I just upgraded to R 3.5.1 and upon issuing the command library(tidyverse) I keep getting R Studio asking me to install each tidyverse application individually.
library(tidyverse)
Error: package or namespace load failed for ‘tidyverse’:
package ‘Rcpp’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
Once I installed (for example) Rcpp it the console then warns me I need to install glue yaml tibble tidyselect purr and every app under the sun.
If I `install.packages("tidyverse") it just says the same error shown above, "package ‘XYZ’ was installed by an R version with different ".
Where can I find the full list of packages to install so I can just issue one command install.packages(c("yaml", "Rcpp", "glue", "tidyselect", etc etc)?
Related
I'm having a bit of a pickle right now with the package tidyverse, that I need for an assignment on layering maps. I tried installing the package using install.packages("tidyverse") and install.packages ("tidyverse", dependencies = TRUE) but when I ran library(tidyverse) it wasn't installed. I searched online and found that I had an older version of RStudio IDE so I uploaded the latest version (1.3.1056).
After installing the newest version, I reinstalled the package but R tells me the following:
"Rtools is required to build R packages but is not currently
installed".
So, I did it, but the R tells me Rtools package is not available for R version 3.5.3.
What can I do to use tidyverse?
It could be a permissions issue, try setting the directory for where you install R packages/libraries on your computer using libpaths. I have to do this on my work laptop because the university has it set up to store things like this in a tempporary directory on the remote server which isn't desirable.
.libPaths("C:/R")
.libPaths()
I need to install few packages that should be installed with remotes::install_github() like
"acidgenomics/basejump" or "satijalab/seurat".
During the installation, it need to upgrade few other packages version. The BiocManager::install program cannot find those versions and I had to install those dependencies packages version with:
R CMD INSTALL IRanges_2.20.2.tar.gz
Then other packages, that use the same packages stop working. like DESeq2,
I get the error:
Error: package or namespace load failed for ‘DESeq2’:
objects ‘rowSums’, ‘colSums’, ‘rowMeans’, ‘colMeans’ are not exported by 'namespace:S4Vectors'
I found few answers that say it happen (like url)
remotes::install_github() isn't picking up the correct Bioconductor
devel repos, whereas installing with BiocManager::install() does work
as expected.
we have the R 3.6.0 installed as a module and a lot of users uses the same R version. I need all packages to work for everyone.
How can I make all variety packages versions to work?
Finally, I install new version of R 3.6.3 with Bioconductor 3.10 and all the packages install right.
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 am fairly new to R. I have tried to google my question, and tried a few things, to no avail.
I am working on a MAC * High Sierra version 10.13.5
I am working with R * R version 3.5.0 (2018-04-23) -- "Joy in Playing"
I am unable to install the package "gtools", and I don't know what to do to make it work??
install.packages("gtools", type="source")
Warning: unable to access index for repository https://mirrors.sorengard.com/cran/src/contrib:
cannot open URL 'https://mirrors.sorengard.com/cran/src/contrib/PACKAGES'
Warning message:
package ‘gtools’ is not available (for R version 3.5.0)
I have also tried to install from a file saved on my computer, but this did not work either
library(gtools)
Error: package or namespace load failed for ‘gtools’:
package ‘gtools’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
You could try specifying a specific repository, for example:
install.packages("gtools", repos="https://cran.rstudio.com/")
Why are you using install from source? typically to install a package u only need to use the command
install.packages("gtools")
Then it will automatically ask u for a mirror to download from. It seems like "gtools" is available for R 3.5, so try to download it from another mirror and it should work.
On my Win 7 Ent x64 I installed RStudio R-3.4.2.
I installed few packages that I need (RPostgreSQL, sqldf, etc..)
But when I'm executing code, these libraries give me errors:
library(RPostgreSQL)
Error: package ‘RPostgreSQL’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
In addition: Warning message:
package ‘RPostgreSQL’ was built under R version 3.5.0
All of the packages are downloaded from CRAN. RPostgrSQL is 0.6-2 version.
I'm pretty sure that solution is quite simple, but I searched a lot and still cannot find the solution.
How did you install the package RPostgreSQL? If you used
install.packages("RPostgreSQL") on your Windows it installed using binaries, which may have been built using a different R version. In your case, 3.5.0 vs 3.4.2.
Try using install.packages("RPostgreSQL", type="source"). This way your machine will compile the package from source using your version of R, and it should work.
If the package needs C/C++/Fortran compilation, you will als need RTools installed on your machine.
You can try to find all packages installed with the old version R like this:
grep 'Built: R 3.4' /usr/local/lib/R/site-library/*/DESCRIPTION > temp
and then you can uninstall the packages with remove.packages()