将dada2安装到通过condas安装的R版本中(installing dada2 into a version of R that was installed through condas)

 我有一个通过condas安装R的环境（我目前使用R与jupyter笔记本，所以这是有道理的一点）。 我想在这个版本的R中使用dada2。 
 
 根据这个网站https://anaconda.org/bioconda/bioconductor-dada2正确的命令来实现这一点是 
 
 conda install -c bioconda bioconductor-dada2 
 
 这给我以下错误 
 
 获取包元数据.............解决包的规格：。 
 
 
 
 不可分析的错误：发现以下规范存在冲突： - 生物导体 - 数据2 - >生物导体 - 生物导体> = 2.32.1 - >生物导体 - 生物共同体> = 0.15.6 - > r 3.3.1 * - > r碱基3.3。 1 - r-glue使用“conda info”查看每个软件包的依赖关系。 
 
 
 如果我运行conda info package r-glue我可以看到它取决于r-base 3.4.1。 
 
 另一种方法也行不通： 
 
 我也尝试进入R并从那里安装，但我无法获得任何软件包来安装R软件包 
 
 source("https://bioconductor.org/biocLite.R")
 biocLite("dada2")
 
 给我一个非常长的输出，但缺点是一堆依赖返回错误 
 
 
 
 错误：编译包'RcppParallel'失败*删除'/ home / jacob / anaconda3 / lib / R / library / RcppParallel'错误：依赖'S4Vectors'不可用于包'IRanges'*删除'/ home / jacob / anaconda3 / lib / R / library / IRanges'错误：依赖关系'S4Vectors'，'IRanges'，'matrixStats'不可用于包'DelayedArray' 
 
 
 然后更多的东西，并在最后 
 
 错误：依赖'Biostrings'，'ShortRead'，'RcppParallel'不可用于包'dada2'*删除'/ home / jacob / anaconda3 / lib / R / library / dada2' 
 
 
 
 下载的源码包在'/ tmp / Rtmptx8OqE / downloaded_pa​​ckages'中更新'.Library'中包的HTML索引制作'packages.html'...完成旧包：'curl'，'dplyr'，'foreign'，' haven'，'httpuv'，'mgcv'，'purrr'，'Rcpp'，'TTR'，'xts'更新全部/部分/无？ [A / S / N]： 
 
 
 然后所有的更新都失败了。 
 
 是否正确的答案是不尝试在R中使用dada2和condas，而只是使用condas独立版本的R，还是有一些我缺少的方法？ 
 
 我在ubuntu linux 16.04和conda 3.2.23上运行R版本3.4.1，以获得更多价值。 

I have an environment with R installed through condas (I currently use R with jupyter notebook, so this made sense at one point). I would like to use dada2 with this version of R.
 
As per this site https://anaconda.org/bioconda/bioconductor-dada2 the correct command to make this happen is
 
 conda install -c bioconda bioconductor-dada2 
 
which gives me the following error
 
Fetching package metadata ............. Solving package specifications: .
 
 
 
UnsatisfiableError: The following specifications were found to be in conflict: - bioconductor-dada2 -> bioconductor-biostrings >=2.32.1 -> bioconductor-biocgenerics >=0.15.6 -> r 3.3.1* -> r-base 3.3.1 - r-glue Use "conda info " to see the dependencies for each package.
 
 
If I run conda info package r-glue I can see that it depends on r-base 3.4.1.
 
Alternative approach that also doesn't work:
 
I also tried going into R and installing from there, but I can't get any packages to install with R packages
 
 source("https://bioconductor.org/biocLite.R")
 biocLite("dada2")
 
Gives me a really long output, but the short of it is that a bunch of the dependencies return errors 
 
 
 
ERROR: compilation failed for package ‘RcppParallel’ * removing ‘/home/jacob/anaconda3/lib/R/library/RcppParallel’ ERROR: dependency ‘S4Vectors’ is not available for package ‘IRanges’ * removing ‘/home/jacob/anaconda3/lib/R/library/IRanges’ ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘matrixStats’ are not available for package ‘DelayedArray’
 
 
and then more stuff and at the end
 
ERROR: dependencies ‘Biostrings’, ‘ShortRead’, ‘RcppParallel’ are not available for package ‘dada2’ * removing ‘/home/jacob/anaconda3/lib/R/library/dada2’
 
 
 
The downloaded source packages are in ‘/tmp/Rtmptx8OqE/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Old packages: 'curl', 'dplyr', 'foreign', 'haven', 'httpuv', 'mgcv', 'purrr', 'Rcpp', 'TTR', 'xts' Update all/some/none? [a/s/n]:
 
 
and then all of the updates fail too.
 
Is the correct answer to not try to use dada2 with condas in R and rather just use a condas independent version of R, or is there some way that I am missing?
 
I am running R version 3.4.1 on ubuntu linux 16.04 and conda 3.2.23 for what that is worth.

原文：https://stackoverflow.com/questions/45556517