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谢老师您好我今天上午参加你在华中农业大学的报告研究生

wangguiqian 2023-06-28 04:06:33

您好！

谢老师请问，我主要是运用R语言的，主要是通过VS-code的上面的jupyter来调用服务器上面的R但是很多时候安装R包的时候例如：“seurat”时候显示no-zero ，但是在我本地电脑的R上面安装可以正常运行请问这个是什么原因？

祝：身体健康、工作顺利！

9 Comments

yihui 2023-06-28 09:57:54

出现 non-zero status 的可能性不唯一，所以很难讲，比如文件夹不可写、代码编译失败、缺少系统依赖，等等。没有更多错误信息了吗？

wangguiqian 2023-06-28 13:39:19

谢老师你看我有时候安装包的时候就是经常出现这样问题

yihui 2023-06-28 14:29:48

有些包是旧版本的 R 下面安装的，你升级 R 之后需要重装它们。

update.packages(ask = FALSE, checkBuilt = TRUE)

又及：能复制文本就复制文本粘贴出来，不需要截图。

wangguiqian 2023-06-28 13:57:43

例如当我再次安装这个包的时候就也会出现这样的问题，但是在我本地的电脑上的R的进行安装就没有问题，这个全部在通过VS-code远程连接Linux服务器使用R时出现问题

wangguiqian 2023-06-28 14:08:48

wangguiqian 2023-06-28 15:12:48

update.packages(ask = FALSE,checkBuilt = TRUE)

Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘cluster’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘collections’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘commonmark’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘curl’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘digest’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘fansi’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘fastmap’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘foreign’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘fs’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘jsonlite’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘KernSmooth’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘lattice’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘lazyeval’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘lpSolve’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘MASS’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘nnet’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘pbdZMQ’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘png’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘ps’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘Rcpp’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘rpart’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘spatial’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘stringi’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘utf8’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘vctrs’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘xfun’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘xml2’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘yaml’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘zip’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘class’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘tibble’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘lintr’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘pkgdepends’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘readxl’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘roxygen2’ had non-zero exit status”
Warning message in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
“installation of package ‘styler’ had non-zero exit status”
Updating HTML index of packages in '.Library'

Making 'packages.html' ...
done

yihui 2023-06-28 15:22:09

我不知道为什么所有的包都安装失败，你可以尝试只安装其中一个，看有没有更多错误信息，比如 install.packages('commonmark')。

wangguiqian 2023-06-28 15:26:39

install.packages("commonmark")

Warning message in install.packages("commonmark"):
“installation of package ‘commonmark’ had non-zero exit status”
Updating HTML index of packages in '.Library'

Making 'packages.html' ...
done

请问谢老师为什么会出现这个问题我使用本地电脑的R没有问题，但是使用远程服务器的R时总会出现这个问题

wangguiqian 2023-06-28 15:27:16

BiocManager::install(checkBuilt=TRUE)

Installing package(s) 'BiocVersion'

wangguiqian 2023-06-28 15:28:53

但是我使用conda安装就没有问题,conda install r-commonmark 就可以正常安装这个R包

yihui 2023-06-28 15:30:02

我不熟悉 Conda，它可能有它特殊的包的管理机制。

wangguiqian 2023-06-28 15:32:29

因为我主要使用VScode的来调用R的但是目前，我没有找到这个问题的解决方法，请问谢老师是否可以明天我找老师当面帮忙解决一下呢？我是华中农业大学的研究生，今天很荣幸参加老师您的报告

yihui 2023-06-28 23:52:59

嗯，等休息的时间我看看吧，但还是那句话，我对 Conda 不熟，不一定能帮到你。