Tinypliny's Journal

08/17/2011 12:53 #54967

Install R on debian without an internet connection.
Category: linux

R needs all these packages to install on debian. So essentially, if my /var/cache/apt/archives/ had these packages already then it wouldn't need to download anything from the net. With these packages already there, R would install instantly without need for an internet connection.

This is the r-base install procedure on debian output from the terminal.

Unpacking liberror-perl (from .../liberror-perl_0.17-1_all.deb) ...
Selecting previously deselected package git.
Unpacking git (from .../git_1%3a1.7.2.5-2_amd64.deb) ...
Selecting previously deselected package autopoint.
Unpacking autopoint (from .../autopoint_0.18.1.1-3_all.deb) ...
Selecting previously deselected package autotools-dev.
Unpacking autotools-dev (from .../autotools-dev_20100122.1_all.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-3_amd64.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_amd64.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
Selecting previously deselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
Selecting previously deselected package dpatch.
Unpacking dpatch (from .../archives/dpatch_2.0.31_all.deb) ...
Selecting previously deselected package gfortran-4.4.
Unpacking gfortran-4.4 (from .../gfortran-4.4_4.4.5-8_amd64.deb) ...
Selecting previously deselected package gfortran.
Unpacking gfortran (from .../gfortran_4%3a4.4.5-1_amd64.deb) ...
Selecting previously deselected package libblas-dev.
Unpacking libblas-dev (from .../libblas-dev_1.2-8_amd64.deb) ...
Selecting previously deselected package libbz2-dev.
Unpacking libbz2-dev (from .../libbz2-dev_1.0.5-6_amd64.deb) ...
Selecting previously deselected package libjpeg62-dev.
Unpacking libjpeg62-dev (from .../libjpeg62-dev_6b1-1_amd64.deb) ...
Selecting previously deselected package liblapack-dev.
Unpacking liblapack-dev (from .../liblapack-dev_3.2.1-8_amd64.deb) ...
Selecting previously deselected package libsys-hostname-long-perl.
Unpacking libsys-hostname-long-perl (from .../libsys-hostname-long-perl_1.4-2_all.deb) ...
Selecting previously deselected package libmail-sendmail-perl.
Unpacking libmail-sendmail-perl (from .../libmail-sendmail-perl_0.79.16-1_all.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_amd64.deb) ...
Selecting previously deselected package libpcrecpp0.
Unpacking libpcrecpp0 (from .../libpcrecpp0_8.02-1.1_amd64.deb) ...
Selecting previously deselected package libpcre3-dev.
Unpacking libpcre3-dev (from .../libpcre3-dev_8.02-1.1_amd64.deb) ...
Preparing to replace libpng12-0 1.2.44-1 (using .../libpng12-0_1.2.44-1+squeeze1_amd64.deb) ...
Unpacking replacement libpng12-0 ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_amd64.deb) ...
Selecting previously deselected package libpng12-dev.
Unpacking libpng12-dev (from .../libpng12-dev_1.2.44-1+squeeze1_amd64.deb) ...
Selecting previously deselected package libreadline6-dev.
Unpacking libreadline6-dev (from .../libreadline6-dev_6.1-3_amd64.deb) ...
Selecting previously deselected package libreadline-dev.
Unpacking libreadline-dev (from .../libreadline-dev_6.1-3_amd64.deb) ...
Selecting previously deselected package patchutils.
Unpacking patchutils (from .../patchutils_0.3.1-2_amd64.deb) ...
Selecting previously deselected package tcl8.5.
Unpacking tcl8.5 (from .../tcl8.5_8.5.8-2_amd64.deb) ...
Selecting previously deselected package tk8.5.
Unpacking tk8.5 (from .../tk8.5_8.5.8-1_amd64.deb) ...
Selecting previously deselected package r-base-core.
Unpacking r-base-core (from .../r-base-core_2.13.1-1~squeezecran.0_amd64.deb) ...
Selecting previously deselected package r-cran-boot.
Unpacking r-cran-boot (from .../r-cran-boot_1.3-2-1~squeezecran.2.13.1_all.deb) ...
Selecting previously deselected package r-cran-cluster.
Unpacking r-cran-cluster (from .../r-cran-cluster_1.14.0-1~squeezecran.2.13.1_amd64.deb) ...
Selecting previously deselected package r-cran-foreign.
