I'm trying to use the package rDEA. I have most recent r version 3.4.4 ("Someone to Lean On"). I'm using most recent R Studio 1.1.423.
I get the error compilation failed for package 'rDEA'. Can anyone help?
Precise details:
install.packages("rDEA")
Package which is only available in source form, and may need
compilation of C/C++/Fortran: ‘rDEA’
Do you want to attempt to install these from sources?
y/n:
I type y, and get the following:
installing the source package ‘rDEA’
trying URL 'https://cran.rstudio.com/src/contrib/rDEA_1.2-5.tar.gz'
Content type 'application/x-gzip' length 57007 bytes (55 KB)
==================================================
downloaded 55 KB
* installing *source* package ‘rDEA’ ...
** package ‘rDEA’ successfully unpacked and MD5 sums checked
** libs
/bin/sh: line 0: cd: GLPK: No such file or directory
make: *** [GLPK.ts] Error 1
ERROR: compilation failed for package ‘rDEA’
* removing
‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rDEA’
Warning in install.packages :
installation of package ‘rDEA’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/b1/_pstgqks0r3gb3t972tk8zh00000gn/T/RtmpuvqGid/downloaded_packages’
Related
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 RWeka in RStudio 1.2.5033
I have tried many different ways to install it, I re-installed Java64. Here is my latest try:
install.packages("rJava")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/Jesse's PC/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
There is a binary version available but the source version is later:
binary source needs_compilation
rJava 0.9-12 0.9-13 TRUE
installing the source package ‘rJava’
trying URL 'https://cran.rstudio.com/src/contrib/rJava_0.9-13.tar.gz'
Content type 'application/x-gzip' length 664898 bytes (649 KB)
downloaded 649 KB
* installing *source* package 'rJava' ...
** package 'rJava' successfully unpacked and MD5 sums checked
** using staged installation
Generate Windows-specific files (src/jvm-w32) ...
make: Entering directory '/c/Users/JESSE'~1/AppData/Local/Temp/RtmpuOekjT/R.INSTALL24344ae86868/rJava/src/jvm-w32'
c:/Rtools/mingw_64/bin/dlltool --as c:/Rtools/mingw_64/bin/as --input-def jvm64.def --kill-at --dllname jvm.dll --output-lib libjvm.dll.a
make: c:/Rtools/mingw_64/bin/dlltool: Command not found
make: *** [Makefile:20: libjvm.dll.a] Error 127
make: Leaving directory '/c/Users/JESSE'~1/AppData/Local/Temp/RtmpuOekjT/R.INSTALL24344ae86868/rJava/src/jvm-w32'
ERROR: configuration failed for package 'rJava'
* removing 'C:/Users/Jesse's PC/Documents/R/win-library/3.6/rJava'
* restoring previous 'C:/Users/Jesse's PC/Documents/R/win-library/3.6/rJava'
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\Jesse's PC\AppData\Local\Temp\Rtmps5Y5TC\downloaded_packages’
I am trying install rentrez in Rstudio and it fails (error below). But I cannot find the config.log to interpret the error. Any help appreciated locating file or installing rentrez. I am doing this with R version R version 3.6.1 (2019-07-05) on Mac OS 10.14.6. Thanks
Error:
install.packages("rentrez") also installing the dependency ‘XML’
>trying URL 'https://cran.rstudio.com/src/contrib/XML_3.98-1.20.tar.gz'
>Content type 'application/x-gzip' length 1600829 bytes (1.5 MB)
downloaded 1.5 MB
>trying URL 'https://cran.rstudio.com/src/contrib/rentrez_1.2.2.tar.gz'
>Content type 'application/x-gzip' length 79029 bytes (77 KB)
downloaded 77 KB
>installing source package ‘XML’ ...
>** package ‘XML’ successfully unpacked and MD5 sums checked **
> using staged installation
> checking for gcc... x86_64-apple-darwin13.4.0-clang checking whether the C compiler works... no
>configure: error: in /private/var/folders/f0/3d9kdp5j09x5xpv5t0_zq6b80000gn/T/Rtmpp98Wvu/R.INSTALLaf61110a6db/XML':
configure: error: C compiler cannot create executables
Seeconfig.log' for more details ERROR: configuration failed for package ‘XML’
>removing ‘/opt/anaconda3/lib/R/library/XML’ Warning in install.packages : installation of package ‘XML’ had non-zero exit status ERROR: dependency ‘XML’ is not available for package ‘rentrez’
removing ‘/opt/anaconda3/lib/R/library/rentrez’ Warning in install.packages : installation of package ‘rentrez’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/f0/3d9kdp5j09x5xpv5t0_zq6b80000gn/T/RtmpxDMasm/downloaded_packages’
Updating HTML index of packages in '.Library' Making 'packages.html' ... done
I have looked for the config.log file in the working directory I am in when I enter the
install.packages("rentrez") command.
I also tried to look for it in /private/var/folders/f0/3d9kdp5j09x5xpv5t0_zq6b80000gn/T/RtmpxDMasm/downloaded_packages’, however RtmpxDMasm/downloaded_packages does not exist. Is it being deleted with the config.log file in the failed install? What should I do next?
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 am trying to install PostgreSQL package on R version 3.1.2. running on Linux.
I get the following error...
Installing package into ‘/usr/lib64/R/library’ (as ‘lib’ is unspecified) trying URL 'http://cran.cnr.berkeley.edu/src/contrib/RPostgreSQL_0.4.tar.gz' Content type 'application/x-gzip' length 477352 bytes (466 Kb) opened URL
==================================================
downloaded 466 Kb
* installing *source* package ‘RPostgreSQL’ ...
** package ‘RPostgreSQL’ successfully unpacked and MD5 sums checked
sh: ./configure: /bin/sh: bad interpreter: Permission denied
ERROR: configuration failed for package ‘RPostgreSQL’
* removing ‘/usr/lib64/R/library/RPostgreSQL’
> The downloaded source packages are in
> ‘/tmp/RtmpANw7OS/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning
> message: In install.packages("RPostgreSQL") : installation of here`package ‘RPostgreSQL’ had non-zero exit status
Any ideas on how to resolve this?
This looks odd:
./configure: /bin/sh: bad interpreter: Permission denied
Is your /bin/sh unsual or in bad shape? What happens when you (manually) untar the sources and run ./configure ?