R-3.1.0: biocLite("vsn") removes all files in /
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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? -- output of sessionInfo(): > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=C [5] LC_MONETARY=C LC_MESSAGES=de_DE.UTF-8 [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- Sent via the guest posting facility at bioconductor.org.
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Dan Tenenbaum ★ 8.2k
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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 > > -- output of sessionInfo(): > > > sessionInfo() > R version 3.1.0 (2014-04-10) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C > [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=C > [5] LC_MONETARY=C LC_MESSAGES=de_DE.UTF-8 > [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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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/ 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()' f?r Details dazu. R ist ein Gemeinschaftsprojekt mit vielen Beitragenden. Tippen Sie 'contributors()' f?r mehr Information und 'citation()', um zu erfahren, wie R oder R packages in Publikationen zitiert werden k?nnen. Tippen Sie 'demo()' f?r einige Demos, 'help()' f?r on-line Hilfe, oder 'help.start()' f?r 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.t ar.gz' Content type 'application/x-gzip' length 114002 bytes (111 Kb) URL ge?ffnet ================================================== 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 ge?ffnet ... 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 ge?ffnet ... 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 ge?ffnet ================================================== 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 m?glich: 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 ?berpr?ft mv: das Verschieben von ?/usr/lib64/R/library/MASS? nach ?/usr/lib64/R/library/00LOCK-MASS/MASS? ist nicht m?glich: 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 ?berpr?ft mv: das Verschieben von ?/usr/lib64/R/library/slam? nach ?/usr/lib64/R/library/00LOCK-slam/slam? ist nicht m?glich: 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 m?glich: 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 m?glich: 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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----- 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()' f?r Details dazu. > R ist ein Gemeinschaftsprojekt mit vielen Beitragenden. > Tippen Sie 'contributors()' f?r mehr Information und 'citation()', > um zu erfahren, wie R oder R packages in Publikationen zitiert werden > k?nnen. > Tippen Sie 'demo()' f?r einige Demos, 'help()' f?r on-line Hilfe, > oder > 'help.start()' f?r 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 ge?ffnet > ================================================== > downloaded 111 Kb > versuche URL > 'http://bioconductor.org/packages/3.0/bioc/src/contrib/preprocessCor e_1.27.0.tar.gz' > Content type 'application/x-gzip' length 120390 bytes (117 Kb) > URL ge?ffnet > > ... > > 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 ge?ffnet > ... > > 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 ge?ffnet > ================================================== > 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 > m?glich: 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 ?berpr?ft > mv: das Verschieben von ?/usr/lib64/R/library/MASS? nach > ?/usr/lib64/R/library/00LOCK-MASS/MASS? ist nicht m?glich: 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 ?berpr?ft > mv: das Verschieben von ?/usr/lib64/R/library/slam? nach > ?/usr/lib64/R/library/00LOCK-slam/slam? ist nicht m?glich: 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 m?glich: 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 m?glich: 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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In general, this is better resolved by 1) Creating a directory /usr/lib64/R/site-library and change it permissions to what you want. Specifically, due to settings in R, if this directory is group writable, everything R installs here becomes group writable as well. In my institution we basically have a group containing people with permission to install packages system- wide and this is the group which owns this directory. 2) Run your installation scripts, like biocLite. You can check that 1) has been achieved by starting R and executing R> .libPaths() You should see the site-library at the beginning of the vector. The only thing is that packages shipped with R, like MASS is install in library, not site-library, so you cannot update these without system privileges. Best, Kasper On Sun, May 18, 2014 at 1:32 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > > > ----- Original Message ----- > > From: "Juergen Rose" <rose@rz.uni-potsdam.de> > > To: "Dan Tenenbaum" <dtenenba@fhcrc.org> > > Cc: "Juergen Rose [guest]" <guest@bioconductor.org>, "vsn Maintainer" < > huber@ebi.ac.uk>, bioconductor@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@bioconductor.org> > > > > To: bioconductor@r-project.org, rose@rz.uni-potsdam.de > > > > Cc: "vsn Maintainer" <huber@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@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. 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@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@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@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@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. > > > > > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Am Sonntag, den 18.05.2014, 10:32 -0700 schrieb Dan Tenenbaum: > > ----- 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 -> ... > > > > 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/ ... > > > > -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 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 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 Maybe I should do this only for bioconductor R-packages. Is there an easy way to find out, which installed R-packages are installed with 'biocLite("pkg")'? Juergen
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----- 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 10:39:03 AM > Subject: Re: [BioC] R-3.1.0: biocLite("vsn") removes all files in / > > Am Sonntag, den 18.05.2014, 10:32 -0700 schrieb Dan Tenenbaum: > > > > ----- 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 > > > > > -> > ... > > > > > 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/ > ... > > > > > -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 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 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 > > Maybe I should do this only for bioconductor R-packages. Is there an > easy way to find out, which installed R-packages are installed with > 'biocLite("pkg")'? > Bioconductor packages can have dependencies on CRAN packages so you need to be able to install those too. biocLite() installs CRAN as well as Bioconductor packages. BTW, I think Kasper's suggestion is a good one. Dan > Juergen > > > > >
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