网站出现的的问题,什么网站可以有人做详情页,网站搭建教程零基础,云服务器做网站R | R包安装报错-github连接速度慢或无法访问 | metaboanalystR | Retip | rJava安装 一、metaboanalystR 安装1.1 Bioconductor报错#xff0c;无网络连接1.2 github520-修改hosts文件 二、retip安装2.1 rJava包加载报错及安装2.2 安装Retip包 三、从Bioconductor安装Rdisop报… R | R包安装报错-github连接速度慢或无法访问 | metaboanalystR | Retip | rJava安装 一、metaboanalystR 安装1.1 Bioconductor报错无网络连接1.2 github520-修改hosts文件 二、retip安装2.1 rJava包加载报错及安装2.2 安装Retip包 三、从Bioconductor安装Rdisop报错及解决方式四、Bioconductor安装报错总结 一、metaboanalystR 安装
Error: Bioconductor version cannot be validated; no internet connection?-2019-06-19 BiocManager安装R包失败——Bioconductor version cannot be validated Windows电脑使用Rstudio会有多少错误呢
1.1 Bioconductor报错无网络连接
报错问题
Error: Bioconductor version cannot be validated; no internet connection? See #troubleshooting section in vignettepacman::p_load(c(impute, pcaMethods, globaltest, GlobalAncova, Rgraphviz, preprocessCore, genefilter, sva, limma, KEGGgraph, siggenes,BiocParallel, MSnbase, multtest,RBGL,edgeR,fgsea,httr,qs))
将程序包安装入‘C:/Users/hp/AppData/Local/R/win-library/4.3’
(因为‘lib’没有被指定)
Warning: 无法在貯藏處http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/4.3中读写索引:cannot open URL http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/4.3/PACKAGES
trying URL https://bioconductor.org/packages/3.17/bioc/bin/windows/contrib/4.3/BiocVersion_3.17.1.zip
Content type application/zip length 8264 bytes
downloaded 8264 bytes1.2 github520-修改hosts文件 metaboanalystR 百度搜索github520 修改host文件 安装metaboanalystR首先需要手动安装依赖包SSPA但安装不成功。
解决方法
– 找到系统中的hosts 文件 Windows 系统C:\Windows\System32\drivers\etc\hosts
– 以文本形式打开hosts 文件图片中为笔者2023-11-8修改
– 复制Github520信息并粘贴在上述打开的hosts文件中保存。
注
由于是在系统路径下无法直接保存该文件可将其先另存到桌面再从桌面拖到C:\Windows\System32\drivers\etc\hosts路径下接下来重启RStudio即可正常访问github并下载安装R包了该文件内容可能需要定期更新不能访问github时就可以重复以上操作。 devtools::install_github(https://github.com/mvaniterson/SSPA)
Downloading GitHub repo mvaniterson/SSPAHEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?1: All
2: CRAN packages only
3: None
4: vctrs (0.6.3 - 0.6.4) [CRAN]
5: fansi (1.0.4 - 1.0.5) [CRAN]Enter one or more numbers, or an empty line to skip updates: 1
vctrs (0.6.3 - 0.6.4 ) [CRAN]
fansi (1.0.4 - 1.0.5 ) [CRAN]
qvalue (NA - 2.32.0) [CRAN]
Installing 3 packages: vctrs, fansi, qvalue
将程序包安装入‘C:/Users/hp/AppData/Local/R/win-library/4.3’
(因为‘lib’没有被指定)
trying URL https://mirrors.sjtug.sjtu.edu.cn/cran/bin/windows/contrib/4.3/vctrs_0.6.4.zip
Content type application/zip length 1334820 bytes (1.3 MB)
downloaded 1.3 MBtrying URL https://mirrors.sjtug.sjtu.edu.cn/cran/bin/windows/contrib/4.3/fansi_1.0.5.zip
Content type application/zip length 314105 bytes (306 KB)
downloaded 306 KBtrying URL https://bioconductor.org/packages/3.17/bioc/bin/windows/contrib/4.3/qvalue_2.32.0.zip
Content type application/zip length 2809146 bytes (2.7 MB)
downloaded 2.7 MB程序包‘vctrs’打开成功MD5和检查也通过
Warning: 无法将拆除原来安装的程序包‘vctrs’
Warning: 回复了‘vctrs’
程序包‘fansi’打开成功MD5和检查也通过
程序包‘qvalue’打开成功MD5和检查也通过下载的二进制程序包在C:\Users\hp\AppData\Local\Temp\RtmpCAEEVQ\downloaded_packages里
── R CMD build ───────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file C:\Users\hp\AppData\Local\Temp\RtmpCAEEVQ\remotes52045d417c\mvaniterson-SSPA-6846d55/DESCRIPTION
─ preparing SSPA:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a data/datalist file should be added
─ building SSPA_2.11.0.tar.gz将程序包安装入‘C:/Users/hp/AppData/Local/R/win-library/4.3’
(因为‘lib’没有被指定)
* installing *source* package SSPA ...