Unpacking r-cran-foreign (from .../r-cran-foreign_0.8.44-1~squeezecran.2.13.1_amd64.deb) ...
Selecting previously deselected package r-cran-mass.
Unpacking r-cran-mass (from .../r-cran-mass_7.3-13-1~squeezecran.2.13.1_amd64.deb) ...
Selecting previously deselected package r-cran-kernsmooth.
Unpacking r-cran-kernsmooth (from .../r-cran-kernsmooth_2.23-6-1~squeezecran.2.13.1_amd64.deb) ...
Selecting previously deselected package r-cran-lattice.
Unpacking r-cran-lattice (from .../r-cran-lattice_0.19-30-1~squeezecran.2.13.1_amd64.deb) ...
Selecting previously deselected package r-cran-nlme.
Unpacking r-cran-nlme (from .../r-cran-nlme_3.1.101-1~squeezecran.2.13.1_amd64.deb) ...
Selecting previously deselected package r-cran-matrix.
Unpacking r-cran-matrix (from .../r-cran-matrix_0.999375-50-1~squeezecran.2.13.1_amd64.deb) ...
Selecting previously deselected package r-cran-mgcv.
Unpacking r-cran-mgcv (from .../r-cran-mgcv_1.7-6-1~squeezecran.2.13.1_amd64.deb) ...
Selecting previously deselected package r-cran-survival.
Unpacking r-cran-survival (from .../r-cran-survival_2.36-9-1~squeezecran.2.13.1_amd64.deb) ...
Selecting previously deselected package r-cran-rpart.
Unpacking r-cran-rpart (from .../r-cran-rpart_3.1.50-1~squeezecran.2.13.1_amd64.deb) ...
Selecting previously deselected package r-cran-class.
Unpacking r-cran-class (from .../r-cran-class_7.3-3-1~squeezecran.2.13.1_amd64.deb) ...
Selecting previously deselected package r-cran-nnet.
Unpacking r-cran-nnet (from .../r-cran-nnet_7.3-1-1~squeezecran.2.13.1_amd64.deb) ...
Selecting previously deselected package r-cran-spatial.
Unpacking r-cran-spatial (from .../r-cran-spatial_7.3-2-1~squeezecran.2.13.1_amd64.deb) ...
Selecting previously deselected package r-cran-codetools.
Unpacking r-cran-codetools (from .../r-cran-codetools_0.2-8-1~squeezecran.2.13.1_all.deb) ...
Selecting previously deselected package r-recommended.
Unpacking r-recommended (from .../r-recommended_2.13.1-1~squeezecran.0_all.deb) ...
Selecting previously deselected package r-base.
Unpacking r-base (from .../r-base_2.13.1-1~squeezecran.0_all.deb) ...
Selecting previously deselected package r-base-dev.
Unpacking r-base-dev (from .../r-base-dev_2.13.1-1~squeezecran.0_all.deb) ...
Selecting previously deselected package r-doc-html.
Unpacking r-doc-html (from .../r-doc-html_2.13.1-1~squeezecran.0_all.deb) ...
Selecting previously deselected package r-base-html.
Unpacking r-base-html (from .../r-base-html_2.13.1-1~squeezecran.0_all.deb) ...
Processing triggers for man-db ...
Processing triggers for install-info ...
Processing triggers for menu ...
Setting up liberror-perl (0.17-1) ...
Setting up git (1:1.7.2.5-2) ...
Setting up autopoint (0.18.1.1-3) ...
Setting up autotools-dev (20100122.1) ...
Setting up html2text (1.3.2a-15) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.0.0) ...
Setting up cdbs (0.4.89) ...
Setting up dpatch (2.0.31) ...
Setting up gfortran-4.4 (4.4.5-8) ...
Setting up gfortran (4:4.4.5-1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode.
Setting up libblas-dev (1.2-8) ...
update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode.
Setting up libbz2-dev (1.0.5-6) ...
Setting up libjpeg62-dev (6b1-1) ...
Setting up liblapack-dev (3.2.1-8) ...
update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode.
Setting up libsys-hostname-long-perl (1.4-2) ...
Setting up libmail-sendmail-perl (0.79.16-1) ...
Setting up libncurses5-dev (5.7+20100313-5) ...
Setting up libpcrecpp0 (8.02-1.1) ...
Setting up libpcre3-dev (8.02-1.1) ...
Setting up libpng12-0 (1.2.44-1+squeeze1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Setting up libpng12-dev (1.2.44-1+squeeze1) ...
Setting up libreadline6-dev (6.1-3) ...
Setting up libreadline-dev (6.1-3) ...
Setting up patchutils (0.3.1-2) ...
Setting up tcl8.5 (8.5.8-2) ...
Setting up tk8.5 (8.5.8-1) ...
update-alternatives: using /usr/bin/wish8.5 to provide /usr/bin/wish (wish) in auto mode.
Setting up r-base-core (2.13.1-1~squeezecran.0) ...
Setting R_PAPERSIZE_USER default to 'a4'

