Bug#695411: (no subject)
bit over my head. As a reminder, the problem is this:
Message-ID: <20130107213444.6883.35009.reportbug@qnap.local>
X-Mailer: reportbug 4.12.6
Date: Mon, 07 Jan 2013 22:34:44 +0100
R 2.15.2 compiled on Debian stable:
> sub(".*\\.", "", "/path/to/file.ext")
[1] "ext"
R 2.15.2 compiled in a Debian unstable chroot:
> sub(".*\\.", "", "/path/to/file.ext")
[1] "/path/to/fileext"
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Bug#695411: Fails to load built-in datasets on armel
Package: r-base-core Severity: normal Sorry for the incomplete message. I had expressed that I think it would be good to have a test case written in C, that calls tre_regcomp(), tre_regwcomp() and tre_regexec() in a similar way as do_gsub() would do, which is the C function being called by sub(). However, I would need some help, as the code in grep.c appears to be a bit too difficult for me. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Bug#695411: Fails to load built-in datasets on armel
Package: r-base-core
Severity: normal
I have started on a test case (attached), but, as mentioned, I did not succeed
to figure out exactly how the tre functions are being called under these
circumstances. Any help would be appreciated.
#include
#include
int main(int argc, char *argv[])
{
if(argc!=3)
{
printf("Usage: %s [regexp] [string]\n\n", argv[0]);
} else {
printf("Regular expression: %s\n", argv[1]);
printf("String to search in: %s\n", argv[2]);
}
regex_t regex;
int reti;
reti = tre_regcomp(®ex, argv[1], REG_EXTENDED); // Maybe tre_regwcomp() needs to be used here...
if (reti) {
fprintf(stderr, "Could not compile regex: %s\n", argv[1]); return(1);
}
/* Now tre_regexec() would need to be called in the way it is called by do_gsub() from src/main/grep.c in the R sources
and the result would need to be returned.
*/
// reti = tre_regexec(®ex, argv[2], 0, NULL, 0);
tre_regfree(®ex);
return(0);
}
Bug#695008: installation-reports: Acer TM8371 nicely installed, partitioning could be improved, suspend to RAM broken
Hi, Am Montag, 3. Dezember 2012, 17:43:03 schrieb Brian Potkin: > On Mon 03 Dec 2012 at 11:08:00 +0100, Johannes Ranke wrote: > > As I was not concentrated during the disk partitioning process, the > > partition manager wanted to use my USB flash drive used for booting the > > installer for the system installation, and I only noticed when the > > partitioning table was already written. [Snip] > > I wonder why this could happen, but I believe it should not be possible > > to select the medium from which the installer was booted as a system > > disk in the partitioning manager. > > The user may have good reasons to install Debian in the free space of > the device holding the installer. You actually tried to format the whole > device, part of which was mounted, so, as you observe, this was not > allowed by mkfs.whatever. Agreed. > The whole device can be used if the netboot mini.iso is written to it. > This is a valid thing to do (Debian on a flash drive). Your suggestion > would prevent it happening. Ah, I didn't know that. However, in my case (netinst image on USB) a seemingly valid selection in the partition manager caused my USB stick to be unusable. I think the installer may be able to disallow this scenario, but I do not know how to distinguish between the case where using the whole drive is possible from the case where it is not. > [Snip] > > > As detailed above, the partition manager at first wanted to use my USB > > flash drive from which the installer was loaded, as a system disk. > > This occurred because you instructed it to do that. Losing concentration > at the partitioning stage can be fatal. :) :) > Apart from this little glitch it would appear the installer has behaved > faultlessly and you successfully booted into the new system. Thank you > for your report. Very welcome! -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Bug#695411: r-base-core: Fails to load built-in datasets on armel
