Install/Compiling Errors with R Packages: tidyverse and caret - r

I recently had to install RStudio and the R language onto a new Macbook. It seemed to install the packages normally but when I started run some newly written code, the console would not execute tidyverse and caret even though it said it was downloaded. This is what shows up in the console and it's the same messages for both caret and tidyverse:
> install.packages("tidyverse")
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/tidyverse_1.3.1.tgz'
Content type 'application/x-gzip' length 421072 bytes (411 KB)
==================================================
downloaded 411 KB
The downloaded binary packages are in
/var/folders/pl/w9k_0l4d4snfgcv53rp2t_4m0000gn/T//RtmpWScbjK/downloaded_packages
> library(tidyverse)
Error: package or namespace load failed for ‘tidyverse’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘Rcpp’
I even tried to install it on just R and not RStudio too and This is the message that comes up for both tidyverse and caret when I try to install Rcpp both ways on just R and RStudio:
> install.packages("Rcpp")
There is a binary version available but the source version is later:
binary source needs_compilation
Rcpp 1.0.8.2 1.0.8.3 TRUE
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes
installing the source package ‘Rcpp’
trying URL 'https://cloud.r-project.org/src/contrib/Rcpp_1.0.8.3.tar.gz'
Content type 'application/x-gzip' length 3086192 bytes (2.9 MB)
==================================================
downloaded 2.9 MB
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp’
The downloaded source packages are in
‘/private/var/folders/pl/w9k_0l4d4snfgcv53rp2t_4m0000gn/T/Rtmp53AysU/downloaded_packages’
Warning message:
In install.packages("Rcpp") :
installation of package ‘Rcpp’ had non-zero exit status
I'm not sure what's going wrong and I'm not seeing any solution on here or other sites that are working for me, I'd appreciate any help with this since I use R alot. If more info is needed please comment, thanks.

It could be that you need to reinstall the rlang package. You can use this code to reinstall this package:
remove.packages("rlang")
install.packages("rlang")
After that you can load the packages tidyverse and caret again:
library(tidyverse)
library(caret)
Check this question for more info: Error: package or namespace load failed for ‘tidyverse’ in loadNamespace

Related

I am unable to install ggplot, there occurs some error

there is this long error message when i try to install ggplot, please someone help me. Thanks!
install.packages("ggplot2")
Installing package into ‘C:/Users/HP/Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
also installing the dependency ‘rlang’
There are binary versions available but the source versions are later:
binary source needs_compilation
rlang 0.3.4 1.0.1 TRUE
ggplot2 3.1.1 3.3.5 FALSE
Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/rlang_0.3.4.zip'
Content type 'application/zip' length 1080437 bytes (1.0 MB)
downloaded 1.0 MB
package ‘rlang’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\HP\AppData\Local\Temp\Rtmpwfvrv8\downloaded_packages
installing the source package ‘ggplot2’
trying URL 'https://cran.rstudio.com/src/contrib/ggplot2_3.3.5.tar.gz'
Content type 'application/x-gzip' length 3063309 bytes (2.9 MB)
downloaded 2.9 MB
installing source package 'ggplot2' ...
** package 'ggplot2' successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
namespace 'rlang' 0.3.4 is being loaded, but >= 0.4.10 is required
ERROR: lazy loading failed for package 'ggplot2'
removing 'C:/Users/HP/Documents/R/win-library/3.4/ggplot2'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-34~1.1/bin/i386/R" CMD INSTALL -l "C:\Users\HP\Documents\R\win-library\3.4" C:\Users\HP\AppData\Local\Temp\Rtmpwfvrv8/downloaded_packages/ggplot2_3.3.5.tar.gz' had status 1
Warning in install.packages :
installation of package ‘ggplot2’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\HP\AppData\Local\Temp\Rtmpwfvrv8\downloaded_packages’
It's saying your "rlang" version is outdated. Update that, it should be fine. Update all the libraries, that's a good practice while installing packages. (you do the same from tool option in menubar of Rstudio and update package)

