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无法在MacOS M1 Monterey上安装Stringi R软件包

发布于 2025-02-04 18:48:27 字数 8247 浏览 4 评论 0原文

我无法在我的MacBook Pro（运行Macos Monterey）上安装R软件包Stringi，并使用新的M1＆amp; ARM64建筑。关于类似问题的帖子有很多帖子，但是我收到的错误消息是我以前从未见过的。

当我在rstudio中运行install.packages（“ stringi”）时，我会收到以下错误消息：

stri_brkiter.cpp:60:9: error: use of undeclared identifier
      'isNull'
    if (isNull(opts_brkiter)) {
        ^

我猜我在这里有某种编译器不匹配 - 不应该有'未宣布标识符的错误来自cran包。不过，我不确定如何解决该问题，而且我无法在线找到其他人收到类似消息的示例。我已经在网上看到了很多类似错误的，但是这些错误的修复程序并没有帮助我解决此isnull（）错误。

Note ：上面的线只是消息输出的误差部分。有关完整的错误文本，请参见下文。

> install.packages("stringi")
Installing package into ‘/Users/<username>/r_libs’
(as ‘lib’ is unspecified)
Package which is only available in source form, and may need
  compilation of C/C++/Fortran: ‘stringi’
Do you want to attempt to install these from sources? (Yes/no/cancel) yes
installing the source package ‘stringi’

Content type 'application/x-gzip' length 7578882 bytes (7.2 MB)
==================================================
downloaded 7.2 MB

* installing *source* package ‘stringi’ ...
** package ‘stringi’ successfully unpacked and MD5 sums checked
** using staged installation
checking for R_HOME... /Library/Frameworks/R.framework/Resources
checking for R... /Library/Frameworks/R.framework/Resources/bin/R
checking for endianness... little
checking for R >= 3.1.0 for C++11 use... yes
checking for R < 3.4.0 for CXX1X flag use... no
checking for cat... /bin/cat
checking for local ICUDT_DIR... icu69/data
checking for gcc... clang -arch arm64
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 -arch arm64 accepts -g... yes
checking for clang -arch arm64 option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -arch arm64 -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 elf.h usability... no
checking elf.h presence... no
checking for elf.h... no
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -arch arm64 -std=gnu++11 accepts -g... yes
checking whether the C++ compiler supports the long long type... yes
checking whether the compiler implements namespaces... yes
checking whether the compiler supports Standard Template Library... yes
checking whether std::map is available... yes
checking for pkg-config... /opt/homebrew/bin/pkg-config
checking with pkg-config for the system ICU4C... 70.1
checking for ICU4C >= 55... yes
checking for additional required CPPFLAGS, LDFLAGS, and LIBS... done
checking whether an ICU4C-based project can be built... yes
checking programmatically for sufficient U_ICU_VERSION_MAJOR_NUM... yes
checking programmatically if U_CHARSET_IS_UTF8 is defined and set... yes
checking the capabilities of the ICU data library (ucnv, uloc, utrans)... yes
checking the capabilities of the ICU data library (ucol)... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/uconfig_local.h
config.status: creating src/install.libs.R

*** stringi configure summary:
    ICU_FOUND=1
    STRINGI_CXXSTD=CXX_STD=CXX11
    STRINGI_CFLAGS=   -fPIC
    STRINGI_CPPFLAGS=-I. -I/opt/homebrew/Cellar/icu4c/70.1/include   -UDEBUG -DNDEBUG
    STRINGI_CXXFLAGS=   -fPIC
    STRINGI_LDFLAGS=-L/opt/homebrew/Cellar/icu4c/70.1/lib
    STRINGI_LIBS=-licui18n -licuuc -licudata

*** Compiler settings used:
    CC=clang -arch arm64
    LD=clang++ -arch arm64 -std=gnu++14
    CFLAGS=-falign-functions=64 -Wall -g -O2 -fPIC
    CPPFLAGS=-I/opt/R/arm64/include   -UDEBUG -DNDEBUG
    CXX=clang++ -arch arm64 -std=gnu++11
    CXXFLAGS=-falign-functions=64 -Wall -g -O2 -fPIC
    LDFLAGS=
    LIBS=

