[BioC] R-3.1.0: biocLite("vsn") removes all files in /
Dan Tenenbaum
dtenenba at fhcrc.org
Sun May 18 19:32:02 CEST 2014
----- Original Message -----
> From: "Juergen Rose" <rose at rz.uni-potsdam.de>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Cc: "Juergen Rose [guest]" <guest at bioconductor.org>, "vsn Maintainer" <huber at ebi.ac.uk>, bioconductor at r-project.org
> Sent: Sunday, May 18, 2014 3:38:34 AM
> Subject: Re: [BioC] R-3.1.0: biocLite("vsn") removes all files in /
>
> Am Sonntag, den 18.05.2014, 00:03 -0700 schrieb Dan Tenenbaum:
> > Hi Juergen,
> >
> > ----- Original Message -----
> > > From: "Juergen Rose [guest]" <guest at bioconductor.org>
> > > To: bioconductor at r-project.org, rose at rz.uni-potsdam.de
> > > Cc: "vsn Maintainer" <huber at ebi.ac.uk>
> > > Sent: Saturday, May 17, 2014 11:09:44 PM
> > > Subject: [BioC] R-3.1.0: biocLite("vsn") removes all files in /
> > >
> > > I had the following files in /:
> > >
> > > root at 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 at 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. I know it is a risk to run scripts from the internet as
> > > root. But what would be the alternative to install a bioconductor
> > > package for all users?
> > >
> >
> > I don't know why this happened. We'll need to investigate further.
> >
> > However, you could install BiocInstaller (the package that provides
> > biocLite()) as follows (you don't need to be root):
> >
> > install.packages("BiocInstaller",
> > repos="http://bioconductor.org/packages/3.0/bioc")
> >
> > Then you can install packages as follows:
> > library(BiocInstaller)
> > biocLite("vsn")
> >
> > Note that you don't have to be root to install packages tha are
> > accessible to all users.
> > You just have to install them to a directory that you have
> > permissions to write to.
> >
> > You can start R (as any user) and see where it will look for
> > packages by doing:
> >
> > .libPaths()
> >
> > Then arrange to give yourself (a non-root user) write permissions
> > to that directory, and then install packages with biocLite() as
> > described above. If the installation is indeed removing files from
> > /, it should now not be able to do so if it doesn't have
> > permission to do so.
> >
> > Dan
>
> Thanks Dan,
>
> I tried this. I am belonging to group portage and the R-packages are
> installed under /usr/lib64/R/library. Therefore I changed the group
> of /usr/lib64/R/library to portage and made it writable by portage:
>
> root at lynx2:/root(21)# ll -d /usr/lib64/R/library
> drwxrwxr-x 40 root portage 4096 May 18 12:10 /usr/lib64/R/library/
Maybe try changing permissions recursively?
sudo chgrp -R portage /usr/lib64/R/library
Dan
>
> Then I tried as user rose to install vsn (some empty lines removed):
>
> rose at lynx2:/home/rose(1)$ R
>
> R version 3.1.0 (2014-04-10) -- "Spring Dance"
> Copyright (C) 2014 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
> R ist freie Software und kommt OHNE JEGLICHE GARANTIE.
> Sie sind eingeladen, es unter bestimmten Bedingungen weiter zu
> verbreiten.
> Tippen Sie 'license()' or 'licence()' für Details dazu.
> R ist ein Gemeinschaftsprojekt mit vielen Beitragenden.
> Tippen Sie 'contributors()' für mehr Information und 'citation()',
> um zu erfahren, wie R oder R packages in Publikationen zitiert werden
> können.
> Tippen Sie 'demo()' für einige Demos, 'help()' für on-line Hilfe,
> oder
> 'help.start()' für eine HTML Browserschnittstelle zur Hilfe.
> Tippen Sie 'q()', um R zu verlassen.
>
> > .libPaths()
> [1] "/usr/lib64/R/library"
> > library(BiocInstaller)
> Bioconductor version 3.0 (BiocInstaller 1.15.5), ?biocLite for help
> > biocLite("vsn")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 3.0 (BiocInstaller 1.15.5), R version
> 3.1.0.