package or namespace load failure

I don't know what happened but this NAMESPACE LOAD FAILURE is coming every time I call the forecast package.
So I have used this line of code
install.packages("forecast",repos = c("http://rstudio.org/_packages",
"http://cran.rstudio.com"))
This was the console message that I got after running this code
Installing package into ‘C:/Users/adarsh/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
Warning in install.packages :
unable to access index for repository
http://rstudio.org/_packages/bin/windows/contrib/3.5:
cannot open URL
'http://rstudio.org/_packages/bin/windows/contrib/3.5/PACKAGES'
There is a binary version available but the
source version is later:
binary source needs_compilation
forecast 8.6 8.7 TRUE
Binaries will be installed
trying URL
'http://cran.rstudio.com/bin/windows/contrib/3.5/forecast_8.6.zip'
Content type 'application/zip' length 2345112 bytes (2.2 MB)
downloaded 2.2 MB
package ‘forecast’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\adarsh\AppData\Local\Temp\RtmpQ58pju\downloaded_packages
I checked whether this was also the case with other packages.
install.packages("tseries")
Installing package into ‘C:/Users/adarsh/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
Warning in install.packages :
dependency ‘quadprog’ is not available
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/tseries_0.10-46.zip'
Content type 'application/zip' length 414767 bytes (405 KB)
downloaded 405 KB
package ‘tseries’ successfully unpacked and MD5 sums checked**
**The downloaded binary packages are in
C:\Users\adarsh\AppData\Local\Temp\RtmpQ1vu1H\downloaded_packages**
library(tseries)
Error: package or namespace load failed for ‘tseries’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘quadprog’
In addition: Warning message:
package ‘tseries’ was built under R version 3.5.3
Same error happened again. Please anyone help me.
I downloaded the " quadprog " package from the cran repository and saved it as zip file at C://Users/yourname/Documents/package_file.zip .
Then used the option Package Archive File (.zip; .tar.gz) in R studio and installed the above package.
Thank you

Different version of GlobalOptions package in R

I'm trying to install the package "circlize" and I am having trouble resolving what seems to be a simple error.
When I run:
install.packages("circlize")
It says:
Installing package into ‘*file location*/3.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
dependency ‘GlobalOptions’ is not available
There is a binary version available but the source version is later:
binary source needs_compilation
circlize 0.3.10 0.4.3 FALSE
installing the source package ‘circlize’
trying URL 'https://mirrors.sorengard.com/cran/src/contrib/circlize_0.4.3.tar.gz'
Content type 'application/x-gzip' length 2456906 bytes (2.3 MB)
downloaded 2.3 MB
* installing *source* package 'circlize' ...
** package 'circlize' successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
namespace 'GlobalOptions' 0.0.11 is being loaded, but >= 0.0.12 is required
ERROR: lazy loading failed for package 'circlize'
* removing '*file location*/3.2/circlize'
Warning in install.packages :
running command '"*file location*/x64/R" CMD INSTALL -l "*file location*\3.2" *file location*/downloaded_packages/circlize_0.4.3.tar.gz' had status 1
Warning in install.packages :
installation of package ‘circlize’ had non-zero exit status
The downloaded source packages are in
‘*file location*\downloaded_packages’
These parts seem most relevant to me:
dependency ‘GlobalOptions’ is not available
namespace 'GlobalOptions' 0.0.11 is being loaded, but >= 0.0.12 is required
When I run sessionInfo() I see under "other attached packages": [1] GlobalOptions_0.0.11
My best guess is that I have the wrong version of GlobalOptions -- I see that GlobalOptions v0.0.13 is available here, but being new to R, I'm not sure what to do now to get the right version up and running.
I'd really appreciate if someone could tell me where I should look next. (I looked through the documentation within that link, but I'm still lost about what to do now.) Thanks!
If you have R version >=3.3.0 you should
install GlobalOptions_0.0.13 from CRAN
install.packages("GlobalOptions")
quit and restart R
re-install circlize from source as before.
If you have an older R version, update R to a more recent version first.

