Dear list, Just upgraded to MacOS Mavericks, fresh install of R 3.0.2 and trying to install a previous version of my QCA package (the most recent one source file, which passed the R CMD check --as-cran with R 3.0.1) I seem to have some difficulties in the C code, apparently it doesn't find some headers (please see below): ===========$ R CMD INSTALL --no-multiarch QCA.history/QCA_1.1-1.tar.gz * installing to library ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library’ * installing *source* package ‘QCA’ ... ** libs llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c allSol.c -o allSol.o In file included from allSol.c:1: /Library/Frameworks/R.framework/Resources/include/R.h:28:20: error: stdlib.h: No such file or directory /Library/Frameworks/R.framework/Resources/include/R.h:29:73: error: stdio.h: No such file or directory In file included from /Library/Frameworks/R.framework/Resources/include/R.h:30, from allSol.c:1: /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h:15:25: error: limits.h: No such file or directory In file included from allSol.c:1: /Library/Frameworks/R.framework/Resources/include/R.h:31:18: error: math.h: No such file or directory In file included from /Library/Frameworks/R.framework/Resources/include/R.h:44, from allSol.c:1: /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:26:47: error: string.h: No such file or directory In file included from allSol.c:2: /Library/Frameworks/R.framework/Resources/include/Rinternals.h:862: error: expected declaration specifiers or ‘...’ before ‘FILE’ /Library/Frameworks/R.framework/Resources/include/Rinternals.h:865: error: expected declaration specifiers or ‘...’ before ‘FILE’ allSol.c: In function ‘allSol’: allSol.c:62: warning: implicit declaration of function ‘div’ allSol.c:62: error: request for member ‘quot’ in something not a structure or union allSol.c:62: error: request for member ‘rem’ in something not a structure or union allSol.c:213: error: request for member ‘quot’ in something not a structure or union allSol.c:213: error: request for member ‘rem’ in something not a structure or union allSol.c:279: error: request for member ‘quot’ in something not a structure or union allSol.c:279: error: request for member ‘rem’ in something not a structure or union make: *** [allSol.o] Error 1 ERROR: compilation failed for package ‘QCA’ * removing ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/QCA’ * restoring previous ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/QCA’ =========== It doesn't find stdlib.h, stdio.h, limits.h, math.h, string.h (etc, basically all important ones). I have Xcode version 5.0.2 installed, do I need anything else installed in the system? Thank you, Adrian -- Adrian Dusa University of Bucharest Romanian Social Data Archive 1, Schitu Magureanu Bd. 050025 Bucharest sector 5 Romania Tel.:+40 21 3126618 \ +40 21 3120210 / int.101 Fax: +40 21 3158391 [[alternative HTML version deleted]]
This is an R-sig-mac issue, so Cc:ed there. I have seen this after an upgrade to Mavericks: you have a partial installation of the pre-Mavericks Xcode Command Line Tools after the upgrade (which removed some of it). See the current R-admin manual for how to use the CRAN binary of R 3.0.2 with Mavericks. Or get R_patched from r.research.att.com, which will change the compiler specs for you. On 06/02/2014 08:49, Adrian Du?a wrote:> Dear list, > > Just upgraded to MacOS Mavericks, fresh install of R 3.0.2 and trying to > install a previous version of my QCA package (the most recent one source > file, which passed the R CMD check --as-cran with R 3.0.1) > > I seem to have some difficulties in the C code, apparently it doesn't find > some headers (please see below): > > ===========> $ R CMD INSTALL --no-multiarch QCA.history/QCA_1.1-1.tar.gz > * installing to library > ???