Unable to install the car package

fynn · January 4, 2021, 9:21pm

Hey,

I tried many, many times to install my package "car". It literally drives me crazy for days that I can't fix it by myself.

This is what I tried:

 install.packages("car", dependencies = TRUE)

Everything seems fine until now

The downloaded binary packages are in
/var/folders/47/f8jhnb1x4_s154gd7x181kpc0000gn/T//RtmpjJkprs/downloaded_packages

But when I want to load the package with "library(car)" it shows me this in red:

Fehler: package or namespace load failed for ‘car’ in dyn.load(file, DLLpath = DLLpath, ...):
 kann shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/libs/Rcpp.so' nicht laden:
  dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/libs/Rcpp.so, 6): Symbol not found: _EXTPTR_PTR
  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/libs/Rcpp.so
  Expected in: /Library/Frameworks/R.framework/Resources/lib/libR.dylib
 in /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/libs/Rcpp.so
Zusätzlich: Warnmeldung:
Paket ‘car’ wurde unter R Version 4.0.2 erstellt

I have read here in the community that I need to install the Rcpp package and that is what I tried as well, as seen below.

> install.packages("Rcpp",dependencies = TRUE)
versuche URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/Rcpp_1.0.5.tgz'
Content type 'application/x-gzip' length 3215939 bytes (3.1 MB)
==================================================
downloaded 3.1 MB


The downloaded binary packages are in
	/var/folders/47/f8jhnb1x4_s154gd7x181kpc0000gn/T//RtmpjJkprs/downloaded_packages

> library(Rcpp)
Fehler: package or namespace load failed for ‘Rcpp’ in dyn.load(file, DLLpath = DLLpath, ...):
 kann shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/libs/Rcpp.so' nicht laden:
  dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/libs/Rcpp.so, 6): Symbol not found: _EXTPTR_PTR
  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/libs/Rcpp.so
  Expected in: /Library/Frameworks/R.framework/Resources/lib/libR.dylib
 in /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/libs/Rcpp.so
Zusätzlich: Warnmeldung:
Paket ‘Rcpp’ wurde unter R Version 4.0.2 erstellt

and when I then tried to use library(car) again, it showed me the same error message as before...

I have tried now so many things and I really have no idea what to do anymore, but it must have something to do with the Rcpp package!

Can anyone help me with this issue, you will be my hero!

Thanks in advance,
Fynn

(Sorry that the error messages are in German )

technocrat · January 4, 2021, 9:35pm

Das ist kein Problem

Looks like you're under macOS. When you installed Rcpp were you given a message "binary version is available, but source version is later"? If so, did you take the yes option? When this happens under macOS and doesn't succeed the first time, the best thing to do is to take the no option on the second attempt.

If you have a compiler toolchain set up compiling from source will sometimes work. Without one (XCode and its cli utility) it will always fail.

fynn · January 4, 2021, 10:12pm

Hey,

when I installed Rcpp I wasn't asked anything, but it automatically installed it as a binary package.

I tried it with the source type, but I got another error, as seen below.
I can't take no option.

install.packages("Rcpp", type = "source")
versuche URL 'https://cran.rstudio.com/src/contrib/Rcpp_1.0.5.tar.gz'
Content type 'application/x-gzip' length 2950521 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

* installing *source* package ‘Rcpp’ ...
** Paket ‘Rcpp’ erfolgreich entpackt und MD5 Summen überprüft
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fPIC  -Wall -g -O2  -c api.cpp -o api.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fPIC  -Wall -g -O2  -c attributes.cpp -o attributes.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fPIC  -Wall -g -O2  -c barrier.cpp -o barrier.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fPIC  -Wall -g -O2  -c date.cpp -o date.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fPIC  -Wall -g -O2  -c module.cpp -o module.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fPIC  -Wall -g -O2  -c rcpp_init.cpp -o rcpp_init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Rcpp.so api.o attributes.o barrier.o date.o module.o rcpp_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Rcpp/00new/Rcpp/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rcpp)

