org.Hs.eg.db安装

org.Hs.eg.db安装

我先把问题解决的办法给出来吧。这个是安装成功了的。

1.去http://www.bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html下载安装包

但是你要注意自己下载的位置在哪，记住路径。后面安装的时候会用到的。

然后直接在你的R里面输入以下的代码，记得额，前面的路径和包名要对得上额。

install.packages("C:/Users/Administrator/Downloads/org.Hs.eg.db_3.7.0.tar.gz",repos=NULL, type="source")

之后，我们再来检查一下是否安装成功

library("org.Hs.eg.db")

返回来的可能是这样的：

Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
    colnames, colSums, dirname, do.call, duplicated, eval, evalq,
    Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
    lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
    rowSums, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

恭喜你安装成功。

下面是我安装出错的方法，也许某个时候，你用这些方法然后安装上了呢。

一

source("http://bioconductor.org/biocLite.R")
options(repos=structure(c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))) 
biocLite("org.Hs.eg.db")

Warning message:
"'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
  package instead."Bioconductor version 3.8 (BiocInstaller 1.32.1), ?biocLite for help
Warning message:
"'biocLite' is deprecated.
Use 'BiocManager::install' instead.
See help("Deprecated")"BioC_mirror: https://bioconductor.org
Using Bioconductor 3.8 (BiocInstaller 1.32.1), R 3.5.3 (2019-03-11).
Installing package(s) 'org.Hs.eg.db'
installing the source package 'org.Hs.eg.db'

Warning message in install.packages(pkgs = doing, lib = lib, ...):
"installation of package 'org.Hs.eg.db' had non-zero exit status"Old packages: 'backports', 'devtools', 'nlme', 'remotes'

二

BiocManager::install("org.Hs.eg.db", version = "3.8")

Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.3 (2019-03-11)
Installing package(s) 'org.Hs.eg.db'
installing the source package ‘org.Hs.eg.db’

trying URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Hs.eg.db_3.7.0.tar.gz'
Content type 'application/x-gzip' length 77962833 bytes (74.4 MB)
downloaded 74.4 MB

* installing *source* package 'org.Hs.eg.db' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Error : package 'Biobase' required by 'AnnotationDbi' could not be found
ERROR: lazy loading failed for package 'org.Hs.eg.db'
* removing 'C:/Program Files/R/R-3.5.3/library/org.Hs.eg.db'
In R CMD INSTALL

The downloaded source packages are in
	‘C:\Users\Administrator\AppData\Local\Temp\RtmpE9zaN3\downloaded_packages’
Update old packages: 'backports', 'devtools', 'nlme', 'remotes'
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source versions are later:
           binary  source needs_compilation
backports   1.1.3   1.1.4              TRUE
devtools    2.0.1   2.0.2             FALSE
nlme      3.1-137 3.1-139              TRUE
remotes     2.0.2   2.0.4             FALSE

  Binaries will be installed
trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.5/backports_1.1.3.zip'
Content type 'application/zip' length 65892 bytes (64 KB)
downloaded 64 KB

trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.5/nlme_3.1-137.zip'
Content type 'application/zip' length 2346045 bytes (2.2 MB)
downloaded 2.2 MB

package ‘backports’ successfully unpacked and MD5 sums checked
package ‘nlme’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\Administrator\AppData\Local\Temp\RtmpE9zaN3\downloaded_packages
installing the source packages ‘devtools’, ‘remotes’

trying URL 'http://cran.rstudio.com/src/contrib/devtools_2.0.2.tar.gz'
Content type 'application/x-gzip' length 388141 bytes (379 KB)
downloaded 379 KB

trying URL 'http://cran.rstudio.com/src/contrib/remotes_2.0.4.tar.gz'
Content type 'application/x-gzip' length 117119 bytes (114 KB)
downloaded 114 KB

* installing *source* package 'remotes' ...
** 成功将'remotes'程序包解包并MD5和检查
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'remotes'
    finding HTML links ... 好了
    available_packages                      html  
    bioc_install_repos                      html  
    download_version                        html  
    github_refs                             html  
    gitlab_pat                              html  
    install_bioc                            html  
    install_bitbucket                       html  
    install_cran                            html  
    install_deps                            html  
    install_dev                             html  
    install_git                             html  
    install_github                          html  
    install_gitlab                          html  
    install_local                           html  
    install_svn                             html  
    install_url                             html  
    install_version                         html  
    package_deps                            html  
    parse-git-repo                          html  
    standardise_dep                         html  
    update_packages                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (remotes)
In R CMD INSTALL
* installing *source* package 'devtools' ...
** 成功将'devtools'程序包解包并MD5和检查
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'devtools'
    finding HTML links ... 好了
    as.package                              html  
    bash                                    html  
    build                                   html  
    build_manual                            html  
    build_readme                            html  
    build_site                              html  
    build_vignettes                         html  
    check                                   html  
    finding level-2 HTML links ... done

