RMongo安裝失敗，分段故障在Ubuntu

我已經爲過去的幾個小時試圖安裝RMongo包以下的輸出：RMongo安裝失敗，分段故障在Ubuntu

> 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

我也發現了同樣的錯誤嘗試安裝xlsx。

我不知道在過去的發行版中發生了什麼變化，因爲我已經在Ubuntu 16.04.2和Ubuntu 17.04上試了這個，結果相同。

這是R環境在Ubuntu 16.04.2發行說明：

> 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

什麼可以發生任何想法？

來源

2017-06-21 asuka

這並沒有回答我遇到的與RMongo相關的問題，但是爲我解決了這個問題，所以我希望它能夠有用。

我繼續做一些測試。由於這個問題是在RMongo突然停止工作時開始的，考慮到我有一個類似的工作正常，我開始比較兩種環境。

我檢查了，因爲出現故障，進行一些軟件更新系統（你可以在下面檢查它們）：

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

所以，我通過一個本包檢查之一，事實證明問題的根源在於新內核4.4.0-81。

爲了確保這是問題的根源，我已經被Ubuntu發行版推出了與以前的版本，我曾在我的筆記本電腦的內核：4.4.0-79

這是安裝的結果：

> 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’

兩種封裝，XLSX和RMongo，現已成功安裝並正常工作。

我還檢查XLSX和RMongo之間的關係，恐怕這個問題下面是rJava（常見應用）。事實上，爲了確保這一點，我已經用其他軟件包rJava相關的（RWeka）進行了測試，並且我遇到了同樣的問題，在更改內核版本後解決。

== == UPDATE

最後內核更新後，從4.4.0-81至4.4.0-83，該問題已得到修復。

來源

2017-06-22 12:27:51 asuka

同樣的問題（至少對於軟件包「xlsx」）發生在Ubuntu 14.04 LTS內核3.13.0-121-generic。使用以前的內核（3.13.0-119-generic）進行引導時，安裝工作並加載庫。

UPDATE：問題出現14.04 LTS的新內核3.13.0-123泛型

來源

2017-06-22 14:05:15

Debian和內核4.9.0-3-amd64在這裏也是一樣。 – vodka

的linux-image-3.13.0-121泛型和linux-圖像4.4.0-81在Ubuntu要解決-generic包含Stack Clash vulnerability的修復程序。

請注意使用內核更新來修復此漏洞。當前的補丁破壞了許多java（sun/oracle和openjdk）應用程序。見Bug #1699772: linux-image-4.4.0-81-generic, linux-image-3.13.0-121-generic Regression: many user-space apps crashing。解決方案是使用舊內核臨時重啓系統（在Trusty中爲linux-image-3.13.0-119-generic）。

Ubuntu內核開發者will prepare new patch in a few days。

更新：修復此漏洞修復此漏洞（至少image-4.4.0-83-generic，linux-image-4.8.0-58-generic，linux-image-4.10.0-26-generic）和用戶空間程序的問題。

來源

2017-06-24 16:36:59 N0rbert

最後一次內核更新後，從4.4.0-81到4.4.0-83，問題已修復。 – asuka

RMongo安裝失敗，分段故障在Ubuntu

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