Hi Ben, On 27 December 2009 at 13:27, Ben Goodrich wrote: | -----BEGIN PGP SIGNED MESSAGE----- | Hash: SHA1 | | | Package: r-base-core | Version: 2.10.1-2 | Severity: normal | | Hi Dirk, | | I just updated my systems (I am seeing this on i386 too) a few minutes | ago, and now R seems to have a problem loading some packages installed | from CRAN (but everything was working fine before I updated everyhing; I | had R 2.10.1 RC before). The error message comes from read.dcf(), but it | is hard to investigate further because the error is thrown by the line | that says | | return(.Internal(readDCF(file, fields)))
Weird that nobody else -- including, say, me and cranberries (!!) sees that. I am running 2.10.1-2 as well. Can you poke around, nuke whatever ~/.R* you have etc ? Dirk, just in from taking the girls sledding. | | For example, | | R version 2.10.1 (2009-12-14) | Copyright (C) 2009 The R Foundation for Statistical Computing | ISBN 3-900051-07-0 | | R is free software and comes with ABSOLUTELY NO WARRANTY. | You are welcome to redistribute it under certain conditions. | Type 'license()' or 'licence()' for distribution details. | | Natural language support but running in an English locale | | R is a collaborative project with many contributors. | Type 'contributors()' for more information and | 'citation()' on how to cite R or R packages in publications. | | Type 'demo()' for some demos, 'help()' for on-line help, or | 'help.start()' for an HTML browser interface to help. | Type 'q()' to quit R. | | > library(rrcov) | Loading required package: robustbase | Loading required package: pcaPP | Loading required package: mvtnorm | pcaPP 0.1-1 loaded | Error in read.dcf(file.path(lib, pkg, "DESCRIPTION"), "Version") : | Line starting 'P ...' is malformed! | In addition: Warning message: | package 'pcaPP' was built under R version 2.9.2 and help may not work | correctly | Error : .onLoad failed in 'loadNamespace' for 'rrcov' | Error: package/namespace load failed for 'rrcov' | | > .libPaths() | [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library" | [3] "/usr/lib/R/library" "/usr/lib64/R/library" | | The first line starting with 'P' in rrcov/DESCRIPTION is "Package: | rrcov". I also get this error when I try to reinstall rrcov via R CMD | INSTALL . But it is not just a rrcov issue | | > ip <- installed.packages(lib = .libPaths()[1]) | There were 45 warnings (use warnings() to see them) | > warnings() | Warning messages: | 1: read.dcf() error on file | '/usr/local/lib/R/site-library/accuracy/DESCRIPTION' | 2: read.dcf() error on file | '/usr/local/lib/R/site-library/arm/DESCRIPTION' | 3: read.dcf() error on file | '/usr/local/lib/R/site-library/batch/DESCRIPTION' | 4: read.dcf() error on file | '/usr/local/lib/R/site-library/boolean/DESCRIPTION' | 5: read.dcf() error on file | '/usr/local/lib/R/site-library/clusterGeneration/DESCRIPTION' | 6: read.dcf() error on file | '/usr/local/lib/R/site-library/compositions/DESCRIPTION' | 7: read.dcf() error on file | '/usr/local/lib/R/site-library/corpcor/DESCRIPTION' | 8: read.dcf() error on file | '/usr/local/lib/R/site-library/debug/DESCRIPTION' | 9: read.dcf() error on file | '/usr/local/lib/R/site-library/ellipse/DESCRIPTION' | 10: read.dcf() error on file | '/usr/local/lib/R/site-library/energy/DESCRIPTION' | 11: read.dcf() error on file | '/usr/local/lib/R/site-library/FactoMineR/DESCRIPTION' | 12: read.dcf() error on file | '/usr/local/lib/R/site-library/FAiR/DESCRIPTION' | 13: read.dcf() error on file | '/usr/local/lib/R/site-library/GPArotation/DESCRIPTION' | 14: read.dcf() error on file | '/usr/local/lib/R/site-library/graph/DESCRIPTION' | 15: read.dcf() error on file | '/usr/local/lib/R/site-library/gWidgets/DESCRIPTION' | 16: read.dcf() error on file | '/usr/local/lib/R/site-library/gWidgetsRGtk2/DESCRIPTION' | 17: read.dcf() error on file | '/usr/local/lib/R/site-library/gWidgetstcltk/DESCRIPTION' | 18: read.dcf() error on file | '/usr/local/lib/R/site-library/MCMCpack/DESCRIPTION' | 19: read.dcf() error on file '/usr/local/lib/R/site-library/mi/DESCRIPTION' | 20: read.dcf() error on file | '/usr/local/lib/R/site-library/mice/DESCRIPTION' | 21: read.dcf() error on file | '/usr/local/lib/R/site-library/mosaiq/DESCRIPTION' | 22: read.dcf() error on file | '/usr/local/lib/R/site-library/multicore/DESCRIPTION' | 23: read.dcf() error on file | '/usr/local/lib/R/site-library/mvbutils/DESCRIPTION' | 24: read.dcf() error on file | '/usr/local/lib/R/site-library/mvnmle/DESCRIPTION' | 25: read.dcf() error on file | '/usr/local/lib/R/site-library/mvnormtest/DESCRIPTION' | 26: read.dcf() error on file | '/usr/local/lib/R/site-library/nFactors/DESCRIPTION' | 27: read.dcf() error on file | '/usr/local/lib/R/site-library/pcaPP/DESCRIPTION' | 28: read.dcf() error on file | '/usr/local/lib/R/site-library/polycor/DESCRIPTION' | 29: read.dcf() error on file | '/usr/local/lib/R/site-library/psych/DESCRIPTION' | 30: read.dcf() error on file | '/usr/local/lib/R/site-library/qtbase/DESCRIPTION' | 31: read.dcf() error on file | '/usr/local/lib/R/site-library/qtdevice/DESCRIPTION' | 32: read.dcf() error on file | '/usr/local/lib/R/site-library/qtgui/DESCRIPTION' | 33: read.dcf() error on file | '/usr/local/lib/R/site-library/qtpaint/DESCRIPTION' | 34: read.dcf() error on file | '/usr/local/lib/R/site-library/qtutils/DESCRIPTION' | 35: read.dcf() error on file | '/usr/local/lib/R/site-library/R2WinBUGS/DESCRIPTION' | 36: read.dcf() error on file | '/usr/local/lib/R/site-library/RBGL/DESCRIPTION' | 37: read.dcf() error on file | '/usr/local/lib/R/site-library/rgenoud/DESCRIPTION' | 38: read.dcf() error on file | '/usr/local/lib/R/site-library/Rgraphviz/DESCRIPTION' | 39: read.dcf() error on file | '/usr/local/lib/R/site-library/rrcov/DESCRIPTION' | 40: read.dcf() error on file | '/usr/local/lib/R/site-library/scatterplot3d/DESCRIPTION' | 41: read.dcf() error on file '/usr/local/lib/R/site-library/sem/DESCRIPTION' | 42: read.dcf() error on file | '/usr/local/lib/R/site-library/sfsmisc/DESCRIPTION' | 43: read.dcf() error on file | '/usr/local/lib/R/site-library/SparseM/DESCRIPTION' | 44: read.dcf() error on file | '/usr/local/lib/R/site-library/tcltk2/DESCRIPTION' | 45: read.dcf() error on file | '/usr/local/lib/R/site-library/tensorA/DESCRIPTION' | | Maybe it is some kind of encoding issue? I am pasting all of the | packages that got dist-upgraded right before this problem started | happening at the very bottom of this email, but I don't see any likely | suspects. | | I also have r-devel installed from svn on the i386 machine and loading | rrcov or similar packages seems to work fine with r-devel. Also | debianized R packages still load fine in all cases. | | Thanks, | Ben | | - -- System Information: | Debian Release: squeeze/sid | APT prefers unstable | APT policy: (500, 'unstable') | Architecture: amd64 (x86_64) | | Kernel: Linux 2.6.32-0.slh.8-sidux-amd64 (SMP w/2 CPU cores; PREEMPT) | Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8) | Shell: /bin/sh linked to /bin/dash | | Versions of packages r-base-core depends on: | hi