Question

我想要使用Affymetrix中的read.affybatch()命令打开一些affy数据。我已经下载了biocLite和affy包没有任何问题，但是一旦我尝试使用read命令读取我的.CEL文件，就会出现以下问题：

Library - package hgu133acdf not installed
Library - package hgu133acdf not installed
In addition: Warning messages:
1: In read.affybatch(filenames = "MonoHypo_U133A_04_12_03.CEL", "MonoC_U133A_04_12_03.CEL",  :
  Incompatible phenoData object. Created a new one.

2: running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.2\library" C:\windows\TEMP\RtmpKKBTXV/downloaded_packages/hgu133acdf_2.18.0.tar.gz' had status 1 
3: In install.packages(cdfname, lib = lib, repos = biocinstallRepos(),  :
  installation of package ‘hgu133acdf’ had non-zero exit status
4: missing cdf environment! in show(AffyBatch) 
5: running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.2\library" C:\windows\TEMP\RtmpKKBTXV/downloaded_packages/hgu133acdf_2.18.0.tar.gz' had status 1 
6: In install.packages(cdfname, lib = lib, repos = biocinstallRepos(),  :
  installation of package ‘hgu133acdf’ had non-zero exit status

所以，问题似乎是这个hgu133acdf包，但是使用BioConductor中的命令来安装这个包我得到以下错误：

biocLite("hgu133acdf")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘hgu133acdf’
installing the source package ‘hgu133acdf’

trying URL 'https://bioconductor.org/packages/3.4/data/annotation/src/contrib/hgu133acdf_2.18.0.tar.gz'
Content type 'application/x-gzip' length 1732200 bytes (1.7 MB)
downloaded 1.7 MB

'\\filestore.soton.ac.uk\users\rl1e15\mydocuments\PhD\PhD Year 1 2016-2017\Analysis\In Silico\R\Hypoxia and Normoxia Monocytes'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
ERROR: unable to create 'C:/Program Files/R/R-3.3.2/library/hgu133acdf'

The downloaded source packages are in
    ‘C:\Windows\Temp\RtmpKKBTXV\downloaded_packages’
Warning messages:
1: running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.2\library" C:\windows\TEMP\RtmpKKBTXV/downloaded_packages/hgu133acdf_2.18.0.tar.gz' had status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘hgu133acdf’ had non-zero exit status

我已尝试使用hgu133acdf将biocLite("hgu133acdf", lib="C:/Program Files/R/R-3.3.2/library")安装到我的本地驱动器，但会出现相同的non-zero exit status。有时它告诉我需要更新nlme所以我尝试了，但nlme_3.1-130与R-3-3-2不兼容，或者当我更新软件包时，它仍然无法正常工作。

Answer 1

所以，如果有人好奇，经过几个小时的R玩，我终于找到了解决方案。由于我有一台工作笔记本电脑，因此不会自动允许管理权限，因此我将所有软件包下载的目录的安全性设置为允许所有内容。我以管理员身份运行R，安装了所有必要的软件包，当我尝试read.affybatch（）命令时，这些软件包一直处于标记状态，并且它有效！

为什么我不能在使用RStudio的biocLite（“affy”）中使用函数read.affybatch（）？

1 个答案: