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?
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'm trying to get R installed as a kernel for jupyter notebook. I am follwing the instructions at: https://irkernel.github.io/installation/ but when I try to install IRkernel I get:
also installing the dependency 'uuid'
trying URL 'https://cran.mtu.edu/src/contrib/uuid_0.1-4.tar.gz'
Content type 'application/x-gzip' length 49544 bytes (48 KB)
==================================================
downloaded 48 KB
trying URL 'https://cran.mtu.edu/src/contrib/IRkernel_1.1.tar.gz'
Content type 'application/x-gzip' length 52805 bytes (51 KB)
==================================================
downloaded 51 KB
* installing *source* package 'uuid' ...
** package 'uuid' 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/y2/38gkkc0s7d52_mr_s6zfj7m80000gq/T/Rtmpru6fsM/R.INSTALL92f935860c3f/uuid':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package 'uuid'
* removing '/anaconda3/lib/R/library/uuid'
ERROR: dependency 'uuid' is not available for package 'IRkernel'
* removing '/anaconda3/lib/R/library/IRkernel'
The downloaded source packages are in
'/private/var/folders/y2/38gkkc0s7d52_mr_s6zfj7m80000gq/T/Rtmpg79DeD/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages("IRkernel") :
installation of package 'uuid' had non-zero exit status
2: In install.packages("IRkernel") :
installation of package 'IRkernel' had non-zero exit status
Can someone please tell me the problem?emphasized text
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 was facing this problem while installing R package devtools. My R studio is in Anaconda, and it's the latest version. The code is this:
install.packages("devtools")
And I got response as follows:
also installing the dependency ‘git2r’
trying URL 'https://cran.rstudio.com/src/contrib/git2r_0.21.0.tar.gz'
Content type 'application/x-gzip' length 1155512 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/src/contrib/devtools_1.13.5.tar.gz'
Content type 'application/x-gzip' length 486555 bytes (475 KB)
==================================================
downloaded 475 KB
* installing *source* package ‘git2r’ ...
** package ‘git2r’ successfully unpacked and MD5 sums checked
checking build system type... x86_64-apple-darwin17.6.0
checking host system type... x86_64-apple-darwin17.6.0
checking for gcc... x86_64-apple-darwin13.4.0-clang
checking whether the C compiler works... no
configure: error: in `/private/var/folders/mh/df2k68vs4g3714qyztvg2y980000gn/T/RtmppuLmjL/R.INSTALL8f6b17805a/git2r':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘git2r’
* removing ‘/Users/nora/anaconda3/lib/R/library/git2r’
Warning in install.packages :
installation of package ‘git2r’ had non-zero exit status
ERROR: dependency ‘git2r’ is not available for package ‘devtools’
* removing ‘/Users/nora/anaconda3/lib/R/library/devtools’
Warning in install.packages :
installation of package ‘devtools’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/mh/df2k68vs4g3714qyztvg2y980000gn/T/Rtmpyjv9BV/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
To fix this problem, I've tried the following but nothing changed:
check Xcode and command line tools, and make surethe command line tools is the latest version.
update all the anaconda package.
update homebrew
update gcc
restart my laptop.
Now I've installed this package by using this code in terminal:
conda install -c r r-devtools
when I type install.packages("devtools") in my R console, nothing seems wrong and I saw feedback as following:
trying URL 'https://cran.rstudio.com/src/contrib/devtools_1.13.5.tar.gz'
Content type 'application/x-gzip' length 486555 bytes (475 KB)
==================================================
downloaded 475 KB
* installing *source* package ‘devtools’ ...
** package ‘devtools’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (devtools)
The downloaded source packages are in
‘/private/var/folders/mh/df2k68vs4g3714qyztvg2y980000gn/T/Rtmpyjv9BV/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
But I'm not sure whether I still have C compiler problem. If so, I still want to fix that for future's convenience. And still, I don't know why I countered this problem in the first place.
I cannot install the XML package on my rstudio. I use anaconda. Below is the log when I try to install:
install.packages("XML") trying URL
'https://cran.rstudio.com/src/contrib/XML_3.98-1.11.tar.gz' Content
type 'application/x-gzip' length 1599537 bytes (1.5 MB)
================================================== downloaded 1.5 MB
installing source package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked checking for gcc... x86_64-apple-darwin13.4.0-clang checking for C compiler
default output file name... configure: error: C compiler cannot
create executables See `config.log' for more details. ERROR:
configuration failed for package ‘XML’
removing ‘/Users/Anton/anaconda3/lib/R/library/XML’ Warning in install.packages : installation of package ‘XML’ had non-zero exit
status
The downloaded source packages are in
‘/private/var/folders/jw/4ff5f8y91h3g0973h3s7zr9h0000gn/T/RtmpRfb8mV/downloaded_packages’
Updating HTML index of packages in '.Library' Making 'packages.html'
... done
Any ideas?