brew安装后无法将软件包安装到R

Question

我花了大约一个小时来调试这个程序，但我认为最好的假设是，除了brew install r和install.packages("tidycensus")以及其他几个包之外，我什么也没有尝试过，以确定它是否是tidycensus。

如果有什么我能提供的信息请告诉我。我最近擦去了我的新Mac的硬盘，重新开始工作。

install.packages("tidycensus")的输出：

> install.packages("tidycensus")
Installing package into ‘/usr/local/lib/R/3.5/site-library’
(as ‘lib’ is unspecified)
also installing the dependencies ‘rgdal’, ‘sf’, ‘tigris’, ‘units’

trying URL 'https://cloud.r-project.org/src/contrib/rgdal_1.3-4.tar.gz'
Content type 'application/x-gzip' length 1664774 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

trying URL 'https://cloud.r-project.org/src/contrib/sf_0.6-3.tar.gz'
Content type 'application/x-gzip' length 7973054 bytes (7.6 MB)
==================================================
downloaded 7.6 MB

trying URL 'https://cloud.r-project.org/src/contrib/tigris_0.7.tar.gz'
Content type 'application/x-gzip' length 72980 bytes (71 KB)
==================================================
downloaded 71 KB

trying URL 'https://cloud.r-project.org/src/contrib/units_0.6-0.tar.gz'
Content type 'application/x-gzip' length 912393 bytes (891 KB)
==================================================
downloaded 891 KB

trying URL 'https://cloud.r-project.org/src/contrib/tidycensus_0.4.6.tar.gz'
Content type 'application/x-gzip' length 1615516 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
configure: R_HOME: /usr/local/Cellar/r/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... no
no
configure: error: gdal-config not found or not executable.
ERROR: configuration failed for package ‘rgdal’
* removing ‘/usr/local/lib/R/3.5/site-library/rgdal’
* installing *source* package ‘units’ ...
** package ‘units’ successfully unpacked and MD5 sums checked
configure: units: 0.6-0
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ accepts -g... yes
checking how to run the C++ preprocessor... clang++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... no
checking for _Bool... no
checking for error_at_line... no
checking for gcc... clang
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking for XML_ParserCreate in -lexpat... yes
checking udunits2.h usability... no
checking udunits2.h presence... no
checking for udunits2.h... no
checking udunits2/udunits2.h usability... no
checking udunits2/udunits2.h presence... no
checking for udunits2/udunits2.h... no
checking for ut_read_xml in -ludunits2... no
configure: error: in `/private/var/folders/69/wy4n7cc10n5fg5_bc8glmms80000gn/T/RtmpPtsVPP/R.INSTALLf8694f0bf387/units':
configure: error: 
--------------------------------------------------------------------------------
  libudunits2.so not found!

  If the udunits2 library is installed in a non-standard location, use:

    --configure-args='--with-udunits2-lib=/usr/local/lib'

  for example, if the library was not found, and/or

    --configure-args='--with-udunits2-include=/usr/include/udunits2'

  if the header was not found, replacing paths with appropriate values for your
  installation. You can alternatively use the UDUNITS2_INCLUDE and UDUNITS2_LIBS
  environment variables.

  If udunits2 is not installed, please install it.
  It is required for this package.
--------------------------------------------------------------------------------

See `config.log' for more details
ERROR: configuration failed for package ‘units’
* removing ‘/usr/local/lib/R/3.5/site-library/units’
ERROR: dependency ‘units’ is not available for package ‘sf’
* removing ‘/usr/local/lib/R/3.5/site-library/sf’
ERROR: dependencies ‘rgdal’, ‘sf’ are not available for package ‘tigris’
* removing ‘/usr/local/lib/R/3.5/site-library/tigris’
ERROR: dependencies ‘sf’, ‘tigris’, ‘units’ are not available for package ‘tidycensus’
* removing ‘/usr/local/lib/R/3.5/site-library/tidycensus’

The downloaded source packages are in
    ‘/private/var/folders/69/wy4n7cc10n5fg5_bc8glmms80000gn/T/Rtmp8iit6a/downloaded_packages’
Warning messages:
1: In install.packages("tidycensus") :
  installation of package ‘rgdal’ had non-zero exit status
2: In install.packages("tidycensus") :
  installation of package ‘units’ had non-zero exit status
3: In install.packages("tidycensus") :
  installation of package ‘sf’ had non-zero exit status
4: In install.packages("tidycensus") :
  installation of package ‘tigris’ had non-zero exit status
5: In install.packages("tidycensus") :
  installation of package ‘tidycensus’ had non-zero exit status
> install.packages('tidycensus')
Installing package into ‘/usr/local/lib/R/3.5/site-library’
(as ‘lib’ is unspecified)
also installing the dependencies ‘rgdal’, ‘sf’, ‘tigris’, ‘units’

