Ubuntu中的分段错误导致RMongo安装失败

Question

过去几个小时，我一直试图安装RMongo包，输出如下：

> install.packages("RMongo")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
trying URL 'https://repo.bppt.go.id/cran/src/contrib/RMongo_0.0.25.tar.gz'
Content type 'application/x-gzip' length 4169519 bytes (4.0 MB)
==================================================
downloaded 4.0 MB

* installing *source* package ‘RMongo’ ...
** package ‘RMongo’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Segmentation fault (core dumped)
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/RMongo’

The downloaded source packages are in
    ‘/tmp/RtmpHZoomn/downloaded_packages’
Warning message:
In install.packages("RMongo") :
  installation of package ‘RMongo’ had non-zero exit status

我还发现了安装xlsx的相同错误。

我不知道在过去的发行版中发生了什么变化，因为我用Ubuntu16.04.2和Ubuntu17.04尝试了这个版本，结果是一样的。

这是对Ubuntu16.04.2发行版中R环境的描述：

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=es_ES.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=es_ES.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=es_ES.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C       
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
loaded via a namespace (and not attached):
[1] compiler_3.4.0 tools_3.4.0    tcltk_3.4.0

知道会发生什么吗？

Answer 1

linux 3.13.0-121-泛型和linux 4.4.0-81泛型包含堆栈冲突漏洞的修复。

小心内核更新，它修复了这个漏洞。当前的修补程序破坏了许多java (sun/oracle和openjdk)应用程序。见Bug #1699772: linux-映像-4.4.0-81-泛型，linux-映像-3.13.0-121-泛型回归:许多用户空间应用程序崩溃。解决方案是用旧内核临时重新启动系统(Linux-Image-3.13.0-119-在可靠的情况下通用)。

Ubuntu内核开发者几天后会准备新补丁。

更新：最新更新(至少图像-4.4.0-83-泛型，linux 4.8.0-58泛型，linux 4.10.0-26通用)修复了用户空间程序的漏洞和问题。

Answer 2

这并不能解决我在RMongo中遇到的问题，而是为我解决了这个问题，所以我希望它是有用的。

我一直在做一些测试。由于这个问题是在RMongo突然停止工作时开始的，并且考虑到我有一个正常工作的类似安装，我开始比较这两个环境。

我已经检查过，在失败的系统中，执行了一些软件更新(您可以在下面检查它们)：

The following NEW packages will be installed
  libmircommon7 libmircore1 linux-headers-4.4.0-81 linux-headers-4.4.0-81-generic linux-image-4.4.0-81-generic
  linux-image-extra-4.4.0-81-generic
The following packages will be upgraded:
  click firefox firefox-locale-en flashplugin-installer gir1.2-click-0.4 google-chrome-stable grub-common grub-pc
  grub-pc-bin grub2-common libc-bin libc-dev-bin libc6 libc6:i386 libc6-dbg libc6-dev libclick-0.4-0 libepoxy0
  libgnutls-openssl27 libgnutls30 libmirclient9 libmircookie2 libmirprotobuf3 libmwaw-0.3-3 libnss3 libnss3-nssdb
  libqt5concurrent5 libqt5core5a libqt5dbus5 libqt5gui5 libqt5network5 libqt5opengl5 libqt5printsupport5 libqt5sql5
  libqt5sql5-sqlite libqt5test5 libqt5widgets5 libqt5xml5 libssl-dev libssl-doc libssl1.0.0 libvlc5 libvlccore8
  libzzip-0-13 linux-firmware linux-headers-generic linux-image-generic linux-libc-dev locales multiarch-support
  openssl python3-click-package vlc vlc-data vlc-nox vlc-plugin-notify vlc-plugin-samba

因此，我已经逐一检查了这个包，结果发现问题的根源是新内核4.4.0-81。

为了确保这是问题的根源，我通过Ubuntu发行版启动了我笔记本中内核的早期版本：4.4.0-79

这是安装的结果：

> install.packages("RMongo")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
trying URL 'https://pbil.univ-lyon1.fr/CRAN/src/contrib/RMongo_0.0.25.tar.gz'
Content type 'application/x-gzip' length 4169519 bytes (4.0 MB)
==================================================
downloaded 4.0 MB

* installing *source* package ‘RMongo’ ...
** package ‘RMongo’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (RMongo)

The downloaded source packages are in
    ‘/tmp/RtmpJScKfz/downloaded_packages’
> install.packages("xlsx")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://pbil.univ-lyon1.fr/CRAN/src/contrib/xlsx_0.5.7.tar.gz'
Content type 'application/x-gzip' length 312839 bytes (305 KB)
==================================================
downloaded 305 KB

* installing *source* package ‘xlsx’ ...
** package ‘xlsx’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (xlsx)

The downloaded source packages are in
    ‘/tmp/RtmpJScKfz/downloaded_packages’

这两个包，xlsx和RMongo，现在都已成功安装和运行。

我还检查了xlsx和RMongo之间的关系，恐怕下面的问题是rJava (公共依赖项)。事实上，为了确定这一点，我对其他依赖于rJava的包(RWeka)进行了测试，并且在更改内核版本后解决了同样的问题。

==更新==

在上一次内核更新之后，从4.4.0-81到4.4.0-83，这个问题已经解决了。

Answer 3

同样的问题(至少对于包"xlsx")发生在Ubuntu14.04LTS中，内核为3.13.0-121-泛型。当使用前一个内核(3.13.0-119-泛型)启动时，安装工作和库加载。

更新:新内核3.13.0-123-泛型似乎解决了Ubuntu14.04LTS中的问题