Conda 构建 R 包在 MacOS Mojave 上的 C 编译器问题上失败

Question

我正在尝试使用 conda 安装一个名为treatSens 的 R 包，以便在 Jupyter 笔记本中使用它。我执行的命令：

conda install conda-build conda skeleton cran treatSens conda build r-treatsens conda install -c local r-treatsens

我得到了关于 C 编译器的错误

* installing *source* package ‘dbarts’ ...
** package ‘dbarts’ successfully unpacked and MD5 sums checked
checking for gcc... x86_64-apple-darwin13.4.0-clang
checking whether the C compiler works... no
configure: error: in `/Users/myusername/anaconda3/conda-bld/r-dbarts_1543961434509/myenvname':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘dbarts’

我的 clang 版本：

clang version 4.0.1 (tags/RELEASE_401/final)
Target: x86_64-apple-darwin18.2.0
Thread model: posix
InstalledDir: /Users/myusername/anaconda3/envs/myenvname/bin

查看我看到的 config.log 文件

configure:3570: x86_64-apple-darwin13.4.0-clang -V >&5
clang-4.0: error: argument to '-V' is missing (expected 1 value)
clang-4.0: error: no input files
configure:3581: $? = 1
configure:3570: x86_64-apple-darwin13.4.0-clang -qversion >&5
clang-4.0: error: unknown argument: '-qversion'
clang-4.0: error: no input files
configure:3581: $? = 1
configure:3601: checking whether the C compiler works
configure:3623: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/myusername/anaconda3/envs/work/conda-bld/r-dbarts_1543961045662/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include -fdebug-prefix-map=/Users/myusername/anaconda3/envs/work/conda-bld/r-dbarts_1543961045662/work=/usr/local/src/conda/r-dbarts-0.9_5 -fdebug-prefix-map=/Users/myusername/anaconda3/envs/work/conda-bld/r-dbarts_1543961045662/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/myusername/anaconda3/envs/work/conda-bld/r-dbarts_1543961045662/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/myusername/anaconda3/envs/work/conda-bld/r-dbarts_1543961045662/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib -L/Users/myusername/anaconda3/envs/work/conda-bld/r-dbarts_1543961045662/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib conftest.c  >&5
ld: warning: ignoring file /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd
ld: dynamic main executables must link with libSystem.dylib for architecture x86_64
clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation)

使用特定版本的 Apple C 编译器构建 Conda 似乎存在问题。我的猜测是我需要为 conda build 定制 C 编译器。所以我的问题变成了

1. 我需要什么正确的 gcc 版本。
2. 如何为 conda build 设置它。

Answer 1

您必须做几件事才能在 MacOS Mojave 中正确构建。出于对我来说很神秘的原因，Anaconda 的人是not keen 来使这一切顺利进行，这对于我们这些使用深奥的 R 包的人来说尤其令人抓狂。我将写截至 2019-04-20 的最新内容：

1.安装 Xcode (v10.2.1)

2。在开源倾向于期望找到它们的地方安装标头。从命令行：

open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg

3.安装命令行工具

• 作为一种带牙套的方法，我从https://developer.apple.com/download/more/ 下载并安装了 DMG Command_Line_Tools_macOS_10.14_for_Xcode_10.2.1
• 我相信这也是xcode-select --install所做的。如果您运行该命令（安装工具后），您应该会看到消息

xcode-select: error: command line tools are already installed, use "Software Update" to install updates

4.下载旧版 MacOS SDK 文件的副本。比如来自here

5.创建目录/opt

sudo mkdir /opt

6.在那里复制 SDK 文件

sudo cp -r ~/Downloads/MacOSX10.9.sdk /opt/

sudo chmod -R a+rX /opt

7.创建一个conda_build_config.yaml 文件，该文件将被 Conda-build 和相关软件引用。它应该包含以下内容

macos_min_version:
  - 10.9
macos_machine:
  - x86_64-apple-darwin13.4.0
MACOSX_DEPLOYMENT_TARGET:
  - 10.9
CONDA_BUILD_SYSROOT:            # [osx]
  - /opt/MacOSX10.9.sdk          # [osx]

在终端中，您可以这样做：

mkdir ~/.conda || echo 'Dir already present'
echo "macos_min_version:" >> ~/.conda/conda_build_config.yaml
echo "  - 10.9" >> ~/.conda/conda_build_config.yaml
echo "macos_machine:" >> ~/.conda/conda_build_config.yaml
echo "  - x86_64-apple-darwin13.4.0" >> ~/.conda/conda_build_config.yaml
echo "MACOSX_DEPLOYMENT_TARGET:" >> ~/.conda/conda_build_config.yaml
echo "  - 10.9" >> ~/.conda/conda_build_config.yaml
echo "CONDA_BUILD_SYSROOT:" >> ~/.conda/conda_build_config.yaml
echo "  - /opt/MacOSX10.9.sdk" >> ~/.conda/conda_build_config.yaml

8.通过您的.condarc 告诉 Conda 您的 YAML 文件。它应该包含以下行：

conda_build:   
  config_file: ~/.conda/conda_build_config.yaml

可以使用

echo "conda_build:" >> ~/.condarc
echo "  config_file: ~/.conda/conda_build_config.yaml" >> ~/.condarc

Answer 2

作为一种快速而肮脏的解决方法（来自comment），我能够使用 RStudio 中的以下代码在 R 中安装包（在 conda env 中打开）

Sys.setenv(CONDA_BUILD_SYSROOT="/")

现在，您可以通过 RStudio 控制台安装任何 R 包，例如

install.packages("tidyverse")

希望这会有所帮助。