r - 尽管C++ 11可用，但正在更新R.3.5.1 C++ 11依赖关系中的Rgdal ...

当我从3.4.4更新到3.5.1后，通过从源代码进行编译来更新(或至少尝试)rgdal软件包时，我遇到了一个一切都进行得很好的奇怪问题，但是由于“ undefined symbol ”错误:

** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for ‘rgdal’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/usr/local/lib/R/site-library/rgdal/libs/rgdal.so':
  /usr/local/lib/R/site-library/rgdal/libs/rgdal.so: undefined symbol: _ZNK10OGRFeature16GetFieldAsDoubleEi
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/rgdal’
* restoring previous ‘/usr/local/lib/R/site-library/rgdal’

The downloaded source packages are in
        ‘/tmp/RtmpHu6D0N/downloaded_packages’
Warning message:
In install.packages("rgdal") :
  installation of package ‘rgdal’ had non-zero exit status

当运行echo _ZNK10OGRFeature16GetFieldAsDoubleEi | c++filt时，我得到的输出OGRFeature::GetFieldAsDouble(int) const并不能帮助我。我已经从https://trac.osgeo.org/gdal/wiki/DownloadSource安装了GDAL，如CRAN软件包站点上所建议的那样，该文件显示我已经安装了GDAL 2.3.1。

奇怪的是，更新失败了，因为已经安装了该软件包，因此应该已经满足依赖关系。热烈欢迎您提出任何有关如何解决此问题的指示。

由于过去几周没有任何建议，我决定卸载rgdal，然后重新安装。有趣的是，现在我声称我的系统(Ubuntu 16.04.5 LTS)不支持C++ 11，尽管检查表明它在那里(C++11 support available):

* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
configure: R_HOME: /usr/lib/R
configure: CC: gcc -std=gnu99
configure: CXX: g++
configure: C++11 support available
configure: rgdal: 1.3-4
checking for /usr/bin/svnversion... yes
configure: svn revision: 766
checking for gdal-config... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.3.1
checking C++11 support for GDAL >= 2.3.0... yes
checking GDAL version >= 1.11.4... yes
checking gdal: linking with --libs only... no
checking gdal: linking with --libs and --dep-libs... no
In file included from /usr/local/include/gdal.h:45:0,
                 from gdal_test.cc:1:
/usr/local/include/cpl_port.h:187:6: error: #error Must have C++11 or newer.
 #    error Must have C++11 or newer.
      ^
In file included from /usr/local/include/gdal.h:49:0,
                 from gdal_test.cc:1:
/usr/local/include/cpl_minixml.h:202:47: error: expected template-name before '<' token
 class CPLXMLTreeCloser: public std::unique_ptr<CPLXMLNode, CPLXMLTreeCloserDeleter>
                                               ^
/usr/local/include/cpl_minixml.h:202:47: error: expected '{' before '<' token
/usr/local/include/cpl_minixml.h:202:47: error: expected unqualified-id before '<' token
In file included from /usr/local/include/ogr_api.h:45:0,
                 from /usr/local/include/gdal.h:50,
                 from gdal_test.cc:1:
/usr/local/include/ogr_core.h:79:28: error: expected '}' before end of line
/usr/local/include/ogr_core.h:79:28: error: expected declaration before end of line
In file included from /usr/local/include/gdal.h:45:0,
                 from gdal_test.cc:1:
/usr/local/include/cpl_port.h:187:6: error: #error Must have C++11 or newer.
 #    error Must have C++11 or newer.
      ^
In file included from /usr/local/include/gdal.h:49:0,
                 from gdal_test.cc:1:
/usr/local/include/cpl_minixml.h:202:47: error: expected template-name before '<' token
 class CPLXMLTreeCloser: public std::unique_ptr<CPLXMLNode, CPLXMLTreeCloserDeleter>
                                               ^
/usr/local/include/cpl_minixml.h:202:47: error: expected '{' before '<' token
/usr/local/include/cpl_minixml.h:202:47: error: expected unqualified-id before '<' token
In file included from /usr/local/include/ogr_api.h:45:0,
                 from /usr/local/include/gdal.h:50,
                 from gdal_test.cc:1:
/usr/local/include/ogr_core.h:79:28: error: expected '}' before end of line
/usr/local/include/ogr_core.h:79:28: error: expected declaration before end of line
configure: Install failure: compilation and/or linkage problems.
configure: error: GDALAllRegister not found in libgdal.
ERROR: configuration failed for package ‘rgdal’
* removing ‘/usr/local/lib/R/site-library/rgdal’

