mzR package not available Bioconductor, trying to install xcms

0
votes

I keep hitting dependency issues when trying to install xcms on Ubuntu 10.04. With the current tack i'm installing xcms from source.

Here is the trace: rob@rob-desktop:~/Desktop$ sudo R CMD INSTALL xcms/ * installing to library ‘/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’

So I googled for a while to try to figure out how to install mzR.

I tried to open R and use:

source("http://bioconductor.org/biocLite.R") biocLite("mzR")

which gets me: Using R version 2.10.1, biocinstall version 2.5.11. Installing Bioconductor version 2.5 packages: [1] "mzR" Please wait...

Warning in install.packages(pkgs = pkgs, repos = repos, ...) : argument 'lib' is missing: using '/home/rob/R/x86_64-pc-linux-gnu-library/2.10' Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ‘mzR’ is not available

Any clues?

2
rbioconductor
FYI I am aware of this post, but note that the rebuild in question is not working in this case. stackoverflow.com/questions/11181691/… – user1385440
Please edit your question rather than adding a comment. You can then delete the comment. – Dirk Eddelbuettel

2 Answers

2
votes

A few quick ones:

  • Ubuntu 10.04 is two-and-a-half years old. Maybe you want to consider upgrading?

  • R 2.10.1 is also that old. You always surely want to upgrade. You can upgrade this rather painlessly by looking at src/bin/linux/ubuntu/ on any CRAN mirror.

  • mzR depends on our Rcpp package

  • Rcpp, if you want recent version, requires a recent R. So I would really upgrade R if I were you.

0
votes

In addition to Dirk's answer, note that mzR requires a more recent version of R and Bioconductor; mzR has been available since BioC 2.9 (R-2.14). In general, it is advised to use the latest R for Bioc usage.