Package: r-base-core Version: 2.15.2-1 Severity: normal Hi Dirk, while checking if R could be useful on my NAS, I noticed that the built-in datasets are not loaded. I am writing this bug report from a fresh sid chroot environment. A short version of the session I just had: R version 2.15.2 (2012-10-26) -- "Trick or Treat" Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: arm-unknown-linux-gnueabi (32-bit) [snip] > stackloss Fehler: Objekt 'stackloss' nicht gefunden > data(stackloss) Warning message: In data(stackloss) : data set 'stackloss' not found > data() no data sets found [snip] However, the datasets are all there $ ls /usr/lib/R/library/datasets/data/ AirPassengers.R JohnsonJohnson.RUCBAdmissions.R airquality.tab eurodist.R nottem.R sunspot.year.R BJsales.R LakeHuron.R UKDriverDeaths.R anscombe.R faithful.R occupationalStatus.R sunspots.R BOD.R LifeCycleSavings.R UKLungDeaths.R attenu.R freeny.Rprecip.R swiss.tab CO2.rda Loblolly.R UKgas.R attitude.R infert.Rpresidents.R treering.R ChickWeight.R Nile.R USAccDeaths.R austres.R iris.R pressure.Rtrees.R DNase.R Orange.RUSArrests.tab beavers.R iris3.R quakes.tabuspop.R EuStockMarkets.R OrchardSprays.R USJudgeRatings.R cars.R islands.R randu.R volcano.R Formaldehyde.RPlantGrowth.R USPersonalExpenditure.R chickwts.R lh.Rrivers.R warpbreaks.R HairEyeColor.RPuromycin.R VADeaths.R co2.R longley.R rock.tab women.R Harman23.cor.RSeatbelts.R WWWusage.R crimtab.rda lynx.R sleep.R Harman74.cor.RTheoph.RWorldPhones.R discoveries.R morley.tab stackloss.R Indometh.RTitanic.R ability.cov.Resoph.R mtcars.Rstate.R InsectSprays.RToothGrowth.R airmiles.R euro.R nhtemp.Rsunspot.month.R Trying to help data() does not help: > data(stackloss, package = "datasets", lib.loc = "/usr/lib/R/library") Warning message: In data(stackloss, package = "datasets", lib.loc = "/usr/lib/R/library") : data set 'stackloss' not found Some additional information that may or may not help: Strangely enough, an R 2.15.2 backport to squeeze on this same box does not do lazy-loading either, but at least finds the dataset using data(): > stackloss Fehler: Objekt 'stackloss' nicht gefunden > data(stackloss) > head(stackloss) Air.Flow Water.Temp Acid.Conc. stack.loss 1 80 27 89 42 2 80 27 88 37 3 75 25 90 37 4 62 24 87 28 5 62 22 87 18 6 62 23 87 18 Any idea? Let me know what I can do to help. Cheers, Johannes -- System Information: Debian Release: wheezy/sid APT prefers unstable APT policy: (500, 'unstable') Architecture: armel (armv5tel) Kernel: Linux 2.6.32-5-kirkwood Locale: LANG=C, LC_CTYPE=C (charmap=ANSI_X3.4-1968) Shell: /bin/sh linked to /bin/dash Versions of packages r-base-core depends on: ii libblas3 [libblas.so.3] 1.2.20110419-5 ii libbz2-1.0 1.0.6-4 ii libc62.13-37 ii libcairo21.12.2-2 ii libgcc1 1:4.7.2-4 ii libgfortran3 4.7.2-4 ii libglib2.0-0 2.33.12+really2.32.4-3 ii libgomp1 4.7.2-4 ii libice6 2:1.0.8-2 ii libjpeg8 8d-1 ii liblapack3 [liblapack.so.3] 3.4.1-6 ii liblzma5 5.1.1alpha+20120614-2 ii libpango1.0-01.30.0-1 ii libpaper-utils 1.1.24+nmu2 ii libpcre3 1:8.31-1 ii libpng12-0 1.2.49-3 ii libreadline6 6.2-9 ii libsm6 2:1.2.1-2 ii libtiff4 3.9.6-9 ii libx11-6 2:1.5.0-1 ii libxext6 2:1.3.1-2 ii libxss1 1:1.2.2-1 ii libxt6 1:1.1.3-1 ii tcl8.5 8.5.11-2 ii tk8.58.5.11-2 ii ucf 3.0025+nmu3 ii unzip6.0-8 ii xdg-utils1.1.0~rc1+gi
Bug#695411: r-base-core: Fails to load built-in datasets on armel
> | > stackloss
> | Fehler: Objekt 'stackloss' nicht gefunden
> | > data(stackloss)
> | Warning message:
> | In data(stackloss) : data set 'stackloss' not found
> | no data sets found
> | Any idea? Let me know what I can do to help.
>
> Hm.
>
> Sounds like we'd need an arm box to do development on to look at the R code
> / metadata ?
(sorry for the delay, I was on the phone for quite a while)
Well, I believe I could let you log into my NAS if I I configure my router
appropriately :) It is running Debian stable and the abovementioned sid
chroot.
Meanwhile, I have had a go at debugging using debug(). The problem appears in
the function fileExt defined in the very beginning of data().
fileExt <- function(x) {
db <- grepl("\\.[^.]+\\.(gz|bz2|xz)$", x)
ans <- sub(".*\\.", "", x)
ans[db] <- sub(".*\\.([^.]+\\.)(gz|bz2|xz)$", "\\1\\2",
x[db])
ans
}
Guess what, adding perl=TRUE to the second line gives the right extension.
I just verified that after
> fix(data)
and doing the abovementioned change using my favorite text editor
I can load the data using
> data(stackloss)
However, I do not fully understand what the code does (the first line results
in db being FALSE, and I do not see how it makes sense later to index ans
using FALSE...)
So I have the feeling maybe it should be discussed upstream why regular
expressions on arm behave so different (broken) and what should be done about
it (use PCRE, considering Adam Conrads viewpoint on #679180 ?).
Beware that lazyloading still does not work after this workaround.
Cheers,
Johannes
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Bug#695411: r-base-core: Fails to load built-in datasets on armel
> | So I have the feeling maybe it should be discussed upstream why regular > | expressions on arm behave so different (broken) and what should be done > | about it (use PCRE, considering Adam Conrads viewpoint on #679180 ?). > > R Core is not too responsive these days to postings on r-devel. Maybe we > should crystalize this into a written bug report for their bugzilla system? > I did file something there and it did get picked up... I just found a bug report with the same symptoms in the bugzilla http://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15087 and added the link to here. > > arm* may matter more with Chromebooks and all that bringing volume to the > architecture. People may hack more on it... Yes, may well be... > | Beware that lazyloading still does not work after this workaround. > | > | Cheers, > | > | Johannes -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Bug#695411: r-base-core: Fails to load built-in datasets on armel
> I just found a bug report with the same symptoms in the bugzilla > > http://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15087 > > and added the link to here. I added some more information on the bug in the R bugzilla, documenting that the sub() function behaves correctly when R 2.15.2 is compiled on Debian stable, while it is buggy when compiled on Debian unstable (both armel platform). -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Bug#695012: kde-workspace: Suspend not working after upgrade squeeze->wheezy
Package: kde-workspace Version: 4:4.8.4-5 Followup-For: Bug #695012 Control: reassign pm-utils Dear maintainter(s) of pm-utils I believe kde-workspace depends on pm-utils for the suspend-resume process. I noticed that using pm-suspend from the command line has the same problem as described in this report. I tried all the quirks listed with pm-suspend --help. None of those alleviate the problem (suspend seems to work correctly, computer reboots instead of waking up on pressing a key). I turned on debugging once, but I did not succeed in making use of the log in /var/log/pm-suspend.log. Kind regards, Johannes -- System Information: Debian Release: wheezy/sid APT prefers testing APT policy: (650, 'testing'), (600, 'unstable') Architecture: amd64 (x86_64) Kernel: Linux 3.2.0-4-amd64 (SMP w/1 CPU core) Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Versions of packages kde-workspace depends on: ii freespacenotifier 4:4.8.4-5 ii kde-window-manager 4:4.8.4-5 ii kde-workspace-bin 4:4.8.4-5 ii klipper 4:4.8.4-5 ii ksysguard 4:4.8.4-5 ii systemsettings 4:4.8.4-5 Versions of packages kde-workspace recommends: pn kdm ii kinfocenter 4:4.8.4-5 ii kmenuedit4:4.8.4-5 kde-workspace suggests no packages. -- no debconf information -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Bug#695012: kde-workspace: Suspend not working after upgrade squeeze->wheezy
Package: kde-workspace Version: 4:4.8.4-5 Followup-For: Bug #695012 Control: reassign 695012 pm-utils Another try to reassign this bug report, with (hopefully) corrected syntax Johannes -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Bug#690275: python-indigo: Does not use the Hill convention for GrossFormula
Package: python-indigo Version: 1.0.0-2 Severity: normal Dear debichem maintainers, Upstream has indigo 1.1.5, and since 1.1.3 they use the Hill convention for their GrossFormula function. It would be great if the latest upstream version could be packaged, because the molecular formulas given by 1.0.0 are not what would be expected and therefore the GrossFormula function does not completely fulfil its purpose. Maybe it is worth to mention that indigo works very nicely for me apart from this. It is great for generating standardised structure representations from SMILES codes, calculating molecular weights to go with it and I am sure for many other chemoinformatics tasks. Kind regards, Johannes Ranke P.S.: I am actually using python-indigo and indigo-utils at work on a Debian stable system, so you can ignore the system information given below. -- System Information: Debian Release: wheezy/sid APT prefers precise-updates APT policy: (500, 'precise-updates'), (500, 'precise-security'), (500, 'precise'), (100, 'precise-backports') Architecture: amd64 (x86_64) Kernel: Linux 3.2.0-31-generic (SMP w/3 CPU cores) Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Bug#690275: python-indigo: Does not use the Hill convention for GrossFormula
Hi ... > I will take a look at uploading indigo-1.1.5 to experimental at least > and then backporting it to squeeze, but the build system has changed > since 1.0.0 (at least they are using CMake now, not some home-grown > Makefiles), so it might take a bit. Sounds great! I would like to offer some help, but ... I do not know so much about packaging and cmake, so I believe I would not be of much help... I could have a go at the backporting bit, but you would have to upload as I am not a dd. Cheers, Johannes -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Bug#695008: installation-reports: Acer TM8371 nicely installed, partitioning could be improved, suspend to RAM broken