我的devtools::session_info()是以下内容:

Session info ------------------------------------------------------------------
 setting  value
 version  R version 3.5.1 (2018-07-02)
 system   x86_64, linux-gnu
 ui       X11
 language en_US:en
 collate  en_US.UTF-8
 tz       Europe/Brussels
 date     2018-07-28

Packages ----------------------------------------------------------------------
 package   * version date       source
 base      * 3.5.1   2018-07-03 local
 compiler    3.5.1   2018-07-03 local
 datasets  * 3.5.1   2018-07-03 local
 devtools  * 1.13.6  2018-06-27 CRAN (R 3.5.1)
 digest      0.6.15  2018-01-28 CRAN (R 3.5.1)
 graphics  * 3.5.1   2018-07-03 local
 grDevices * 3.5.1   2018-07-03 local
 memoise     1.1.0   2017-04-21 CRAN (R 3.5.1)
 methods   * 3.5.1   2018-07-03 local
 stats     * 3.5.1   2018-07-03 local
 tools       3.5.1   2018-07-03 local
 utils     * 3.5.1   2018-07-03 local
 withr       2.1.2   2018-03-15 CRAN (R 3.5.1)

最佳答案

就我而言，解决方案是更新我的~/.R/Makevars配置。

  CC=clang
  CXX=clang++
  PKG_CFLAGS= -g -O2

我在我的CXX定义中添加了 -std = gnu++ 11

  CC=clang
  CXX=clang++ -std=gnu++11
  PKG_CFLAGS= -g -O2

在此之后，不再出现编译问题和相关错误(至少到目前为止我的测试中没有)

推理

上面引出了一个问题-为什么？以我的经验，使用rgdal进行的新R 3.5.1安装不会出现编译错误，而从3.4.4进行升级会出现编译错误。我的感觉是R和rgdal软件包配置之间存在相互作用，导致C++ 11编译标志未激活。 rgdal需要并使用C++ 11功能。请参阅Makevar-下面的概述。

引文:

R Installation and Administration

R Using Makevars

How do I enable C++11 in gcc?

编译示例:

Makevars中没有-std=gnu++11标志[错误]

> install.packages("rgdal")
--2018-08-10 21:31:58--  https://cran.rstudio.com/src/contrib/rgdal_1.3-4.tar.gz
Resolving cran.rstudio.com (cran.rstudio.com)... 52.84.17.191
Connecting to cran.rstudio.com (cran.rstudio.com)|52.84.17.191|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1664774 (1.6M) [application/x-gzip]
Saving to: ‘/var/folders/md/03gdc4c14z18kbqwpfh4jdfc0000gr/T//RtmpidZNr4/downloaded_packages/rgdal_1.3-4.tar.gz’

/var/folders/md/03gdc4c14z18kbqwpfh4jd 100%[============================================================================>]   1.59M  --.-KB/s    in 0.04s

2018-08-10 21:31:58 (35.6 MB/s) - ‘/var/folders/md/03gdc4c14z18kbqwpfh4jdfc0000gr/T//RtmpidZNr4/downloaded_packages/rgdal_1.3-4.tar.gz’ saved [1664774/1664774]

* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
configure: R_HOME: /Users/***/.Renv/versions/3.5.1/lib/R
configure: CC: clang
configure: CXX: clang++
configure: C++11 support available
configure: rgdal: 1.3-4
checking for /usr/bin/svnversion... yes
configure: svn revision: 766
checking for gdal-config... /usr/local/opt/gdal2/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.3.1
checking C++11 support for GDAL >= 2.3.0... yes
checking GDAL version >= 1.11.4... yes
checking gdal: linking with --libs only... no
checking gdal: linking with --libs and --dep-libs... no
In file included from gdal_test.cc:1:
In file included from /usr/local/Cellar/gdal2/2.3.1/include/gdal.h:45:
/usr/local/Cellar/gdal2/2.3.1/include/cpl_port.h:187:6: error: Must have C++11 or newer.
#    error Must have C++11 or newer.
     ^
1 error generated.
In file included from gdal_test.cc:1:
In file included from /usr/local/Cellar/gdal2/2.3.1/include/gdal.h:45:
/usr/local/Cellar/gdal2/2.3.1/include/cpl_port.h:187:6: error: Must have C++11 or newer.
#    error Must have C++11 or newer.
     ^
1 error generated.
configure: Install failure: compilation and/or linkage problems.
configure: error: GDALAllRegister not found in libgdal.
ERROR: configuration failed for package ‘rgdal’
* removing ‘/Users/***/.Renv/versions/3.5.1/lib/R/library/rgdal’

