我无法安装任何 Bioconductor 包:“readRDS(dest) 中的错误:从连接读取错误" [英] I can't install any Bioconductor package: "Error in readRDS(dest) : error reading from connection"
问题描述
您好(这是我的第一条消息，所以如果有什么不对的地方，我很抱歉)，
我已经遇到这个问题几天了.我无法安装新软件包，我读过类似的 问题 但就我而言，问题仅在我尝试安装新的 Bioconductor 包时出现(或者当我删除旧的并尝试重新安装时).问题是我总是得到下一条消息的一些变化(在这个例子中我试图安装 ComplexHeatmap):
BiocManager::install(ComplexHeatmap")<块引用>
Bioconductor 版本 3.12 (BiocManager 1.30.13), R 4.0.0 (2020-04-24)安装包BiocVersion"，ComplexHeatmap"也在安装依赖关系shape"、rjson"、BiocGenerics"、circlize"、GetoptLong"、色彩空间"、线索"、RColorBrewer"、GlobalOptions"、png"、开罗"、S4Vectors"、IRanges"、matrixStats"
无法打开网址
'https://bioconductor.org/packages/3.12/data/annotation/bin/windows/contrib/4.0/PACKAGES.rds':HTTP 状态为404 Not Found"旧包:installr"、boot"、'类'，'集群'，'codetools'，'外国'，'KernSmooth'，'格子'，质量"、矩阵"、mgcv"、nlme"、nnet"、空间"、生存"更新全部/部分/无?[a/s/n]:更新全部/部分/无?[a/s/n]:
它告诉我必须安装 X 包，所以我键入a"；这发生了:
<块引用>readRDS(dest) 错误:从连接读取错误
第一次尝试后，我只收到第二条消息，直到我重新启动 R.
我试过了:
- 开始新的 Rscripts(或 Rmarkdowns)会话
- 删除所有包(直接删除文件夹)
- 卸载并重新安装 R 和 RStudio(尝试不同版本，R 降至 4.0)
- 重启 R 和计算机
我尝试安装以前版本的 BiocManager，但无法安装.一切都在更新.非常感谢您的关注，感谢您的帮助.
这是 BiocManager 的一个已知问题1.30.13.通过运行以下命令安装开发版本:
install.packages(devtools")devtools::install_github("Bioconductor/BiocManager", ref="ghost-binary-repo")Hello (this is my first message so, I'm sorry if there is something wrong),
I have been having this problem for a couple of days now. I can't install new packages, I have read a similar question but in my case, the problem only occurs when I try to install a new Bioconductor package (or when I delete an old one and try to reinstall it). The thing is that I always got some variation of the next message (in this example I am trying to install ComplexHeatmap):
BiocManager::install("ComplexHeatmap")
Bioconductor version 3.12 (BiocManager 1.30.13), R 4.0.0 (2020-04-24) Installing package(s) 'BiocVersion', 'ComplexHeatmap' also installing the dependencies �shape�, �rjson�, �BiocGenerics�, �circlize�, �GetoptLong�, �colorspace�, �clue�, �RColorBrewer�, �GlobalOptions�, �png�, �Cairo�, �S4Vectors�, �IRanges�, �matrixStats�
cannot open URL
'https://bioconductor.org/packages/3.12/data/annotation/bin/windows/contrib/4.0/PACKAGES.rds': HTTP status was '404 Not Found'Old packages: 'installr', 'boot', 'class', 'cluster', 'codetools', 'foreign', 'KernSmooth', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', 'spatial', 'survival' Update all/some/none? [a/s/n]: Update all/some/none? [a/s/n]:
It says to me that I must install X packages, so I type "a" and this happens:
Error in readRDS(dest) : error reading from connection
After the first attempt, I only get the second message until I restart R.
I have tried:
- Start new sessions of Rscripts (or Rmarkdowns)
- Remove all packages (by deleting the folders, directly)
- Uninstall and reinstall R and RStudio (trying different versions, down to 4.0 for R)
- Reboot R and the computer
I tried to install a previous version of BiocManager, but I am not able to do it. Everything is updated. Thank you very much for your attention I would appreciate your help.
This is a known issue with BiocManager 1.30.13. Install the developmental version by running the following:
install.packages("devtools")
devtools::install_github("Bioconductor/BiocManager", ref="ghost-binary-repo")
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