libatlas3gf-base [libla 3.6.0-24 Automatically Tuned Linear Algebra | ii libblas3gf [libblas.so. 1.2-2 Basic Linear Algebra Subroutines 3 | ii libbz2-1.0 1.0.5-3 high-quality block-sorting file co | ii libc6 2.10.2-2 GNU C Library: Shared libraries | ii libcairo2 1.8.8-2 The Cairo 2D vector graphics libra | ii libgfortran3 4.4.2-7 Runtime library for GNU Fortran ap | ii libglib2.0-0 2.22.3-2 The GLib library of C routines | ii libice6 2:1.0.6-1 X11 Inter-Client Exchange library | ii libjpeg62 6b-15 The Independent JPEG Group's JPEG | ii liblapack3gf [liblapack 3.2.1-2 library of linear algebra routines | ii libpango1.0-0 1.26.2-1 Layout and rendering of internatio | ii libpaper-utils 1.1.23+nmu1 library for handling paper charact | ii libpcre3 7.8-3 Perl 5 Compatible Regular Expressi | ii libpng12-0 1.2.41-1 PNG library - runtime | ii libreadline6 6.0-5 GNU readline and history libraries | ii libsm6 2:1.1.1-1 X11 Session Management library | ii libtiff4 3.9.2-1 Tag Image File Format (TIFF) libra | ii libx11-6 2:1.3.2-1 X11 client-side library | ii libxext6 2:1.0.4-1 X11 miscellaneous extension librar | ii libxss1 1:1.1.3-1 X11 Screen Saver extension library | ii libxt6 1:1.0.7-1 X11 toolkit intrinsics library | ii perl 5.10.1-8 Larry Wall's Practical Extraction | ii tcl8.5 8.5.8-2 Tcl (the Tool Command Language) v8 | ii tk8.5 8.5.8-1 Tk toolkit for Tcl and X11, v8.5 - | ii ucf 3.0025 Update Configuration File: preserv | ii unzip 6.0-1 De-archiver for .zip files | ii xdg-utils 1.0.2-6.1 desktop integration utilities from | ii zip 3.0-1 Archiver for .zip files | ii zlib1g 1:1.2.3.4.dfsg-2 compression library - runtime | | Versions of packages r-base-core recommends: | ii r-base-dev 2.10.1-2 GNU R installation of auxiliary GN | ii r-doc-html 2.10.1-2 GNU R html manuals for statistical | ii r-recommended 2.10.1-2 GNU R collection of recommended pa | | Versions of packages r-base-core suggests: | pn ess <none> (no description available) | ii r-base-html 2.10.1-2 GNU R html docs for statistical co | ii r-doc-info 2.10.1-2 GNU R info manuals statistical com | ii r-doc-pdf 2.10.1-2 GNU R pdf manuals for statistical | ii r-mathlib 2.10.1-2 GNU R standalone mathematics libra | | | Calculating upgrade... Done | The following NEW packages will be installed: | librasqal2 linux-headers-2.6.32-2.slh.3-sidux-amd64 | linux-image-2.6.32-2.slh.3-sidux-amd64 | The following packages have been kept back: | gcj-jre-headless gij libatlas-base-dev libatlas-test libatlas3gf-base | libpoppler-qt4-3 mysql-client | mysql-server xserver-xorg-input-kbd xserver-xorg-input-mouse | xserver-xorg-input-vmmouse | xserver-xorg-video-apm xserver-xorg-video-ark xserver-xorg-video-chips | xserver-xorg-video-cirrus | xserver-xorg-video-fbdev xserver-xorg-video-i128 | xserver-xorg-video-mach64 xserver-xorg-video-mga | xserver-xorg-video-neomagic xserver-xorg-video-nv | xserver-xorg-video-r128 xserver-xorg-video-rendition | xserver-xorg-video-s3 xserver-xorg-video-s3virge | xserver-xorg-video-siliconmotion xserver-xorg-video-sis | xserver-xorg-video-sisusb xserver-xorg-video-tdfx | xserver-xorg-video-trident xserver-xorg-video-tseng | xserver-xorg-video-v4l xserver-xorg-video-vesa xserver-xorg-video-vmware | xserver-xorg-video-voodoo | The following packages will be upgraded: | acpid adduser apt apt-utils bsdmainutils cdbs cpp-4.4 cups cups-bsd | cups-client cups-common cups-ppdc | cupsddk distro-defaults dosfstools dpkg dpkg-dev file firmware-linux | firmware-linux-free | firmware-linux-nonfree fll-iso2usb fluxbox fontconfig