那些遇到过的问题

在R.3.5.1 C++ 11依赖中更新Rgdal ...虽然C++ 11可用

FM *_*hof 9 r gdal c++11 rgdal

当我在将R从3.4.4更新到3.5.1之后通过从源代码编译来更新(或至少尝试)rgdal包时,我遇到一个奇怪的问题,一切顺利,但命名空间加载由于"未定义的符号"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
Run Code Online (Sandbox Code Playgroud)

在跑步的时候,echo _ZNK10OGRFeature16GetFieldAsDoubleEi | c++filt我得到的输出OGRFeature::GetFieldAsDouble(int) const并没有让我学到很多东西.我已经安装了GDAL从https://trac.osgeo.org/gdal/wiki/DownloadSource,在CRAN包网站这表明我有GDAL 2.3.1安装的建议.

奇怪的是,更新失败,因为软件包已经安装,因此应该满足依赖性.有关如何解决此问题的任何指示都受到热烈欢迎.

由于我在过去几周没有得到任何建议,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,尽管检查说它在那里(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’
Run Code Online (Sandbox Code Playgroud)

我devtools::session_info()的内容如下:

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)
Run Code Online (Sandbox Code Playgroud)

Tec*_*e01 5

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
Run Code Online (Sandbox Code Playgroud)

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
Run Code Online (Sandbox Code Playgroud)

在此之后,编译问题和相关错误不再发生(至少在我的测试中到目前为止)

推理

上面提出了一个问题 - 为什么？带有rgdal的R 3.5.1的新安装(根据我的经验)没有表现出编译错误,而从3.4.4升级则表示编译错误.我的感觉是R和rgdal包配置之间存在交互,导致C++ 11编译标志未被激活.rgdal需要并使用C++ 11功能.请参阅Makevar - 以下概述.

引文:

编译示例:

-std=gnu++11Makevars中没有标志[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
Run Code Online (Sandbox Code Playgroud)

添加-std=gnu++11到Makevars

> 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
Run Code Online (Sandbox Code Playgroud)

MakeVars - 概述:

Makevars是一个makefile,它覆盖由R生成的默认makefile(位于file.path(R.home("etc"),"Makeconf")).这允许您在能够设置所需标志的同时利用R的默认行为.这些是最常用的标志:

  • PKG_LIBS 链接器标志.常见的用途是PKG_LIBS = $(BLAS_LIBS).这允许您使用与R相同的BLAS库.

  • PKG_CFLAGS和PKG_CXXFLAGS C和C++标志.最常用于使用-D设置define指令.

PKG_CPPFLAGS 预处理程序标志(不是C++标志!).最常用于设置包含-I的目录.将自动包含DESCRIPTION中LinkingTo字段中列出的任何包 - 您无需显式添加它.

我希望上述内容有助于指明解决方案的方向.

  • 谢谢你的全面答复.最后,事实证明,在我的情况下,手动和自动安装的gdal库之间存在冲突(http://r-sig-geo.2731867.n2.nabble.com/Problems-with-installing-rgdal -on-Ubuntu的QUOT检查的GDAL联与 - 库 - 仅-NO-QUOT-td7590255.html).通过遵循该帖子上的建议,我终于可以在我的机器上安装rgdal了. (3认同)

归档时间：

查看次数：

800 次

最近记录：

7 年，1 月 前
如何在gcc中启用C++ 11？ 109
错误:找不到gdal-config 57
在Ubuntu 16.04上安装python GDAL 2.1 41
更多相关链接
相关归档
在linux下的GCC中使用std :: thread的正确链接选项是什么？ 87
如何按组获取摘要统计信息 61
C++ 11与非平凡成员的匿名联合 27
与整数斗争(最大整数) 23
R向导的参考 18
如何从基地模拟功能？ 12
重载成员函数的decltype 10
c ++ 0x std :: shared_ptr vs. boost :: shared_ptr 8
B.Stroustrup新书中的优化和多线程 7
什么可以使用std :: remove_extent？ 6
难疑归档
在jQuery中添加表行 2331
正确使用IDisposable接口 1586
LINQ中的多个"order by" 1537
Git如何处理符号链接？ 1515
是否有快速Git命令来查看旧版本的文件？ 1438
如何在python字符串中打印文字大括号字符并在其上使用.format？ 1320
检查Bash shell脚本中是否存在输入参数 1223
wait()和sleep()之间的区别 1158
如何配置Visual Studio代码以始终在新选项卡中打开文件？ 1078
jQuery的jquery-1.10.2.min.map触发了404(未找到) 1051