R语言笔记——'org.Hs.eg.db'脱坑记录

R语言笔记——'org.Hs.eg.db'脱坑记录

'org.Hs.eg.db'是发布在bioconductor平台上面的一个数据库文件，该包中装有较多的主流数据资料文件，但是小编在安装该包的过程中遇到了一些问题，通过浏览各大平台的资料以及自己实操，现已解决'org.Hs.eg.db'包的安装问题，接下来对于该包安装过程中遇到的问题进行简要分享。

1.'BiocManager'包

  • 下载'BiocManager'包中的问题

if (!requireNamespace("BiocManager", quietly = TRUE))
options(BioC_mirror="http://mirrors.ustc.edu.cn/bioc/") 
install.packages("BiocManager")
library("BiocManager")
#报错信息
Bioconductor version '3.12' requires R version '4.0'; use
  `BiocManager::install(version = '3.13')` with R version 4.1; see
  https://bioconductor.org/install
Bioconductor version '3.12' is out-of-date; the current release version '3.13' is
  available with R version '4.1'; see https://bioconductor.org/install

  • 解决办法

BiocManager::install(version = '3.13') #由于R版本较新，按照提示中的相关信息，安装最新版本的BiocManager()即可
#运行信息，更新Bioconductor()中的数据包
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Upgrade 23 packages to Bioconductor version '3.13'? [y/n]: 
y
#package安装过程较多，在此省略
  • 在这里注意看BiocManager::install(version = '3.13') with R version 4.1，提示当前版本的R，需要配套3.13版本的BiocManager

2.'org.Hs.eg.db'包

  • 下载“org.Hs.eg.db“包中的问题
library("BiocManager")
BiocManager::install("org.Hs.eg.db")
#报错信息
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Installing package(s) 'org.Hs.eg.db'
安装源码包‘org.Hs.eg.db’

试开URL’https://bioconductor.org/packages/3.13/data/annotation/src/contrib/org.Hs.eg.db_3.13.0.tar.gz'
Content type 'application/x-gzip' length 83002050 bytes (79.2 MB)
downloaded 79.2 MB

* installing *source* package 'org.Hs.eg.db' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
错误: package 'S4Vectors' 0.28.1 was found, but >= 0.29.19 is required by 'IRanges'
停止执行 #这里有error信息，注意看
ERROR: lazy loading failed for package 'org.Hs.eg.db'
* removing 'C:/Program Files/R/R-4.1.0/library/org.Hs.eg.db'

The downloaded source packages are in
    ‘C:\Users\Administrator\AppData\Local\Temp\RtmpgTlmcL\downloaded_packages’
Warning message:
In .inet_warning(msg) :
  installation of package ‘org.Hs.eg.db’ had non-zero exit status
  • 解决办法
#针对上文问题，安装'S4Vectors'包
BiocManager::install("S4Vectors")
#运行信息，安装'S4Vectors'包
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for
details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Old packages: 'gert', 'RCurl', 'readr', 'survival', 'XML'
Update all/some/none? [a/s/n]: 
a
#package安装信息较多，在此省略
······
#再次安装”org.Hs.eg.db“包
  • 下载'org.Hs.eg.db'包中的问题
#再次安装”org.Hs.eg.db“包
BiocManager::install("org.Hs.eg.db")
#运行信息，再次报错
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories'
for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Installing package(s) 'org.Hs.eg.db'
安装源码包‘org.Hs.eg.db’

试开URL’https://bioconductor.org/packages/3.13/data/annotation/src/contrib/org.Hs.eg.db_3.13.0.tar.gz'
Content type 'application/x-gzip' length 83002050 bytes (79.2 MB)
downloaded 79.2 MB

* installing *source* package 'org.Hs.eg.db' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for 'AnnotationDbi' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 不存在叫'GenomeInfoDbData'这个名字的程辑包 
错误: 无法载入程辑包'AnnotationDbi'
停止执行 #以上error信息表明，需要单独安装'GenomeInfoDbData'以及'AnnotationDbi'包
ERROR: lazy loading failed for package 'org.Hs.eg.db'
* removing 'C:/Program Files/R/R-4.1.0/library/org.Hs.eg.db'
  • 解决办法
#根据报错提示，安装'GenomeInfoDbData'以及'AnnotationDbi'包
BiocManager::install("AnnotationDbi")
#运行信息
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories'
for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Old packages: 'gert', 'RCurl', 'readr', 'survival', 'XML'
Update all/some/none? [a/s/n]: 
a
#package运行信息较多，在此省略
···
BiocManager::install("GenomeInfoDbData")
#运行信息
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories'
for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Installing package(s) 'GenomeInfoDbData'
安装源码包‘GenomeInfoDbData’