** libs
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/homebrew/Cellar/icu4c/70.1/include   -UDEBUG -DNDEBUG  -I/opt/R/arm64/include  -fPIC -fPIC  -falign-functions=64 -Wall -g -O2  -c stri_brkiter.cpp -o stri_brkiter.o
stri_brkiter.cpp:60:9: error: use of undeclared identifier
      'isNull'
    if (isNull(opts_brkiter)) {
        ^
stri_brkiter.cpp:130:9: error: use of undeclared identifier
      'isNull'
    if (isNull(opts_brkiter)) {
        ^
stri_brkiter.cpp:171:9: error: use of undeclared identifier
      'isNull'
    if (isNull(opts_brkiter)) {
        ^
3 errors generated.
make: *** [stri_brkiter.o] Error 1
ERROR: compilation failed for package ‘stringi’
* removing ‘/Users/<username>/r_libs/stringi’
* restoring previous ‘/Users/<username>/r_libs/stringi’

The downloaded source packages are in
    ‘/private/var/folders/qc/whkk090506v2qjy698yf25m80000gq/T/RtmpvLUDID/downloaded_packages’
Warning message:
In install.packages("stringi") :
  installation of package ‘stringi’ had non-zero exit status

我已经尝试在R Studio和命令行中安装Stringi，因此一些建议的帖子可能更有效，但是我通过这两种方法都会收到相同的错误。

最初，编译器无法找到ICU4C库（这也阻止了我安装stringi），但是我能够通过运行<来指向pkg-config。代码> brew link ICU4C -force ，然后解决了。

我尝试过的其他命令（DID 不是修复了它）：

install.packages('stringi', configure.args='--disable-cxx11')

install.packages("stringi", configure.args = "--with-extra-cxxflags='--std=c++11'")

完全删除我的makevars文件无法解决问题。

我已经检查了许多有关So＆amp;的主要/流行的问题。 github（包括 this ， this ， https://stackoverflow.com/questions/48866862/cannot-install-stringi-stringi-since-since-command-line-line-tools-tools-undate"> this ， this 等）。我认为我已经达到了对这些东西的理解的边缘。

我公认的非专家假设是，这与我下载的编译器，我完成的M1架构解决方法和/或我的makevars文件有关以前（较旧的）MacBook之前没有任何问题。

系统信息：

  • OS： Mac OS Monterey（V 12.2）w/a apple m1 max芯片
  • r： r版本4.2.0
  • rstudio： rstudio版本1.4.1717
  • Xcode ：Xcode版本13.3.1
  • 已安装GCC/GFORTRAN gcc 和其他库，并使用homebrew＆amp;将下载位置添加到$路径

我的makevars文件：

此文件是根据此处，此处，在这里，和在这里。

CC=/opt/homebrew/bin/gcc-11
CXX=/opt/homebrew/bin/g++-11

FC=/opt/homebrew/bin/gfortran-11
F77=/opt/homebrew/bin/gfortran-11
FLIBS=-L/opt/homebrew/opt/gfortran/lib -lgfortran -lquadmath -lm

CFLAGS=-I/opt/homebrew/include
CXXFLAGS=-O3 -Wall -pipe -Wno-unused -pedantic
CXX11FLAGS=-O3 -Wall -pipe -Wno-unused -pedantic

这个错误看起来对任何人是否熟悉，还是有人对我可以做的修复可以做什么？我已经尝试了很多解决方法，所以我很抱歉，如果我遗漏了任何东西，请告诉我是否有其他信息有用！

谢谢！

原文

I have been unable to install the R package stringi on my Macbook Pro (running MacOS Monterey) with the new M1 & arm64 architecture. There are a number of posts on SO describing similar problems, but the error message I'm receiving is something I haven't seen before.

When I run install.packages("stringi") in RStudio, I receive the following error message:

stri_brkiter.cpp:60:9: error: use of undeclared identifier
      'isNull'
    if (isNull(opts_brkiter)) {
        ^

I'm guessing there is some kind of compiler mismatch going on here - there shouldn't be 'undeclared identifier' errors coming from a CRAN package. I'm not sure how to fix the problem, though, and I wasn't able to find any examples online of others getting a similar message. I've seen a lot of similar errors online, but the fixes for those haven't helped me get around this isNull() error.

Note: The lines above are just the error portion of the message output. See below for full error text.

> install.packages("stringi")
Installing package into ‘/Users/<username>/r_libs’
(as ‘lib’ is unspecified)
Package which is only available in source form, and may need
  compilation of C/C++/Fortran: ‘stringi’
Do you want to attempt to install these from sources? (Yes/no/cancel) yes
installing the source package ‘stringi’

Content type 'application/x-gzip' length 7578882 bytes (7.2 MB)
==================================================
downloaded 7.2 MB

* installing *source* package ‘stringi’ ...
** package ‘stringi’ successfully unpacked and MD5 sums checked
** using staged installation
checking for R_HOME... /Library/Frameworks/R.framework/Resources
checking for R... /Library/Frameworks/R.framework/Resources/bin/R
checking for endianness... little
checking for R >= 3.1.0 for C++11 use... yes
checking for R < 3.4.0 for CXX1X flag use... no
checking for cat... /bin/cat
checking for local ICUDT_DIR... icu69/data
checking for gcc... clang -arch arm64
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 -arch arm64 accepts -g... yes
checking for clang -arch arm64 option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -arch arm64 -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 elf.h usability... no
checking elf.h presence... no
checking for elf.h... no
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -arch arm64 -std=gnu++11 accepts -g... yes
checking whether the C++ compiler supports the long long type... yes
checking whether the compiler implements namespaces... yes
checking whether the compiler supports Standard Template Library... yes
checking whether std::map is available... yes
checking for pkg-config... /opt/homebrew/bin/pkg-config
checking with pkg-config for the system ICU4C... 70.1
checking for ICU4C >= 55... yes
checking for additional required CPPFLAGS, LDFLAGS, and LIBS... done
checking whether an ICU4C-based project can be built... yes
checking programmatically for sufficient U_ICU_VERSION_MAJOR_NUM... yes
checking programmatically if U_CHARSET_IS_UTF8 is defined and set... yes
checking the capabilities of the ICU data library (ucnv, uloc, utrans)... yes
checking the capabilities of the ICU data library (ucol)... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/uconfig_local.h
config.status: creating src/install.libs.R

*** stringi configure summary:
    ICU_FOUND=1
    STRINGI_CXXSTD=CXX_STD=CXX11
    STRINGI_CFLAGS=   -fPIC
    STRINGI_CPPFLAGS=-I. -I/opt/homebrew/Cellar/icu4c/70.1/include   -UDEBUG -DNDEBUG
    STRINGI_CXXFLAGS=   -fPIC
    STRINGI_LDFLAGS=-L/opt/homebrew/Cellar/icu4c/70.1/lib
    STRINGI_LIBS=-licui18n -licuuc -licudata

*** Compiler settings used:
    CC=clang -arch arm64
    LD=clang++ -arch arm64 -std=gnu++14
    CFLAGS=-falign-functions=64 -Wall -g -O2 -fPIC
    CPPFLAGS=-I/opt/R/arm64/include   -UDEBUG -DNDEBUG
    CXX=clang++ -arch arm64 -std=gnu++11
    CXXFLAGS=-falign-functions=64 -Wall -g -O2 -fPIC
    LDFLAGS=
    LIBS=

** libs
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/homebrew/Cellar/icu4c/70.1/include   -UDEBUG -DNDEBUG  -I/opt/R/arm64/include  -fPIC -fPIC  -falign-functions=64 -Wall -g -O2  -c stri_brkiter.cpp -o stri_brkiter.o
stri_brkiter.cpp:60:9: error: use of undeclared identifier
      'isNull'
    if (isNull(opts_brkiter)) {
        ^
stri_brkiter.cpp:130:9: error: use of undeclared identifier
      'isNull'
    if (isNull(opts_brkiter)) {
        ^
stri_brkiter.cpp:171:9: error: use of undeclared identifier
      'isNull'
    if (isNull(opts_brkiter)) {
        ^
3 errors generated.
make: *** [stri_brkiter.o] Error 1
ERROR: compilation failed for package ‘stringi’
* removing ‘/Users/<username>/r_libs/stringi’
* restoring previous ‘/Users/<username>/r_libs/stringi’

The downloaded source packages are in
    ‘/private/var/folders/qc/whkk090506v2qjy698yf25m80000gq/T/RtmpvLUDID/downloaded_packages’
Warning message:
In install.packages("stringi") :
  installation of package ‘stringi’ had non-zero exit status

I've tried installing stringi both in R Studio and on the command line, which some SO posts suggested may be more effective, but I receive the same errors via both methods.

Initially, the compiler was unable to find the ICU4C library (which also prevented me from installing stringi), but I was able to point pkg-config to the library by running brew link icu4c --force and that resolved it.

Other commands I've tried (that did NOT fix it):

install.packages('stringi', configure.args='--disable-cxx11')

install.packages("stringi", configure.args = "--with-extra-cxxflags='--std=c++11'")

Fully removing my Makevars file didn't resolve the issue.