Package: installation-reports Severity: normal Tags: d-i Dear Maintainer, As I was not concentrated during the disk partitioning process, the partition manager wanted to use my USB flash drive used for booting the installer for the system installation, and I only noticed when the partitioning table was already written. Then, I got a warning that the installer could not "inform the kernel" of the change in the partitioning table, presumably because the device was mounted. I wonder why this could happen, but I believe it should not be possible to select the medium from which the installer was booted as a system disk in the partitioning manager. I had to put the installer on the USB drive again and restart the process. Partitioning: Also, it turned out that the 10 GB proposed as default for the root partition, when choosing a separate /home partition, was not enough for my KDE4 installation (well, not only KDE4...), so I had trouble when I installed my package list via dpkg --set-selections. Package selection: It was also problematic that dselect was not installed per default, as I wanted to recover my package list from the predecessor system via dpkg --set-selections. Please consider putting it back into the list of packages installed per default. Sound: I had to start alsamixer to unmute channel "speaker". This is not obvious for GUI users. Suspend to RAM: This does not work any more. I am currently looking for the appropriate plasma component to file a bug report on this. Thanks for your kind attention, Johannes -- Package-specific info: Boot method: USB flash drive Image version: debian-wheezy-DI-b4-amd64-netinst.iso Date: Machine: Acer Travelmate 8371 Partitions: DateisystemTyp 1K-Blöcke Benutzt Verfügbar Verw% Eingehängt auf rootfs rootfs 9611492 8841268281984 97% / udev devtmpfs 10240 0 102400% /dev tmpfs tmpfs 198860 7041981561% /run /dev/disk/by-uuid/004a0d93-feb6-416b-9534-7d3fa4db5cfa ext4 9611492 8841268281984 97% / tmpfs tmpfs 5120 0 51200% /run/lock tmpfs tmpfs 1206860 0 12068600% /run/shm /dev/sda6 ext4 478661528 372713672 81633184 83% /home Base System Installation Checklist: [O] = OK, [E] = Error (please elaborate below), [ ] = didn't try it Initial boot: [O] Detect network card:[O] Configure network: [O] Detect CD: [ ] Load installer modules: [O] Clock/timezone setup: [O] User/password setup:[O] Detect hard drives: [O] Partition hard drives: [E] Install base system:[O] Install tasks: [O] Install boot loader:[O] Overall install:[O] Comments/Problems: As detailed above, the partition manager at first wanted to use my USB flash drive from which the installer was loaded, as a system disk. -- Please make sure that the hardware-summary log file, and any other installation logs that you think would be useful are attached to this report. Please compress large files using gzip. Once you have filled out this report, mail it to sub...@bugs.debian.org. == Installer lsb-release: == DISTRIB_ID=Debian DISTRIB_DESCRIPTION="Debian GNU/Linux installer" DISTRIB_RELEASE="7.0 (wheezy) - installer build 20121114" X_INSTALLATION_MEDIUM=cdrom == Installer hardware-summary: == uname -a: Linux time 3.2.0-4-amd64 #1 SMP Debian 3.2.32-1 x86_64 GNU/Linux lspci -knn: 00:00.0 Host bridge [0600]: Intel Corporation Mobile 4 Series Chipset Memory Controller Hub [8086:2a40] (rev 07) lspci -knn: Subsystem: Acer Incorporated [ALI] Device [1025:0283] lspci -knn: Kernel driver in use: agpgart-intel lspci -knn: 00:02.0 VGA compatible controller [0300]: Intel Corporation Mobile 4 Series Chipset Integrated Graphics Controller [8086:2a42] (rev 07) lspci -knn: Subsystem: Acer Incorporated [ALI] Device [1025:0283] lspci -knn: 00:02.1 Display controller [0380]: Intel Corporation Mobile 4 Series Chipset Integrated Graphics Controller [8086:2a43] (rev 07) lspci -knn: Subsystem: Acer Incorporated [ALI] Device [1025:0283] lspci -knn: 00:1a.0 USB controller [0c03]: Intel Corporation 82801I (ICH9 Family) USB UHCI Controller #4 [8086:2937] (rev 03) lspci -knn: Subsystem: Acer Incorporated [ALI] Device [1025:0283] lspci -knn: Kernel driver in use: uhci_hcd lspci -knn: 00:1a.1 USB controller [0c03]: Intel Corporation 82801I (ICH9 Family) USB UHCI Controller #5 [8086:2938] (rev 03) lspci -knn: Subsystem: Acer Incorporated [ALI] Device [102
Bug#695012: kde-workspace: Suspend not working after upgrade squeeze->wheezy
Package: kde-workspace Version: 4:4.8.4-4 Severity: normal Dear Maintainer, After a fresh installation of Debian wheezy on my ACER TravelMate 8371 laptop, suspend/resume is not working any more. Maybe it has to do with my package selection, as I used the list of installed packages in squeeze for selecting packages in wheezy via dpkg --get-selection and dpkg --set-selection. Please let me know what kind for further information I should supply. Kind regards, Johannes -- System Information: Debian Release: wheezy/sid APT prefers testing APT policy: (500, 'testing') Architecture: amd64 (x86_64) Kernel: Linux 3.2.0-4-amd64 (SMP w/1 CPU core) Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Versions of packages kde-workspace depends on: ii freespacenotifier 4:4.8.4-4 ii kde-window-manager 4:4.8.4-4 ii kde-workspace-bin 4:4.8.4-4 ii klipper 4:4.8.4-4 ii ksysguard 4:4.8.4-4 ii systemsettings 4:4.8.4-4 Versions of packages kde-workspace recommends: pn kdm ii kinfocenter 4:4.8.4-4 ii kmenuedit4:4.8.4-4 kde-workspace suggests no packages. -- no debconf information -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Bug#438823: r-base-core: valgrind throws an error when R starts on amd64