试开URL’https://bioconductor.org/packages/3.13/data/annotation/src/contrib/GenomeInfoDbData_1.2.6.tar.gz'
Content type 'application/x-gzip' length 10973004 bytes (10.5 MB)
downloaded 10.5 MB

* installing *source* package 'GenomeInfoDbData' ...
** using staged installation
** data
** inst
** help
*** installing help indices
  converting help for package 'GenomeInfoDbData'
    finding HTML links ... done
    GenomeInfoDbData-package                html  
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomeInfoDbData)

The downloaded source packages are in
    ‘C:\Users\Administrator\AppData\Local\Temp\RtmpgTlmcL\downloaded_packages’
Old packages: 'gert', 'RCurl', 'readr', 'survival', 'XML'
Update all/some/none? [a/s/n]: 
a
#package运行信息较多，在此省略
···
#安装完之后，再安装“org.Hs.eg.db“包
BiocManager::install("org.Hs.eg.db")
#运行信息
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories'
for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Installing package(s) 'org.Hs.eg.db'
安装源码包‘org.Hs.eg.db’

试开URL’https://bioconductor.org/packages/3.13/data/annotation/src/contrib/org.Hs.eg.db_3.13.0.tar.gz'
Content type 'application/x-gzip' length 83002050 bytes (79.2 MB)
downloaded 79.2 MB

* installing *source* package 'org.Hs.eg.db' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'org.Hs.eg.db'
    finding HTML links ... done
    org.Hs.egACCNUM                         html  
    org.Hs.egALIAS2EG                       html  
    org.Hs.egBASE                           html  
    org.Hs.egCHR                            html  
    org.Hs.egCHRLENGTHS                     html  
    org.Hs.egCHRLOC                         html  
    org.Hs.egENSEMBL                        html  
    org.Hs.egENSEMBLPROT                    html  
    org.Hs.egENSEMBLTRANS                   html  
    org.Hs.egENZYME                         html  
    org.Hs.egGENENAME                       html  
    org.Hs.egGENETYPE                       html  
    org.Hs.egGO                             html  
    org.Hs.egMAP                            html  
    org.Hs.egMAPCOUNTS                      html  
    org.Hs.egOMIM                           html  
    org.Hs.egORGANISM                       html  
    org.Hs.egPATH                           html  
    org.Hs.egPFAM                           html  
    org.Hs.egPMID                           html  
    org.Hs.egPROSITE                        html  
    org.Hs.egREFSEQ                         html  
    org.Hs.egSYMBOL                         html  
    org.Hs.egUCSCKG                         html  
    org.Hs.egUNIPROT                        html  
    org.Hs.eg_dbconn                        html  
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (org.Hs.eg.db)
The downloaded source packages are in
    ‘C:\Users\Administrator\AppData\Local\Temp\RtmpgTlmcL\downloaded_packages’
Old packages: 'gert', 'RCurl', 'readr', 'survival', 'XML'
Update all/some/none? [a/s/n]: 
a
#package运行信息较多，在此省略
···
#安装完之后，library(org.Hs.eg.db)就不会报错了
library(org.Hs.eg.db)
  • 错误: package 'S4Vectors' 0.28.1 was found, but >= 0.29.19 is required by 'IRanges'停止执行第一个问题在于'S4Vectors'版本太低，导致“org.Hs.eg.db“安装失败，通过BiocManager::install()重新安装'S4Vectors'即可；
  • 再次安装“org.Hs.eg.db“提示报错，报错信息如下：Error: package or namespace load failed for 'AnnotationDbi' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):不存在叫'GenomeInfoDbData'这个名字的程辑包 错误: 无法载入程包'AnnotationDbi'，主要问题在于未安装'GenomeInfoDbData''AnnotationDbi'两个数据包，通过BiocManager::install()安装'GenomeInfoDbData''AnnotationDbi'即可。

3.经验

  • 仔细看程序报错，并解读程序报错的原因；
  • 安装包保存地址中切记不要出现中文，文件夹的命名最好以英文为主；
  • 要学会用搜索引擎找寻自己的问题，要及时bioconductor社区交流学习。
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