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CRAN R 包的 conda 構建失敗

[英]conda build fails for CRAN R packages

 原文  2018-03-30 10:49:37  7   1    r/ conda/ cran/ conda-build

問題描述

我正在嘗試使用此處顯示的方法從 CRAN 包構建 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 為例——這個包在 conda-forge 上已經作為 r-rann 存在，但我用它來測試構建過程是否正常工作。

在構建過程中，將執行包含$R CMD INSTALL --build .行的腳本“conda_build.sh” $R CMD INSTALL --build . . 我的問題是構建過程失敗並出現錯誤Fatal error: cannot open file 'CMD': No such file or directory ，與我嘗試構建的包無關。 我不知道環境變量（？）“CMD”應該來自哪里。

我采取了以下步驟：

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

我還測試了從 pip 構建 Python 包，這些工作沒有任何問題，所以這似乎不是我的 Miniconda 安裝的普遍問題。

我的系統：

  • Ubuntu 17.10
  • Miniconda 3，版本 4.4.10

這是構建過程的完整日志：

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 創建的內容：

#!/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

創建的 meta.yaml conda 的內容：

{% 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

任何幫助將不勝感激！

1 個解決方案

解決方案1
 2 已采納  2018-03-31 11:19:11

“CMD”是 R 命令行指令。 在 conda-build 期間，您下載 RANN 的源代碼，然后在臨時環境中使用 R 從中構建一個包，然后（臨時）安裝它以檢查它是否有效。

該行只是告訴 R 構建包rann 。 當您開發 R 包時，您使用R CMD build <my_package>或R CMD INSTALL --build <my_package>來制作該包的可安裝存檔。

看起來您的 conda-build 找不到 R 來構建包，盡管這通常是在運行 conda-build 時設置的臨時環境中完成的； 並且構建過程幾乎肯定會安裝r-base因此沒有真正的理由不找到 R。

我已經使用 conda-build 3.7.2 和 conda 4.3.34 以及 R v3.4.1（帶有詳細輸出）在 windows-subsystem for linux（實際上是 Ubuntu 16.04）下運行代碼

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

它嘗試在我的系統上運行Rscript CMD INSTALL --build ，而不是R CMD build 。 前者不是通常在 R 下構建包的方式，正是在這一步引發了“無法找到文件 CMD”錯誤，所以我更詳細地研究了它。

首先，我將 meta.yaml 與 conda - forge 上的進行了比較。 運行要求中沒有 libgcc，而 conda 骨架設置的 yaml 中的構建要求中沒有 r-base - 我添加了這些並重建了（盡管我懷疑這些會導致問題）。 這沒有解決任何問題，“找不到 CMD”錯誤仍然拋出。

我檢查了conda-build 的變更日志。 從 3.7.2 版本開始，Rscript 用於運行測試而不是 R。 我恢復到 conda-build=3.7.1：

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

現在，我通過了對 R CMD INSTALL --build ... 的調用，但在編譯過程中仍然發生錯誤； 所以我還沒有解決這個問題。

盡管如此，您最初發布的錯誤似乎是由於 conda-build 的更改（在測試包時使用 Rscript 而不是 R）導致的，導致構建 R 包時出現問題。 請您將問題交叉引用到 conda-build github 上。

<-- 編輯-->

經過一番搜索，我通過 a) 安裝 gfortran 和 b) 使用 conda-build 3.6.0 來創建框架並構建包來使其工作。 conda-build 的 3.7.0/1 拋出了一個與版本號相關的錯誤（沒有 --version XXX 參數，conda-skeleton 在命名空間沒有版本時拋出錯誤；使用 --version XXX 參數，conda-skeleton 拋出R 包未實現的版本號錯誤）。

上述錯誤已在conda-build 3.8.0 中修復，但我還沒有使用過

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