> | > | I noticed this problem with R 2.5.1 (binary from Debian unstable or > | source from CRAN); do you want me to try the SVN version of R? > > Could be the compiler, could be R. FWIW the debian/rules specifies gcc 4.2 > as per > > > # edd 03 Apr 2006 switch to gfortran > # edd 04 Apr 2006 use optimflags, build per-compiler flags later > # edd 26 Jun 2007 need 4.2 for fortran linking > fortrancompiler = F77=gfortran-4.2 > compiler = gcc-4.2 > cxxcompiler = g++-4.2 > optimflags= -O3 -pipe > Just for your information, if you use the sources from CRAN for debian etch, debian/rules contains # edd 03 Apr 2006 switch to gfortran # edd 04 Apr 2006 use optimflags, build per-compiler flags later # edd 26 Jun 2007 need 4.2 for fortran linking # jranke 30 Jun 2007 obviously 4.2 not needed for backporters :) fortrancompiler = F77=gfortran compiler= gcc cxxcompiler = g++ optimflags = -O3 -pipe Could this be problematic? Johannes -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Bug#438823: r-base-core: valgrind throws an error when R starts on amd64
* Ben Goodrich <[EMAIL PROTECTED]> [070821 16:00]: > Johannes Ranke wrote: > >> | > >> | I noticed this problem with R 2.5.1 (binary from Debian unstable or > >> | source from CRAN); do you want me to try the SVN version of R? > >> > >> Could be the compiler, could be R. FWIW the debian/rules specifies gcc 4.2 > >> as per > >> > >> > >> # edd 03 Apr 2006 switch to gfortran > >> # edd 04 Apr 2006 use optimflags, build per-compiler flags later > >> # edd 26 Jun 2007 need 4.2 for fortran linking > >> fortrancompiler= F77=gfortran-4.2 > >> compiler = gcc-4.2 > >> cxxcompiler= g++-4.2 > >> optimflags = -O3 -pipe > >> > > > > Just for your information, if you use the sources from CRAN for debian > > etch, debian/rules contains > > > > # edd 03 Apr 2006 switch to gfortran > > # edd 04 Apr 2006 use optimflags, build per-compiler flags later > > # edd 26 Jun 2007 need 4.2 for fortran linking > > # jranke 30 Jun 2007 obviously 4.2 not needed for backporters :) > > fortrancompiler = F77=gfortran > > compiler= gcc > > cxxcompiler = g++ > > optimflags = -O3 -pipe > > > > Could this be problematic? > > > > Johannes > > > > I should have clarified: the test with the CRAN source was with the > vanilla source (http://cran.r-project.org/src/base/R-2/R-2.5.1.tar.gz). > I didn't apply any Debian patches or do anything except ./configure; > make, which I guess would imply that the CRAN source was compiled with > gcc 4.1.3. Anyway, aside from producing the same valgrind error as with > the binary from the unstable repo, and perhaps suggesting that the bug > is not with r-base-core per se, I am not sure the test with the CRAN > source is too interesting. Oh, I thought you had used the Debian source package from CRAN. > Maybe I did not fully understand the point you were making? No, only my point was based on a misunderstanding. Thanks for the clarification. Johannes -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Bug#456938: openoffice.org-java-common: fails to upgrade
Package: openoffice.org-java-common Version: 2.2.1-9~bpo40+1 Severity: grave Justification: renders package unusable On upgrade I get: Preparing to replace openoffice.org-java-common 2.2.1-9~bpo40+1 (using .../openoffice.org-java-common_1%3a2.3.1-2~bpo40+1_all.deb) ... Unpacking replacement openoffice.org-java-common ... dpkg: error processing /var/cache/apt/archives/openoffice.org-java-common_1%3a2.3.1-2~bpo40+1_all.deb (--unpack): trying to overwrite `/usr/lib/openoffice/program/classes/hsqldb.jar', which is also in package openoffice.org-base Errors were encountered while processing: /var/cache/apt/archives/openoffice.org-java-common_1%3a2.3.1-2~bpo40+1_all.deb E: Sub-process /usr/bin/dpkg returned an error code (1) -- System Information: Debian Release: 4.0 APT prefers stable APT policy: (500, 'stable'), (1, 'experimental') Architecture: amd64 (x86_64) Shell: /bin/sh linked to /bin/bash Kernel: Linux 2.6.18-3-xen-amd64 Locale: [EMAIL PROTECTED], [EMAIL PROTECTED] (charmap=ISO-8859-15) Versions of packages openoffice.org-java-common depends on: ii bsh2.0b4-4 Java scripting environment (BeanSh ii libxalan2-java 2.7.0-1 XSL Transformations (XSLT) process ii libxerces2-java2.8.1-1 Validating XML parser for Java wit ii openoffice.org-common 1:2.3.1-2~bpo40+1 OpenOffice.org office suite archit openoffice.org-java-common recommends no packages. -- no debconf information -- Dr. Johannes Ranke [EMAIL PROTECTED] Key ID: F649AF90 UFT Bremen, Leobenerstr. 1 +49 421 218 63373 D-28359 Bremen http://www.uft.uni-bremen.de/chemie/ranke -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Bug#457057: (no subject)
Hi Diego, I am not sure if you mail reached the right audience - I received it because I am subscribed to the "boot" package which is a library for the R program for statistical computing, and has little to do with booting or installing debian. Nevertheless I feel sorry that you lost access to your Windows system. I hope you will be able to restore all your personal data. Best regards, Johannes Ranke * Diego de Soto <[EMAIL PROTECTED]> [071219 13:20]: > > Package: installation-reportsBoot method: <4.0 r1 "Etch" - Official i386 > BC Binary - 1 20070820 - 20:20 CD> Image version: <4.0 r1 "Etch" - Official > i386 BC Binary - 1 20070820 - 20:20 CD> Date: <14 Dec. 2007>Machine: Pavilion dv6519ea> Processor: Intel Core 2 Duo T7100 Memory: 1 GB RAM, 120 > GB HD Partitions: <3 GB ext2 & 3 GB swap area>Output of lspci -nn and > lspci -vnn: not sure