    check_failures                          html  
    check_man                               html  
    check_rhub                              html  
    check_win                               html  
    clean_vignettes                         html  
    dev_mode                                html  
    dev_packages                            html  
    devtest                                 html  
    devtools-deprecated                     html  
    devtools                                html  
Rd warning: C:/Users/Administrator/AppData/Local/Temp/RtmpQZU020/R.INSTALL1cbc72d7b29/devtools/man/devtools.Rd:28: file link 'as.person' in package 'utils' does not exist and so has been treated as a topic
    document                                html  
    dr_devtools                             html  
    dr_github                               html  
    git_checks                              html  
    github_pat                              html  
    has_tests                               html  
    install                                 html  
    install_deps                            html  
    is.package                              html  
    lint                                    html  
    load_all                                html  
    loaded_packages                         html  
    missing_s3                              html  
    package_file                            html  
    r_env_vars                              html  
    reexports                               html  
Rd warning: C:/Users/Administrator/AppData/Local/Temp/RtmpQZU020/R.INSTALL1cbc72d7b29/devtools/man/reexports.Rd:39: file link 'has_devel' in package 'pkgbuild' does not exist and so has been treated as a topic
Rd warning: C:/Users/Administrator/AppData/Local/Temp/RtmpQZU020/R.INSTALL1cbc72d7b29/devtools/man/reexports.Rd:39: file link 'find_rtools' in package 'pkgbuild' does not exist and so has been treated as a topic
Rd warning: C:/Users/Administrator/AppData/Local/Temp/RtmpQZU020/R.INSTALL1cbc72d7b29/devtools/man/reexports.Rd:43: file link 'github_pull' in package 'remotes' does not exist and so has been treated as a topic
Rd warning: C:/Users/Administrator/AppData/Local/Temp/RtmpQZU020/R.INSTALL1cbc72d7b29/devtools/man/reexports.Rd:43: file link 'github_release' in package 'remotes' does not exist and so has been treated as a topic
Rd warning: C:/Users/Administrator/AppData/Local/Temp/RtmpQZU020/R.INSTALL1cbc72d7b29/devtools/man/reexports.Rd:43: file link 'dev_package_deps' in package 'remotes' does not exist and so has been treated as a topic
    release                                 html  
    release_checks                          html  
    reload                                  html  
    revdep                                  html  
    run_examples                            html  
    save_all                                html  
    show_news                               html  
    source_gist                             html  
    source_url                              html  
    spell_check                             html  
    submit_cran                             html  
    system_check                            html  
    system_output                           html  
    test                                    html  
    uninstall                               html  
    wd                                      html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (devtools)
In R CMD INSTALL

The downloaded source packages are in
	‘C:\Users\Administrator\AppData\Local\Temp\RtmpE9zaN3\downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘org.Hs.eg.db’ had non-zero exit status
Error in substring(html, match + 6, match + attr(match, "match.length") -  : 
  invalid multibyte string at '<9d>
<5f>Journal of Statistical Software_, *22*(4), pp. 1-20. doi: 10.18637/jss.v022.i04 (URL:
http://doi.org/10.18637/jss.v022.i04).
</p>
<p>See ade4 website: <a href="http://pbil.univ-lyon1.fr/ADE-4/">http://pbil.univ-lyon1.fr/ADE-4/</a>
</p>


<h3>See Also</h3>

<p><code>ade4TkGUI</code>, <code>adegenet</code>, <code>adehabitat</code>, <code>adegraphics</code></p>

<hr /><div style="text-align: center;">[Package <em>ade4</em> version 1.7-13 <a href="00Index.html">Index</a>]</div>
</body></html>'
Error in substring(html, match + 6, match + attr(match, "match.length") -  : 
  invalid multibyte string at '<9d>
<5f>Journal of Statistical Software_, *22*(4), pp. 1-20. doi: 10.18637/jss.v022.i04 (URL:
http://doi.org/10.18637/jss.v022.i04).
</p>
<p>See ade4 website: <a href="http://pbil.univ-lyon1.fr/ADE-4/">http://pbil.univ-lyon1.fr/ADE-4/</a>
</p>


<h3>See Also</h3>

<p><code>ade4TkGUI</code>, <code>adegenet</code>, <code>adehabitat</code>, <code>adegraphics</code></p>

<hr /><div style="text-align: center;">[Package <em>ade4</em> version 1.7-13 <a href="00Index.html">Index</a>]</div>
</body></html>'
Error in substring(html, match + 6, match + attr(match, "match.length") -  : 
  invalid multibyte string at '<9d>
<5f>Journal of Statistical Software_, *22*(4), pp. 1-20. doi: 10.18637/jss.v022.i04 (URL:
http://doi.org/10.18637/jss.v022.i04).
</p>
<p>See ade4 website: <a href="http://pbil.univ-lyon1.fr/ADE-4/">http://pbil.univ-lyon1.fr/ADE-4/</a>
</p>


<h3>See Also</h3>

<p><code>ade4TkGUI</code>, <code>adegenet</code>, <code>adehabitat</code>, <code>adegraphics</code></p>

<hr /><div style="text-align: center;">[Package <em>ade4</em> version 1.7-13 <a href="00Index.html">Index</a>]</div>
</body></html>'