[Rd] Rebuilding and re-checking of downstream dependencies on CRAN Mac build machines

Hadley Wickham h@w|ckh@m @end|ng |rom gm@||@com
Thu Mar 26 22:40:26 CET 2020 

If I do install.packages("dplyr", type = "source"), I see:

Installing package into ‘/Users/hadley/R’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/dplyr_0.8.5.tar.gz'
Content type 'application/x-gzip' length 1378766 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

* installing *source* package ‘dplyr’ ...
** package ‘dplyr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
ccache clang++ -Qunused-arguments
 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR
-DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT
-DBOOST_NO_AUTO_PTR  -I"/Users/hadley/R/BH/include"
-I"/Users/hadley/R/plogr/include" -I"/Users/hadley/R/Rcpp/include"
-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-I/usr/local/include  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o
RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/dplyr.h:4:
In file included from ../inst/include/dplyr/main.h:6:
In file included from ../inst/include/dplyr/workarounds/static_assert.h:17:
In file included from /Users/hadley/R/BH/include/boost/config.hpp:57:
In file included from
/Users/hadley/R/BH/include/boost/config/platform/macos.hpp:28:
In file included from
/Users/hadley/R/BH/include/boost/config/detail/posix_features.hpp:18:
In file included from
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:655:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/gethostuuid.h:39:17:
error: unknown type name 'uuid_t'
int gethostuuid(uuid_t, const struct timespec *)
__OSX_AVAILABLE_STARTING(__MAC_10_5, __IPHONE_NA);
                ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/dplyr.h:4:
In file included from ../inst/include/dplyr/main.h:6:
In file included from ../inst/include/dplyr/workarounds/static_assert.h:17:
In file included from /Users/hadley/R/BH/include/boost/config.hpp:57:
In file included from
/Users/hadley/R/BH/include/boost/config/platform/macos.hpp:28:
In file included from
/Users/hadley/R/BH/include/boost/config/detail/posix_features.hpp:18:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:662:27:
error: unknown type name 'uuid_t'; did you mean 'uid_t'?
int      getsgroups_np(int *, uuid_t);
                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_uid_t.h:31:31:
note: 'uid_t' declared here
typedef __darwin_uid_t        uid_t;
                              ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/dplyr.h:4:
In file included from ../inst/include/dplyr/main.h:6:
In file included from ../inst/include/dplyr/workarounds/static_assert.h:17:
In file included from /Users/hadley/R/BH/include/boost/config.hpp:57:
In file included from
/Users/hadley/R/BH/include/boost/config/platform/macos.hpp:28:
In file included from
/Users/hadley/R/BH/include/boost/config/detail/posix_features.hpp:18:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:664:27:
error: unknown type name 'uuid_t'; did you mean 'uid_t'?
int      getwgroups_np(int *, uuid_t);
                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_uid_t.h:31:31:
note: 'uid_t' declared here
typedef __darwin_uid_t        uid_t;
                              ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/dplyr.h:4:
In file included from ../inst/include/dplyr/main.h:6:
In file included from ../inst/include/dplyr/workarounds/static_assert.h:17:
In file included from /Users/hadley/R/BH/include/boost/config.hpp:57:
In file included from
/Users/hadley/R/BH/include/boost/config/platform/macos.hpp:28:
In file included from
/Users/hadley/R/BH/include/boost/config/detail/posix_features.hpp:18:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:727:31:
error: unknown type name 'uuid_t'; did you mean 'uid_t'?
int      setsgroups_np(int, const uuid_t);
                                  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_uid_t.h:31:31:
note: 'uid_t' declared here
typedef __darwin_uid_t        uid_t;
                              ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/dplyr.h:4:
In file included from ../inst/include/dplyr/main.h:6:
In file included from ../inst/include/dplyr/workarounds/static_assert.h:17:
In file included from /Users/hadley/R/BH/include/boost/config.hpp:57:
In file included from
/Users/hadley/R/BH/include/boost/config/platform/macos.hpp:28:
In file included from
/Users/hadley/R/BH/include/boost/config/detail/posix_features.hpp:18:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:729:31:
error: unknown type name 'uuid_t'; did you mean 'uid_t'?
int      setwgroups_np(int, const uuid_t);
                                  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_uid_t.h:31:31:
note: 'uid_t' declared here
typedef __darwin_uid_t        uid_t;
                              ^
In file included from RcppExports.cpp:5:
In file included from ./../inst/include/dplyr_types.h:4:
In file included from ../inst/include/dplyr/data/GroupedDataFrame.h:8:
In file included from ../inst/include/tools/SymbolMap.h:4:
In file included from ../inst/include/tools/hash.h:10:
In file included from /Users/hadley/R/BH/include/boost/unordered_map.hpp:17:
In file included from
/Users/hadley/R/BH/include/boost/unordered/unordered_map.hpp:19:
In file included from /Users/hadley/R/BH/include/boost/move/move.hpp:30:
In file included from /Users/hadley/R/BH/include/boost/move/iterator.hpp:27:
/Users/hadley/R/BH/include/boost/move/detail/iterator_traits.hpp:29:1:
warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/hadley/R/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note:
expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:866:53:
note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace
_LIBCPP_ABI_NAMESPACE {
                                                    ^
1 warning and 5 errors generated.
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘dplyr’
* removing ‘/Users/hadley/R/dplyr’
* restoring previous ‘/Users/hadley/R/dplyr’