what this means and don't have time to find out, sorry > Base System Installation Checklist: [O] = OK, [E] = Error (please elaborate > below), [ ] = didn't try itInitial boot: [O] Detect network > card:[O] Configure network: [E] Detect CD: [O] Load > installer modules: [O?] Detect hard drives: [O] Partition hard drives: > [O] Install base system:[E] Clock/timezone setup: [O] User/password > setup:[O] Install tasks: [ ] Install boot loader:[ ] > Overall install:[E]Comments/Problems: I don't remember if the loading of the installer modules went well; hence > the question mark. When setting up the network, I get an error message: > "Network autoconfiguration failed". This may simply be due to the fact that I > don't have an internet connection. When I try to install the base system, I > get the following error messages: "Debootstrap Error" and "Failed to > determine the codename for the release." Also, due in part to the > non-intuitive nature of the installation instructions, I deleted part of > Windows (enough so that I no longer had access to it) during the partitioning > process.> > > > - > Never miss a thing. Make Yahoo your homepage. -- Dr. Johannes Ranke [EMAIL PROTECTED] Key ID: F649AF90 UFT Bremen, Leobenerstr. 1 +49 421 218 63373 D-28359 Bremen http://www.uft.uni-bremen.de/chemie/ranke -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Bug#463348: rkward 0.4.9-2 does not start if there is no libRblas.so
Hi, I can confirm this behavior on my amd64 unstable box. rkward needs to be recompiled, because it is linked to blas (although Thomas said blas symbols are not used anywhere). The same issue arose with rkward 0.5, and also with the R package mgcv, which is linked against blas. I am filing a bug report against mgcv in a minute so Dirk can force a recompile there, too. Best regards, Johannes * Ben Goodrich <[EMAIL PROTECTED]> [080131 04:20]: > Package: rkward > Version: 0.4.9-2 > Severity: important > > Hi Thomas, > > rkward 0.4.9-2 fails to start on amd64 > > [EMAIL PROTECTED]:~$ rkward > /usr/bin/rkward.bin: error while loading shared libraries: libRblas.so: > cannot open shared object file: No such file or directory > > [EMAIL PROTECTED]:~$ ls /usr/lib/R/lib > libRlapack.so libR.so > > See http://packages.debian.org/sid/amd64/r-base-core/filelist ; > r-base-core does not provide libRblas.so anymore. > > I think this is related to the most recent update of R in unstable, > which involved a mini-transition relating to BLAS. For me, r-base-dev > got held back in a dist-upgrade due to refblas3-dev, but I asked Dirk > and he said it was okay to install r-base-dev separately, which kicked > refblas3-dev but added libblas-dev. Anyway, now there is no libRblas.so > anywhere on the system, but R does work. > > On my 32bit with 0.5.x, there is also no libRblas.so, but rkward starts > fine. > > Thanks, > Ben > > -- System Information: > Debian Release: lenny/sid > APT prefers unstable > APT policy: (500, 'unstable') > Architecture: amd64 (x86_64) > > Kernel: Linux 2.6.23.14-slh64-smp-1 (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/bash > > Versions of packages rkward depends on: > ii kdelibs4c2a4:3.5.8.dfsg.1-7 core libraries and binaries > for al > ii libacl12.2.45-1 Access control list shared > library > ii libart-2.0-2 2.3.20-1 Library of functions for 2D > graphi > ii libattr1 1:2.4.39-1Extended attribute shared > library > ii libaudio2 1.9.1-1 Network Audio System - > shared libr > ii libc6 2.7-6 GNU C Library: Shared libraries > ii libfam02.7.0-13.1Client library to control > the FAM > ii libfontconfig1 2.5.0-2 generic font configuration > library > ii libfreetype6 2.3.5-1+b1FreeType 2 font engine, > shared lib > ii libgcc11:4.3-20080127-1 GCC support library > ii libgfortran2 4.2.2-7 Runtime library for GNU > Fortran ap > ii libice62:1.0.4-1 X11 Inter-Client Exchange > library > ii libidn11 1.1-1 GNU libidn library, > implementation > ii libjpeg62 6b-14 The Independent JPEG > Group's JPEG > ii libpcre3 7.6-1 Perl 5 Compatible Regular > Expressi > ii libpng12-0 1.2.15~beta5-3PNG library - runtime > ii libqt3-mt 3:3.3.7-9 Qt GUI Library (Threaded > runtime v > ii libsm6 2:1.0.3-1+b1 X11 Session Management library > ii libstdc++6 4.3-20080127-1The GNU Standard C++ Library v3 > ii libx11-6 2:1.0.3-7 X11 client-side library > ii libxcursor11:1.1.9-1 X cursor management library > ii libxext6 1:1.0.3-2 X11 miscellaneous extension > librar > ii libxft22.1.12-2 FreeType-based font drawing > librar > ii libxi6 2:1.1.3-1 X11 Input extension library > ii libxinerama1 1:1.0.2-1 X11 Xinerama extension library > ii libxrandr2 2:1.2.2-1 X11 RandR extension library > ii libxrender11:0.9.4-1 X Rendering Extension > client libra > ii libxt6 1:1.0.5-3 X11 toolkit intrinsics library > ii php4-cli 6:4.4.6-2+b1 command-line interpreter > for the p > ii r-base-core2.6.1-2 GNU R core of statistical > computin > ii zlib1g 1:1.2.3.3.dfsg-11 compression library - runtime > > Versions of packages rkward recommends: > ii r-base-html 2.6.1-2GNU R html docs for > statistical co > > -- no debconf information > > -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Bug#463374: r-cran-mgcv: library fails to load on amd64
