This is my first time building an R package, and doing it with the help of devtools and roxygen2. After writing a simple func in the R directory and making a DESCRIPTION file with devtools, I try to build and reload for the first time but I get an error -
==> devtools::document(roclets=c('rd', 'collate', 'namespace'))
First time using roxygen2 4.0. Upgrading automatically...
Documentation completed
==> R CMD INSTALL --no-multiarch --with-keep.source TestPack
...
ERROR: a 'NAMESPACE' file is required
Which is odd because I have selected in my build configurations that roxygen2 should be making this for me. A man directory is made when building and reloading but nothing else.
Related
I'm currently making a R package (tessellation) which includes some C code. When I do some modifications and click "Install and restart" in RStudio, I get this error:
==> Rcmd.exe INSTALL --no-multiarch --with-keep.source tessellation
* installing to library 'C:/PortableApps/R/R-4.1.2/App/R-Portable/library'
* installing *source* package 'tessellation' ...
ERROR: cannot remove earlier installation, is it in use?
When I do "Restart R session" before "Install and restart", sometimes this works, sometimes not. So I have to close the project and reopen it, and this is annoying. Do you know what could I do to work more conveniently?
You need to be sure that the process is not being used (or loaded into R's search path) for the package. I suggest stopping all R sessions, deleting the installed package folder manually, start an R vanilla session, check the attached packages/search path, and finally attempt re-installation/building the package:
# from terminal
R --vanilla
# check search path
ls()
search()
# attempt installing package
devtools::install() # or devtools::build()
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 unable to generate .Rd documentation files for my package using RStudio and Roxygen2. First, let me mention that I have gone through similar problems posted here and have already done the following:
Roxygen2 blocks initiated at the beginning of file with a #'
Configured Build Tools>Checked generate documentation with Roxygen> Configure > Checked all fields under 'Use roxygen to generate' and 'Automatically roxygenize when running'
Made sure there were no .Rd files in the 'man' folder
And even after that, when I perform a 'Build and Reload' on RStudio I get the following output (please note the line that reads: No man pages found in package MYPACKAGE:
=
=> devtools::document(roclets=c('rd', 'collate', 'namespace', 'vignette'))
>
Updating MYPACKAGE documentation
Loading MYPACKAGE
Documentation completed
==> Rcmd.exe INSTALL --no-multiarch --with-keep.source MYPACKAGE
installing to library C:/Users/user/Documents/R/win-library/3.3
installing source package 'MYPACKAGE' ...
** R
** data
* moving datasets to lazyload DB
** preparing package for lazy loading
No man pages found in package 'MYPACKAGE'
** help
* installing help indices
** building package indices
** testing if installed package can be loaded
DONE (MYPACKAGE)
Edit:
Upon further investigation, it appears that this was caused by the fact that I have sub-directories within my R directory, which is not supported by default. A possible solution was located here which, however, I haven't yet tried out. I will report back with the outcome as soon as I am able to perform the tests.
I had the same error. roxygen2 was creating correctly the md files in the /man directory but they were not found at compilation time. I had the following error.
No man pages found in package
After a bit of time I found that in one of the R file I had a source statement
source("C:/Users/vaulot/Google Drive/Scripts/R library/dv_function_pr2.R")
My guess is that there was some code in the source file interfering with roxygen2.
I am confused. I was used to the following flow when creating packages:
create new package in RStudio using gui (named e.g. testPackage
modify some files (let's say DESCRIPTION for beginning)
write:
-
library(devtools)
document()
check()
load_all()
But now, for some reason document() does not propagate changes in DESCRIPTION to testPackage-package.Rd in man folder anymore. I get the following when using document():
> document()
Updating testPackage documentation
Loading testPackage
First time using roxygen2 4.0. Upgrading automatically...
When I run check() I see in one of the lines:
Warning:
...r/packages/testPackage.Rcheck/00_pkg_src/testPackage/man/testPackage-package.Rd:32: All text must be in a section
Unfortunately, there is no additional information in 00install.out as indiciated by check(). I am on Windows, R 3.1.2, RStudio 0.98.1091, devtools 1.7.0, roxygen2 4.1.0.
Did the process change or I have some inconsistent set of packages installed?
I was trying to install RTextTools package for R, but failed. Here is the output from the screen
> > install.packages("RTextTools")
Warning in install.packages("RTextTools") :
argument 'lib' is missing: using 'C:\Users\datamining\Documents/R/win-library/2.10'
--- Please select a CRAN mirror for use in this session ---
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.10
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
package ‘RTextTools’ is not available
What's the reason for this problem, and how to fix it? Thanks.
There are two distinct, but related, issues:
You are running version 2.10 of R which is two years old. CRAN supports only the current version with pre-built binaries. You could try installing from source.
RTextTools, as can be seen on its CRAN page also requires at least R version 2.13.
So in short: you should upgrade.
I have resolved the issue. I have Download RTextTools From Given Link.
https://cran.r-project.org/src/contrib/Archive/RTextTools/
and copy RTextTools_1.4.2.tar.gz file in project root folder then run this command in project folder in terminal
"R CMD INSTALL RTextTools_1.4.2.tar.gz"
After running this command I receive below error
"ERROR: dependencies ‘SparseM’, ‘randomForest’, ‘tree’, ‘e1071’, ‘ipred’, ‘caTools’, ‘maxent’, ‘glmnet’, ‘tau’ are not available for package ‘RTextTools’".
Now install each dependencies from RStudio or RConsole (Any Editor used by you) by simply running this code.
install.packages("caTools").
Install all 9 required packages One By One (In My Case it was 9 Packages Dependencies required by RTextTools) all packages will be installed except 'maxent'.
Now download maxent from the given link.
https://cran.r-project.org/src/contrib/Archive/maxent/.
and copy maxent_1.3.3.1.tar file in project folder then run this command in project folder in terminal.
"R CMD INSTALL maxent_1.3.3.1.tar"
Now For RTextTools Run this command again in Terminal.
"R CMD INSTALL RTextTools_1.4.2.tar.gz"
All is done Now..
But the Last Step is
Load the RTextTools using.
library(RTextTools)
You will see one more Error: Load SparseM Now Loading SparseM use code below.
library(SparseM)
and in the last Load RTextTools
library(RTextTools)
RTextTools is dependent on a number of packages, most of which require R 2.13+. You should always keep R updated to the latest version, since each update contains numerous bug fixes and performance enhancements.
If you can't install packages from repository or the packages are not available anymore, just follow this steps:
Install.packages("devtools")
check -- library("devtools")
install_github("cran/maxent")
install_github("cran/RTextTools")