
I think this is the fourth attempt to send this blessed message, so let's hope this gets through without any 'unprocessed' or 'ignored' in-lines on auto-reply.
I wish to report to you some strange problems I'm experiencing with installing packages directly into my -R- 2.15.1 (there is an indirect solution, which I note below). First, here's some essential information:
> sessionInfo()R version 2.15.1 (2012-06-22)
Platform: i686-pc-linux-gnu (32-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8       
 [4] LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] tools_2.15.1
Essentially, some packages are installing 'at the front end' and some are not, but this has only been happening since I re-enabled the 'other software sources' inside the Muon Software Centre settings on my Kubuntu 12.04 OS (I only discovered earlier this month that they are always disabled when Kubuntu upgrades to the next full version). Fixing this automatically triggered the updates for the latest version of -R- (successfully installed), but when I then attempted to install the -lme4- package shortly afterwards
> install.packages("lme4")Installing package(s) into ‘/home/clive/R/i686-pc-linux-gnu-library/2.15’(as ‘lib’ is unspecified)trying URL 'http://cran.ma.imperial.ac.uk/src/contrib/lme4_0.999999-0.tar.gz'Content type 'application/x-gzip' length 1074142 bytes (1.0 Mb)opened URL==================================================downloaded 1.0 Mb
* installing *source* package ‘lme4’ ...** package ‘lme4’ successfully unpacked and MD5 sums checked** libs/usr/share/R/share/make/shlib.mk:6: warning: overriding commands for target `lme4.so'Makevars:7: warning: ignoring old commands for target `lme4.so'gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/usr/lib/R/library/Matrix/include" -I"/usr/lib/R/library/stats/include"   -fpic  -O3 -pipe  -g  -c init.c -o init.ogcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/usr/lib/R/library/Matrix/include" -I"/usr/lib/R/library/stats/include"   -fpic  -O3 -pipe  -g  -c lmer.c -o lmer.ogcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/usr/lib/R/library/Matrix/include" -I"/usr/lib/R/library/stats/include"   -fpic  -O3 -pipe  -g  -c local_stubs.c -o local_stubs.ogcc -std=gnu99 -shared -o lme4.so init.o lmer.o local_stubs.o -llapack -lblas -lgfortran -lm -L/usr/lib/R/lib -lR/usr/bin/ld: cannot find -llapack/usr/bin/ld: cannot find -lblas/usr/bin/ld: cannot find -lgfortrancollect2: ld returned 1 exit statusmake: *** [lme4.so] Error 1ERROR: compilation failed for package ‘lme4’* removing ‘/home/clive/R/i686-pc-linux-gnu-library/2.15/lme4’Warning in install.packages :  installation of package ‘lme4’ had non-zero exit status
The downloaded source packages are in	‘/tmp/RtmpUFK3Hz/downloaded_packages’
it failed. It also failed for -rms-
> install.packages("rms")Installing package(s) into ‘/home/clive/R/i686-pc-linux-gnu-library/2.15’(as ‘lib’ is unspecified)also installing the dependency ‘Hmisc’
trying URL 'http://cran.ma.imperial.ac.uk/src/contrib/Hmisc_3.9-3.tar.gz'Content type 'application/x-gzip' length 573945 bytes (560 Kb)opened URL==================================================downloaded 560 Kb
trying URL 'http://cran.ma.imperial.ac.uk/src/contrib/rms_3.5-0.tar.gz'Content type 'application/x-gzip' length 368054 bytes (359 Kb)opened URL==================================================downloaded 359 Kb
* installing *source* package ‘Hmisc’ ...** package ‘Hmisc’ successfully unpacked and MD5 sums checked** libsgcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c Hmisc.c -o Hmisc.ogfortran   -fpic  -O3 -pipe  -g  -c cidxcn.f -o cidxcn.o/bin/bash: gfortran: command not foundmake: *** [cidxcn.o] Error 127ERROR: compilation failed for package ‘Hmisc’* removing ‘/home/clive/R/i686-pc-linux-gnu-library/2.15/Hmisc’Warning in install.packages :  installation of package ‘Hmisc’ had non-zero exit statusERROR: dependency ‘Hmisc’ is not available for package ‘rms’* removing ‘/home/clive/R/i686-pc-linux-gnu-library/2.15/rms’Warning in install.packages :  installation of package ‘rms’ had non-zero exit status
The downloaded source packages are in	‘/tmp/RtmpUFK3Hz/downloaded_packages’
and for -lmtest-
> install.packages("lmtest")Installing package(s) into ‘/home/clive/R/i686-pc-linux-gnu-library/2.15’(as ‘lib’ is unspecified)trying URL 'http://cran.ma.imperial.ac.uk/src/contrib/lmtest_0.9-30.tar.gz'Content type 'application/x-gzip' length 176106 bytes (171 Kb)opened URL==================================================downloaded 171 Kb
* installing *source* package ‘lmtest’ ...** package ‘lmtest’ successfully unpacked and MD5 sums checked** libsgfortran   -fpic  -O3 -pipe  -g  -c pan.f -o pan.o/bin/bash: gfortran: command not foundmake: *** [pan.o] Error 127ERROR: compilation failed for package ‘lmtest’* removing ‘/home/clive/R/i686-pc-linux-gnu-library/2.15/lmtest’Warning in install.packages :  installation of package ‘lmtest’ had non-zero exit status
The downloaded source packages are in	‘/tmp/RtmpUFK3Hz/downloaded_packages’
It did, however, work for -car-> install.packages("car")Installing package(s) into ‘/home/clive/R/i686-pc-linux-gnu-library/2.15’(as ‘lib’ is unspecified)trying URL 'http://cran.ma.imperial.ac.uk/src/contrib/car_2.0-12.tar.gz'Content type 'application/x-gzip' length 319291 bytes (311 Kb)opened URL==================================================downloaded 311 Kb* installing *source* package ‘car’ ...** package ‘car’ successfully unpacked and MD5 sums checked** R** data**  moving datasets to lazyload DB** inst** byte-compile and prepare package for lazy loading** help*** installing help indices** building package indices** testing if installed package can be loaded* DONE (car)The downloaded source packages are in        ‘/tmp/RtmpHQHTwB/downloaded_packages’
and for -ggplot2- (output much too long to include here!). This has never happened to me in all the years I have casually used -R-, either on Windows or Linux. This problem is now occurring regardless of whether I use RStudio, as I am currently (v0.96.304), or when running -R- from the Konsole terminal; although this would be perhaps unsurprising to you. All of the above attempts had the option to install dependencies selected.
