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CRAN R 包的 conda 构建失败

[英]conda build fails for CRAN R packages

 原文  2018-03-30 10:49:37  8   1    r/ conda/ cran/ conda-build

问题描述

我正在尝试使用此处显示的方法从 CRAN 包构建 conda-forge 上不存在的 R conda 包： https ://www.anaconda.com/blog/developer-blog/conda-data-science/

我以 R 包 rann 为例——这个包在 conda-forge 上已经作为 r-rann 存在，但我用它来测试构建过程是否正常工作。

在构建过程中，将执行包含$R CMD INSTALL --build .行的脚本“conda_build.sh” $R CMD INSTALL --build . . 我的问题是构建过程失败并出现错误Fatal error: cannot open file 'CMD': No such file or directory ，与我尝试构建的包无关。 我不知道环境变量（？）“CMD”应该来自哪里。

我采取了以下步骤：

  1. conda skeleton cran rann
  2. conda build r-rann

我还测试了从 pip 构建 Python 包，这些工作没有任何问题，所以这似乎不是我的 Miniconda 安装的普遍问题。

我的系统：

  • Ubuntu 17.10
  • Miniconda 3，版本 4.4.10

这是构建过程的完整日志：

eega@eega-nb:~/workspace$ conda build r-rann/
Adding in variants from internal_defaults
INFO:conda_build.variants:Adding in variants from internal_defaults
Attempting to finalize metadata for r-rann
INFO:conda_build.metadata:Attempting to finalize metadata for r-rann
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.4.10
  latest version: 4.5.0

Please update conda by running

    $ conda update -n base conda


Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.4.10
  latest version: 4.5.0

Please update conda by running

    $ conda update -n base conda


Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.4.10
  latest version: 4.5.0

Please update conda by running

    $ conda update -n base conda


BUILD START: ['r-rann-2.5.1-r341h599a50d_0.tar.bz2']
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.4.10
  latest version: 4.5.0

Please update conda by running

    $ conda update -n base conda



## Package Plan ##

  environment location: /tmp/conda-builds/r-rann_1522400915206/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold


The following NEW packages will be INSTALLED:

    bzip2:           1.0.6-1          conda-forge
    ca-certificates: 2018.1.18-0      conda-forge
    cairo:           1.14.10-0        conda-forge
    curl:            7.59.0-0         conda-forge
    fontconfig:      2.12.6-0         conda-forge
    freetype:        2.8.1-0          conda-forge
    gettext:         0.19.8.1-0       conda-forge
    glib:            2.55.0-0         conda-forge
    graphite2:       1.3.11-0         conda-forge
    gsl:             2.1-2            conda-forge
    harfbuzz:        1.7.6-0          conda-forge
    icu:             58.2-0           conda-forge
    jpeg:            9b-2             conda-forge
    krb5:            1.14.2-0         conda-forge
    libffi:          3.2.1-3          conda-forge
    libgcc:          7.2.0-h69d50b8_2            
    libgcc-ng:       7.2.0-hdf63c60_3            
    libiconv:        1.15-0           conda-forge
    libpng:          1.6.34-0         conda-forge
    libssh2:         1.8.0-2          conda-forge
    libstdcxx-ng:    7.2.0-hdf63c60_3            
    libtiff:         4.0.9-0          conda-forge
    libxml2:         2.9.8-0          conda-forge
    ncurses:         5.9-10           conda-forge
    openssl:         1.0.2n-0         conda-forge
    pango:           1.40.14-0        conda-forge
    pcre:            8.39-0           conda-forge
    pixman:          0.34.0-1         conda-forge
    r-base:          3.4.1-3          conda-forge
    readline:        7.0-0            conda-forge
    tk:              8.6.7-0          conda-forge
    xz:              5.2.3-0          conda-forge
    zlib:            1.2.11-0         conda-forge

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.4.10
  latest version: 4.5.0

Please update conda by running

    $ conda update -n base conda


Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.4.10
  latest version: 4.5.0

Please update conda by running

    $ conda update -n base conda



## Package Plan ##

  environment location: /tmp/conda-builds/r-rann_1522400915206/_build_env


The following NEW packages will be INSTALLED:

    binutils_impl_linux-64: 2.28.1-had2808c_3            
    binutils_linux-64:      7.2.0-26                     
    gcc_impl_linux-64:      7.2.0-habb00fd_3             
    gcc_linux-64:           7.2.0-26                     
    gxx_impl_linux-64:      7.2.0-hdf63c60_3             
    gxx_linux-64:           7.2.0-26                     
    libstdcxx-ng:           7.2.0-hdf63c60_3             
    make:                   4.2.1-0           conda-forge

