When I try to redownload packages like digest I get this error.
installing the source package ‘digest’
trying URL 'https://cran.rstudio.com/src/contrib/digest_0.6.23.tar.gz'
Content type 'application/x-gzip' length 143316 bytes (139 KB)
downloaded 139 KB
installing *source* package ‘digest’ ...
package ‘digest’ 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 ‘digest’
removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/digest’
Warning in install.packages :
installation of package ‘digest’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/rn/2fyqm2wd6qs5pq5ttswtffvh0000gn/T/Rtmpv0Vy8N/downloaded_packages’
Any help would be greatly appreciated
Related
I have installed the 'MCMCpack' package on my R using the code install.packages("MCMCpack") successfully.
also installing the dependency ‘quantreg’
There are binary versions available but the source versions are later:
binary source needs_compilation
quantreg 5.85 5.94 TRUE
MCMCpack 1.6-0 1.6-3 TRUE
Do you want to install from sources the packages which need compilation? (Yes/no/cancel) Yes
installing the source packages ‘quantreg’, ‘MCMCpack’
trying URL 'https://cran.rstudio.com/src/contrib/quantreg_5.94.tar.gz'
Content type 'application/x-gzip' length 1025290 bytes (1001 KB)
==================================================
downloaded 1001 KB
trying URL 'https://cran.rstudio.com/src/contrib/MCMCpack_1.6-3.tar.gz'
Content type 'application/x-gzip' length 1030533 bytes (1006 KB)
==================================================
downloaded 1006 KB
* installing *source* package ‘quantreg’ ...
** package ‘quantreg’ 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 ‘quantreg’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/quantreg’
Warning in install.packages :
installation of package ‘quantreg’ had non-zero exit status
ERROR: dependency ‘quantreg’ is not available for package ‘MCMCpack’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/MCMCpack’
Warning in install.packages :
installation of package ‘MCMCpack’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/xp/077px4z927d5jplc0wg9701r0000gn/T/RtmpAgOlHz/downloaded_packages’
But when I enter library(MCMCpack), it returns this error message:
Error in library("MCMCpack") : there is no package called ‘MCMCpack’
What might be the problem here? There seems no issue in installing the package beforehand.
I have installed the 'MCMCpack' package on my R using the code install.packages("MCMCpack") successfully.
No, your installation of MCMCpack was unsuccessful, as is clearly indicated by the error & warning messages.
Of note,
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
This is usually the result of the Command Line Tools not having been installed (correctly). You can install the Xcode Command Line Tools with
xcode-select --install
Then re-issue
install.packages("MCMCpack")
I am using RStudio 2022.02.3 Build 492 for mac. I am trying to install the package Rdpack as a requirement to load another package and it does not work. Could you please help to tell me what the problem is and what I should do to solve it. And here is the error message I received:
install.packages('Rdpack')
also installing the dependency ‘rbibutils’
There are binary versions available but the source versions are later:
binary source needs_compilation
rbibutils 2.2.7 2.2.8 TRUE
Rdpack 2.3 2.3.1 FALSE
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
installing the source packages ‘rbibutils’, ‘Rdpack’
trying URL 'https://cran.rstudio.com/src/contrib/rbibutils_2.2.8.tar.gz'
Content type 'application/x-gzip' length 882817 bytes (862 KB)
==================================================
downloaded 862 KB
trying URL 'https://cran.rstudio.com/src/contrib/Rdpack_2.3.1.tar.gz'
Content type 'application/x-gzip' length 703156 bytes (686 KB)
==================================================
downloaded 686 KB
* installing *source* package ‘rbibutils’ ...
** package ‘rbibutils’ 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 ‘rbibutils’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rbibutils’
Warning in install.packages :
installation of package ‘rbibutils’ had non-zero exit status
ERROR: dependency ‘rbibutils’ is not available for package ‘Rdpack’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rdpack’
Warning in install.packages :
installation of package ‘Rdpack’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/r2/_r7yln992kq1x9pg298ql_s40000gn/T/RtmpMko8Ru/downloaded_packages’
Thank you so much for your help!
I am trying to install package "RecordLinkage" in Mac but I get this error message.
I already tried to type "no" for "Do you want to attempt to install these from sources?" and it does not work either.
Any advice/suggestions, please?
Package which is only available in source form, and may need compilation of C/C++/Fortran:
‘RecordLinkage’
Do you want to attempt to install these from sources? (Yes/no/cancel) yes
installing the source package ‘RecordLinkage’
trying URL 'https://cran.rstudio.com/src/contrib/RecordLinkage_0.4-12.1.tar.gz'
Content type 'application/x-gzip' length 759438 bytes (741 KB)
==================================================
downloaded 741 KB
* installing *source* package ‘RecordLinkage’ ...