Package: r-cran-mgcv Version: 1.3-29-1 Severity: important After upgrading to R 2.6.1-2 I get > library(mgcv) Error in dyn.load(file, ...) : unable to load shared library '/usr/lib/R/library/mgcv/libs/mgcv.so': libRblas.so: cannot open shared object file: No such file or directory This is caused by the recent changes in refblas packaging and can be fixed by a recompile against the current R version in the archive. Thanks, Johannes -- System Information: Debian Release: lenny/sid APT prefers unstable APT policy: (500, 'unstable'), (500, 'stable'), (1, 'experimental') Architecture: amd64 (x86_64) Kernel: Linux 2.6.23-1-amd64 (SMP w/1 CPU core) Locale: [EMAIL PROTECTED], [EMAIL PROTECTED] (charmap=ISO-8859-15) Shell: /bin/sh linked to /bin/bash Versions of packages r-cran-mgcv depends on: ii libc6 2.7-6GNU C Library: Shared libraries ii libgcc1 1:4.3-20080127-1 GCC support library ii libgfortran24.2.2-7 Runtime library for GNU Fortran ap ii r-base-core 2.6.1-2 GNU R core of statistical computin r-cran-mgcv recommends no packages. -- no debconf information -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Bug#463463: postinst fails if there is no /dev/shm/resolvconf/*
Package: resolvconf Version: 1.38 Severity: important I wanted network-manager-dev and network-manager-kde, so something pulled resolvconf. When it failed to install I removed it, and then: stiller:/home/ranke# LANG=C apt-get install resolvconf Reading package lists... Done Building dependency tree Reading state information... Done The following NEW packages will be installed: resolvconf 0 upgraded, 1 newly installed, 0 to remove and 2 not upgraded. Need to get 0B/50.8kB of archives. After this operation, 270kB of additional disk space will be used. Reading package fields... Done Reading package status... Done Retrieving bug reports... Done Parsing Found/Fixed information... Done /bin/sh: /usr/bin/apt-listchanges: No such file or directory Preconfiguring packages ... Selecting previously deselected package resolvconf. (Reading database ... 386489 files and directories currently installed.) Unpacking resolvconf (from .../resolvconf_1.38_all.deb) ... Setting up resolvconf (1.38) ... resolvconf.postinst: Info: Migrating /dev/shm/resolvconf to /lib/init/rw/resolvconf cp: cannot stat `/dev/shm/resolvconf/*': No such file or directory dpkg: error processing resolvconf (--configure): subprocess post-installation script returned error exit status 1 Errors were encountered while processing: resolvconf E: Sub-process /usr/bin/dpkg returned an error code (1) I don't have /dev/shm/resolvconf: stiller:/home/ranke# ls -l /dev/shm insgesamt 0 drwxr-xr-x 2 root root 60 31. Jan 16:53 network Here some parts of dpkg.log: stiller:/var/log# cat dpkg.log | grep resolvconf 2008-01-31 20:15:17 install resolvconf 1.37 1.38 2008-01-31 20:15:17 status half-installed resolvconf 1.37 2008-01-31 20:15:17 status unpacked resolvconf 1.38 2008-01-31 20:15:17 status unpacked resolvconf 1.38 2008-01-31 20:15:29 status unpacked resolvconf 1.38 2008-01-31 20:15:29 status unpacked resolvconf 1.38 2008-01-31 20:15:29 status unpacked resolvconf 1.38 2008-01-31 20:15:29 status unpacked resolvconf 1.38 2008-01-31 20:15:29 status unpacked resolvconf 1.38 2008-01-31 20:15:29 status unpacked resolvconf 1.38 2008-01-31 20:15:29 status unpacked resolvconf 1.38 2008-01-31 20:15:29 status unpacked resolvconf 1.38 2008-01-31 20:15:29 status unpacked resolvconf 1.38 2008-01-31 20:15:29 status unpacked resolvconf 1.38 2008-01-31 20:15:30 status unpacked resolvconf 1.38 2008-01-31 20:15:30 status unpacked resolvconf 1.38 2008-01-31 20:15:30 status unpacked resolvconf 1.38 2008-01-31 20:15:30 status half-configured resolvconf 1.38 2008-01-31 20:15:50 status half-configured resolvconf 1.38 2008-01-31 20:19:04 status half-configured resolvconf 1.38 2008-01-31 20:19:06 remove resolvconf 1.38 1.38 2008-01-31 20:19:06 status half-configured resolvconf 1.38 2008-01-31 20:19:06 status half-installed resolvconf 1.38 2008-01-31 20:19:06 status config-files resolvconf 1.38 2008-01-31 20:19:06 status config-files resolvconf 1.38 2008-01-31 20:21:07 install resolvconf 1.38 1.38 2008-01-31 20:21:07 status half-installed resolvconf 1.38 2008-01-31 20:21:07 status unpacked resolvconf 1.38 2008-01-31 20:21:07 status unpacked resolvconf 1.38 -- System Information: Debian Release: lenny/sid Architecture: amd64 (x86_64) Kernel: Linux 2.6.23-1-amd64 (SMP w/1 CPU core) Locale: [EMAIL PROTECTED], [EMAIL PROTECTED] (charmap=ISO-8859-15) Shell: /bin/sh linked to /bin/bash Versions of packages resolvconf depends on: ii coreutils 6.10-3 The GNU core utilities ii debconf [debconf-2.0] 1.5.19 Debian configuration management sy ii lsb-base 3.1-24 Linux Standard Base 3.1 init scrip resolvconf recommends no packages. -- debconf information: resolvconf/bad-pppoeconf-hook: * resolvconf/downup-interfaces: * resolvconf/link-tail-to-original: false resolvconf/bad-pppconfig-hook: resolvconf/linkify-resolvconf: true resolvconf/disable-bad-hooks: true resolvconf/bad-xisp-hook: -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Bug#463463: Acknowledgement (postinst fails if there is no /dev/shm/resolvconf/*)