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Source cache directory is: /tmp/conda-builds/src_cache
Found source in cache: RANN_2.5.1_75277e5d8a.tar.gz
Extracting download
source tree in: /tmp/conda-builds/r-rann_1522400915206/work
INFO: activate-binutils_linux-64.sh made the following environmental changes:
+ADDR2LINE=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-addr2line
+AR=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-ar
+AS=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-as
+CXXFILT=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++filt
+ELFEDIT=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-elfedit
+GPROF=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-gprof
+HOST=x86_64-conda_cos6-linux-gnu
+LD_GOLD=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-ld.gold
+LD=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-ld
+NM=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-nm
+OBJCOPY=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-objcopy
+OBJDUMP=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-objdump
+RANLIB=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-ranlib
+READELF=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-readelf
+SIZE=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-size
+STRINGS=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-strings
+STRIP=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-strip
INFO: activate-gcc_linux-64.sh made the following environmental changes:
+CC=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc
+CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/tmp/conda-builds/r-rann_1522400915206/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
+_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
+CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2
+CPP=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-cpp
+DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -I/tmp/conda-builds/r-rann_1522400915206/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
+DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og
+GCC_AR=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc-ar
+GCC_NM=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc-nm
+GCC_RANLIB=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc-ranlib
+GCC=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc
+LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,-rpath,/tmp/conda-builds/r-rann_1522400915206/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -L/tmp/conda-builds/r-rann_1522400915206/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib
INFO: activate-gxx_linux-64.sh made the following environmental changes:
+CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/tmp/conda-builds/r-rann_1522400915206/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
+CXX=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++
+DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -I/tmp/conda-builds/r-rann_1522400915206/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
+GXX=/tmp/conda-builds/r-rann_1522400915206/_build_env/bin/x86_64-conda_cos6-linux-gnu-g++
Fatal error: cannot open file 'CMD': No such file or directory
Traceback (most recent call last):
  File "/home/eega/miniconda3/bin/conda-build", line 6, in <module>
    sys.exit(conda_build.cli.main_build.main())
  File "/home/eega/miniconda3/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 420, in main
    execute(sys.argv[1:])
  File "/home/eega/miniconda3/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 411, in execute
    verify=args.verify)
  File "/home/eega/miniconda3/lib/python3.6/site-packages/conda_build/api.py", line 199, in build
    notest=notest, need_source_download=need_source_download, variants=variants)
  File "/home/eega/miniconda3/lib/python3.6/site-packages/conda_build/build.py", line 2097, in build_tree
    notest=notest,
  File "/home/eega/miniconda3/lib/python3.6/site-packages/conda_build/build.py", line 1370, in build
    utils.check_call_env(cmd, env=env, cwd=src_dir, stats=build_stats)
  File "/home/eega/miniconda3/lib/python3.6/site-packages/conda_build/utils.py", line 301, in check_call_env
    return _func_defaulting_env_to_os_environ('call', *popenargs, **kwargs)
  File "/home/eega/miniconda3/lib/python3.6/site-packages/conda_build/utils.py", line 280, in _func_defaulting_env_to_os_environ
    raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-e', '/tmp/conda-builds/r-rann_1522400915206/work/conda_build.sh']' returned non-zero exit status 2.

build.sh conda 创建的内容：

#!/bin/bash

if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then
  export DISABLE_AUTOBREW=1
  mv DESCRIPTION DESCRIPTION.old
  grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
  $R CMD INSTALL --build .
else
  mkdir -p $PREFIX/lib/R/library/RANN
  mv * $PREFIX/lib/R/library/RANN
fi

创建的 meta.yaml conda 的内容：

{% set version = '2.5.1' %}

{% set posix = 'm2-' if win else '' %}
{% set native = 'm2w64-' if win else '' %}

package:
  name: r-rann
  version: {{ version|replace("-", "_") }}

source:
  fn: RANN_2.5.1.tar.gz
  url:
    - {{ cran_mirror }}/src/contrib/RANN_2.5.1.tar.gz
    - {{ cran_mirror }}/src/contrib/Archive/RANN/RANN_2.5.1.tar.gz
  sha256: 75277e5d8a13ca01ff387f99d403268a8077862d4e95b076b74fb1b5538a8546

build:
  merge_build_host: True  # [win]
  # If this is a new build for the same version, increment the build number.
  number: 0

  # This is required to make R link correctly on Linux.
  rpaths:
    - lib/R/lib/
    - lib/

# Suggests: testthat
requirements:
  build:
    - {{ compiler('c') }}          # [not win]
    - {{ compiler('cxx') }}        # [not win]
    - {{native}}toolchain          # [win]
    - {{posix}}filesystem          # [win]
    - {{posix}}make

  host:
    - r-base

  run:
    - r-base
    - {{native}}gcc-libs           # [win]

test:
  commands:
    # You can put additional test commands to be run here.
    - $R -e "library('RANN')"           # [not win]
    - "\"%R%\" -e \"library('RANN')\""  # [win]

  # You can also put a file called run_test.py, run_test.sh, or run_test.bat
  # in the recipe that will be run at test time.