Errors installing "dplyr" in r

Question: unable to install dplyr in R... code below. Anyone offer any solutions?
I'm on a mac osx sierra and R Version 1.0.136
> install.packages("dplyr")
There is a binary version available but the source version
is later:
binary source needs_compilation
dplyr 0.5.0 0.7.0 TRUE
Do you want to install from sources the package which needs compilation?
y/n:
y
installing the source package ‘dplyr’
trying URL 'https://cran.rstudio.com/src/contrib/dplyr_0.7.0.tar.gz'
Content type 'application/x-gzip' length 690938 bytes (674 KB)
==================================================
downloaded 674 KB
* installing *source* package ‘dplyr’ ...
** package ‘dplyr’ successfully unpacked and MD5 sums checked
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘dplyr’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/dplyr’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/dplyr’
Warning in install.packages :
installation of package ‘dplyr’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/ll/6vx1dr1n5bb9zwbv1z9v53z00000gn/T/RtmpitMpQn/downloaded_packages’
> library(dplyr)
Error: package or namespace load failed for ‘dplyr’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘DBI’
Not sure why this isn't working! Tried to download manually and it didn't work either (similar/same warnings/errors)
A new dplyr version was accepted into CRAN yesterday. Usually CRAN provides packages for both Windows and OSX in binary form, but it takes up to 48 hours for CRAN to provide the compiled packages.
When you try to install a package in that time window, R asks you to either install the previous binary version or the new version from source. If you decide to install the version from source you will need to have a c++ compiler.
The easiest thing for you to do is to either install the previous binary package or wait until the latest version gets compiled at CRAN.
Checkout https://cran.r-project.org/web/packages/dplyr/index.html to see if the binaries for your OS are already available.
Update: It seems there are some issues with the latest dplyr version, and the OSX compilation seems to fail. More info here: https://cran.r-project.org/web/checks/check_results_dplyr.html. I would rather stay with 0.5.0 until those issues are ironed out.

unable to install packages("caret") completely in R version 3.2.3

> require("caret")
Loading required package: caret
Loading required package: lattice
Loading required package: ggplot2
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘pbkrtest’
So I found that there is lack of "pbkrtest" then I tried to reinstall it.
> install.packages("pbkrtest")
Installing package into ‘C:/Users/ADMIN/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
There is a binary version available but the source version is
later:
binary source needs_compilation
pbkrtest 0.4-2 0.4-3 FALSE
installing the source package ‘pbkrtest’
trying URL 'https://rweb.crmda.ku.edu/cran/src/contrib/pbkrtest_0.4- 3.tar.gz'
Content type 'application/x-gzip' length 164415 bytes (160 KB)
downloaded 160 KB
* installing *source* package 'pbkrtest' ...
** package 'pbkrtest' successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by 'stats::sigma' when loading 'pbkrtest'
Error : object 'sigma' is not exported by 'namespace:stats'
ERROR: lazy loading failed for package 'pbkrtest'
* removing 'C:/Users/ADMIN/Documents/R/win-library/3.2/pbkrtest'
The downloaded source packages are in
‘C:\Users\ADMIN\AppData\Local\Temp\Rtmpk7mJT0\downloaded_packages’
Warning messages:
1: running command '"D:/R-3.2.3/bin/x64/R" CMD INSTALL -l
"C:\Users\ADMIN\Documents\R\win-library\3.2"
C:\Users\ADMIN\AppData\Local\Temp\Rtmpk7mJT0/downloaded_packages/pbkrtest_0.4- 3.tar.gz' had status 1
2: In install.packages("pbkrtest") :
installation of package ‘pbkrtest’ had non-zero exit status
It seems like that the installation keeps failing.
As a result, I couldn't use other code using caret packages.
I faced this problem as well on Windows 7. I did following steps in the sequence and it worked.
a) Make sure your R version is updated latest R release 3.2.3
b) The default sources seems to be installing Unix version. So I manually downloaded https://cran.r-project.org/web/packages/pbkrtest/index.html for windows
c) Use manually install function from R menu to install the package.
Cheers,
Ratan
Check version of R by typing version in your console.
If version is not "version.string R version 3.3.2" or later then
Install new version of R from https://cran.r-project.org/bin/windows/base/
Update R version using Tools => Global Options in RStudio.
install package using "install.packages("caret")" in your console.
do require(caret).
test using ?createDataPartition.

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