** using staged installation
** libs
using C compiler: gcc.exe (GCC) 12.3.0
gcc -ID:/Program Files/R/R-4.3.1/include -DNDEBUG -ID:/Apps install/Rtools/rtools43/x86_64-w64-mingw32.static.posix/include -O2 -Wall -mfpmathsse -msse2 -mstackrealign -c Rinit.c -o Rinit.o
Rinit.c:8:40: warning: missing braces around initializer [-Wmissing-braces]8 | static const R_CMethodDef cMethods[] {| ^
gcc -ID:/Program Files/R/R-4.3.1/include -DNDEBUG -ID:/Apps install/Rtools/rtools43/x86_64-w64-mingw32.static.posix/include -O2 -Wall -mfpmathsse -msse2 -mstackrealign -c massdist.c -o massdist.o
gcc -ID:/Program Files/R/R-4.3.1/include -DNDEBUG -ID:/Apps install/Rtools/rtools43/x86_64-w64-mingw32.static.posix/include -O2 -Wall -mfpmathsse -msse2 -mstackrealign -c nncg.c -o nncg.o
nncg.c: In function objf:
nncg.c:57:11: warning: *c[0] may be used uninitialized [-Wmaybe-uninitialized]57 | return(c[0]);| ~~^~~~
gcc -shared -s -static-libgcc -o SSPA.dll tmp.def Rinit.o massdist.o nncg.o -LD:/Apps install/Rtools/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LD:/Apps install/Rtools/rtools43/x86_64-w64-mingw32.static.posix/lib -LD:/Program Files/R/R-4.3.1/bin/x64 -lR
installing to C:/Users/hp/AppData/Local/R/win-library/4.3/00LOCK-SSPA/00new/SSPA/libs/x64
** R
** data
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SSPA)
Warning message:
In file.copy(savedcopy, lib, recursive TRUE) :problem copying C:\Users\hp\AppData\Local\R\win-library\4.3\00LOCK\vctrs\libs\x64\vctrs.dll to C:\Users\hp\AppData\Local\R\win-library\4.3\vctrs\libs\x64\vctrs.dll: Permission denied安装metaboanalystR,
问题未安装R包“crmn”手动安装后再本地安装“metaboanalystR”安装成功。
二、retip安装
R语言rJava包安装载入及JAVA环境配置 Rxlsx/rJava无法加载的解决方法——java安装及版本查询
2.1 rJava包加载报错及安装 devtools::install_github(https://github.com/PaoloBnn/Retip)
Downloading GitHub repo PaoloBnn/RetipHEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?1: All
2: CRAN packages only
3: None
4: vctrs (0.6.3 - 0.6.4) [CRAN]Enter one or more numbers, or an empty line to skip updates: 1
vctrs (0.6.3 - 0.6.4) [CRAN]
Installing 1 packages: vctrs
将程序包安装入‘C:/Users/hp/AppData/Local/R/win-library/4.3’
(因为‘lib’没有被指定)
trying URL https://mirrors.sjtug.sjtu.edu.cn/cran/bin/windows/contrib/4.3/vctrs_0.6.4.zip
Content type application/zip length 1334820 bytes (1.3 MB)
downloaded 1.3 MB程序包‘vctrs’打开成功MD5和检查也通过
Warning: 无法将拆除原来安装的程序包‘vctrs’
Warning: 回复了‘vctrs’下载的二进制程序包在C:\Users\hp\AppData\Local\Temp\Rtmp0WG2OO\downloaded_packages里
── R CMD build ───────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file C:\Users\hp\AppData\Local\Temp\Rtmp0WG2OO\remotes47e451515493\PaoloBnn-Retip-8c23eda/DESCRIPTION ...
