Everytime I give the command for any package, in this case for ggplot2, I get this after a few minutes. I am missing something, but can't figure out what. Thanks in advance!
ERROR: dependency ‘plyr’ is not available for package ‘reshape2’
* removing ‘/home/cj/R/x86_64-pc-linux-gnu-library/2.14/reshape2’
Warning in install.packages :
installation of package ‘reshape2’ had non-zero exit status
ERROR: dependency ‘plyr’ is not available for package ‘scales’
* removing ‘/home/cj/R/x86_64-pc-linux-gnu-library/2.14/scales’
Warning in install.packages :
installation of package ‘scales’ had non-zero exit status
ERROR: dependencies ‘plyr’, ‘reshape2’, ‘scales’ are not available for package ‘ggplot2’
* removing ‘/home/cj/R/x86_64-pc-linux-gnu-library/2.14/ggplot2’
Warning in install.packages :
installation of package ‘ggplot2’ had non-zero exit status
The downloaded packages are in
‘/tmp/RtmpAXVGC6/downloaded_packages’
You are on R 2.14. Please please PLEASE upgrade to something from the last few years -- preferably from the current year such as R 3.2.0, 3.2.1 or the recently-release 3.2.2.
Simply put, you are being unreasonable in trying to expect that current and well-maintained archived for users of the current versions should also work with versions released that many years ago.
Related
I am trying to use package glmmTMB. When I call library(glmmTMB) this is the error message:
">library(glmmTMB)
Error: package or namespace load failed for ‘glmmTMB’ in inDL(x, as.logical(local), as.logical(now), ...):
function 'Rcpp_precious_remove' not provided by package 'Rcpp'
In addition: Warning messages:
1: package ‘glmmTMB’ was built under R version 4.0.5
2: In checkMatrixPackageVersion() :
Package version inconsistency detected.
TMB was built with Matrix version 1.3.4
Current Matrix version is 1.2.18
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
I have tried using install.packages('TMB', type = 'source') with no luck. Any ideas?
It's a FAQ -- search for 'Rcpp_precious_remove' not provided by package 'Rcpp'.
In short you are mixing a NEWER compilatio nof something that was built with Rcpp 1.0.7 present with an older installed version which lacks the symbol.
Fix: install.packages("Rcpp") to get the newer Rcpp. And I generally recommend regular update.packages() runs to avoid these issues.
I'm trying to get stack running for the first time, but running stack setup in an example project (from stack new helloworld new-template) fails with the following output (I skipped the beginning, which I think was normal):
Installing library in
/home/ajl/.stack/programs/x86_64-linux/ghc-7.10.2/lib/ghc7.10.2/ghc_JzwEp1oQ8kA7NFNTGk1ho5 "/home/ajl/.stack/programs/x86_64-linux/ghc-7.10.2/lib/ghc-7.10.2/bin/ghc-pkg" --force --global-package-db "/home/ajl/.stack/programs/x86_64-linux/ghc-7.10.2/lib/ghc-7.10.2/package.conf.d" update rts/dist/package.conf.install
Reading package info from "rts/dist/package.conf.install" ... done.
: Warning: Unrecognized field 420 on line 420
(Skipped unrecognized field for every line 419 down to 1)
: Warning: Unrecognized field 1 on line 1
: missing id field
: invalid package identifier:
: invalid package key:
make[1]: *** [install_packages] Error 1
make: *** [install] Error 2
Installing GHC ...%
I'm on Ubuntu 14.04, running stack 1.0.2. Not sure if it's relevant but I have ghc 7.10.1 with Cabal 1.23.0.0 installed on the system already, which work fine.
I have tried changing the resolver to older LTS versions with older ghc versions. I also tried deleting ~/.stack. Not sure what else to try given the unhelpfulness of the errors.
I figured it out. The GHC build uses grep to make packages.conf.install. I have GREP_OPTIONS=--color=auto -n set in my zsh config. The -n was putting line numbers in front of everything, which was causing the errors.
The reason I couldn't find packages.conf.install anywhere before is because it is made on the fly during GHC make. And stack does that in /tmp.