> Installing package(s) 'vsn'
> also installing the dependencies ‘affyio’, ‘preprocessCore’,
> ‘zlibbioc’,
> ‘Biobase’, ‘affy’, ‘limma’
> versuche URL
> 'http://bioconductor.org/packages/3.0/bioc/src/contrib/affyio_1.33.0.tar.gz'
> Content type 'application/x-gzip' length 114002 bytes (111 Kb)
> URL geöffnet
> ==================================================
> downloaded 111 Kb
> versuche URL
> 'http://bioconductor.org/packages/3.0/bioc/src/contrib/preprocessCore_1.27.0.tar.gz'
> Content type 'application/x-gzip' length 120390 bytes (117 Kb)
> URL geöffnet
>
> ...
>
> installing to /usr/lib64/R/library/affyio/libs
> ** R
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> * DONE (affyio)
> ERROR: dependency ‘Biobase’ is not available for package ‘affy’
> * removing ‘/usr/lib64/R/library/affy’
> ERROR: dependencies ‘Biobase’, ‘affy’ are not available for package
> ‘vsn’
> * removing ‘/usr/lib64/R/library/vsn’
>
> The downloaded source packages are in
> ‘/tmp/Rtmp4RcqFj/downloaded_packages’
> Updating HTML index of packages in '.Library'
> Old packages: 'BiocGenerics', 'MASS', 'RBGL', 'graph', 'slam'
> Update all/some/none? [a/s/n]: a
> versuche URL
> 'http://bioconductor.org/packages/3.0/bioc/src/contrib/BiocGenerics_0.11.2.tar.gz'
> Content type 'application/x-gzip' length 32452 bytes (31 Kb)
> URL geöffnet
> ...
>
> This results in permission errors:
>
> versuche URL 'http://cran.fhcrc.org/src/contrib/slam_0.1-32.tar.gz'
> Content type 'application/x-gzip' length 46672 bytes (45 Kb)
> URL geöffnet
> ==================================================
> downloaded 45 Kb
>
> * installing *source* package ‘BiocGenerics’ ...
> mv: das Verschieben von „/usr/lib64/R/library/BiocGenerics“ nach
> „/usr/lib64/R/library/00LOCK-BiocGenerics/BiocGenerics“ ist nicht
> möglich: Keine Berechtigung
> Warnung in file.copy(f, instdir, TRUE) :
> Problem ./NAMESPACE nach
> /usr/lib64/R/library/BiocGenerics/NAMESPACE
> zu kopieren: Keine Berechtigung
> Warnung in file(file, ifelse(append, "a", "w")) :
> kann Datei '/usr/lib64/R/library/BiocGenerics/DESCRIPTION'
> nicht ?ffnen: Keine Berechtigung
> Error in file(file, ifelse(append, "a", "w")) :
> kann Verbindung nicht ?ffnen
> ERROR: installing package DESCRIPTION failed for package
> ‘BiocGenerics’
> * removing ‘/usr/lib64/R/library/BiocGenerics’
> * installing *source* package ‘MASS’ ...
> ** Paket ‘MASS’ erfolgreich entpackt und MD5 Summen überprüft
> mv: das Verschieben von „/usr/lib64/R/library/MASS“ nach
> „/usr/lib64/R/library/00LOCK-MASS/MASS“ ist nicht möglich: Keine
> Berechtigung
> Warnung in file.copy(f, instdir, TRUE) :
> Problem ./NAMESPACE nach /usr/lib64/R/library/MASS/NAMESPACE zu
> kopieren: Keine Berechtigung
> Warnung in file(file, ifelse(append, "a", "w")) :
> kann Datei '/usr/lib64/R/library/MASS/DESCRIPTION' nicht ?ffnen:
> Keine
> Berechtigung
> Error in file(file, ifelse(append, "a", "w")) :
> kann Verbindung nicht ?ffnen
> ERROR: installing package DESCRIPTION failed for package ‘MASS’
> * removing ‘/usr/lib64/R/library/MASS’
> * installing *source* package ‘slam’ ...