  # requires:
    # Put any additional test requirements here.

about:
  home: https://github.com/jefferis/RANN
  license: GPL (>= 3)
  summary: Finds the k nearest neighbours for every point in a given dataset in O(N log N) time
    using Arya and Mount's ANN library (v1.1.3). There is support for approximate as
    well as exact searches, fixed radius searches and 'bd' as well as 'kd' trees. The
    distance is computed using the L2 (Euclidean) metric. Please see package 'RANN.L1'
    for the same functionality using the L1 (Manhattan, taxicab) metric.
  license_family: GPL3

# The original CRAN metadata for this package was:

# Package: RANN
# Title: Fast Nearest Neighbour Search (Wraps ANN Library) Using L2 Metric
# Author: Sunil Arya and David Mount (for ANN), Samuel E. Kemp, Gregory Jefferis
# Maintainer: Gregory Jefferis <jefferis@gmail.com>
# Copyright: ANN library is copyright University of Maryland and Sunil Arya and David Mount. See file COPYRIGHT for details.
# Description: Finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library (v1.1.3). There is support for approximate as well as exact searches, fixed radius searches and 'bd' as well as 'kd' trees. The distance is computed using the L2 (Euclidean) metric. Please see package 'RANN.L1' for the same functionality using the L1 (Manhattan, taxicab) metric.
# URL: https://github.com/jefferis/RANN
# BugReports: https://github.com/jefferis/RANN/issues
# Encoding: UTF-8
# License: GPL (>= 3)
# Suggests: testthat
# Version: 2.5.1
# RoxygenNote: 6.0.1
# NeedsCompilation: yes
# Packaged: 2017-05-19 13:52:30 UTC; jefferis
# Repository: CRAN
# Date/Publication: 2017-05-21 07:56:50 UTC

# See
# http://docs.continuum.io/conda/build.html for
# more information about meta.yaml

任何帮助将不胜感激！

1 个解决方案

解决方案1
 2 已采纳  2018-03-31 11:19:11

“CMD”是 R 命令行指令。 在 conda-build 期间，您下载 RANN 的源代码，然后在临时环境中使用 R 从中构建一个包，然后（临时）安装它以检查它是否有效。

该行只是告诉 R 构建包rann 。 当您开发 R 包时，您使用R CMD build <my_package>或R CMD INSTALL --build <my_package>来制作该包的可安装存档。

看起来您的 conda-build 找不到 R 来构建包，尽管这通常是在运行 conda-build 时设置的临时环境中完成的； 并且构建过程几乎肯定会安装r-base因此没有真正的理由不找到 R。

我已经使用 conda-build 3.7.2 和 conda 4.3.34 以及 R v3.4.1（带有详细输出）在 windows-subsystem for linux（实际上是 Ubuntu 16.04）下运行代码

conda skeleton cran rann
conda build r-rann --R=3.4.1 --debug

它尝试在我的系统上运行Rscript CMD INSTALL --build ，而不是R CMD build 。 前者不是通常在 R 下构建包的方式，正是在这一步引发了“无法找到文件 CMD”错误，所以我更详细地研究了它。

首先，我将 meta.yaml 与 conda - forge 上的进行了比较。 运行要求中没有 libgcc，而 conda 骨架设置的 yaml 中的构建要求中没有 r-base - 我添加了这些并重建了（尽管我怀疑这些会导致问题）。 这没有解决任何问题，“找不到 CMD”错误仍然抛出。

我检查了conda-build 的变更日志。 从 3.7.2 版本开始，Rscript 用于运行测试而不是 R。 我恢复到 conda-build=3.7.1：

conda install conda-build=3.7.1 -vv
conda build r-rann --R=3.4.1 --debug

现在，我通过了对 R CMD INSTALL --build ... 的调用，但在编译过程中仍然发生错误； 所以我还没有解决这个问题。

尽管如此，您最初发布的错误似乎是由于 conda-build 的更改（在测试包时使用 Rscript 而不是 R）导致的，导致构建 R 包时出现问题。 请您将问题交叉引用到 conda-build github 上。

<-- 编辑-->

经过一番搜索，我通过 a) 安装 gfortran 和 b) 使用 conda-build 3.6.0 来创建框架并构建包来使其工作。 conda-build 的 3.7.0/1 抛出了一个与版本号相关的错误（没有 --version XXX 参数，conda-skeleton 在命名空间没有版本时抛出错误；使用 --version XXX 参数，conda-skeleton 抛出R 包未实现的版本号错误）。

上述错误已在conda-build 3.8.0 中修复，但我还没有使用过

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