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/lme4Warning 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/HmiscWarning 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/rmsWarning 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/lmtestWarning 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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