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>'