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Help with "error: no acceptable C compiler found in $PATH"
4 messages · Hari Easwaran, R. Michael Weylandt
Yes, you probably need some sort of C compiler, but why can't you just
download the appropriate binary directly? I just did on OS X 10.5.8
(admittedly for R 2.13.2, not 2.14) with no problems. The output of
sessionInfo()
install.packages("RCurl")
if you don't mind please.
Thanks,
Michael
On Tue, Nov 15, 2011 at 2:12 PM, Hari Easwaran <hariharan.pe at gmail.com> wrote:
Dear all, I am trying to install a package from bioconductor (biomaRt) for which I need the RCurl package. I get the following main error message when I try to install RCurl (and its dependencies). configure: error: no acceptable C compiler found in $PATH See `config.log' for more details. ERROR: configuration failed for package ?RCurl? I searched for possible solutions and read in some online mailing list that I might have to install Xcode to install the gcc compiler. I am not sure if I should do this because I have installed RCurl in previous versions of R without any problems (on this same computer). I upgraded to the latest R (R version 2.14.0) and faced this problem. So I downgraded to R version 2.13.2 and still cannot install RCurl. I think my last successful installation of RCurl was with R version 2.11. Following is the complete error message and my R version details. I really appreciate any help or suggestions. Sincerely, Hari trying URL ' http://watson.nci.nih.gov/cran_mirror/src/contrib/XML_3.4-3.tar.gz' Content type 'application/octet-stream' length 906364 bytes (885 Kb) opened URL ================================================== downloaded 885 Kb trying URL ' http://watson.nci.nih.gov/cran_mirror/src/contrib/RCurl_1.7-0.tar.gz' Content type 'application/octet-stream' length 813252 bytes (794 Kb) opened URL ================================================== downloaded 794 Kb * installing *source* package ?XML? ... checking for gcc... no checking for cc... no checking for cl.exe... no configure: error: no acceptable C compiler found in $PATH See `config.log' for more details. ERROR: configuration failed for package ?XML? * removing ?/Library/Frameworks/R.framework/Versions/2.13/Resources/library/XML? * installing *source* package ?RCurl? ... checking for curl-config... /usr/bin/curl-config checking for gcc... no checking for cc... no checking for cc... no checking for cl... no configure: error: no acceptable C compiler found in $PATH See `config.log' for more details. ERROR: configuration failed for package ?RCurl? * removing ?/Library/Frameworks/R.framework/Versions/2.13/Resources/library/RCurl? * restoring previous ?/Library/Frameworks/R.framework/Versions/2.13/Resources/library/RCurl? The downloaded packages are in ?/private/var/folders/a6/a60JdPfrHC0ZAizZWyNM-E+++TI/-Tmp-/RtmpVjBcvX/downloaded_packages? ? ? ? ?[[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
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1 day later
Hmmmm....strange....if possible, this might be solvable by simply updating to the release version R 2.14. If it's at all possible, I'd start there. Can you find the object it's unhappy about? On my machine, I do the following 1) Open Finder 2) Macintosh HD -> Library -> Frameworks -> R.framework -> Versions -> 2.13 -> Resources -> library -> RCurl -> libs -> x86_64 -> RCurl.so Going the other way, are you sure you have Curl on your system? I'm pretty sure it's standard on all Macs but you never know...follow some of the instructions given here: http://www.omegahat.org/RCurl/FAQ.html You should be able to type curl-config in the terminal and get a meaningful response if it is. Did you change something on the OS level recently? I don't really know why this would have all fallen apart, I just re-reinstalled RCurl on R 2.13.2 OSX 10.5.8 with no problem at all. Michael
On Wed, Nov 16, 2011 at 11:14 AM, Hari Easwaran <hariharan.pe at gmail.com> wrote:
Hi Michael, Thanks for your response. Using the binary seems to solve partially. I am able to install (I think!) RCurl but not able to load the library. Below is the info you required and the error while loading RCurl.
