I am a beginner in R
trying to analyze my scRNA-seq data with velocyto.R in R studio.
Following velocyto tutorial, I tried installing velocyto.R as below:
library(devtools)
install_github("velocyto-team/velocyto.R")
But, an error pops up:
ERROR: compilation failed for package 'velocyto.R'
removing 'C:/Users/USER/Documents/R/win-library/3.6/velocyto.R'
Error: Failed to install 'velocyto.R' from GitHub:
(converted from warning) installation of package ‘C:/Users/USER/AppData/Local/Temp/RtmpukpRFl/file37346a812b86/velocyto.R_0.6.tar.gz’ had non-zero exit status
Is there anyone to face the same problem described above and succeed in resolving it after all?
I desperately need helps!
Thanks
As your error log says C:/..., you probably use Windows. According to velocyto's README it seems that this package runs only on unix-flavored systems with C++11, Open MP, boost, igraph and hdf5c++ libraries.
This can be the problem: read the velocyto's GitHub issue #40, maybe you'll need to run this under WSL...?
Related
I am trying to install the interference package in R. The package is still under development, so one needs to install it from the website:
devtools::install_github('szonszein/interference', ref='0.1.0')
However, I receive the following error message:
ERROR: dependency ‘randnet’ is not available for package ‘interference’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/interference’
Warning message:
In i.p(...) :
installation of package ‘/var/folders/sw/x2n7fwsj6p32wmcz0dfyk5p40000gn/T//RtmpVf6Xns/file58297d4fcf4a/interference_0.1.0.tar.gz’ had non-zero exit status
Even when I install radnet, however, things do not work. Any advice on how to deal with this?
I just tried that install, and it failed because randnet is not available. interference hasn't been updated in more than 2 years, so I think you'll have some work ahead of you: fork its repository, replace all references to randnet with something that is available.
randnet was removed from CRAN about 6 months ago because the authors were unresponsive to bug reports from CRAN. So an alternative would be to install the most recent (buggy!) version by downloading https://cran.r-project.org/src/contrib/Archive/randnet/randnet_0.5.tar.gz and installing that tar.gz file, but it appears the authors are no longer maintaining it, as is also the case for interference. I'd find a different solution.
I've been trying to install the Sleuth package in R all morning and it keeps giving me errors. This is how I tried to install it:
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DESeq2")
BiocManager::install ("rhdf5")
install.packages("devtools")
devtools:: install_github("pachterlab/sleuth")
I did use the library() command.
I get the following error messages:
Error: object 'h5write.default' is not exported by 'namespace:rhdf5'
Execution halted
ERROR: lazy loading failed for package 'sleuth'
removing 'C:/Users/31625/OneDrive/Documents/R/win-library/4.1/sleuth'
I was having the same issue and found that there's current an open issue on Github discussing this problem.
Currently there is a workaround which was shared in the same issue on Github:
Run git clone https://github.com/pachterlab/sleuth
Remove the last line in ./sleuth/NAMESPACE which is the h5write.default that raises the error during installation - ignore the warning in the first line
Then in R: devtools::install('./sleuth/')
It worked for me while using Linux - ZorinOS and R 4.1.2 but it should work on Windows as well.
Someone also opened a PR to fix the whole issue but it seems they are not updating the package anymore (unfortunately).
I install the recipes library just fine using:
install.packages("recipes", dependencies = c("Depends", "Suggests"))
This gives me the following error:
Error in library(recipes) : there is no package called ‘recipes’
I having a bigger issue, I am unable to load caret but it seems the reason I cannot is recipes, so I assume if I solve the recipes issue I will be able to load caret.
This issue is impossible to replicate. You need to answer the following questions:
What is the error message?
What R version are you running?
What is your system?
I tried to install with exactly the same command. Got an error of some missing dependencies, and after running this install.packages(c("caret", "recipes", "klaR", "ipred")) I could finally load "recipes".
os it seems I couldn't install recipes package because of gfortran-4.8 not been available in my system. I followed this and now I can finally load recipes and caret. thank you
I wish to install sentiment140 github package by developer okugami79. I wrote following script for the same:
install.packages("githubinstall")
require(devtools)
library(githubinstall)
install_github('sentiment140', 'okugami79')
library(sentiment)
But it threw an error:
Installation failed: Failed to connect to raw.githubusercontent.com port 443: Timed out
Warning message: Username parameter is deprecated. Please use okugami79/sentiment140
Then I modified installation statement as follows:
install_github('okugami79/sentiment140')
Still it threw an error:
Installation failed: Failed to connect to raw.githubusercontent.com port 443: Timed out
I checked for solution on stackoverflow through following link:
Timeout R package installation from Github
Here, I found a way to install github package by downloading package zip file and installing it in R using:
install.packages("/address/to/zip-package", repos = NULL, type="source")
This also prompts error:
Warning: invalid package 'sentiment-master'
Error: ERROR: no packages specified
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-33~1.3/bin/x64/R" CMD INSTALL -l "C:\Users\u257449\Documents\R\win-library\3.3" "sentiment-master"' had status 1
Warning in install.packages : installation of package ‘sentiment-master’ had non-zero exit status
How should I go about installing required package from github in R ? Your valuable advice/solution is requested.
Thank You !
Just a straightforward pair of functions installed this package from Github source for me on both Windows and OSX.
install.packages("devtools")
devtools::install_github('okugami79/sentiment140')
There may be something unusual about your system setup, in which case, it would be helpful to have your session information. You can get that by entering sessionInfo().
However, note that this package you are looking to install is over 4 years old per the description file on Github. A lot of work has gone into other packages that work with natural language processing and sentiment analysis. The CRAN Task View for Natural Language Processing is a good place to start for an overview of many of these packages that can be installed directly from CRAN. There are many resources that are better maintained. For example, here's a chapter on sentiment analysis using the tidytext package.
I am getting the error below while installing a package:
Warning in install.packages :
unable to move temporary installation ‘E:\R-3.3.2\library\filed603811626\tidytext’ to ‘E:\R-3.3.2\library\tidytext
Please suggest how to resolve this error.
Make sure you install R in your main disk drive (most probably C:/)
This resolves quite a few problems with moving packages that R does when installing.
You can then install all required dependencies with install.packages(c("tm", "tidytext"))