Question

尝试在Ubuntu 10.04上安装xcms时，我一直遇到依赖性问题。目前我正在从源代码安装xcms。

这是跟踪： rob @ rob-desktop：〜/桌面$ sudo R CMD INSTALL xcms / *安装到库'/home/rob/R/x86_64-pc-linux-gnu-library/2.10'

* installing *source* package ‘xcms’ ...
** libs
rm -f massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o
g++ -I/usr/share/R/include      -fpic  -g -O2 -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
massifquant/xcms_massifquant.cpp: In function ‘SEXPREC* massifquant(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
massifquant/xcms_massifquant.cpp:120: warning: deprecated conversion from string constant to ‘char*’
massifquant/xcms_massifquant.cpp:120: warning: deprecated conversion from string constant to ‘char*’
massifquant/xcms_massifquant.cpp:120: warning: deprecated conversion from string constant to ‘char*’
massifquant/xcms_massifquant.cpp:120: warning: deprecated conversion from string constant to ‘char*’
massifquant/xcms_massifquant.cpp:120: warning: deprecated conversion from string constant to ‘char*’
massifquant/xcms_massifquant.cpp:120: warning: deprecated conversion from string constant to ‘char*’
massifquant/xcms_massifquant.cpp:120: warning: deprecated conversion from string constant to ‘char*’
g++ -I/usr/share/R/include      -fpic  -g -O2 -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
g++ -I/usr/share/R/include      -fpic  -g -O2 -c massifquant/Tracker.cpp -o massifquant/Tracker.o
g++ -I/usr/share/R/include      -fpic  -g -O2 -c massifquant/SegProc.cpp -o massifquant/SegProc.o
massifquant/SegProc.cpp: In member function ‘double SegProc::Rf_pt(double, double, int, int)’:
massifquant/SegProc.cpp:361: warning: deprecated conversion from string constant to ‘char*’
g++ -I/usr/share/R/include      -fpic  -g -O2 -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
g++ -I/usr/share/R/include      -fpic  -g -O2 -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
g++ -I/usr/share/R/include      -fpic  -g -O2 -c obiwarp/mat.cpp -o obiwarp/mat.o
g++ -I/usr/share/R/include      -fpic  -g -O2 -c obiwarp/vec.cpp -o obiwarp/vec.o
g++ -I/usr/share/R/include      -fpic  -g -O2 -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
g++ -I/usr/share/R/include      -fpic  -g -O2 -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++ -I/usr/share/R/include      -fpic  -g -O2 -c xcms_obiwarp.cpp -o xcms_obiwarp.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c fastMatch.c -o fastMatch.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c mzClust_hclust.c -o mzClust_hclust.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c mzROI.c -o mzROI.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c util.c -o util.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c xcms.c -o xcms.o
g++ -shared -o xcms.so massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o -L/usr/lib64/R/lib -lR
** R
** inst
** preparing package for lazy loading
Error : package 'mzR' required by 'xcms' could not be found
ERROR: lazy loading failed for package ‘xcms’
* removing ‘/home/rob/R/x86_64-pc-linux-gnu-library/2.10/xcms’
* restoring previous ‘/home/rob/R/x86_64-pc-linux-gnu-library/2.10/xcms’

所以我用Google搜索了一段时间来试图弄清楚如何安装mzR。

我试图打开R并使用：

源（ “http://bioconductor.org/biocLite.R”） biocLite（ “MZR”）

让我：使用R版本2.10.1，biocinstall版本2.5.11。安装Bioconductor 2.5版软件包： [1]“mzR” 请等一下......

install.packages中的警告（pkgs = pkgs，repos = repos，...）：缺少参数'lib'：使用'/home/rob/R/x86_64-pc-linux-gnu-library/2.10' 警告信息：在getDependencies（pkgs，dependencies，available，lib）中：包'mzR'不可用

任何线索？

Answer 1

一些快速的：

Ubuntu 10.04已有两年半的历史了。也许您想考虑升级？
R 2.10.1也是那么老。你总是想要升级。通过查看任何CRAN镜像上的src/bin/linux/ubuntu/，您可以轻松地升级它。
mzR取决于我们的Rcpp包
Rcpp，如果你想要最近的版本，需要最近的R.所以如果我是你，我真的会升级R.

Answer 2

除了Dirk的回答，请注意mzR需要更新版本的R和Bioconductor;自BioC 2.9（R-2.14）以来mzR已经可用。通常，建议使用最新的R进行Bioc使用。

mzR封装不可用Bioconductor，试图安装xcms

2 个答案: