I have an R package that I successfully submitted to CRAN over a year ago. I am ready to submit an update, however I see in the package check results an error: Package suggested but not available for checking: ‘rgdal’
This R package passes checks with R CMD check --as-cran on macOS, winbuilder with R-devel and on ubuntu. But I don't understand why rgdal was not available for checking in that one instance, and I am trying to avoid this same error cropping up again.
A quick google search shows this same error showing up for quite a few R packages, always only for r-release-osx-x86_64.
Is this something I should be concerned with?
In the end, I was able to ignore this issue, and this was not a problem. The same error did not crop up with the submission of the package update.
Related
Downloaded package from below URL.
Attempted to install using below command; response shown.
library(dalton.rqi,lib.loc='/home/X/Desktop/')
Error: package ‘dalton.rqi’ was built before R 3.0.0: please re-install it
https://my.clevelandclinic.org/departments/anesthesiology/depts/outcomes-research/risk-quantification
It appears this is a compiled package that maybe I don't have the source for? Is there a way to force install of the package? I'm unable to install using Rstudio GUI in its current form as a zip. Tried repackaging to tar.gz has Rstudio was looking for and also had a non-zero exit status error.
Any ideas?
I'm afraid this can't be achieved directly. The error message says it well: to use a package in R it needs to be built on an R version matching yours.
I can suggest two ways to move forward:
Contact the authors, ask for the R sources (it is somewhat surprising they did not make them available in the first place), and build the package yourself.
Downgrade your R version as far back as needed to match the one this pre-built package used.
I updated R 3.4.4 to R 3.5.0 today. And my package cannot pass R CMD check anymore. It fails at checking whether package can be installed ... ERROR.
In another hand my package works, I can install it and use it as long as I don't check it.
The error is the following:
Error: package or namespace load failed for ‘sp’:
package ‘lattice’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
Error : package ‘sp’ could not be loaded
I tried to reinstall lattice these ways:
sudo apt-get --reinstall install r-cran-lattice
or
remove.packages("lattice", lib="~/R/x86_64-pc-linux-gnu-library/3.5")
install.package("lattice")
The package lattice is installed correctly in both cases. But it does not solve my problem. Also I ensured to have a single version of lattice removing either the r-cran one or the self compiled version. Nothing works.
Edit By the way I can do library(sp) or library(lattice) it works. But not with R CMD check
The error message tells you that the binary you are attempting to install comes from an insufficient / incompatible R version.
Two fixes:
Install from source as you did. After that check with AP <- available.packages() that you really only have one.
Use the correct binarie: read this README at CRAN and switch to Michael's 'R 3.5' repos. Many of us have been doing that for weeks.
Lastly, the r-sig-debian list is a friendly place for these questions and more. Subscribe first so that you can post.
I have spent the past several days trying to install RDCOMClient in order to integrate R output in MS Word using R2wd
Thanks to SO, I was finally able to wrestle devtools and other required packages into shape (man, that was way more difficult than it should have been!) but I have not been able to install RDCOMClient
The closest I have come is downloading RDCOMClient_0.93-0.zip and then receiving the error message
"Error: package ‘RDCOMClient’ was built before R 3.0.0: please
re-install it"
I also received the message
"package ‘RDCOMClient’ is not available (for R version 3.4.0)"
at one point.
I have tried the omegahat site as well as github and CRAN with no luck.
I am beginning to think the package is no longer available (I wish I had known that days ago!) but still wonder if I am missing something.
If the package is no longer available for version 3.4.0, can you suggest another package with similar functionality? I am looking to write analyses in MS Word and then embed tables, charts and other output from R.
Thanks!
Yes it is. You need to install Rtools first.
Then you can install RDCOMClient via:
remotes::install_github("omegahat/RDCOMClient")
My end goal is to be able to use the geoR and sp packages in R on an AWS EC2 Linux instance. The first hurdle is getting an older version of R since 3.3 doesn't support TCL/TK (at least that I've found).