sessionInfo()
R version 2.13.2 (2011-09-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base
install.packages("RCurl")
trying URL 'http://watson.nci.nih.gov/cran_mirror/bin/macosx/leopard/contrib/2.13/RCurl_1.7-0.tgz' Content type 'application/octet-stream' length 680511 bytes (664 Kb) opened URL ================================================== downloaded 664 Kb The downloaded packages are in /var/folders/a6/a60JdPfrHC0ZAizZWyNM-E+++TI/-Tmp-//RtmpYE7JLJ/downloaded_packages
library(RCurl)
Loading required package: bitops Error in dyn.load(file, DLLpath = DLLpath, ...) : ? unable to load shared object '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/RCurl/libs/x86_64/RCurl.so': dlopen(/Library/Frameworks/R.framework/Versions/2.13/Resources/library/RCurl/libs/x86_64/RCurl.so, 6): Library not loaded: @rpath/R.framework/Versions/2.13/Resources/lib/libR.dylib ? Referenced from: /Library/Frameworks/R.framework/Versions/2.13/Resources/library/RCurl/libs/x86_64/RCurl.so ? Reason: image not found Error: package/namespace load failed for 'RCurl' Warning: dependency ?Rcompression? is not available also installing the dependency ?XML? Seems like now I need 'Rcompression'. I googled this and found a Rcompression package 'zlib' (http://www.omegahat.org/Rcompression/). However the site says that "zlib for Mac OS X: zlib is already included as part of Mac OS X". I am wondering what to do? To my bliss, why did the previous R version oblivious of these issues! Really appreciate any hep. SIncerely, Hari On Tue, Nov 15, 2011 at 11:33 PM, R. Michael Weylandt <michael.weylandt at gmail.com> wrote:
Yes, you probably need some sort of C compiler, but why can't you just
download the appropriate binary directly? I just did on OS X 10.5.8
(admittedly for R 2.13.2, not 2.14) with no problems. The output of
sessionInfo()
install.packages("RCurl")
if you don't mind please.
Thanks,
Michael
On Tue, Nov 15, 2011 at 2:12 PM, Hari Easwaran <hariharan.pe at gmail.com>
wrote:
Dear all, I am trying to install a package from bioconductor (biomaRt) for which I need the RCurl package. I get the following main error message when I try to install RCurl (and its dependencies). configure: error: no acceptable C compiler found in $PATH See `config.log' for more details. ERROR: configuration failed for package ?RCurl? I searched for possible solutions and read in some online mailing list that I might have to install Xcode to install the gcc compiler. I am not sure if I should do this because I have installed RCurl in previous versions of R without any problems (on this same computer). I upgraded to the latest R (R version 2.14.0) and faced this problem. So I downgraded to R version 2.13.2 and still cannot install RCurl. I think my last successful installation of RCurl was with R version 2.11. Following is the complete error message and my R version details. I really appreciate any help or suggestions. Sincerely, Hari trying URL ' http://watson.nci.nih.gov/cran_mirror/src/contrib/XML_3.4-3.tar.gz' Content type 'application/octet-stream' length 906364 bytes (885 Kb) opened URL ================================================== downloaded 885 Kb trying URL ' http://watson.nci.nih.gov/cran_mirror/src/contrib/RCurl_1.7-0.tar.gz' Content type 'application/octet-stream' length 813252 bytes (794 Kb) opened URL ================================================== downloaded 794 Kb * installing *source* package ?XML? ... checking for gcc... no checking for cc... no checking for cl.exe... no configure: error: no acceptable C compiler found in $PATH See `config.log' for more details. ERROR: configuration failed for package ?XML? * removing ?/Library/Frameworks/R.framework/Versions/2.13/Resources/library/XML? * installing *source* package ?RCurl? ... checking for curl-config... /usr/bin/curl-config checking for gcc... no checking for cc... no checking for cc... no checking for cl... no configure: error: no acceptable C compiler found in $PATH See `config.log' for more details. ERROR: configuration failed for package ?RCurl? * removing ?/Library/Frameworks/R.framework/Versions/2.13/Resources/library/RCurl? * restoring previous ?/Library/Frameworks/R.framework/Versions/2.13/Resources/library/RCurl? The downloaded packages are in ?/private/var/folders/a6/a60JdPfrHC0ZAizZWyNM-E+++TI/-Tmp-/RtmpVjBcvX/downloaded_packages? ? ? ? ?[[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.