/Library/Frameworks/R.framework/Versions/3.0/Resources/library??? > * installing *source* package ???QCA??? ... > ** libs > llvm-gcc-4.2 -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c allSol.c -o allSol.o > In file included from allSol.c:1: > /Library/Frameworks/R.framework/Resources/include/R.h:28:20: error: > stdlib.h: No such file or directory > /Library/Frameworks/R.framework/Resources/include/R.h:29:73: error: > stdio.h: No such file or directory > In file included from > /Library/Frameworks/R.framework/Resources/include/R.h:30, > from allSol.c:1: > /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h:15:25: > error: limits.h: No such file or directory > In file included from allSol.c:1: > /Library/Frameworks/R.framework/Resources/include/R.h:31:18: error: math.h: > No such file or directory > In file included from > /Library/Frameworks/R.framework/Resources/include/R.h:44, > from allSol.c:1: > /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:26:47: error: > string.h: No such file or directory > In file included from allSol.c:2: > /Library/Frameworks/R.framework/Resources/include/Rinternals.h:862: error: > expected declaration specifiers or ???...??? before ???FILE??? > /Library/Frameworks/R.framework/Resources/include/Rinternals.h:865: error: > expected declaration specifiers or ???...??? before ???FILE??? > allSol.c: In function ???allSol???: > allSol.c:62: warning: implicit declaration of function ???div??? > allSol.c:62: error: request for member ???quot??? in something not a structure > or union > allSol.c:62: error: request for member ???rem??? in something not a structure > or union > allSol.c:213: error: request for member ???quot??? in something not a structure > or union > allSol.c:213: error: request for member ???rem??? in something not a structure > or union > allSol.c:279: error: request for member ???quot??? in something not a structure > or union > allSol.c:279: error: request for member ???rem??? in something not a structure > or union > make: *** [allSol.o] Error 1 > ERROR: compilation failed for package ???QCA??? > * removing > ???/Library/Frameworks/R.framework/Versions/3.0/Resources/library/QCA??? > * restoring previous > ???/Library/Frameworks/R.framework/Versions/3.0/Resources/library/QCA??? > ===========> > It doesn't find stdlib.h, stdio.h, limits.h, math.h, string.h (etc, > basically all important ones). > > I have Xcode version 5.0.2 installed, do I need anything else installed in > the system? > > Thank you, > Adrian > > > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
I went through this pain two days ago, but I managed both building R from source and my own packages by following Brian Ripley excellent (as always) pointers on the r-sig-mac mailing list (around october 2013). Look there, and ask further questions on that list. G?ran Brostr?m On 02/06/2014 09:49 AM, Adrian Du?a wrote:> Dear list, > > Just upgraded to MacOS Mavericks, fresh install of R 3.0.2 and trying to > install a previous version of my QCA package (the most recent one source > file, which passed the R CMD check --as-cran with R 3.0.1) > > I seem to have some difficulties in the C code, apparently it doesn't find > some headers (please see below): > > ===========> $ R CMD INSTALL --no-multiarch QCA.history/QCA_1.1-1.tar.gz > * installing to library > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library? > * installing *source* package ?QCA? ... > ** libs > llvm-gcc-4.2 -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c allSol.c -o allSol.o > In file included from allSol.c:1: > /Library/Frameworks/R.framework/Resources/include/R.h:28:20: error: > stdlib.h: No such file or directory > /Library/Frameworks/R.framework/Resources/include/R.h:29:73: error: > stdio.h: No such file or directory > In file included from > /Library/Frameworks/R.framework/Resources/include/R.h:30, > from allSol.c:1: > /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h:15:25: > error: limits.h: No such file or directory > In file included from allSol.c:1: > /Library/Frameworks/R.framework/Resources/include/R.h:31:18: error: math.h: > No such file or directory > In file included from > /Library/Frameworks/R.framework/Resources/include/R.h:44, > from allSol.c:1: > /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:26:47: error: > string.h: No such file or directory > In file included from allSol.c:2: > /Library/Frameworks/R.framework/Resources/include/Rinternals.h:862: error: > expected declaration specifiers or ?...? before ?FILE? > /Library/Frameworks/R.framework/Resources/include/Rinternals.h:865: error: > expected declaration specifiers or ?...? before ?FILE? > allSol.c: In function ?allSol?: > allSol.c:62: warning: implicit declaration of function ?div? > allSol.c:62: error: request for member ?quot? in something not a structure > or union > allSol.c:62: error: request for member ?rem? in something not a structure > or union > allSol.c:213: error: request for member ?quot? in something not a structure > or union > allSol.c:213: error: request for member ?rem? in something not a structure > or union > allSol.c:279: error: request for member ?quot? in something not a structure > or union > allSol.c:279: error: request for member ?rem? in something not a structure > or union > make: *** [allSol.o] Error 1 > ERROR: compilation failed for package ?QCA? > * removing > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/QCA? > * restoring previous > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/QCA? > ===========> > It doesn't find stdlib.h, stdio.h, limits.h, math.h, string.h (etc, > basically all important ones). > > I have Xcode version 5.0.2 installed, do I need anything else installed in > the system? > > Thank you, > Adrian >
Apologies for my late reply, I've been away for a few days. Everything is working fine now, thank you again for your advice. Best wishes, Adrian On Thu, Feb 6, 2014 at 10:49 AM, Adrian Dușa <dusa.adrian@unibuc.ro> wrote:> Dear list, > > Just upgraded to MacOS Mavericks, fresh install of R 3.0.2 and trying to > install a previous version of my QCA package (the most recent one source > file, which passed the R CMD check --as-cran with R 3.0.1) > > I seem to have some difficulties in the C code, apparently it doesn't find > some headers (please see below): > > ===========> $ R CMD INSTALL --no-multiarch QCA.history/QCA_1.1-1.tar.gz > * installing to library > ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library’ > * installing *source* package ‘QCA’ ... > ** libs > llvm-gcc-4.2 -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c allSol.c -o allSol.o > In file included from allSol.c:1: > /Library/Frameworks/R.framework/Resources/include/R.h:28:20: error: > stdlib.h: No such file or directory > /Library/Frameworks/R.framework/Resources/include/R.h:29:73: error: > stdio.h: No such file or directory > In file included from > /Library/Frameworks/R.framework/Resources/include/R.h:30, > from allSol.c:1: > /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin11/4.2.1/include/limits.h:15:25: > error: limits.h: No such file or directory > In file included from allSol.c:1: > /Library/Frameworks/R.framework/Resources/include/R.h:31:18: error: > math.h: No such file or directory > In file included from > /Library/Frameworks/R.framework/Resources/include/R.h:44, > from allSol.c:1: > /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:26:47: error: > string.h: No such file or directory > In file included from allSol.c:2: > /Library/Frameworks/R.framework/Resources/include/Rinternals.h:862: error: > expected declaration specifiers or ‘...’ before ‘FILE’ > /Library/Frameworks/R.framework/Resources/include/Rinternals.h:865: error: > expected declaration specifiers or ‘...’ before ‘FILE’ > allSol.c: In function ‘allSol’: > allSol.c:62: warning: implicit declaration of function ‘div’ > allSol.c:62: error: request for member ‘quot’ in something not a structure > or union > allSol.c:62: error: request for member ‘rem’ in something not a structure > or union > allSol.c:213: error: request for member ‘quot’ in something not a > structure or union > allSol.c:213: error: request for member ‘rem’ in something not a structure > or union > allSol.c:279: error: request for member ‘quot’ in something not a > structure or union > allSol.c:279: error: request for member ‘rem’ in something not a structure > or union > make: *** [allSol.o] Error 1 > ERROR: compilation failed for package ‘QCA’ > * removing > ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/QCA’ > * restoring previous > ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/QCA’ > ===========> > It doesn't find stdlib.h, stdio.h, limits.h, math.h, string.h (etc, > basically all important ones). > > I have Xcode version 5.0.2 installed, do I need anything else installed in > the system? > > Thank you, > Adrian > > -- > Adrian Dusa > University of Bucharest > Romanian Social Data Archive > 1, Schitu Magureanu Bd. > 050025 Bucharest sector 5 > Romania > Tel.:+40 21 3126618 \ > +40 21 3120210 / int.101 > Fax: +40 21 3158391 >-- Adrian Dusa University of Bucharest Romanian Social Data Archive 1, Schitu Magureanu Bd. 050025 Bucharest sector 5 Romania Tel.:+40 21 3126618 \ +40 21 3120210 / int.101 Fax: +40 21 3158391 [[alternative HTML version deleted]]