On 05/19/2014 01:09 AM, Henric Winell wrote:
On 2014-05-18 20:43, peter dalgaard wrote:
On 18 May 2014, at 07:38 , Jeff Newmiller <jdnew...@dcn.davis.ca.us> wrote:
Then you had best not do it again if you don't like that result.
1) This is not the right mailing list for issues having to do with
bioconductor. Please go to the bioconductor mailing list for that.
Hmm, this is one case where I'd really rather not scare people off R-help.
Non-BioC users do use BioC packages from time to time and what Juergen did is
what the BioConductor web pages tells new users to do (probably minus the
as-root bit). A warn-off on R-help seems entirely warranted. Good to see that
Martin Morgan is taking the issue very seriously in his post below.
As a non-BioC user using BioC packages I've always wondered why the standard R
functionality isn't enough. Can someone, please, tell me why 'biocLite()'
should be used?
I've always succeeded installing BioC packages using the standard R tools (as
indicated by Uwe in his reply).
Conversely, I've always succeeded in installing CRAN and Bioc packages via
source("http://bioconductor.org/biocLite.R";)
biocLite(...)
and am more-or-less flummoxed by the extra steps I'm asked to perform (to choose
and set repositories) when I take that rare foray into install.packages()-land!
One point is that http://bioconductor.org actually points to an Amazon
CloudFront address, which means that the content comes from a geographically
proximate and reliable location (this makes choice of repository mostly
irrelevant for normal users, just point to bioconductor.org)
Bioconductor has a repository and release schedule that differs from R
(Bioconductor has a 'devel' branch to which new packages and updates are
introduced, and a stable 'release' branch emitted once every 6 months to which
bug fixes but not new features are introduced).
A consequences of the mismatch between R and Bioconductor release schedules is
that the Bioconductor version identified by Uwe's method is sometimes not the
most recent 'release' available. For instance, R 3.1.1 will likely be introduced
some months before the next Bioc release. After the Bioc release, 3.1.1 users
will be pointed to an out-of-date version of Bioconductor.
A consequence of the distinct 'devel' branch is that Uwe's method sometimes
points only to the 'release' repository, whereas Bioconductor developers and
users wanting leading-edge features wish to access the Bioconductor 'devel'
repository. For instance, the next Bioc release will be available for R.3.1.x,
so Bioconductor developers and leading-edge users need to be able to install the
devel version of Bioconductor packages into the same version (though perhaps
different instance or at least library location) of R that currently supports
the release version.
An indirect consequence of the structured release is that Bioconductor packages
generally have more extensive dependencies with one another, both explicitly via
the usual package mechanisms and implicitly because the repository, release
structure, and Bioconductor community interactions favor re-use of data
representations and analysis concepts across packages. There is thus a higher
premium on knowing that packages are from the same release, and that all
packages are current within the release.
These days, the main purpose of source("http://bioconductor.org/biocLite.R";) is
to install and attach the 'BiocInstaller' package.
In a new installation, the script installs the most recent version of the
BiocInstaller package relevant to the version of R in use, regardless of the
relative times of R and Bioconductor release cycles. The BiocInstaller package
serves as the primary way to identify the version of Bioconductor in use
> library(BiocInstaller)
Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help
Since new features are often appealing to users, but at the same time require an
updated version of Bioconductor, the source() command evaluated in an
out-of-date R will nudge users to upgrade, e.g., in R-2.15.3
> source("http://bioconductor.org/biocLite.R";)
A new version of Bioconductor is available after installing the most
recent version of R; see http://bioconductor.org/install
The biocLite() function is provided by BiocInstaller. This is a wrapper around
install.packages, but with the repository chosen according to the version of
Bioconductor in use, rather than to the version relevant at the time of the
release of R.
biocLite also nudges users to remain current within a release, by default
checking for out-of-date packages and asking if the user would like to update
> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version
3.1.0.
Old packages: 'BBmisc', 'genefilter', 'GenomicAlignments',
'GenomicRanges', 'IRanges', 'MASS', 'reshape2', 'Rgraphviz',
'RJSONIO', 'rtracklayer'
Update all/some/none? [a/s/n]:
The BiocInstaller package provides facilities for switching to the 'devel'
version of Bioconductor
> BiocInstaller::useDevel()
Installing package into ‘/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.1’
(as ‘lib’ is unspecified)
trying URL
'http://bioconductor.org/packages/3.0/bioc/src/contrib/BiocInstaller_1.15.5.tar.gz'
Content type 'application/x-gzip' length 14144 bytes (13 Kb)
opened URL
==================================================
downloaded 13 Kb
* installing *source* package ‘BiocInstaller’ ...
...
Bioconductor version 3.0 (BiocInstaller 1.15.5), ?biocLite for help
'BiocInstaller' changed to version 1.15.5
(at some points in the R / Bioc release cycle use of 'devel' requires use of a
different version of R itself, in which case the attempt to useDevel() fails
with an appropriate message).