Now, after rifling the list archives, I found that the following post
https://stat.ethz.ch/pipermail/r-sig-debian/2011-November/001711.html
pointed to a solution from the terminal, which worked:
clive@clivubu:~$ sudo apt-get install r-cran-lme4[sudo] password for clive: Reading package lists... DoneBuilding dependency tree       Reading state information... DoneThe following NEW packages will be installed  r-cran-lme40 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.Need to get 1,231 kB of archives.After this operation, 1,634 kB of additional disk space will be used.Get:1 http://gb.archive.ubuntu.com/ubuntu/ precise/universe r-cran-lme4 i386 0.999375-42-1 [1,231 kB]Fetched 1,231 kB in 3s (335 kB/s)        Selecting previously unselected package r-cran-lme4.(Reading database ... 199646 files and directories currently installed.)Unpacking r-cran-lme4 (from .../r-cran-lme4_0.999375-42-1_i386.deb) ...Setting up r-cran-lme4 (0.999375-42-1) ...
clive@clivubu:~$ sudo apt-get install r-cran-lmtestReading package lists... DoneBuilding dependency tree       Reading state information... DoneThe following extra packages will be installed:  r-cran-zooThe following NEW packages will be installed  r-cran-lmtest r-cran-zoo0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.Need to get 1,761 kB of archives.After this operation, 2,207 kB of additional disk space will be used.Do you want to continue [Y/n]? yGet:1 http://gb.archive.ubuntu.com/ubuntu/ precise/universe r-cran-zoo i386 1.7-6-1 [1,389 kB]Get:2 http://gb.archive.ubuntu.com/ubuntu/ precise/universe r-cran-lmtest i386 0.9.29-1 [372 kB]Fetched 1,761 kB in 3s (471 kB/s)      Selecting previously unselected package r-cran-zoo.(Reading database ... 199695 files and directories currently installed.)Unpacking r-cran-zoo (from .../r-cran-zoo_1.7-6-1_i386.deb) ...Selecting previously unselected package r-cran-lmtest.Unpacking r-cran-lmtest (from .../r-cran-lmtest_0.9.29-1_i386.deb) ...Setting up r-cran-zoo (1.7-6-1) ...Setting up r-cran-lmtest (0.9.29-1) ...
clive@clivubu:~$ sudo apt-get install r-cran-rmsReading package lists... DoneBuilding dependency tree                                                                                                                                                            Reading state information... Done                                                                                                                                                   The following extra packages will be installed:                                                                                                                                       r-cran-chron r-cran-hmisc                                                                                                                                                         The following NEW packages will be installed                                                                                                                                          r-cran-chron r-cran-hmisc r-cran-rms                                                                                                                                              0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded.Need to get 2,394 kB of archives.After this operation, 2,768 kB of additional disk space will be used.Do you want to continue [Y/n]? yGet:1 http://gb.archive.ubuntu.com/ubuntu/ precise/universe r-cran-chron i386 2.3-42-1 [87.4 kB]Get:2 http://gb.archive.ubuntu.com/ubuntu/ precise/universe r-cran-hmisc i386 3.9-0-1 [1,395 kB]Get:3 http://gb.archive.ubuntu.com/ubuntu/ precise/universe r-cran-rms i386 3.3-3-1 [911 kB]Fetched 2,394 kB in 6s (385 kB/s)                                                                                                                                                  Selecting previously unselected package r-cran-chron.(Reading database ... 199800 files and directories currently installed.)Unpacking r-cran-chron (from .../r-cran-chron_2.3-42-1_i386.deb) ...Selecting previously unselected package r-cran-hmisc.Unpacking r-cran-hmisc (from .../r-cran-hmisc_3.9-0-1_i386.deb) ...Selecting previously unselected package r-cran-rms.Unpacking r-cran-rms (from .../r-cran-rms_3.3-3-1_i386.deb) ...Setting up r-cran-chron (2.3-42-1) ...Setting up r-cran-hmisc (3.9-0-1) ...Setting up r-cran-rms (3.3-3-1) ...
That's good, but the question which now remains is simply this: why are some packages not loading via -install.packages()- when others do? Has anyone else experienced this difficulty? 
I can only hope and trust that any list members reading this have spotted some crucial nugget(s) of information in the output I have provided to suggest an answer.
Many thanks.
Yours, Clive Nicholas 		 	   		  
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