DiffBind安装（二）

DiffBind包现在更新了，但是我还是习惯了用旧的版本，由于我的R语言更新到了4.0，默认安装DiffBind的最新版本，所以我又下载了R语言3.5版本，安装上DiffBind对应的旧版本。

用bioconductor安装DiffBind，要先安装BiocManager，安装的时候一定要联网，否则报错，由于小白用的服务器，这一步就踩坑了，哭唧唧 :(

install.packages("BiocManager")
BiocManager::install("DiffBind")

安装失败：

The downloaded source packages are in
       ‘/tmp/RtmpV6kPB4/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages(...) :
 installation of package ‘DESeq2’ had non-zero exit status
2: In install.packages(...) :
 installation of package ‘systemPipeR’ had non-zero exit status
3: In install.packages(...) :
 installation of package ‘DiffBind’ had non-zero exit status

根据报错要求安装缺失的R包

BiocManager::install("DESeq2")

又安装失败

make: *** [/usr/R-3.5.1/lib/R/etc/Makeconf:168: DESeq2.o] Error 1
ERROR: compilation failed for package ‘DESeq2’
* removing ‘/usr/R-3.5.1/lib/R/library/DESeq2’
The downloaded source packages are in
       ‘/tmp/RtmpV6kPB4/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(...) :
 installation of package ‘DESeq2’ had non-zero exit status

鼓捣了好久，怎么弄都装不成DESeq2，一怒之下重新安装R 3.5版本，害怕自己安装R又会出现各种问题，因此用conda自动安装。我现在用的服务器conda的默认base环境下已经安装了R 4.0版本，因此重新创建环境安装R 3.5版本，这样也可以有两个版本的R语言，方便自己使用。

用conda来重新安装一个R 3.5版本的参考链接如下：
https://www.jianshu.com/p/2e1986296e15
https://www.jianshu.com/p/e326912eb41b

conda create -n R3.5  # 创建名为R3.5的环境
source activate R3.5  #激活环境
conda install r-base=3.5.1 #安装R语言，后面必须加版本号，要不然默认会装最新版本
conda deactivate # 退出当前环境

让我们来看一下安装后的结果，conda的默认base环境下，R语言是R 4.0.3版本

base环境下 R4.0.3版本

进入R3.5环境, R语言是R 3.5.1版本

conda activate R3.5

R3.5 环境下 R 3.5.1版本

重新安装好R 3.5.1，再安装DESeq2试试

install.packages("BiocManager")
library('BiocManager', quietly = TRUE)
BiocManager::install("DESeq2")

又安装失败：

The downloaded source packages are in
       ‘/tmp/RtmpOY7qYy/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages(...) :
 installation of package ‘Hmisc’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘DESeq2’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
 installation of package ‘stringi’ had non-zero exit status

缺失了好多R包，这次用回到liunx，用conda安装R包试试

conda install -c r r-Hmisc
conda install -c r r-stringi

装好后再去R 3.5.1安装DESeq2

BiocManager::install("DESeq2")

这次是出现了警告：

Warning message:
In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
 installation of package ‘stringi’ had non-zero exit status

R包stringi一直装不上，查了好久，有网友解决过该问题
参考链接如下：
http://www.bubuko.com/infodetail-3647996.html
是不能使用默认的ICU库，解决方法如下：

install.packages("stringr", configure.args="--disable-pkg-config")

终于成功安装了stringi包：

** testing if installed package can be loaded
* DONE (stringi)
下载的程序包在
       ‘/tmp/RtmpRuxXQB/downloaded_packages’里
更新'.Library'里的HTML程序包列表
Making 'packages.html' ... 做完了。

这次再安装DESeq2

BiocManager::install("DESeq2")

装好后载入试试：

library("DESeq2")

又出现警告：

Warning messages:
1: In sample.int(.Machine$integer.max - 1L, 1L) :
 '.Random.seed[1]' is not a valid integer, so ignored
2: In stats::runif(1L) :
 '.Random.seed[1]' is not a valid integer, so ignored

无语，心好累，这个小白还没有能力解决，有人知道可以来告诉我。由于不影响使用，我选择了无视 ╮（╯＿╰）╭

走了这么远不能忘记初心啊，装好DESeq2后去安装DiffBind

BiocManager::install("DiffBind")

安装失败：

Warning messages:
1: In install.packages(...) :
 installation of package ‘gplots’ had non-zero exit status
2: In install.packages(...) :
 installation of package ‘DiffBind’ had non-zero exit status

回到liunx用conda安装缺失R包gplots

conda install -c r r-gplots

装好后回到R 3.5再安装DiffBind

BiocManager::install("DiffBind")

又报错了，呜呜呜 ～～～ 〒▽〒：

ERROR: dependency ‘amap’ is not available for package ‘DiffBind’
* removing ‘/software/miniconda3/envs/R3.5/lib/R/library/DiffBind’
The downloaded source packages are in
       ‘/tmp/RtmpRuxXQB/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(...) :
 installation of package ‘DiffBind’ had non-zero exit status

应该是R包amp的默认安装版本太高，手动安装低版本
参考原文链接：https://zhuanlan.zhihu.com/p/129331377

R包amap默认版本
R包amap其他版本的存储位置
R包amap的0.6版本存储位置

download.file("https://cran.r-project.org/src/contrib/Archive/amap/amap_0.6.tar.gz","amap_0.6.tar.gz")
install.packages("amap_0.6.tar.gz",repos=NULL)

成功安装R包amap

*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (amap)

之后再安装DiffBind

BiocManager::install("DiffBind")

成功啦

*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DiffBind)
The downloaded source packages are in
    ‘/tmp/RtmpRuxXQB/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done

载入试试：

library("DiffBind")

和DESeq2一样的警告，啊啊啊～，算了，不影响使用我选择无视，有大神知道可以来告诉小白^_~

Warning messages:
1: In sample.int(.Machine$integer.max - 1L, 1L) :
  '.Random.seed[1]' is not a valid integer, so ignored
2: In stats::runif(1L) :
  '.Random.seed[1]' is not a valid integer, so ignored