The downloaded source packages are in
	‘/private/var/folders/47/f8jhnb1x4_s154gd7x181kpc0000gn/T/RtmpjJkprs/downloaded_packages’
> library("Rcpp")
Fehler: package or namespace load failed for ‘Rcpp’ in get(Info[i, 1], envir = env):
 lazy-load database '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/R/Rcpp.rdb' is corrupt
Zusätzlich: Warnmeldung:
In get(Info[i, 1], envir = env) : internal error -3 in R_decompress1

I will try to figure out, what you meant with your second part.

technocrat · January 4, 2021, 10:44pm

 lazy-load database '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/R/Rcpp.rdb' is corrupt

Try

remove.packages("Rcpp")
install.packages("Rcpp")

Come back if you continue to have problems, and I'll fire up my old AirBook to see if I can reproduce the issue and help troubleshoot.

fynn · January 4, 2021, 11:05pm

That didn't work, I tried it multiple times. I feel kinda lost.

("insert the I'm in danger meme")

nirgrahamuk · January 4, 2021, 11:43pm

I'm a sometimes windows sometimes linux user, so I can't speak from personal experience.
but I did google around and found this:

andresrcs · January 5, 2021, 12:19am

It seems to be an issue with the CRAN version of Rcpp for MacOS systems, can you try installing this way?

install.packages("Rcpp", repos="https://rcppcore.github.io/drat")

This is the GitHub issue for reference

github.com/RcppCore/Rcpp

Many packages are broken on Mac with CRAN version of Rcpp -- unless 10.11 SDK is used as on CRAN

opened 05:42PM - 26 Mar 20 UTC

closed 09:02PM - 09 Apr 20 UTC

wch

The CRAN version of httpuv will not build using the CRAN version of Rcpp, on Mac…. Simple example: ```R install.packages("Rcpp") install.packages("httpuv", type = "source") ``` (For more info, see https://github.com/rstudio/httpuv/issues/260#issuecomment-604115061 and other comments in that issue.) In that issue, I and others use the Mac system toolchain, but @kevinushey has tested with the CRAN recommended toolchain and ecountered the same problems. I've learned that several other packages have similar problems: http://lists.r-forge.r-project.org/pipermail/rcpp-devel/2020-March/010412.html In that discussion thread, it is claimed that these packages pass R CMD check on CRAN: http://lists.r-forge.r-project.org/pipermail/rcpp-devel/2020-March/010414.html However, @jeroen has informed me that (A) CRAN does not have the resources to re-check downstream dependencies of new packages on Mac, and (B), it does not re-build the downstream dependencies either. I don't know how I could confirm (A) from the public information that CRAN provides, but it is simple to confirm that (B) is true. These are the dates in https://www.r-project.org/nosvn/R.check/r-release-osx-x86_64/ : * Rcpp_1.0.4.tgz: 2020-03-18 * httpuv_1.5.2.tgz: 2019-09-12 * dplyr_0.8.5.tgz: 2020-03-08 These dates show that Rcpp's downstream dependencies were NOT rebuilt on Mac. So from all this, I feel fairly confident that the CRAN version of Rcpp does actually break its downstream dependencies on Mac. I know that the issue is fixed in the development version of Rcpp, and I think that this is very strong reason to release a new version of Rcpp to CRAN.

technocrat · January 5, 2021, 2:50am

Finally got XCode to update to 12.3, and this setup worked.

> install.packages("Rcpp")
Installing package into ‘/Users/rc/Library/R/4.0/library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/Rcpp_1.0.5.tgz'
Content type 'application/x-gzip' length 3215939 bytes (3.1 MB)
==================================================
downloaded 3.1 MB


> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

other attached packages:
[1] Rcpp_1.0.5

loaded via a namespace (and not attached):
[1] compiler_4.0.3 tools_4.0.3   
>

fynn · January 5, 2021, 10:39am

Thanks buddy, you're the best! I tried around and somehow everything started to work again.

system · January 26, 2021, 10:39am

This topic was automatically closed 21 days after the last reply. New replies are no longer allowed.

If you have a query related to it or one of the replies, start a new topic and refer back with a link.