I am facing the following errors while trying to install the caret package in R.
g++: error: /tmp/Rtmp2Tos7n/R.INSTALL2e6e30153a74/nloptr/nlopt-2.4.2/lib/libnlopt_cxx.a:
No such file or directory make: *** [nloptr.so] Error 1
ERROR: compilation failed for package ‘nloptr’
* removing ‘/rmt/csfiles/pgrads/mava290/R/x86_64-suse-linux-gnu-library/3.1/nloptr’
Warning in install.packages :
installation of package ‘nloptr’ had non-zero exit status
ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
* removing ‘/rmt/csfiles/pgrads/mava290/R/x86_64-suse-linux-gnu-library/3.1/lme4’
Warning in install.packages :
installation of package ‘lme4’ had non-zero exit status
ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
* removing ‘/rmt/csfiles/pgrads/mava290/R/x86_64-suse-linux-gnu-library/3.1/pbkrtest’
Warning in install.packages :
installation of package ‘pbkrtest’ had non-zero exit status
ERROR: dependency ‘lme4’ is not available for package ‘BradleyTerry2’
* removing ‘/rmt/csfiles/pgrads/mava290/R/x86_64-suse-linux-gnu-library/3.1/BradleyTerry2’
Warning in install.packages :
installation of package ‘BradleyTerry2’ had non-zero exit status
ERROR: dependency ‘pbkrtest’ is not available for package ‘car’
* removing ‘/rmt/csfiles/pgrads/mava290/R/x86_64-suse-linux-gnu-library/3.1/car’
Warning in install.packages :
installation of package ‘car’ had non-zero exit status
ERROR: dependencies ‘car’, ‘BradleyTerry2’ are not available for package ‘caret’
* removing ‘/rmt/csfiles/pgrads/mava290/R/x86_64-suse-linux-gnu-library/3.1/caret’
Warning in install.packages :
installation of package ‘caret’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpG9dYqn/downloaded_packages’
I looked into this other question that had a similar problem
Dependency issue while installing caret package in R
The solution for this problem was to install each of the dependencies first, but they all had the same error message. For example:
>install.packages('nloptr')
g++: error: /tmp/RtmpgEn54A/R.INSTALL7015350f0d03/nloptr/nlopt-2.4.2/lib/libnlopt_cxx.a: No such file or directory
make: *** [nloptr.so] Error 1
ERROR: compilation failed for package ‘nloptr’
* removing ‘/rmt/csfiles/pgrads/mava290/R/x86_64-suse-linux-gnu-library/3.1/nloptr’
Warning in install.packages :
installation of package ‘nloptr’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpG9dYqn/downloaded_packages’
I also tried changing the repos ie. install.packages('caret', repos='http://cran.rstudio.com/') but it dint work either.
My session info is given below:
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-suse-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_3.1.2
I recently encountered the problem with nlopt as well. It was easily solved by installing nlopt-devel and its associated dependencies from YaST (or your preferred package manager).
I was hoping to add a comment first. On Jan 28, 2015, there was an addition to the nloptr package in github that possibly broke the compilation. I used a workaround by installing from an older version with the command
install.packages("http://cran.r-project.org/src/contrib/Archive/nloptr/nloptr_1.0.0.tar.gz",
repos=NULL, type="source")
As mentioned in this R help forum:
http://r.789695.n4.nabble.com/can-t-install-rugarch-and-nloptr-packages-in-R-3-01-opensuse-linux-td4669649.html
add the line to the src/Makevars file
mv .libs lib; \
between
make install; \
ls | grep -v ^include$$ | grep -v ^lib$$ | xargs rm -rf; \
This will remove the compilation error and you would be able to install nloptr package. I have tested this for nloptr_1.0.0.tar.gz .
I solve this issue by installing first "car" from synaptic (use filter with "cran-car").
And then I install "caret" with rstudio but I guess it will work also for R.