Creating config file /etc/R/Renviron with new version
Setting up r-cran-boot (1.3-2-1~squeezecran.2.13.1) ...
Setting up r-cran-cluster (1.14.0-1~squeezecran.2.13.1) ...
Setting up r-cran-foreign (0.8.44-1~squeezecran.2.13.1) ...
Setting up r-cran-mass (7.3-13-1~squeezecran.2.13.1) ...
Setting up r-cran-kernsmooth (2.23-6-1~squeezecran.2.13.1) ...
Setting up r-cran-lattice (0.19-30-1~squeezecran.2.13.1) ...
Setting up r-cran-nlme (3.1.101-1~squeezecran.2.13.1) ...
Setting up r-cran-matrix (0.999375-50-1~squeezecran.2.13.1) ...
Setting up r-cran-mgcv (1.7-6-1~squeezecran.2.13.1) ...
Setting up r-cran-survival (2.36-9-1~squeezecran.2.13.1) ...
Setting up r-cran-rpart (3.1.50-1~squeezecran.2.13.1) ...
Setting up r-cran-class (7.3-3-1~squeezecran.2.13.1) ...
Setting up r-cran-nnet (7.3-1-1~squeezecran.2.13.1) ...
Setting up r-cran-spatial (7.3-2-1~squeezecran.2.13.1) ...
Setting up r-cran-codetools (0.2-8-1~squeezecran.2.13.1) ...
Setting up r-recommended (2.13.1-1~squeezecran.0) ...
Setting up r-base (2.13.1-1~squeezecran.0) ...
Setting up r-base-dev (2.13.1-1~squeezecran.0) ...
Setting up r-doc-html (2.13.1-1~squeezecran.0) ...
Setting up r-base-html (2.13.1-1~squeezecran.0) ...

And this is the actual list of packages I need:

autopoint_0.18.1.1-3_all.deb
autopoint_0.18.1.1-4_all.deb
autotools-dev_20100122.1_all.deb
autotools-dev_20110511.1_all.deb
cdbs_0.4.89_all.deb
cdbs_0.4.96_all.deb
debhelper_8.0.0_all.deb
debhelper_8.9.4_all.deb
dpatch_2.0.31_all.deb
gettext_0.18.1.1-3_amd64.deb
gettext_0.18.1.1-4_amd64.deb
gfortran_4%3a4.4.5-1_amd64.deb
gfortran_4%3a4.6.1-2_amd64.deb
gfortran-4.4_4.4.5-8_amd64.deb
gfortran-4.6_4.6.1-6_amd64.deb
git_1%3a1.7.2.5-2_amd64.deb
html2text_1.3.2a-15_amd64.deb
intltool-debian_0.35.0+20060710.1_all.deb
libblas3gf_1.2.20110419-1_amd64.deb
libblas-dev_1.2.20110419-1_amd64.deb
libblas-dev_1.2-8_amd64.deb
libbz2-dev_1.0.5-6_amd64.deb
liberror-perl_0.17-1_all.deb
libjpeg62-dev_6b1-1_amd64.deb
liblapack-dev_3.2.1-8_amd64.deb
liblapack-dev_3.3.1-1_amd64.deb
libmail-sendmail-perl_0.79.16-1_all.deb
libncurses5-dev_5.7+20100313-5_amd64.deb
libpcre3_8.12-4_amd64.deb
libpcre3-dev_8.02-1.1_amd64.deb
libpcre3-dev_8.12-4_amd64.deb
libpcrecpp0_8.02-1.1_amd64.deb
libpcrecpp0_8.12-4_amd64.deb
libpng12-0_1.2.44-1+squeeze1_amd64.deb
libpng12-0_1.2.46-3_amd64.deb
libpng12-dev_1.2.44-1+squeeze1_amd64.deb
libpng12-dev_1.2.46-3_amd64.deb
libreadline6_6.2-2_amd64.deb
libreadline6-dev_6.1-3_amd64.deb
libreadline6-dev_6.2-2_amd64.deb
libreadline-dev_6.1-3_amd64.deb
libreadline-dev_6.2-2_amd64.deb
libsys-hostname-long-perl_1.4-2_all.deb
libunistring0_0.9.3-3_amd64.deb
libunistring0_0.9.3-4_amd64.deb
patchutils_0.3.1-2_amd64.deb
patchutils_0.3.2-1_amd64.deb
pdftk_1.41+dfsg-10+squeeze1_amd64.deb
perl_5.12.4-3_amd64.deb
perl-base_5.12.4-3_amd64.deb
perl-modules_5.12.4-3_all.deb
po-debconf_1.0.16+nmu1_all.deb
r-base_2.13.1-1~squeezecran.0_all.deb
r-base-core_2.13.1-1~squeezecran.0_amd64.deb
r-base-dev_2.13.1-1~squeezecran.0_all.deb
r-base-html_2.13.1-1~squeezecran.0_all.deb
rcconf_2.5_all.deb
r-cran-boot_1.3-2-1~squeezecran.2.13.1_all.deb
r-cran-class_7.3-3-1~squeezecran.2.13.1_amd64.deb
r-cran-cluster_1.14.0-1~squeezecran.2.13.1_amd64.deb
r-cran-codetools_0.2-8-1~squeezecran.2.13.1_all.deb
r-cran-foreign_0.8.44-1~squeezecran.2.13.1_amd64.deb
r-cran-kernsmooth_2.23-6-1~squeezecran.2.13.1_amd64.deb
r-cran-lattice_0.19-30-1~squeezecran.2.13.1_amd64.deb
r-cran-mass_7.3-13-1~squeezecran.2.13.1_amd64.deb
r-cran-matrix_0.999375-50-1~squeezecran.2.13.1_amd64.deb
r-cran-mgcv_1.7-6-1~squeezecran.2.13.1_amd64.deb
r-cran-nlme_3.1.101-1~squeezecran.2.13.1_amd64.deb
r-cran-nnet_7.3-1-1~squeezecran.2.13.1_amd64.deb
r-cran-rpart_3.1.50-1~squeezecran.2.13.1_amd64.deb
r-cran-spatial_7.3-2-1~squeezecran.2.13.1_amd64.deb
r-cran-survival_2.36-9-1~squeezecran.2.13.1_amd64.deb
r-doc-html_2.13.1-1~squeezecran.0_all.deb
r-recommended_2.13.1-1~squeezecran.0_all.deb
subversion_1.6.12dfsg-6_amd64.deb
tcl8.5_8.5.10-1_amd64.deb
tcl8.5_8.5.8-2_amd64.deb
tk8.5_8.5.10-1_amd64.deb
tk8.5_8.5.8-1_amd64.deb
tkdiff_1%3a4.1.4-1_all.deb
tzdata_2011d-0squeeze1_all.deb
tzdata-java_2011d-0squeeze1_all.deb
zlib1g-dev_1%3a1.2.3.4.dfsg-3_amd64.deb

Of course versions etc. would change with time. But that is what updates are for.

Followed by more internal R packages within R:

install.packages(â€˜Hmiscâ€™)
install.packages('rms')
install.packages('ggplot2')
install.packages('haplo.stats')
install.packages('plyr')
install.packages('reshape')

Then subversion:

The following extra packages will be installed:
libapr1 libaprutil1 libneon27-gnutls libserf-0-0 libsvn1
Suggested packages:
subversion-tools db4.8-util
The following NEW packages will be installed:
libapr1 libaprutil1 libneon27-gnutls libserf-0-0 libsvn1
subversion

Procedure:
Selecting previously deselected package libapr1.
(Reading database ... 101103 files and directories currently installed.)
Unpacking libapr1 (from .../libapr1_1.4.2-6+squeeze3_amd64.deb) ...
Selecting previously deselected package libaprutil1.
Unpacking libaprutil1 (from .../libaprutil1_1.3.9+dfsg-5_amd64.deb) ...
Selecting previously deselected package libneon27-gnutls.
Unpacking libneon27-gnutls (from .../libneon27-gnutls_0.29.3-3_amd64.deb) ...
Selecting previously deselected package libserf-0-0.
Unpacking libserf-0-0 (from .../libserf-0-0_0.3.1-1_amd64.deb) ...
Selecting previously deselected package libsvn1.
Unpacking libsvn1 (from .../libsvn1_1.6.12dfsg-6_amd64.deb) ...
Selecting previously deselected package subversion.
Unpacking subversion (from .../subversion_1.6.12dfsg-6_amd64.deb) ...
Processing triggers for man-db ...
Setting up libapr1 (1.4.2-6+squeeze3) ...
Setting up libaprutil1 (1.3.9+dfsg-5) ...
Setting up libneon27-gnutls (0.29.3-3) ...
Setting up libserf-0-0 (0.3.1-1) ...
Setting up libsvn1 (1.6.12dfsg-6) ...
Setting up subversion (1.6.12dfsg-6) ...