** package ‘RecordLinkage’ 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 ‘RecordLinkage’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RecordLinkage’
Warning in install.packages :
installation of package ‘RecordLinkage’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/sp/jy_rk5ts16sbrlkd2mbpg0m00000gn/T/RtmpDWiWEt/downloaded_packages’
On my Macbook 10.15 in RStudio I attempted to install ggplot2, however I get errors for dependencies related to digest and rlang. I did perform a xcode-select --install to install that and also rebooted my Mac.
However it seems R can't locate xcode.
I notice that the error messages complain about the xcode path. Is this a red herring or is that the root of the problem?
Metroids-MacBook-Air:~ metroid$ xcode-select -p
/Applications/Xcode.app/Contents/Developer
What should the path be set to and why isn't it set by default?
Any thoughts?
Please see below:
> install.packages("ggplot2")
also installing the dependencies ‘digest’, ‘rlang’
There are binary versions available but the source versions are later:
binary source needs_compilation
digest 0.6.21 0.6.22 TRUE
rlang 0.4.0 0.4.1 TRUE
Do you want to install from sources the packages which need compilation? (Yes/no/cancel) Yes
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/ggplot2_3.2.1.tgz'
Content type 'application/x-gzip' length 3973186 bytes (3.8 MB)
==================================================
downloaded 3.8 MB
The downloaded binary packages are in
/var/folders/q5/pqd495t95fq3tjtbxbdsvv_00000gn/T//Rtmp8aJzND/downloaded_packages
installing the source packages ‘digest’, ‘rlang’
trying URL 'https://cran.rstudio.com/src/contrib/digest_0.6.22.tar.gz'
Content type 'application/x-gzip' length 141968 bytes (138 KB)
==================================================
downloaded 138 KB
trying URL 'https://cran.rstudio.com/src/contrib/rlang_0.4.1.tar.gz'
Content type 'application/x-gzip' length 797012 bytes (778 KB)
==================================================
downloaded 778 KB
* installing *source* package ‘digest’ ...
** package ‘digest’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
dyld: Symbol not found: _kConditionalConnectionRequirementTimeWindowStartTime
Referenced from: /Applications/Xcode.app/Contents/Developer/usr/bin/../../../SharedFrameworks/DVTFoundation.framework/Versions/A/DVTFoundation
Expected in: /System/Library/Frameworks/CFNetwork.framework/Versions/A/CFNetwork
in /Applications/Xcode.app/Contents/Developer/usr/bin/../../../SharedFrameworks/DVTFoundation.framework/Versions/A/DVTFoundation
make: error: unable to locate xcodebuild, please make sure the path to the Xcode folder is set correctly!
make: error: You can set the path to the Xcode folder using /usr/bin/xcode-select -switch
ERROR: compilation failed for package ‘digest’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/digest’
Warning in install.packages :
installation of package ‘digest’ had non-zero exit status
* installing *source* package ‘rlang’ ...
** package ‘rlang’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
dyld: Symbol not found: _kConditionalConnectionRequirementTimeWindowStartTime
Referenced from: /Applications/Xcode.app/Contents/Developer/usr/bin/../../../SharedFrameworks/DVTFoundation.framework/Versions/A/DVTFoundation
Expected in: /System/Library/Frameworks/CFNetwork.framework/Versions/A/CFNetwork
in /Applications/Xcode.app/Contents/Developer/usr/bin/../../../SharedFrameworks/DVTFoundation.framework/Versions/A/DVTFoundation
make: error: unable to locate xcodebuild, please make sure the path to the Xcode folder is set correctly!
make: error: You can set the path to the Xcode folder using /usr/bin/xcode-select -switch
ERROR: compilation failed for package ‘rlang’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rlang’
Warning in install.packages :
installation of package ‘rlang’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/q5/pqd495t95fq3tjtbxbdsvv_00000gn/T/Rtmp8aJzND/downloaded_packages’
>
I updated R to the latest version "R version 3.3.3 (2017-03-06)". I am using macOS Mojave.
Now, when I am trying to knit the code in the Markdown, I get an error. I figured this is because I don't have an updated version of the "yaml" package. However, when I am trying to update the "yaml" package, I get the following errors:
installing the source package ‘yaml’
trying URL 'https://cran.rstudio.com/src/contrib/yaml_2.2.0.tar.gz'
Content type 'application/x-gzip' length 89447 bytes (87 KB)
==================================================
downloaded 87 KB
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
unknown timezone 'zone/tz/2019a.1.0/zoneinfo/America/Chicago'
* installing *source* package ‘yaml’ ...
** package ‘yaml’ 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 ‘yaml’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/yaml’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/yaml’
Warning in install.packages :
installation of package ‘yaml’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/_r/cgv1gmqx1vzgv25k1k805lyw0000gn/T/RtmpagnKIL/downloaded_packages’