After unpacking R-3.2.5.tar.gz and following the instructions in the INSTALL file (along with these configure options), a search in the config.log shows the following for TCL and TK:
configure:32908: checking for tclConfig.sh
configure:32950: checking for tclConfig.sh in library (sub)directories
configure:33143: checking for tcl.h
conftest.c:228:17: fatal error: tcl.h: No such file or directory
#include <tcl.h>
config.status:1893: creating src/library/tcltk/DESCRIPTION
config.status:1893: creating src/library/tcltk/Makefile
config.status:1893: creating src/library/tcltk/src/Makefile
ac_cv_env_TCLTK_CPPFLAGS_set=
ac_cv_env_TCLTK_CPPFLAGS_value=
ac_cv_env_TCLTK_LIBS_set=
ac_cv_env_TCLTK_LIBS_value=
r_cv_header_tcl_h=no
TCLTK_CPPFLAGS=''
TCLTK_LIBS=''
TCL_CONFIG=''
use_tcltk='no'
R installs successfully, but running capabilities("tcltk") confirms that something went wrong, as it returns FALSE.
Following the hints here, I searched for tclConfig.sh and tkConfig.sh, and realized I hadn't installed the appropriate dependencies, namely tcl-devel, and tk-devel.
Running yum list available shows a package for tcl-devel.x86_64 but nothing for tk. I downloaded source files for TCL and TK from here, but couldn't find source files for any devel packages.
So now I'm at a loss on how to proceed. Has anyone been through this process that can shed some light on it?
UPDATE
After reading the comment below, I'm afraid I didn't do my due diligence in researching TCL/TK and R 3.3.
My very early efforts to troubleshoot the whole problem consisted of the following workflow- First, without even considering an older version of R, I ran install.packages("geoR") in 3.3.2. This resulted in installation of package 'geoR' had non-zero exit status, along with:
Error: package 'tcltk' does not have a namespace
ERROR: lazy loading failed for package 'geoR'
So, naturally, I ran install.packages("tcltk") which resulted in package 'tcltk' is not available (for R version 3.3.2)
As I mentioned before, this was very early on. I took the message literally and didn't think to look further into TCL/TK for 3.3, but instead started looking to get an earlier version of R, since I had been successfully running geoR and sp on another system that had R 3.2.5.
I would like to submit a package (DLMtool) to the CRAN repository. When I check the package with R CMD check --as-cran I receive only 1 note regarding the new submission.
However when I submit the package I am receiving feedback from the R core team regarding errors that I do not receive. For example:
Quitting from lines 261-262 (DLMtool.Rnw)
Error: processing vignette 'DLMtool.Rnw' failed with diagnostics:
one node produced an error: NAs are not allowed in subscripted assignments
I cannot recreate this error by running the code myself. But that isn't the point of this post: I'm not worried about specific errors, rather my inability to detect these myself. To this point Prof. Ripley has been very patient. I desperately don't want to waste any more of his time or any of the R core team by using them as a step-by-step checking process.
How can I recreate the CRAN package check process if --as-cran is insufficient?
A similar question has been asked regarding a previous version of R that was not answered satisfactorily as far as I can tell:
CRAN package check finds warning that R CMD check --as-cran doesn't
Cheers,
Tom
I'm using Windows 7 x64, RStudio 0.98.507 and R 3.1.1 x64.
Submitting a package to CRAN still fills me a with a sense of uneasiness, despite having been successful on a number of occasions.
Some things to check:
Ensure you are using the correct process
Specifically, use:
R CMD build pkg
R CMD check pkg_version.tar.gz
Make sure you check using the current version of R, as well as the development branch, R-devel (http://cran.r-project.org/bin/windows/base/rdevel.html)
Submit your package to the windows builder (http://win-builder.r-project.org/)
Make sure you have read, and completely understood, every single sentence of the CRAN submission policy (http://cran.r-project.org/web/packages/policies.html)
Submit your package using the online submission form (http://cran.r-project.org/submit.html)
Then hope for the best.
To be honest, every individual I have dealt with on the CRAN build team have been very patient and helpful.