08/17/2011 12:20 #54966

Pipe it through
Category: linux

somecommand goes here > some output goes here

For example:

ls > filename

lists all names in that directory in a neat little text file called "filename" (that doesn't even need an extension because linux *just knows*(tm) what that file is without need for extensions.

Simple stuff, but fun when you learn it.

08/17/2011 08:39 #54963

Hating big hair.
Category: whine

While I am hating on non-specific things, let me rant about about my hair as well.

That is not even an exaggeration. At this point my hair is bigger than my head and that is a really bad place to be in. Not only is it completey out of control and curling all over the place, it is also making my head feel heavy. I really should chop it all off.

Only, I thought I could let it grow for a bit but that is backfiring. The ugly phase is taking its toll.

enknot - 08/18/11 08:23
Oh and take a picture. it must be so cute right now. Indian hair is like gold.

enknot - 08/18/11 08:23
Can i pleaaaaase play with it before you freak out and cut it all off again.

tinypliny - 08/18/11 03:13
Hmm. I can't quite make up my mind if you are saying that just to see how far the ugliness can go or if you are just saying it to be polite... lol

paul - 08/17/11 21:05
I think its cute.

metalpeter - 08/17/11 16:53
Have you ever tried a Mohawk! You could if you really want to do the extreme Mohawk keep the mohawk and instead of setting one on the clippers go and Stay bald with the mohawk.......

08/16/2011 19:37 #54960

Out of salt.
Category: eating in

Again.

My new year resolution (HA HA) has been shot to hell because somehow I am right back to eating a canister of salt every 2 months.

I am somewhat worried that my end will be horrific with uncontrolled hypertension and associated kidney disease. But I am hoping I can make a deal with (e:Paul) to amputate my kidneys and heart out (with two different rusty elegant Victorian saws) at that point and die more peacefully (and in style). I also want to hire Malibu to sing some Sinatra melody during the "surgery".

I am off to get salt.

And chick peas.

And let's not forget the tomatoes.

08/16/2011 17:28 #54957

Losing my patience
Category: whine

I am really losing my patience with people who just can't seem to see the obvious or who have trouble thinking straight.

It's a sign that either I am reaching a point where I am not able to think straight myself or a point where I have no time for anything else other than my dissertation.

If it's the second, I hope I finish soon.

If I don't, I will end up as the most anti-social impatient jerk on this planet who views every second person with contempt. Seriously, the "quality-me" has been taking a nose-dive in the past week or so because everything other than finishing my dissertation seems irrelevant and every person who whines that things are more complex than what they want to make an effort to learn seems like a lazy no-gooder. I am also increasingly hating on former influences in my life who made me feel like crap at any point in the time I spent with them. I don't think I am an unreasonable person in general and I make a ton of effort to get along with people all the time. So their behaviour to me seems inexcusable now. I think I have come to a decision to put them on perennial ignore, going forwards. I cannot deal with such pettiness in my life anymore.

I know this non-humble intolerant ridiculously stupid phase has to end. I am seeing myself going from a person I am always comfortable being to a person I detest and totally not proud of. It is times such as these I wonder if 95% of intolerance in the world comes from people just being too busy with their own problems and not having any time or inclination to see anyone else's point of views. Or is it that they have finally come to a conclusion that their short lives on this planet is not worth wasting agonizing over things that seem like they are not quite right.

Disclaimer: This is just me ranting over non-specific things mainly because I need my dissertation work to go faster and have no mindspace anymore to think patiently about things in general. You can safely ignore this post altogether because it's definitely not about you. The things and people who are annoying me definitely don't know about this blog or the fact that I whine non-specifically on it. Some of them don't even know I exist. LOL

PS: I think the main reason behind all this intolerance is that I need to finish my dissertation. Every day that passes grates on my nerves and makes me lose one more pound to sleepless anxiety, adds one more extra dimension to my nightmares. It's not pretty.

paul - 08/16/11 23:46
I love your intolerance.

metalpeter - 08/16/11 18:20
Never thought of that in terms of intolerance but it makes sense though.......