CRAN R 包的 conda 构建失败
conda build fails for CRAN R packages
我正在尝试使用此处显示的方法从 CRAN 包构建一个 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，执行包含行 $R CMD INSTALL --build . 的脚本 "conda_build.sh"。我的问题是构建过程失败并出现错误 Fatal error: cannot open file 'CMD': No such file or directory，与我尝试构建的包无关。我不知道环境变量（？）"CMD" 应该从哪里来。
我采取了以下步骤：
conda skeleton cran rannconda build r-rann
我还测试了从 pip 构建 Python 包，这些包没有任何问题，所以看起来这不是我的 Miniconda 安装的普遍问题。
我的系统：
- Ubuntu 17.10
- Miniconda 3，版本 4.4.10
这里是构建过程的完整日志：
eega@eega-nb:~/workspace$ 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.
conda 创建的 build.sh 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
conda 创建的 meta.yaml 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
如有任何帮助，我们将不胜感激！
"CMD" 是一个 R command-line 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> 制作该包的可安装存档。
看起来你的 conda-build 找不到 R 来构建包，尽管这通常是在 运行ning 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 所以没有真正的理由不找到 R.
我 运行 windows-subsystem 下 linux 的代码（有效 Ubuntu 16.04）与 conda-build 3.7.2 和 conda 4.3.34 ，以及 R v3.4.1（详细输出）
conda skeleton cran rann
conda build r-rann --R=3.4.1 --debug
它试图在我的系统上 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 "Cannot find file CMD" 错误，因此我对其进行了更详细的研究。
首先，我将 meta.yaml 与 conda-forge 进行了比较。 run-requirements 中缺少 libgcc，而 conda skeleton 设置的 yaml 中 build-requirements 中缺少 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，"Could not find CMD" 错误仍然存在。
我查看了 conda-build 的更新日志。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ccall，但是在编译过程中仍然出现错误；所以我还没有解决问题。
尽管如此，您最初 post 所了解的错误似乎是由于对 conda-build 的更改（使用 Rscript 而不是
R when testing packages）导致构建 R 包时出现问题。请post issue cross-referencing 这个问题给 conda-build github,
<-- 编辑 -->
经过一些搜索，我通过 a) 安装 gfort运行 和 b) 使用 conda-build 3.6.0 创建框架和构建包来实现它。 conda-build 的 3.7.0/1 引发了与版本号相关的错误（没有 --version XXX 参数，conda-skeleton 引发了命名空间没有版本的错误；使用 --version XXX 参数， conda-skeleton 抛出一个错误，即未为 R 包实现版本号。
以上错误已在conda-build 3.8.0中修复，但我还没有使用
我正在尝试使用此处显示的方法从 CRAN 包构建一个 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，执行包含行 $R CMD INSTALL --build . 的脚本 "conda_build.sh"。我的问题是构建过程失败并出现错误 Fatal error: cannot open file 'CMD': No such file or directory，与我尝试构建的包无关。我不知道环境变量（？）"CMD" 应该从哪里来。
我采取了以下步骤：
conda skeleton cran rannconda build r-rann
我还测试了从 pip 构建 Python 包，这些包没有任何问题，所以看起来这不是我的 Miniconda 安装的普遍问题。
我的系统：
- Ubuntu 17.10
- Miniconda 3，版本 4.4.10
这里是构建过程的完整日志：
eega@eega-nb:~/workspace$ 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.
conda 创建的 build.sh 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
conda 创建的 meta.yaml 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
如有任何帮助，我们将不胜感激！
"CMD" 是一个 R command-line 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> 制作该包的可安装存档。
看起来你的 conda-build 找不到 R 来构建包，尽管这通常是在 运行ning 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 所以没有真正的理由不找到 R.
我 运行 windows-subsystem 下 linux 的代码（有效 Ubuntu 16.04）与 conda-build 3.7.2 和 conda 4.3.34 ，以及 R v3.4.1（详细输出）
conda skeleton cran rann
conda build r-rann --R=3.4.1 --debug
它试图在我的系统上 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 "Cannot find file CMD" 错误，因此我对其进行了更详细的研究。
首先，我将 meta.yaml 与 conda-forge 进行了比较。 run-requirements 中缺少 libgcc，而 conda skeleton 设置的 yaml 中 build-requirements 中缺少 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，"Could not find CMD" 错误仍然存在。
我查看了 conda-build 的更新日志。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ccall，但是在编译过程中仍然出现错误；所以我还没有解决问题。
尽管如此，您最初 post 所了解的错误似乎是由于对 conda-build 的更改（使用 Rscript 而不是 R when testing packages）导致构建 R 包时出现问题。请post issue cross-referencing 这个问题给 conda-build github,
<-- 编辑 -->
经过一些搜索，我通过 a) 安装 gfort运行 和 b) 使用 conda-build 3.6.0 创建框架和构建包来实现它。 conda-build 的 3.7.0/1 引发了与版本号相关的错误（没有 --version XXX 参数，conda-skeleton 引发了命名空间没有版本的错误；使用 --version XXX 参数， conda-skeleton 抛出一个错误，即未为 R 包实现版本号。
以上错误已在conda-build 3.8.0中修复，但我还没有使用