Hadley


On Thu, Mar 26, 2020 at 4:05 PM Simon Urbanek <simon.urbanek using r-project.org>
wrote:

> Winston,
>
> the Mac CRAN build builds a package only if either is true:
> 1) the package has not passed checks
> 2) there is a new version of the package since last successful build+check
>
> The old build machine doesn't have the capacity to do full re-builds (it
> would take over 24h - currently the nightly build of packages takes 16-22
> hours), but we're currently building a new setup for R 4.0.0 on new
> hardware and as a part of it we are planning to setup a "mac-builder"
> similar to what is currently available for Windows.
>
> That said, I have run httpuv by hand on the CRAN build machine (against
> Rcpp 1.0.4) and I saw no issues. I have seen the discussion on Rcpp, but so
> far no one actually posted details of what is breaking (nor do your links
> include any actual details on this). I'd love to help, but the lack fo a
> useful report makes this impossible. If you have any actual leads, please
> post them. The CRAN machine uses the tools that are available on CRAN:
> https://cran.r-project.org/bin/macosx/tools/ (clang-7 and gfortran-6.1
> for 3.6.x)
>
> Cheers,
> Simon
>
>
> > On 27/03/2020, at 7:38 AM, Winston Chang <winstonchang1 using gmail.com>
> wrote:
> >
> > I have two questions about the CRAN machines that build binary
> > packages for Mac. When a new version of a package is released,
> >  (A) Do the downstream dependencies get re-checked?
> >  (B) Do the downstream dependencies get re-built?
> >
> > I have heard (but do not know for sure) that the answer to (A) is no,
> > the downstream dependencies do not get rechecked.
> >
> > From publicly available information on the CRAN web server, it looks
> > like the answer to (B) is also no, the downstream dependencies do not
> > get rebuilt. Looking at
> > https://www.r-project.org/nosvn/R.check/r-release-osx-x86_64/, I see
> > the following dates for these binary packages:
> >
> > - Rcpp_1.0.4.tgz: 2020-03-18
> > - httpuv_1.5.2.tgz: 2019-09-12
> > - dplyr_0.8.5.tgz: 2020-03-08
> >
> > Rcpp was released recently, and httpuv and dplyr (which are downstream
> > dependencies of Rcpp) have older dates, which indicates that these
> > binary packages were not rebuilt when Rcpp was released.
> >
> > In my particular case, I'm interested in the httpuv package (which I
> > maintain). I and several others have not been able to get the CRAN
> > version of httpuv to compile using the CRAN version of Rcpp on Mac.
> > (It seems to compile fine on other platforms.) I have heard from
> > maintainers of other Rcpp-dependent packages that they also can't get
> > their packages to compile on Mac, using both the default Mac compiler
> > toolchain and the CRAN-recommended toolchain, which uses clang 7.
> >
> > For more technical details about the cause of breakage, see:
> > https://github.com/RcppCore/Rcpp/issues/1060
> > https://github.com/rstudio/httpuv/issues/260
> >
> > If the CRAN Mac build machine is indeed able to build httpuv against
> > the current version of Rcpp, it would be really helpful to have more
> > information about the system configuration. If it is not able to
> > rebuild httpuv and other packages against Rcpp, then this is a
> > problem. Among other things, it prevents people from building their
> > packages from source using CRAN versions of packages, and it also
> > means that none of these packages can release a new version, because
> > the binaries can't be built on Mac.
> >
> > -Winston
> >
> > ______________________________________________
> > R-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
> ______________________________________________
> R-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>


-- 
http://hadley.nz

	[[alternative HTML version deleted]]

More information about the R-devel mailing list