如何从bioconductor (而不是CRAN)安装软件包？

Question

在this教程中，它说

source("http://www.bioconductor.org/biocLite.R")
biocLite("limma")
library(limma)

这将返回各种错误。

这是在尝试从bioconductor下载并安装吗?如果是，还有其他方法吗？

Answer 1

@dc37的答案是正确的，并且与您在BioConductor网页上找到的答案相对应。

因为这既是一个相对常见的任务，也是一个可以在命令行上完成的任务，所以我最近在littler的GitHub存储库中添加了一个助手脚本，现在我可以这样做了

edd@rob:~$ installBioc.r limma
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29)
Installing package(s) 'limma'
trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/limma_3.42.2.tar.gz'
Content type 'application/x-gzip' length 1494662 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

* installing *source* package ‘limma’ ...
** using staged installation
** libs
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O3 -Wall -pipe -pedantic  -std=gnu99 -c init.c -o init.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O3 -Wall -pipe -pedantic  -std=gnu99 -c normexp.c -o normexp.o
normexp.c: In function ‘fit_saddle_nelder_mead’:
normexp.c:165:78: warning: ISO C forbids passing argument 9 of ‘nmmin’ between function pointer and ‘void *’ [-Wpedantic]
  165 |   nmmin(3, par, parsOut, Fmin, normexp_m2loglik_saddle, fail, abstol, intol, &ex, alpha, beta, gamma, trace, fncount, maxit);
      |                                                                              ^~~
In file included from normexp.c:12:
/usr/share/R/include/R_ext/Applic.h:73:51: note: expected ‘void *’ but argument is of type ‘void (*)()’
   73 |     int *fail, double abstol, double intol, void *ex,
      |                                             ~~~~~~^~
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O3 -Wall -pipe -pedantic  -std=gnu99 -c weighted_lowess.c -o weighted_lowess.o
ccache gcc -Wl,-S -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o limma.so init.o normexp.o weighted_lowess.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-limma/00new/limma/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (limma)

The downloaded source packages are in
    ‘/tmp/downloaded_packages’
edd@rob:~$ 

Answer 2

本教程使用的是先前版本的Bioconductor，现在使用版本3.10，您必须使用BiocManager而不是BiocLite，并传递以下命令(如此处所述：https://bioconductor.org/packages/release/bioc/html/limma.html)：

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("limma")

有关BiocManager和Bioconductor的更多信息可以在这里找到：https://bioconductor.org/install/