I've checked many of the major/popular related questions on SO & Github (including this, this, this, this, this etc). I think I've reached the edge of my understanding of this stuff, though.

My admittedly non-expert assumption is that this has to do with the compilers I've downloaded, the M1 architecture workarounds I've done, and/or my Makevars file, as I've installed stringi on previous (older) Macbooks before without any issue.

System info:

  • OS: Mac OS Monterey (v 12.2) w/ an Apple M1 Max chip
  • R: R version 4.2.0
  • RStudio: RStudio version 1.4.1717
  • Xcode: Xcode version 13.3.1
  • Installed gcc/gfortran and other libraries using Homebrew & added download location to $PATH

My Makevars file:

This file was built based on advice from here, here, here, and here.

CC=/opt/homebrew/bin/gcc-11
CXX=/opt/homebrew/bin/g++-11

FC=/opt/homebrew/bin/gfortran-11
F77=/opt/homebrew/bin/gfortran-11
FLIBS=-L/opt/homebrew/opt/gfortran/lib -lgfortran -lquadmath -lm

CFLAGS=-I/opt/homebrew/include
CXXFLAGS=-O3 -Wall -pipe -Wno-unused -pedantic
CXX11FLAGS=-O3 -Wall -pipe -Wno-unused -pedantic

Does this error look familiar to anyone, or does anyone have suggestions of what I could do next to fix this? I've tried a lot of workarounds so I apologize if I've left anything out, please let me know if any other information could be useful!

Thanks!

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评论（2）

熊抱啵儿 2025-02-11 18:48:27

对于那些返回相同问题的人，似乎stringi无法在r v.4.2。*（请参阅在这里和在这里）。降级至R v.4.1.1足以在我的计算机上解决此问题，并在下面的会话信息上进行修复。

降级之前：

   platform       x86_64-apple-darwin17.0     
                    arch           x86_64                      
                    os             darwin17.0                  
                    system         x86_64, darwin17.0          
                    status                                     
                    major          4                           
                    minor          2.1                         
                    year           2022                        
                    month          06                          
                    day            23                          
                    svn rev        82513                       
                    language       R                           
                    version.string R version 4.2.1 (2022-06-23)
                    nickname       Funny-Looking Kid

降级后：

platform       x86_64-apple-darwin17.0     
arch           x86_64                      
os             darwin17.0                  
system         x86_64, darwin17.0          
status                                     
major          4                           
minor          1.1                         
year           2021                        
month          08                          
day            10                          
svn rev        80725                       
language       R                           
version.string R version 4.1.1 (2021-08-10)
nickname       Kick Things

For those returning with this same problem, it seems stringi fails to build specifically under R v.4.2.* (see here and here). Downgrading to R v.4.1.1 was sufficient to fix this on my machine, with session info below.

Prior to downgrade:

   platform       x86_64-apple-darwin17.0     
                    arch           x86_64                      
                    os             darwin17.0                  
                    system         x86_64, darwin17.0          
                    status                                     
                    major          4                           
                    minor          2.1                         
                    year           2022                        
                    month          06                          
                    day            23                          
                    svn rev        82513                       
                    language       R                           
                    version.string R version 4.2.1 (2022-06-23)
                    nickname       Funny-Looking Kid

After downgrade:

platform       x86_64-apple-darwin17.0     
arch           x86_64                      
os             darwin17.0                  
system         x86_64, darwin17.0          
status                                     
major          4                           
minor          1.1                         
year           2021                        
month          08                          
day            10                          
svn rev        80725                       
language       R                           
version.string R version 4.1.1 (2021-08-10)
nickname       Kick Things
回复 原文
羁〃客ぐ 2025-02-11 18:48:27

除非您绝对需要编译源版本，否则目前有一个二进制ARM版本。 （显然，将来的人们需要更改版本号）

install.packages("https://cran.r-project.org/bin/macosx/big-sur-arm64/contrib/4.1/stringi_1.7.6.tgz", 
                  repos = NULL, type = .Platform$pkgType)

我想知道在您尝试过的那一刻，在这方面，rstudio的默认存储库是否不完整？

Unless you absolutely need to have source compiled version, there is a binary arm version at the moment. (Obviously people in the future will need to change the version numbers)

install.packages("https://cran.r-project.org/bin/macosx/big-sur-arm64/contrib/4.1/stringi_1.7.6.tgz", 
                  repos = NULL, type = .Platform$pkgType)

I'm wondering if the default repository for Rstudio was not complete in this regard at the point you tried this?

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