要学会say no / 开普饭

最近在更新一个R包的时候，发生了如下所示的报错：

3: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ' hdf5r ’ had non-zero exit status 4: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ' RcppArmadillo ’ had non-zero exit status

既然 hdf5r 和 RcppArmadillo包报错了，就先安装它们，首先是hdf5r ，第一次尝试安装它：

> BiocManager::install('hdf5r') 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details


replacement repositories:

    CRAN: https://cran.rstudio.com/
Bioconductor version 3.11 (BiocManager 1.30.12), R 4.0.2 (2020-06-22)

Installing package(s) 'hdf5r'

There is a binary version available but the source version is later: binary source needs_compilation hdf5r 1.3.2 1.3.3 TRUE # 在这里不小心选择了yes Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes installing the source package 'hdf5r’

然后可怕的事情就出来了：

configure: error: hdf5 does not seem to be installed on your platform. Please install the hdf5 library. The required HDF5 library files can be installed as follows: - Debian-based (e.g. Debian >= 8.0, Ubuntu >= 15.04): 'sudo apt-get install libhdf5-dev' - Old Debian-based (e.g Debian < 8.0, Ubuntu < 15.04): Install from source (see INSTALL) - OS X using Homebrew: 'brew install hdf5' - RPM-based (e.g Fedora): 'sudo yum install hdf5-devel' ERROR: configuration failed for package 'hdf5r’ * removing '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/hdf5r’ * restoring previous '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/hdf5r’

我看了看我的系统，再次尝试 brew install hdf5 ，然后又是一堆报错：

==> Summary 🍺 /usr/local/Cellar/gcc/10.2.0_4: 1,465 files, 339.5MB ==> Installing hdf5 dependency: szip ==> Pouring szip--2.1.1_1.big_sur.bottle.tar.gz 🍺 /usr/local/Cellar/szip/2.1.1_1: 11 files, 143.1KB ==> Installing hdf5 ==> Pouring hdf5--1.12.0_3.big_sur.bottle.tar.gz

Error: Permission denied @ apply2files - /usr/local/lib/docker/cli-plugins

在这样的报错的纠结中，我回忆起来了以前其实遇到过这样的问题：

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) no trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/hdf5r_1.3.2.tgz' Content type 'application/x-gzip' length 5041178 bytes (4.8 MB) ================================================== downloaded 4.8 MB


The downloaded binary packages are in

 /var/folders/2x/l4fzfvy17gz94j1sz6klhyjh0000gn/T//RtmpeVVDPq/downloaded_packages

Old packages: 'hdf5r', 'RcppArmadillo'

Update all/some/none? [a/s/n]: 

n

> library(hdf5r)

Attaching package: 'hdf5r’

也就是说在最开始面临是否编译的选择，只需要选择no就好了：

Do you want to install from sources the package which needs compilation? (Yes/no/cancel)

要学会say no

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