able to install the package (as evidenced by the welcome message) and then have a runtime error from incompatible versions.
...
* DONE (PosteriorBootstrap)
Reloading attached PosteriorBootstrap
Welcome to PosteriorBootstrap, a parallel approach for adaptive non-parametric learning
Error: package ‘StanHeaders’ 2.18.1 was found, but > 2.18.1 is required by ‘rstan’
In addition: Warning message:
version 2.18.1.10 of ‘StanHeaders’ masked by 2.18.1 in /usr/lib/R/site-library
Execution halted
I do not have StanHeaders anywhere in my code so I suspect the problem is between different packages. How can I solve this problem with versions?
As #nicola wrote in the comments, the fix is to reinstall StanHeaders with:
install.packages("StanHeaders")
The previous code may have stopped working because of a new version of R, but I could not determine the cause.
I used to use Julia in Jupyter notebook. I uninstalled yesterday the .julia directory because of other issues and after Pkg.add(IJulia) Im getting a building error related to ZMQ. the full error is below.
julia> Pkg.build("ZMQ")
INFO: Building Homebrew
Already up-to-date.
INFO: Building ZMQ
Warning: staticfloat/juliatranslated/zeromq32-3.2.5 already installed, it's just not linked.
Error: Formulae found in multiple taps:
* staticfloat/juliadeps/zeromq32
* staticfloat/juliatranslated/zeromq32
Please use the fully-qualified name e.g. staticfloat/juliadeps/zeromq32 to refer the formula.
=================================[ ERROR: ZMQ ]=================================
LoadError: failed process: Process(`/Users/pacagal/.julia/v0.5/Homebrew/deps/usr/bin/brew link staticfloat/juliatranslated/zeromq32 --force`, ProcessExited(1)) [1]
while loading /Users/pacagal/.julia/v0.5/ZMQ/deps/build.jl, in expression starting on line 35
================================================================================
================================[ BUILD ERRORS ]================================
WARNING: ZMQ had build errors.
- packages with build errors remain installed in /Users/pacagal/.julia/v0.5
- build the package(s) and all dependencies with `Pkg.build("ZMQ")`
- build a single package by running its `deps/build.jl` script
================================================================================
I have also run the build.jl file but I am getting an error too.
I was having the same issue this morning. In the terminal I ran brew install zmq and that resolved the issue.
I still had to run julia>Pkg.build("Nettle") after installing zmq and after that IJulia is running fine.
I was building an R package on https://travis-ci.org/ and got an error:
The command "tlmgr update --self" failed and exited with 25 during .
The last lines of Travis CI output:
When I call devtools::check() locally on Windows 10 in RStudio no errors nor warnings arise.
I found that tlmgr concerns with LaTeX/TexLive packages, and In Travis CI documentation "Building an R Project" it's written that some LaTeX/TexLive may be need to be installed if vignettes require. (Note: there are no vignettes in my package yet.)
Configuration in .travis.yml file:
language: R
sudo: false
cache: packages
r_github_packages:
- jimhester/covr
after_success:
- Rscript -e 'covr::codecov()'
My question: what is the cause of the problem and how to solve it?
It seems that tlmgr can't accessing the current repository, you can rollback the repository to the archived version with:
tlmgr option repository ftp://tug.org/historic/systems/texlive/2015/tlnet-final
which gaves
tlmgr: setting default package repository to ftp://tug.org/historic/systems/texlive/2015/tlnet-final
Source: A little trick with tlmgr: Unknown directive …containerchecksum error
I am having a tough time installing R-packages that are not available in the Anaconda repositories. My attempts so far can be found here How to install R-packages not in the conda repositories?.
Currently, I am trying to build the R-package rafalib for conda by following the instructions from this article under the heading Building a conda R package.
The first part works fine.
conda skeleton cran rafalib
Out:
Tip: install CacheControl to cache the CRAN metadata
Fetching metadata from http://cran.r-project.org/
Writing recipe for rafalib
Done
The build command runs into errors
conda build r-rafalib
Out:
Removing old build environment
Removing old work directory
BUILD START: r-rafalib-1.0.0-r3.2.2_0
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata: ......
Solving package specifications: .
Error: Packages missing in current linux-64 channels:
- r 3.2.2*
- r-rcolorbrewer
I have r 3.2.2-64bit installed via conda and it runs without problems. I also already have r-colorbrewer installed via conda and I can use that package without issues in R. Why am I getting these errors when trying to build a conda package?
I am on Linux (Antergos, an Arch derivative) with kernel 4.4.5-1-ARCH.
UPDATE 2015/04/19
Thanks to this answer, I found out that I could include the dependencies by building them separately in the same directory as the package I want to install. That didn't work for me, but I also read that I can include a channel in the build command with -c, just as when installing. So now I do:
conda build -c r r-rafalib
This gets passed all the dependency problems, but after fetching, extracting and linking packages, it fails. Here is the end of the error message.
Removing old work directory
Source cache directory is: /home/joel/anaconda2/conda-bld/src_cache
Downloading source to cache: rafalib_1.0.0.tar.gz
Downloading http://cran.r-project.org/src/contrib/rafalib_1.0.0.tar.gz
rafalib_1.0.0. 100% |#######################| Time: 0:00:00 4.87 MB/s
Success
Extracting download
Package: r-rafalib-1.0.0-r3.2.2_0
source tree in: /home/joel/anaconda2/conda-bld/work/rafalib
+ mv DESCRIPTION DESCRIPTION.old
+ grep -v '^Priority: ' DESCRIPTION.old
+ /home/joel/anaconda2/envs/_build/bin/R CMD INSTALL --build .
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
Command failed: /bin/bash -x -e /home/joel/drafts/r-rafalib/build.sh
The error sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook is the same as I encounter when using install.packages() as reported here.
There is some related discussion in this thread. I have tried to get around this error by installing different versions of ncurses, including this patched version, and I have tried to link the readline libraries, as suggested here, but I keep running into the same error. I'm quite lost at this point and any help to solve this would be greatly appreciated.
Although I started out with a different problem, the final solution turned out to be the same as I posted elsewhere How to install R-packages not in the conda repositories?. I am adding it here for completeness.
In the end, I got around the rl_event_hookproblems by following the approach recommended here and symlinking anaconda's libreadline to the system one:
mv ~/anaconda3/lib/libreadline.s.6.2 ~/anaconda3/lib/libreadline.s.6.2.bak
ln -s /usr/lib/libreadline.so.6.3 ~/anaconda3/lib/libreadline.s.6.2
I am still having troubles installing some dependency heavy R-packages due to failure to load shared objects when using install.packages() from withing R. However, simpler packages work fine and I can get most of the dependency heavy packages from anacondas R-repositories.