> ** Paket ‘slam’ erfolgreich entpackt und MD5 Summen überprüft
> mv: das Verschieben von „/usr/lib64/R/library/slam“ nach
> „/usr/lib64/R/library/00LOCK-slam/slam“ ist nicht möglich: Keine
> Berechtigung
> Warnung in file.copy(f, instdir, TRUE) :
> Problem ./NAMESPACE nach /usr/lib64/R/library/slam/NAMESPACE zu
> kopieren: Keine Berechtigung
> Warnung in file(file, ifelse(append, "a", "w")) :
> kann Datei '/usr/lib64/R/library/slam/DESCRIPTION' nicht ?ffnen:
> Keine
> Berechtigung
> Error in file(file, ifelse(append, "a", "w")) :
> kann Verbindung nicht ?ffnen
> ERROR: installing package DESCRIPTION failed for package ‘slam’
> * removing ‘/usr/lib64/R/library/slam’
> * installing *source* package ‘graph’ ...
> mv: das Verschieben von „/usr/lib64/R/library/graph“ nach
> „/usr/lib64/R/library/00LOCK-graph/graph“ ist nicht möglich: Keine
> Berechtigung
> Warnung in file.copy(f, instdir, TRUE) :
> Problem ./NAMESPACE nach /usr/lib64/R/library/graph/NAMESPACE zu
> kopieren: Keine Berechtigung
> Warnung in file(file, ifelse(append, "a", "w")) :
> kann Datei '/usr/lib64/R/library/graph/DESCRIPTION' nicht ?ffnen:
> Keine Berechtigung
> Error in file(file, ifelse(append, "a", "w")) :
> kann Verbindung nicht ?ffnen
> ERROR: installing package DESCRIPTION failed for package ‘graph’
> * removing ‘/usr/lib64/R/library/graph’
> * installing *source* package ‘RBGL’ ...
> mv: das Verschieben von „/usr/lib64/R/library/RBGL“ nach
> „/usr/lib64/R/library/00LOCK-RBGL/RBGL“ ist nicht möglich: Keine
> Berechtigung
> untarring boost include tree...
> Warnung in file.copy(f, instdir, TRUE) :
> Problem ./NAMESPACE nach /usr/lib64/R/library/RBGL/NAMESPACE zu
> kopieren: Keine Berechtigung
> Warnung in file.copy(f, instdir, TRUE) :
> Problem ./NEWS nach /usr/lib64/R/library/RBGL/NEWS zu kopieren:
> Keine
> Berechtigung
> Warnung in file(file, ifelse(append, "a", "w")) :
> kann Datei '/usr/lib64/R/library/RBGL/DESCRIPTION' nicht ?ffnen:
> Keine
> Berechtigung
> Error in file(file, ifelse(append, "a", "w")) :
> kann Verbindung nicht ?ffnen
> ERROR: installing package DESCRIPTION failed for package ‘RBGL’
> * removing ‘/usr/lib64/R/library/RBGL’
>
> The downloaded source packages are in
> ‘/tmp/Rtmp4RcqFj/downloaded_packages’
> Updating HTML index of packages in '.Library'
> Es gab 12 Warnungen (Anzeige mit warnings())
>
> After leaving R I can't find a /usr/lib64/R/library/vsn directory:
>
>
> root at lynx2:/root(23)# ll /usr/lib64/R/library/vsn
> /bin/ls: cannot access /usr/lib64/R/library/vsn: No such file or
> directory
>
>
> The only packages installed today under /usr/lib64/R/library are the
> first five directories of the following list:
>
> rose at lynx2:/home/rose(3)$ ll -t /usr/lib64/R/library/ | head
> insgesamt 168
> drwxrwxr-x 7 rose rose 4096 18. Mai 12:22 affyio/
> drwxrwxr-x 8 rose rose 4096 18. Mai 12:22 limma/
> drwxrwxr-x 9 rose rose 4096 18. Mai 12:22 zlibbioc/
> drwxrwxr-x 8 rose rose 4096 18. Mai 12:22 preprocessCore/
> drwxr-xr-x 8 root root 4096 18. Mai 12:10 BiocInstaller/
> drwxr-xr-x 8 root root 4096 3. Mai 19:06 scatterplot3d/
> drwxr-xr-x 10 root root 4096 16. Apr 09:17 MASS/
> drwxr-xr-x 7 root root 4096 16. Apr 09:17 base/
> drwxr-xr-x 8 root root 4096 16. Apr 09:17 boot/
>
>
> Any further hint is appreciated.
>
>
>
>
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