fontconfig-config | g++-4.4 gcc-4.4 gcc-4.4-base | gcj-4.4-base gcj-4.4-jre-headless gfortran-4.4 | gfxboot-themes-sidux-2009-04-moros-core ggobi git-core | gnome-keyring gnome-pkg-tools gparted grub-common hal help2man | hplip-data iceweasel install-usb-gui | iptables kde-window-manager kdebase-workspace kdebase-workspace-bin | kdebase-workspace-data | kdebase-workspace-kgreet-plugins kdm klipper ksysguard ksysguardd | libboost-program-options1.40.0 | libboost-python1.40-dev libboost-python1.40.0 libboost-regex1.40.0 | libboost-signals1.40.0 libboost1.40-dev | libcaca0 libcucul0 libcups2 libcups2-dev libcupscgi1 libcupsdriver1 | libcupsimage2 libcupsmime1 libcupsppdc1 | libdb4.8 libdjvulibre-text libdjvulibre21 libffi5 libfontconfig1 | libfontconfig1-dev libfribidi0 libgcc1 | libgcj10 libgcr0 libgeoip1 libgfortran3 libglib2.0-0 libglib2.0-dev | libglib2.0-doc libgnome-keyring0 | libgomp1 libgp11-0 libgps19 libgraphviz4 libgtop2-7 libgtop2-common | libhal-storage1 libhal1 libiw30 | libkdecorations4 libkephal4 libkfontinst4 libkscreensaver5 libksgrd4 | libkwineffects1 libkworkspace4 | liblcms1 liblcms1-dev libmagic1 libmozjs2d libmusicbrainz4c2a | libnepomukquery4 libnepomukqueryclient4 | libnewt0.52 libnss3-1d libntfs10 libogg0 libpango1.0-0 | libpango1.0-common libpango1.0-dev | libplasma-applet-system-monitor4 libplasma-geolocation-interface4 | libplasmaclock4 libpoppler-dev | libpoppler-glib-dev libpoppler-glib4 libpoppler-qt-dev libpoppler-qt2 | libpoppler5 libpq-dev libpq5 | libprocesscore4 libprocessui4 libraptor1 librdf0 libsane libsmbclient | libsndfile1 libsnmp-base libsnmp15 | libsolidcontrol4 libsolidcontrolifaces4 libstdc++6 libstdc++6-4.4-dev | libtalloc2 libtaskmanager4 libtheora0 | libudev0 libwbclient0 libweather-ion4 libwxbase2.6-0 libwxbase2.8-0 | libwxgtk2.6-0 libwxgtk2.8-0 | linux-headers-2.6-sidux-amd64 linux-image-2.6-sidux-amd64 linux-libc-dev | maxima maxima-share | mozilla-openoffice.org nano ntfsprogs openjdk-6-jdk openjdk-6-jre | openjdk-6-jre-headless openjdk-6-jre-lib | openoffice.org openoffice.org-base openoffice.org-base-core | openoffice.org-calc openoffice.org-common | openoffice.org-core openoffice.org-draw openoffice.org-filter-mobiledev | openoffice.org-gtk | openoffice.org-help-en-us openoffice.org-impress | openoffice.org-java-common openoffice.org-math | openoffice.org-officebean openoffice.org-pdfimport | openoffice.org-report-builder-bin | openoffice.org-style-andromeda openoffice.org-style-crystal | openoffice.org-style-galaxy | openoffice.org-style-tango openoffice.org-writer pcmciautils | plasma-dataengines-workspace | plasma-widgets-workspace poppler-dbg poppler-utils psmisc pwgen python | python-all python-all-dev | python-cvxopt python-dev python-minimal python-sympy python-uno | python-zconfig r-base r-base-core | r-base-core-dbg r-base-dev r-base-html r-cran-dbi r-cran-multcomp | r-cran-rcmdr r-cran-rcpp r-cran-runit | r-cran-slam r-cran-survival r-doc-html r-doc-info r-doc-pdf r-mathlib | r-recommended samba-common sane-utils | sgml-data sidux-irc sidux-manual-common sidux-manual-en smbclient smbfs | systemsettings ttf-opensymbol udev | uno-libs3 ure whiptail whois wireless-tools wireshark wireshark-common | xfonts-utils xsane xsane-common | xulrunner-1.9.1 zlib1g zlib1g-dev | 238 upgraded, 3 newly installed, 0 to remove and 35 not upgraded. | Need to get 0B/491MB of archives. | After this operation, 166MB of additional disk space will be used. | Do you want to continue [Y/n]? 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