trying URL 'https://cloud.r-project.org/src/contrib/rgdal_1.3-4.tar.gz'
Content type 'application/x-gzip' length 1664774 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

trying URL 'https://cloud.r-project.org/src/contrib/sf_0.6-3.tar.gz'
Content type 'application/x-gzip' length 7973054 bytes (7.6 MB)
==================================================
downloaded 7.6 MB

trying URL 'https://cloud.r-project.org/src/contrib/tigris_0.7.tar.gz'
Content type 'application/x-gzip' length 72980 bytes (71 KB)
==================================================
downloaded 71 KB

trying URL 'https://cloud.r-project.org/src/contrib/units_0.6-0.tar.gz'
Content type 'application/x-gzip' length 912393 bytes (891 KB)
==================================================
downloaded 891 KB

trying URL 'https://cloud.r-project.org/src/contrib/tidycensus_0.4.6.tar.gz'
Content type 'application/x-gzip' length 1615516 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
configure: R_HOME: /usr/local/Cellar/r/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... no
no
configure: error: gdal-config not found or not executable.
ERROR: configuration failed for package ‘rgdal’
* removing ‘/usr/local/lib/R/3.5/site-library/rgdal’
* installing *source* package ‘units’ ...
** package ‘units’ successfully unpacked and MD5 sums checked
configure: units: 0.6-0
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ accepts -g... yes
checking how to run the C++ preprocessor... clang++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... no
checking for _Bool... no
checking for error_at_line... no
checking for gcc... clang
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking for XML_ParserCreate in -lexpat... yes
checking udunits2.h usability... no
checking udunits2.h presence... no
checking for udunits2.h... no
checking udunits2/udunits2.h usability... no
checking udunits2/udunits2.h presence... no
checking for udunits2/udunits2.h... no
checking for ut_read_xml in -ludunits2... no
configure: error: in `/private/var/folders/69/wy4n7cc10n5fg5_bc8glmms80000gn/T/RtmpuOGf6j/R.INSTALLfdd5361d965a/units':
configure: error: 
--------------------------------------------------------------------------------
  libudunits2.so not found!

  If the udunits2 library is installed in a non-standard location, use:

    --configure-args='--with-udunits2-lib=/usr/local/lib'

  for example, if the library was not found, and/or

    --configure-args='--with-udunits2-include=/usr/include/udunits2'

  if the header was not found, replacing paths with appropriate values for your
  installation. You can alternatively use the UDUNITS2_INCLUDE and UDUNITS2_LIBS
  environment variables.

  If udunits2 is not installed, please install it.
  It is required for this package.
--------------------------------------------------------------------------------

See `config.log' for more details
ERROR: configuration failed for package ‘units’
* removing ‘/usr/local/lib/R/3.5/site-library/units’
ERROR: dependency ‘units’ is not available for package ‘sf’
* removing ‘/usr/local/lib/R/3.5/site-library/sf’
ERROR: dependencies ‘rgdal’, ‘sf’ are not available for package ‘tigris’
* removing ‘/usr/local/lib/R/3.5/site-library/tigris’
ERROR: dependencies ‘sf’, ‘tigris’, ‘units’ are not available for package ‘tidycensus’
* removing ‘/usr/local/lib/R/3.5/site-library/tidycensus’

The downloaded source packages are in
    ‘/private/var/folders/69/wy4n7cc10n5fg5_bc8glmms80000gn/T/Rtmp8iit6a/downloaded_packages’
Warning messages:
1: In install.packages("tidycensus") :
  installation of package ‘rgdal’ had non-zero exit status
2: In install.packages("tidycensus") :
  installation of package ‘units’ had non-zero exit status
3: In install.packages("tidycensus") :
  installation of package ‘sf’ had non-zero exit status
4: In install.packages("tidycensus") :
  installation of package ‘tigris’ had non-zero exit status
5: In install.packages("tidycensus") :
  installation of package ‘tidycensus’ had non-zero exit status

Answer 1

我的问题是，在一个非brew的python3安装之后，我有一些杂乱无章的python3配置文件。我删除了python3并重新安装了brew。

我对有同样问题的用户的建议是运行brew doctor。如果您有相同的问题，您的python3配置文件将显示为问题，您可以卸载python3并使用brew install python3重新安装它。

然后，我有一些依赖，我必须解决，一些在R，一些在brew。

@舒适鹰公司在安装和进口install_github()后建议使用devtools也是有帮助的。

Answer 2

对我来说很好。可能的解决办法：

1. 通过github install_github("tidyverse/ggplot2")检查是否安装了ggplot
2. 确认您的R版本是≥3.3.0
3. 通过github install_github("walkerke/tidycensus")安装软件包
4. 检查其他依赖关系