在 Google Colab 中使用 R 库 sf

Question

我正在尝试使用 R 在 Google Colab 中绘制等值线图。

在网上搜索提示后，我发现必须使用库 sf。但是，我发现在Colab上很难安装和调用它。

如果我写：

install.packages("sf")

几分钟后，出现以下错误：

Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)

also installing the dependencies ‘proxy’, ‘e1071’, ‘wk’, ‘classInt’, ‘Rcpp’, ‘s2’, ‘units’


Warning message in install.packages("sf"):
“installation of package ‘units’ had non-zero exit status”
Warning message in install.packages("sf"):
“installation of package ‘sf’ had non-zero exit status”

尽管如此，我在 GitHub (sf installation on google colab throws errors #1572) 中找到了解决方案：

system('sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable')
system('sudo apt-get update')
system('sudo apt-get install libudunits2-dev libgdal-dev libgeos-dev libproj-dev')
install.packages('sf')

这次没有错误。

然而，在调用库（library(sf)）时，出现了新的错误：

Error: package or namespace load failed for ‘sf’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/usr/local/lib/R/site-library/sf/libs/sf.so':
  /usr/lib/libgdal.so.26: undefined symbol: GEOSMakeValid_r
Traceback:

1. library(sf)
2. tryCatch({
 .     attr(package, "LibPath") <- which.lib.loc
 .     ns <- loadNamespace(package, lib.loc)
 .     env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
 . }, error = function(e) {
 .     P <- if (!is.null(cc <- conditionCall(e))) 
 .         paste(" in", deparse(cc)[1L])
 .     else ""
 .     msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
 .         sQuote(package), P, conditionMessage(e))
 .     if (logical.return && !quietly) 
 .         message(paste("Error:", msg), domain = NA)
 .     else stop(msg, call. = FALSE, domain = NA)
 . })
3. tryCatchList(expr, classes, parentenv, handlers)
4. tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. value[[3L]](cond)
6. stop(msg, call. = FALSE, domain = NA)

知道如何解决吗？

谢谢！

Answer 1

感谢 GitHub 用户，我找到了解决方案 (Calling sf on google colab throws errors)

您应该安装 sf 而无需在新的协作笔记本中添加 ubuntugis 存储库：

system("apt-get -y update")
system("apt-get install -y libudunits2-dev libgdal-dev libgeos-dev libproj-dev")
install.packages("sf")
library("sf")

然后没有错误出现：

Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)

also installing the dependencies ‘proxy’, ‘e1071’, ‘wk’, ‘classInt’, ‘Rcpp’, ‘s2’, ‘units’


Linking to GEOS 3.8.0, GDAL 3.0.4, PROJ 7.0.0; sf_use_s2() is TRUE

在 Google Colab 中使用 R 库 sf

Using R library sf in Google Colab

r

sf