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()
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 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.
I'd like to install the latest version of R in RHEL 5 as I tried to install some library (plyr) but it complained a dependency could not be used with my installed version of R: package ‘Rcpp’ is not available (for R version 2.15.2)
2.15.2 is the latest precompiled R binary available for RHEL5 from epel. I guess they stopped updating it. Is compiling from source to get R 3.x my only solution here or there is some binary installer somewhere else? I much rather use something like yum since it take care of all the R dependency packages as well.
I have been trying to install the package "doby" from RStudio (ver 0.98.501 ) on ubuntu 13.04 but it keeps throwing the following warning and the package does not get installed.
Warning in install.packages :
package ‘doBy’ is not available (for R version 2.15.2)
I have followed all the instructions given here :
http://www.r-bloggers.com/installing-r-packages/
Can someone please suggest where I might be going wrong ?
If you are on Ubuntu, please see this README for Ubuntu from CRAN --- it will allow you to get to the current version of R (today 3.0.2, in a few days 3.0.3) with mininal effort.
Once you have a current R version, getting the doBy package (which depends on it) installed is a piece of cake too.
If however you prefer to stay with your version of R, you can manually fetch an older version of doBy from its CRAN archive. Download to, say, /tmp and run R CMD INSTALLby hand on it.
From http://cran.r-project.org/web/packages/doBy/index.html, package doBy depends on R version 3.0 and above. Your R version is 2.15.2. You will need to install a later version of R, and then change the settings in Rstudio to target the updated version.