To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("mcaGUI")
Note: R version >= 2.13
..........................
g++ -shared -L/usr/local/lib64 -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o alphabet.o io.o io_bowtie.o io_soap.o pileup.o readBfaToc.o read_maq_map.o sampler.o util.o xsnap.o -lz
安装至 /home/shenzy/R/x86_64-pc-linux-gnu-library/R-2.13.1/library/ShortRead/libs
** R
** inst
** preparing package for lazy loading
Attaching package: ‘IRanges’
The following object(s) are masked from ‘package:base':
Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
pmin, pmin.int, rbind, rep.int, setdiff, table, union
警告: Class “AssayData” is defined (with package slot ‘Biobase’) but no metadata object found to revise subclass information—not exported? Making a copy in package ‘ShortRead’
** help
*** installing help indices
** building package indices …
** testing if installed package can be loaded
* DONE (ShortRead)
* installing *source* package ‘OTUbase’ …
** R
** inst
** preparing package for lazy loading
Loading required package: IRanges
Attaching package: ‘IRanges’
The following object(s) are masked from ‘package:base':
Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
pmin, pmin.int, rbind, rep.int, setdiff, table, union
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: lattice
Loading required package: Rsamtools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
‘browseVignettes()’. To cite Bioconductor, see
‘citation(“Biobase”)’ and for packages ‘citation(“pkgname”)’.
Attaching package: ‘Biobase’
The following object(s) are masked from ‘package:IRanges':
updateObject
Loading required package: permute
This is vegan 2.0-4
** help
*** installing help indices
** building package indices …
** testing if installed package can be loaded
================================================================================
Welcome to OTUbase version 1.2.0
* DONE (OTUbase)
ERROR: dependency ‘gWidgetsRGtk2’ is not available for package ‘mcaGUI’
* removing ‘/home/shenzy/R/x86_64-pc-linux-gnu-library/R-2.13.1/library/mcaGUI’
The downloaded packages are in
‘/tmp/RtmpvRkW92/downloaded_packages’
Updating HTML index of packages in ‘.Library’
Making packages.html … done
警告信息：
1: In install.packages(pkgs = pkgs, repos = repos, …) :
installation of package ‘RGtk2′ had non-zero exit status
2: In install.packages(pkgs = pkgs, repos = repos, …) :
installation of package ‘gWidgetsRGtk2′ had non-zero exit status
3: In install.packages(pkgs = pkgs, repos = repos, …) :
installation of package ‘mcaGUI’ had non-zero exit status
> biocLite(“gWidgetsRGtk2″)
Using R version 2.13.1, biocinstall version 2.8.4.
Installing Bioconductor version 2.8 packages:
[1] “gWidgetsRGtk2″
Please wait…
also installing the dependency ‘RGtk2’
试开URL’http://cran.fhcrc.org/src/contrib/RGtk2_2.20.24.tar.gz’
Content type ‘application/x-gzip’ length 2784958 bytes (2.7 Mb)
打开了URL
==================================================
downloaded 2.7 Mb
试开URL’http://cran.fhcrc.org/src/contrib/gWidgetsRGtk2_0.0-81.tar.gz’
Content type ‘application/x-gzip’ length 168332 bytes (164 Kb)
打开了URL
==================================================
downloaded 164 Kb
* installing *source* package ‘RGtk2’ …
checking for pkg-config… /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0… yes
checking for INTROSPECTION… no
checking for GTK… no
configure: error: GTK version 2.8.0 required
ERROR: configuration failed for package ‘RGtk2’
* removing ‘/home/shenzy/R/x86_64-pc-linux-gnu-library/R-2.13.1/library/RGtk2’
ERROR: dependency ‘RGtk2’ is not available for package ‘gWidgetsRGtk2’
* removing ‘/home/shenzy/R/x86_64-pc-linux-gnu-library/R-2.13.1/library/gWidgetsRGtk2’
The downloaded packages are in
‘/tmp/RtmpvRkW92/downloaded_packages’
Updating HTML index of packages in ‘.Library’
Making packages.html … done
> biocLite(“RGtk2″)
Using R version 2.13.1, biocinstall version 2.8.4.
Installing Bioconductor version 2.8 packages:
[1] “RGtk2″
Please wait…
you should also install r-cran-rgtk2 and libgtk2.0-dev
> biocLite(“RGtk2″)
tk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lm -lcairo -lpng12 -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lrt -lglib-2.0 -pthread -lgthread-2.0 -lrt -lglib-2.0
安装至 /home/shenzy/R/x86_64-pc-linux-gnu-library/R-2.13.1/library/RGtk2/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices …
** testing if installed package can be loaded
* DONE (RGtk2)
The downloaded packages are in
‘/tmp/RtmpvRkW92/downloaded_packages’
Updating HTML index of packages in ‘.Library’
> biocLite(“gWidgetsRGtk2″)
….
* DONE (gWidgetsRGtk2)
The downloaded packages are in
‘/tmp/RtmpvRkW92/downloaded_packages’
Updating HTML index of packages in ‘.Library’
Making packages.html … done
> biocLite(“mcaGUI”)
Using R version 2.13.1, biocinstall version 2.8.4.
Installing Bioconductor version 2.8 packages:
[1] “mcaGUI”
Please wait…
…..
================================================================================
Welcome to OTUbase version 1.2.0
Loading mcaGUI()
[1] “You can access the mcaGUI vignette by browsing to: ”
[1] “/home/shenzy/R/x86_64-pc-linux-gnu-library/R-2.13.1/library/mcaGUI/doc/An_Introduction_and_User_Guide_for_mcaGUI.pdf”
GUI requires an interactive environment
* DONE (mcaGUI)
The downloaded packages are in
‘/tmp/RtmpvRkW92/downloaded_packages’
Updating HTML index of packages in ‘.Library’
Making packages.html … done
SUCCESS !!!!!
> library(“mcaGUI”)
载入需要的程辑包：lattice
载入需要的程辑包：MASS
载入需要的程辑包：proto
载入需要的程辑包：foreign
载入需要的程辑包：gWidgets
载入需要的程辑包：gWidgetsRGtk2
载入需要的程辑包：OTUbase
载入需要的程辑包：ShortRead
载入需要的程辑包：BiocGenerics
…..
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