The BiocInstaller package also provides biocValid() to test that the installed
packages are not a hodgepodge from different Bioconductor releases (the 'too
new' packages have been installed from source rather than a repository; regular
users would seldom have these).
> biocValid()
* sessionInfo()
R version 3.1.0 Patched (2014-05-06 r65533)
Platform: x86_64-unknown-linux-gnu (64-bit)
...
* Out-of-date packages
...
update with biocLite()
* Packages too new for Bioconductor version '3.0'
...
downgrade with biocLite(c("ShortRead", "BatchJobs"))
Error: 9 package(s) out of date; 2 package(s) too new
Certainly for casual users install.packages() offers a familiar and
not-incorrect way of installing Bioconductor packages. For users who spend a lot
of time in Bioconductor, the features outlined above become increasingly
important and biocLite() is the way to go.
Martin
Henric Winell
2) Running random scripts straight from the internet as root without
reviewing them is exactly the kind of thing any experienced *nix user would
never do. That is why user-level accounts have limits on the things they can
do. I doubt you are supposed to be running anything with your current
directory set to /, ever, especially not logged in as root.
---------------------------------------------------------------------------
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Sent from my phone. Please excuse my brevity.
On May 17, 2014 10:16:46 PM PDT, Juergen Rose <r...@rz.uni-potsdam.de> wrote:
I had the following files in /:
root@caiman:/root(8)# ll /
total 160301
drwxr-xr-x 2 root root 4096 May 16 12:23 bin/
drwxr-xr-x 6 root root 3072 May 14 13:58 boot/
-rw-r--r-- 1 root root 38673 May 14 14:22 boot_local-d.log
lrwxrwxrwx 1 root root 11 Jan 22 2011 data -> data_caiman/
drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/
lrwxrwxrwx 1 root root 23 Dec 29 13:43 data_impala ->
/net/impala/data_impala/
lrwxrwxrwx 1 root root 21 Jan 27 08:13 data_lynx2 ->
/net/lynx2/data_lynx2/
drwxr-xr-x 21 root root 4040 May 14 14:40 dev/
drwxr-xr-x 160 root root 12288 May 17 17:14 etc/
-rw------- 1 root root 15687 Dec 26 13:42 grub.cfg_old
lrwxrwxrwx 1 root root 11 Jan 23 2011 home -> home_caiman/
drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/
lrwxrwxrwx 1 root root 23 Dec 29 13:43 home_impala ->
/net/impala/home_impala/
lrwxrwxrwx 1 root root 21 Jan 27 08:13 home_lynx2 ->
/net/lynx2/home_lynx2/
lrwxrwxrwx 1 root root 5 Mar 30 04:25 lib -> lib64/
drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/
drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/
-rw-r--r-- 1 root root 1797418 May 14 14:22 login.log
drwx------ 2 root root 16384 Jan 20 2011 lost+found/
drwxr-xr-x 2 root root 0 May 14 14:21 misc/
drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/
drwxr-xr-x 4 root root 0 May 17 17:38 net/
drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/
dr-xr-xr-x 270 root root 0 May 14 14:21 proc/
drwx------ 36 root root 4096 May 17 15:00 root/
drwxr-xr-x 30 root root 840 May 16 18:21 run/
drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/
-rw-r--r-- 1 root root 162191459 Jan 13 2011
stage3-amd64-20110113.tar.bz2
dr-xr-xr-x 12 root root 0 May 14 14:21 sys/
drwxrwxrwt 16 root root 1648 May 17 17:14 tmp/
drwxr-xr-x 19 root root 4096 May 6 04:40 usr/
drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/
Then I did as root:
R
source("http://bioconductor.org/biocLite.R";)
biocLite("vsn")
Save workspace image? [y/n/c]: n
root@caiman:/root(15)# ll /
total 93
drwxr-xr-x 2 root root 4096 May 16 12:23 bin/
drwxr-xr-x 6 root root 3072 May 14 13:58 boot/
drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/
drwxr-xr-x 21 root root 4040 May 14 14:40 dev/
drwxr-xr-x 160 root root 12288 May 17 17:14 etc/
drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/
drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/
drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/
drwx------ 2 root root 16384 Jan 20 2011 lost+found/
drwxr-xr-x 2 root root 0 May 14 14:21 misc/
drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/
drwxr-xr-x 2 root root 0 May 17 17:38 net/
drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/
dr-xr-xr-x 272 root root 0 May 14 14:21 proc/
drwx------ 36 root root 4096 May 17 15:00 root/
drwxr-xr-x 30 root root 840 May 16 18:21 run/
drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/
dr-xr-xr-x 12 root root 0 May 17 17:38 sys/
drwxrwxrwt 19 root root 1752 May 17 18:33 tmp/
drwxr-xr-x 19 root root 4096 May 6 04:40 usr/
drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/
I.e., all not directory files in / disappeared. This happens on two
systems.
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