conda的确是一个非常好的工具，对于初学者而言，安装软件就跟用apt/yum软件管理器一样方便。但软件安装后有时会出现的动态库缺失的问题。

以安装软件lefse(https://bioconda.github.io/recipes/lefse/README.html)为例：

首先我设置/添加频道(这个添加顺序是错误的，所以导致后续报错，正确方法见解决方法2):

[root@localhost soft_backup]# conda config --add channels defaults

Warning: 'defaults' already in 'channels' list, moving to the top

[root@localhost soft_backup]# conda config --add channels conda-forge

[root@localhost soft_backup]# conda config --add channels defaults

Warning: 'defaults' already in 'channels' list, moving to the top

[root@localhost soft_backup]# conda config --add channels bioconda

[root@localhost miniconda2]# more ~/.condarc #频道顺序

channels:

- bioconda

- defaults

- conda-forge

[root@localhost soft_backup]#conda create -n lefse lefse

Solving environment: done

## Package Plan ##

environment location: /share/soft/miniconda2

added / updated specs:

– lefse

The following packages will be downloaded:

package                        |  build

—————————–    |—————–

expat-2.2.5                     | he0dffb1_0 186 KB

pyqi-0.3.2                        | py27_0 57 KB              bioconda

ncurses-5.9                     | 10 904 KB                     #说明使用的是默认频道中的ncurses

r-modeltools-0.2_21     | r3.4.1_0 171 KB

singledispatch-3.4.0.3 | py27h9bcb476_0 15 KB

……

click-6.7                          | py27h4225b90_0 103 KB

————————————————————

Total: 408.5 MB

The following NEW packages will be INSTALLED:

backports:           1.0-py27h63c9359_1

backports_abc:  0.5-py27h7b3c97b_0

biom-format:       2.1.6-py27_0 bioconda

blas:                       1.0-mkl

pyparsing:            2.2.0-py27hf1513f8_1

pyqi:                       0.3.2-py27_0          bioconda

pyqt:                       5.6.0-py27h4b1e83c_5

python-dateutil:  2.7.3-py27_0

pytz:                        2018.4-py27_0

qt:                            5.6.2-h974d657_12

r-base:                    3.4.1-3                   conda-forge

r-codetools:          0.2_15-r3.4.1_0

……

xz:                            5.2.4-h14c3975_4

The following packages will be UPDATED:

libedit:      3.1-heed3624_0         –>   3.1.20170329-0 conda-forge

readline:  7.0-ha6073c6_4         –>    7.0-hb321a52_4

The following packages will be DOWNGRADED:

ncurses:    6.0-h9df7e31_2           –>   5.9-10

python:    2.7.14-h1571d57_29    –>   2.7.14-ha6fc286_23

Proceed ([y]/n)? y

Downloading and Extracting Packages

expat-2.2.5                     | 186 KB | ################################# | 100%

graphite2-1.3.11            | 129 KB | ################################# | 100%

readline-7.0                    | 388 KB | ################################# | 100%

future-0.16.0                   | 641 KB | ################################# | 100%

lefse-1.0.8.post1            | 95 KB | ################################## | 100%

pyparsing-2.2.0             | 93 KB | ################################## | 100%

intel-openmp-2018.0. | 705 KB | #################################  | 100%

r-base-3.4.1                   | 23.0 MB | #################################| 100%

xz-5.2.4                            | 366 KB | #################################  | 100%

subprocess32-3.5.1     | 40 KB | ##################################  | 100%

backports_abc-0.5    | 12 KB | ##################################   | 100%

libtiff-4.0.9                     | 566 KB | ################################## | 100%

……

click-6.7                         | 103 KB | ################################## | 100%

Preparing transaction: done

Verifying transaction: done

Executing transaction: done

安装完后出现报错：

(lefse) [root@localhost envs]# run_lefse.py

Traceback (most recent call last):

File "/share/soft/miniconda2/envs/lefse/bin/run_lefse.py", line 4, in

from lefse import *

File "/share/soft/miniconda2/envs/lefse/share/lefse-1.0.8.post1-0/lefse.py", line 3, in

import rpy2.robjects as robjects

File "/share/soft/miniconda2/envs/lefse/lib/python2.7/site-packages/rpy2/robjects/__init__.py", line 16, in

import rpy2.rinterface as rinterface

File "/share/soft/miniconda2/envs/lefse/lib/python2.7/site-packages/rpy2/rinterface/__init__.py", line 92, in

from rpy2.rinterface._rinterface import (baseenv,

ImportError: libiconv.so.2: cannot open shared object file: No such file or directory

#通过一顿百度谷歌，发现上述libiconv.so.2报错是其中运行R时动态库的缺失问题，而rpy2.robjects报错是因为rpy2需要调用R

(lefse) [root@localhost envs]# R

/share/soft/miniconda2/envs/lefse/lib/R/bin/exec/R: error while loading shared libraries: libiconv.so.2: cannot open shared object file: No such file or directory

#差这个库，那我就安装

[root@localhost lib]# conda install -n lefse libiconv

安装完成后又报错：

ImportError: libicuuc.so.54: cannot open shared object file: No such file or directory

#通过/share/soft/miniconda2/envs/lefse/lib中高版本的库链接成对应的低版本解决：ln -s libicuuc.so.58.2 libicuuc.so.54 ，老错误解决，又报新错：

ImportError: libtinfow.so.6: cannot open shared object file: No such file or directory

#通过libtinfow.so.6缺失，一顿百度谷歌，发现只有ncurses包没安装时会抱这个错，而我明明安装了，当我爬贴爬到：https://github.com/samtools/samtools/issues/790 时 发现有人回答通过 conda install -c conda-forge ncurses可以解决。所以：

解决方法一：安装对应频道的ncurses, 虽然前面遇到的问题解决，但在使用过程中还是会报错，所以方法一失效，推荐方法二！

conda install -n lefse -c conda-forge ncurses

解决方法二：

所以究其原因，应该是频道顺序错误导致安装的包不一致。我又仔细看了一下lefse的安装说明，发现lefse安装说明明确说明需要激活bioconda频道，而激活bioconda的正确顺序如下：

[root@localhost miniconda2]# conda config --add channels defaults

Warning: 'defaults' already in 'channels' list, moving to the top

[root@localhost miniconda2]# conda config --add channels conda-forge

Warning: 'conda-forge' already in 'channels' list, moving to the top

[root@localhost miniconda2]# conda config --add channels bioconda

Warning: 'bioconda' already in 'channels' list, moving to the top

[root@localhost miniconda2]# more ~/.condarc

channels:

- bioconda #第一优先级

- conda-forge #第二优先级

- defaults #第三优先级

按上述顺序调整频道的顺序后，正常安装lefse，问题解决:

conda create -n lefse lefse

最后如果你不喜欢用包辅助安装，这里附一下普通自定义安装lefse的链接：http://blog.sciencenet.cn/blog-306699-997026.html

参考：

https://www.jianshu.com/p/f8a0692df264

https://github.com/samtools/samtools/issues/790