The downloaded source packages are in
    ‘/private/var/folders/md/03gdc4c14z18kbqwpfh4jdfc0000gr/T/RtmpidZNr4/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("rgdal") :
  installation of package ‘rgdal’ had non-zero exit status

在Makevars中添加了-std=gnu++11

> install.packages("rgdal")
--2018-08-10 21:34:20--  https://cran.rstudio.com/src/contrib/rgdal_1.3-4.tar.gz
Resolving cran.rstudio.com (cran.rstudio.com)... 52.84.17.191
Connecting to cran.rstudio.com (cran.rstudio.com)|52.84.17.191|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1664774 (1.6M) [application/x-gzip]
Saving to: ‘/var/folders/md/03gdc4c14z18kbqwpfh4jdfc0000gr/T//RtmpidZNr4/downloaded_packages/rgdal_1.3-4.tar.gz’

/var/folders/md/03gdc4c14z18kbqwpfh4jd 100%[============================================================================>]   1.59M  --.-KB/s    in 0.04s

2018-08-10 21:34:20 (43.5 MB/s) - ‘/var/folders/md/03gdc4c14z18kbqwpfh4jdfc0000gr/T//RtmpidZNr4/downloaded_packages/rgdal_1.3-4.tar.gz’ saved [1664774/1664774]

* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
configure: R_HOME: /Users/***/.Renv/versions/3.5.1/lib/R
configure: CC: clang
configure: CXX: clang++ -std=gnu++11
configure: C++11 support available
configure: rgdal: 1.3-4
checking for /usr/bin/svnversion... yes
configure: svn revision: 766
checking for gdal-config... /usr/local/opt/gdal2/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.3.1
checking C++11 support for GDAL >= 2.3.0... yes
checking GDAL version >= 1.11.4... yes
checking gdal: linking with --libs only... yes
checking GDAL: /usr/local/Cellar/gdal2/2.3.1/share/gdal/pcs.csv readable... yes
configure: pkg-config proj exists, will use it
configure: PROJ version: 5.1.0
checking proj_api.h presence and usability... yes
checking PROJ version >= 4.8.0... yes
checking projects.h presence and usability... yes
checking PROJ.4: epsg found and readable... yes
checking PROJ.4: conus found and readable... yes
configure: Package CPP flags:  -I/usr/local/Cellar/gdal2/2.3.1/include -I/usr/local/Cellar/proj/5.1.0/include
configure: Package LIBS:  -L/usr/local/Cellar/gdal2/2.3.1/lib -lgdal -lproj
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/Users/***/.Renv/versions/3.5.1/lib/R/include" -DNDEBUG -I/usr/local/Cellar/gdal2/2.3.1/include -I/usr/local/Cellar/proj/5.1.0/include -I"/Users/***/.Renv/versions/3.5.1/lib/R/library/sp/include" -I/usr/local/opt/gdal2/include -I/usr/local/opt/liblas-gdal2/include -I/usr/local/opt/laszip@2.2/include -I/usr/local/opt/bzip2/include -I/usr/local/opt/zlib/include  -g -O2 -stdlib=libc++ -std=c++11 -fPIC  -g -O2 -c OGR_write.cpp -o OGR_write.o
g++ -std=gnu++11 -I"/Users/***/.Renv/versions/3.5.1/lib/R/include" -DNDEBUG -I/usr/local/Cellar/gdal2/2.3.1/include -I/usr/local/Cellar/proj/5.1.0/include -I"/Users/***/.Renv/versions/3.5.1/lib/R/library/sp/include" -I/usr/local/opt/gdal2/include -I/usr/local/opt/liblas-gdal2/include -I/usr/local/opt/laszip@2.2/include -I/usr/local/opt/bzip2/include -I/usr/local/opt/zlib/include  -g -O2 -stdlib=libc++ -std=c++11 -fPIC  -g -O2 -c gdal-bindings.cpp -o gdal-bindings.o
clang -I"/Users/***/.Renv/versions/3.5.1/lib/R/include" -DNDEBUG -I/usr/local/Cellar/gdal2/2.3.1/include -I/usr/local/Cellar/proj/5.1.0/include -I"/Users/***/.Renv/versions/3.5.1/lib/R/library/sp/include" -I/usr/local/opt/gdal2/include -I/usr/local/opt/liblas-gdal2/include -I/usr/local/opt/laszip@2.2/include -I/usr/local/opt/bzip2/include -I/usr/local/opt/zlib/include  -g -O2 -fPIC  -g -O2  -c init.c -o init.o
clang -I"/Users/***/.Renv/versions/3.5.1/lib/R/include" -DNDEBUG -I/usr/local/Cellar/gdal2/2.3.1/include -I/usr/local/Cellar/proj/5.1.0/include -I"/Users/***/.Renv/versions/3.5.1/lib/R/library/sp/include" -I/usr/local/opt/gdal2/include -I/usr/local/opt/liblas-gdal2/include -I/usr/local/opt/laszip@2.2/include -I/usr/local/opt/bzip2/include -I/usr/local/opt/zlib/include  -g -O2 -fPIC  -g -O2  -c inverser.c -o inverser.o
clang -I"/Users/***/.Renv/versions/3.5.1/lib/R/include" -DNDEBUG -I/usr/local/Cellar/gdal2/2.3.1/include -I/usr/local/Cellar/proj/5.1.0/include -I"/Users/***/.Renv/versions/3.5.1/lib/R/library/sp/include" -I/usr/local/opt/gdal2/include -I/usr/local/opt/liblas-gdal2/include -I/usr/local/opt/laszip@2.2/include -I/usr/local/opt/bzip2/include -I/usr/local/opt/zlib/include  -g -O2 -fPIC  -g -O2  -c local_stubs.c -o local_stubs.o
g++ -std=gnu++11 -I"/Users/***/.Renv/versions/3.5.1/lib/R/include" -DNDEBUG -I/usr/local/Cellar/gdal2/2.3.1/include -I/usr/local/Cellar/proj/5.1.0/include -I"/Users/***/.Renv/versions/3.5.1/lib/R/library/sp/include" -I/usr/local/opt/gdal2/include -I/usr/local/opt/liblas-gdal2/include -I/usr/local/opt/laszip@2.2/include -I/usr/local/opt/bzip2/include -I/usr/local/opt/zlib/include  -g -O2 -stdlib=libc++ -std=c++11 -fPIC  -g -O2 -c ogr_geom.cpp -o ogr_geom.o
clang -I"/Users/***/.Renv/versions/3.5.1/lib/R/include" -DNDEBUG -I/usr/local/Cellar/gdal2/2.3.1/include -I/usr/local/Cellar/proj/5.1.0/include -I"/Users/***/.Renv/versions/3.5.1/lib/R/library/sp/include" -I/usr/local/opt/gdal2/include -I/usr/local/opt/liblas-gdal2/include -I/usr/local/opt/laszip@2.2/include -I/usr/local/opt/bzip2/include -I/usr/local/opt/zlib/include  -g -O2 -fPIC  -g -O2  -c ogr_polygons.c -o ogr_polygons.o
g++ -std=gnu++11 -I"/Users/***/.Renv/versions/3.5.1/lib/R/include" -DNDEBUG -I/usr/local/Cellar/gdal2/2.3.1/include -I/usr/local/Cellar/proj/5.1.0/include -I"/Users/***/.Renv/versions/3.5.1/lib/R/library/sp/include" -I/usr/local/opt/gdal2/include -I/usr/local/opt/liblas-gdal2/include -I/usr/local/opt/laszip@2.2/include -I/usr/local/opt/bzip2/include -I/usr/local/opt/zlib/include  -g -O2 -stdlib=libc++ -std=c++11 -fPIC  -g -O2 -c ogr_proj.cpp -o ogr_proj.o
g++ -std=gnu++11 -I"/Users/***/.Renv/versions/3.5.1/lib/R/include" -DNDEBUG -I/usr/local/Cellar/gdal2/2.3.1/include -I/usr/local/Cellar/proj/5.1.0/include -I"/Users/***/.Renv/versions/3.5.1/lib/R/library/sp/include" -I/usr/local/opt/gdal2/include -I/usr/local/opt/liblas-gdal2/include -I/usr/local/opt/laszip@2.2/include -I/usr/local/opt/bzip2/include -I/usr/local/opt/zlib/include  -g -O2 -stdlib=libc++ -std=c++11 -fPIC  -g -O2 -c ogrdrivers.cpp -o ogrdrivers.o
g++ -std=gnu++11 -I"/Users/***/.Renv/versions/3.5.1/lib/R/include" -DNDEBUG -I/usr/local/Cellar/gdal2/2.3.1/include -I/usr/local/Cellar/proj/5.1.0/include -I"/Users/***/.Renv/versions/3.5.1/lib/R/library/sp/include" -I/usr/local/opt/gdal2/include -I/usr/local/opt/liblas-gdal2/include -I/usr/local/opt/laszip@2.2/include -I/usr/local/opt/bzip2/include -I/usr/local/opt/zlib/include  -g -O2 -stdlib=libc++ -std=c++11 -fPIC  -g -O2 -c ogrsource.cpp -o ogrsource.o
g++ -std=gnu++11 -I"/Users/***/.Renv/versions/3.5.1/lib/R/include" -DNDEBUG -I/usr/local/Cellar/gdal2/2.3.1/include -I/usr/local/Cellar/proj/5.1.0/include -I"/Users/***/.Renv/versions/3.5.1/lib/R/library/sp/include" -I/usr/local/opt/gdal2/include -I/usr/local/opt/liblas-gdal2/include -I/usr/local/opt/laszip@2.2/include -I/usr/local/opt/bzip2/include -I/usr/local/opt/zlib/include  -g -O2 -stdlib=libc++ -std=c++11 -fPIC  -g -O2 -c projectit.cpp -o projectit.o
g++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Users/***/.Renv/versions/3.5.1/lib/R/lib -L/usr/local/opt/gdal2/lib -L/usr/local/opt/liblas-gdal2/lib -L/usr/local/opt/laszip@2.2/lib -L/usr/local/opt/bzip2/lib -L/usr/local/opt/zlib/lib -o rgdal.so OGR_write.o gdal-bindings.o init.o inverser.o local_stubs.o ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o -L/usr/local/Cellar/gdal2/2.3.1/lib -lgdal -lproj -L/Users/***/.Renv/versions/3.5.1/lib/R/lib -lR -Wl,-framework -Wl,CoreFoundation
installing to /Users/***/.Renv/versions/3.5.1/lib/R/library/rgdal/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rgdal)