─ preparing Retip:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building Retip_0.5.4.tar.gz将程序包安装入‘C:/Users/hp/AppData/Local/R/win-library/4.3’
(因为‘lib’没有被指定)
* installing *source* package Retip ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
Error: .onLoad failed in loadNamespace() for rJava, details:call: fun(libname, pkgname)error: JAVA_HOME cannot be determined from the Registry
Execution halted
ERROR: lazy loading failed for package Retip
* removing C:/Users/hp/AppData/Local/R/win-library/4.3/Retip
Warning messages:
1: In file.copy(savedcopy, lib, recursive TRUE) :problem copying C:\Users\hp\AppData\Local\R\win-library\4.3\00LOCK\vctrs\libs\x64\vctrs.dll to C:\Users\hp\AppData\Local\R\win-library\4.3\vctrs\libs\x64\vctrs.dll: Permission denied
2: In i.p(...) :安装程序包‘C:/Users/hp/AppData/Local/Temp/Rtmp0WG2OO/file47e461ac715c/Retip_0.5.4.tar.gz’时退出狀態的值不是0install.packages(rJava)
将程序包安装入‘C:/Users/hp/AppData/Local/R/win-library/4.3’
(因为‘lib’没有被指定)
trying URL https://mirrors.sjtug.sjtu.edu.cn/cran/bin/windows/contrib/4.3/rJava_1.0-6.zip
Content type application/zip length 1300490 bytes (1.2 MB)
downloaded 1.2 MB程序包‘rJava’打开成功MD5和检查也通过下载的二进制程序包在C:\Users\hp\AppData\Local\Temp\Rtmp0WG2OO\downloaded_packages里library(rJava)
Error: package or namespace load failed for ‘rJava’:loadNamespace()里算rJava时.onLoad失败了详细内容调用: fun(libname, pkgname)错误: JAVA_HOME cannot be determined from the RegistryWindows10下的超详细Java安装步骤 Java/JDK下载安装与环境配置Windows 10 超详细的图文版教程
根据以上链接首先安装Java并进行环境配置。
以上加载rJava包成功。
2.2 安装Retip包 devtools::install_github(https://github.com/PaoloBnn/Retip)
Downloading GitHub repo PaoloBnn/RetipHEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?1: All
2: CRAN packages only
3: None
4: vctrs (0.6.3 - 0.6.4) [CRAN]Enter one or more numbers, or an empty line to skip updates: 1
vctrs (0.6.3 - 0.6.4) [CRAN]
Installing 1 packages: vctrs
将程序包安装入‘C:/Users/hp/AppData/Local/R/win-library/4.3’
(因为‘lib’没有被指定)
trying URL https://mirrors.sjtug.sjtu.edu.cn/cran/bin/windows/contrib/4.3/vctrs_0.6.4.zip
Error in download.file(url, destfile, method, mode wb, ...) : cannot open URL https://mirrors.sjtug.sjtu.edu.cn/cran/bin/windows/contrib/4.3/vctrs_0.6.4.zip
In addition: Warning message:
In download.file(url, destfile, method, mode wb, ...) :URL https://mirrors.sjtug.sjtu.edu.cn/cran/bin/windows/contrib/4.3/vctrs_0.6.4.zip: status was Couldnt resolve host name
Warning in download.packages(pkgs, destdir tmpd, available available, :下载程序包‘vctrs’时出了问题
── R CMD build ───────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file C:\Users\hp\AppData\Local\Temp\Rtmp0WG2OO\remotes47e4440c7b54\PaoloBnn-Retip-8c23eda/DESCRIPTION (793ms)
─ preparing Retip:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building Retip_0.5.4.tar.gz将程序包安装入‘C:/Users/hp/AppData/Local/R/win-library/4.3’
(因为‘lib’没有被指定)
* installing *source* package Retip ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Retip)安装成功。
三、从Bioconductor安装Rdisop报错及解决方式
从Bioconductor安装R包报错网络未连接
if (!require(BiocManager, quietly TRUE))install.packages(BiocManager)BiocManager::install(Rdisop)Error: Bioconductor version cannot be validated; no internet connection? See #troubleshooting section in vignetteoptions(download.file.method libcurl) #问题解决if (!require(BiocManager, quietly TRUE))install.packages(BiocManager)BiocManager::install(Rdisop)BiocManager无法安装R包
四、Bioconductor安装报错总结
重启软件及电脑修改host文件安装java