Hope it helps,
Regards
I'm trying to cabal install binary-strict and I get this error:
src/Data/Binary/BitBuilder.hs:205:37:
Ambiguous occurrence `unsafePerformIO'
It could refer to either `Foreign.unsafePerformIO',
imported from `Foreign' at src/Data/Binary/BitBuilder.hs:38:1-14
or `System.IO.Unsafe.unsafePerformIO',
imported from `System.IO.Unsafe' at src/Data/Binary/BitBuilder.hs:42:26-40
(and originally defined in `GHC.IO')
Failed to install binary-strict-0.4.8.1
cabal: Error: some packages failed to install:
binary-strict-0.4.8.1 failed during the building phase. The exception was:
ExitFailure 1
I'm running ghc 7.6.3. If it's relevant, I have binary-0.7.2.3 installed too.
As written, binary-strict only works for base >= 4.7. GHC 7.6.3 uses base = 4.6.* so it will not work. You should file a bug with the maintainer and work around the issue by adding hiding (unsafePerformIO) to the import Foreign line of the file in question.
I only just found out about this. It is now fixed. Also I have listed the git repo in the package details so you can now raise issues and I will know about them. Thanks to Thomas for suggesting the fix.
Today i'm trying to install a good library for visualization and create graphics, named "ggplot2", but i actually have a problems with installation!
There what i have in output:
Installing package into ‘/home/hamsternik/R/x86_64-pc-linux-gnu-library/3.1’ (as ‘lib’ is unspecified)
also installing the dependencies ‘munsell’, ‘scales’, ‘testthat’
trying URL 'http://cran.rstudio.com/src/contrib/munsell_0.4.2.tar.gz' Content type 'application/x-gzip' length 91026 bytes (88 Kb) opened URL ==================================================
downloaded 88 Kb trying URL 'http://cran.rstudio.com/src/contrib/scales_0.2.4.tar.gz' Content type 'application/x-gzip' length 40093 bytes (39 Kb) opened URL ==================================================
downloaded 39 Kb trying URL 'http://cran.rstudio.com/src/contrib/testthat_0.8.1.tar.gz' Content type 'application/x-gzip' length 40777 bytes (39 Kb) opened URL ==================================================
downloaded 39 Kb trying URL 'http://cran.rstudio.com/src/contrib/ggplot2_1.0.0.tar.gz' Content type 'application/x-gzip' length 2351447 bytes (2.2 Mb) opened URL ==================================================
downloaded 2.2 Mb * installing source package ‘munsell’ ... ** package ‘munsell’ successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading Error : package ‘colorspace’ was built before R 3.0.0: please re-install it ERROR: lazy loading failed for package ‘munsell’ * removing ‘/home/hamsternik/R/x86_64-pc-linux-gnu-library/3.1/munsell’
Warning in install.packages : installation of package ‘munsell’ had non-zero exit status * installing source package ‘testthat’ ... ** package ‘testthat’ successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading Error : package ‘digest’ was built before R 3.0.0: please re-install it ERROR: lazy loading failed for package ‘testthat’ * removing ‘/home/hamsternik/R/x86_64-pc-linux-gnu-library/3.1/testthat’
Warning in install.packages : installation of package ‘testthat’ had non-zero exit status ERROR: dependency ‘munsell’ is not available for package ‘scales’ * removing ‘/home/hamsternik/R/x86_64-pc-linux-gnu-library/3.1/scales’
Warning in install.packages : installation of package ‘scales’ had non-zero exit status ERROR: dependency ‘scales’ is not available for package ‘ggplot2’ * removing ‘/home/hamsternik/R/x86_64-pc-linux-gnu-library/3.1/ggplot2’
Warning in install.packages : installation of package ‘ggplot2’ had non-zero exit status The downloaded source packages are in ‘/tmp/RtmpDEeNck/downloaded_packages’
I actually use a debian-stable system (v.7.6) and the next decision was to install "r-cran-ggplot2" in the console.
And when i install them, i think about i having this library, but when i write in Rstudio: library(ggplot2), i take next message: Error: package ‘ggplot2’ was built before R 3.0.0: please re-install it
But i have a the up-to-date version - 3.1.1!
I really don't find any good answers for that question! PLeas, help!
OK, problem is actually done!
All what i make - remove all packages, including 'R-cran-.*' and again install it, but not install all packages which i find by the search command in konsole. I install only r-base, next i install R studio. Thus i can straightforwardly install every package with dependencies and they will be actually installed!