The downloaded source packages are in
    ‘/private/var/folders/md/03gdc4c14z18kbqwpfh4jdfc0000gr/T/RtmpidZNr4/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done

MakeVars-概述:

Makevars是一个覆盖R生成的默认makefile的makefile(位于file.path(R.home(“etc”)，“Makeconf”))。这样一来，您就可以利用R的默认行为，同时可以设置所需的标志。这些是最常用的标志:

PKG_LIBS
链接器标志。常见用法是PKG_LIBS = $(BLAS_LIBS)。这使您可以使用与R.相同的BLAS库。

PKG_CFLAGS 和 PKG_CXXFLAGS
C和C++标志。最常用于通过-D设置定义指令。

PKG_CPPFLAGS
预处理器标志(不是C++标志!)。最常用的设置包括带有-I的目录。在Description的LinkingTo字段中列出的所有软件包都将自动包括在内-您无需显式添加它。

希望以上内容能为您指明解决方案的方向。

关于r - 尽管C++ 11可用，但正在更新R.3.5.1 C++ 11依赖关系中的Rgdal ...，我们在Stack Overflow上找到一个类似的问题： https://stackoverflow.com/questions/51566741/

r - 尽管C++ 11可用，但正在更新R.3.5.1 C++ 11依赖关系中的Rgdal ...

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