OK, I purged the package and reinstalled without problems. I vaguely remember that I aborted debconf when resolvconf was pulled on a similar occasion. Best regards, Johannes * Debian Bug Tracking System <[EMAIL PROTECTED]> [080131 20:50]: > Thank you for the problem report you have sent regarding Debian. > This is an automatically generated reply, to let you know your message has > been received. It is being forwarded to the package maintainers and other > interested parties for their attention; they will reply in due course. > > Your message has been sent to the package maintainer(s): > resolvconf maintainers <[EMAIL PROTECTED]> > > If you wish to submit further information on your problem, please send > it to [EMAIL PROTECTED] (and *not* to > [EMAIL PROTECTED]). > > If you have filed this report in error and wish to close it, please > send mail to [EMAIL PROTECTED] with an explanation > why the bug report should be closed. > > Please do not reply to the address at the top of this message, > unless you wish to report a problem with the Bug-tracking system. > > Debian bug tracking system administrator > (administrator, Debian Bugs database) -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Bug#460745: New upstream version 0.4.9
Dear Marco, it's funny that you supply the changelog, since the maintainer of the package is also the main upstream author, so he is probably aware of the changes :) I am sure he will update the package soon. Cheers, Johannes * Marco Rodrigues <[EMAIL PROTECTED]> [080114 23:50]: > Package: rkward > Severity: wishlist > > Hi! Please update it... > > Changelog: > --- Version 0.4.9 - Jan-14-2008 > > - Improved user interface for CSV import plugin > - Support drawing grids in histogram and stripchart plots > - New plugin: Levene test > - New plugin: Jarque-Bera test (by Germán Márquez Mejía) > - Fixed: Crosstabs plugin produces better output > - Fixed: use.value.labels option was wrong in SPSS import plugin > - Fixed: SPSS tables would only be imported to the workspace, when the edit > option was checked > - Fixed: correct installation of rkward.desktop file > - Use the KDE default fixed spacing font for command log and object viewer > > Thanks > > -- > Marco Rodrigues > > http://Marco.Tondela.org > > > -- Dr. Johannes Ranke [EMAIL PROTECTED] Key ID: F649AF90 UFT Bremen, Leobenerstr. 1 +49 421 218 63373 D-28359 Bremen http://www.uft.uni-bremen.de/chemie/ranke
Bug#460745: New upstream version 0.4.9
Hi, never mind, just thought it would be interesting. And in this way I was made aware of the new upstream version, since I am subscribed to the package on qa.d.o. Johannes * Marco Rodrigues <[EMAIL PROTECTED]> [080115 14:20]: > Hi! > > I don't know if the maintainer is also upstream author =) if I take time to > check that, it will take much more time. > > Thanks for the reminder. > > Johannes Ranke wrote: > >Dear Marco, > > > >it's funny that you supply the changelog, since the maintainer of the > >package is also the main upstream author, so he is probably aware of the > >changes :) I am sure he will update the package soon. > > > >Cheers, > > > >Johannes > > -- > Marco Rodrigues > > http://Marco.Tondela.org > > > -- Dr. Johannes Ranke [EMAIL PROTECTED] Key ID: F649AF90 UFT Bremen, Leobenerstr. 1 +49 421 218 63373 D-28359 Bremen http://www.uft.uni-bremen.de/chemie/ranke -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Bug#432022: wengophone: Please package version 2.1.1
Package: wengophone Version: 2.1.0.dfsg-3+b1 Severity: wishlist Hi, today I had my first success with wengophone 2.1.0 - I was able to make an audio test call. Now can't reproduce anything any more, as I always get a segfault after starting up. Could you package 2.1.1, so we can test if it works any better? Greetings, Johannes -- System Information: Debian Release: lenny/sid APT prefers unstable APT policy: (500, 'unstable'), (1, 'experimental') Architecture: amd64 (x86_64) Kernel: Linux 2.6.20-1-amd64 (SMP w/1 CPU core) Locale: [EMAIL PROTECTED], [EMAIL PROTECTED] (charmap=ISO-8859-15) Shell: /bin/sh linked to /bin/bash Versions of packages wengophone depends on: ii libasound2 1.0.14a-2ALSA library ii libavcodec1d0.cvs20070307-5 ffmpeg codec library ii libavformat1d 0.cvs20070307-5 ffmpeg file format library ii libavutil1d 0.cvs20070307-5 ffmpeg utility library ii libboost-program-option 1.34.0-1 program options library for C++ ii libboost-regex1.34.01.34.0-1 regular expression library for C++ ii libboost-serialization1 1.34.0-1 serialization library for C++ ii libboost-signals1.34.0 1.34.0-1 managed signals and slots library ii libboost-thread1.34.0 1.34.0-1 portable C++ multi-threading ii libc6 2.5-11 GNU C Library: Shared libraries ii libcurl37.16.2-6 Multi-protocol file transfer libra ii libgcc1 1:4.2-20070627-1 GCC support library ii libglib2.0-02.12.12-1The GLib library of C routines ii libgnutls13 1.6.3-1 the GNU TLS library - runtime libr ii libportaudio2 19+svn20070125-1 Portable audio I/O - shared librar ii libqt4-core 4.3.0-2+b1 Qt 4 core non-GUI functionality ru ii libqt4-gui 4.3.0-2+b1 Qt 4 core GUI functionality runtim ii libsamplerate0 0.1.2-5 audio rate conversion library ii libsndfile1 1.0.17-3 Library for reading/writing audio ii libspeex1 1.1.12-3 The Speex Speech Codec ii libssl0.9.8 0.9.8e-5 SSL shared libraries ii libstdc++6 4.2-20070627-1 The GNU Standard C++ Library v3 ii libuuid11.40-1 universally unique id library ii libx11-62:1.0.3-7X11 client-side library ii libxml2 2.6.29.dfsg-1GNOME XML library wengophone recommends no packages. -- no debconf information -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Bug#432022: wengophone: Please package version 2.1.1
* Marco Nenciarini <[EMAIL PROTECTED]> [070707 10:30]: > On Fri, Jul 06, 2007 at 09:33:23PM +0200, Johannes Ranke wrote: > > Package: wengophone > > Version: 2.1.0.dfsg-3+b1 > > Severity: wishlist > > > > > > Hi, > > > > today I had my first success with wengophone 2.1.0 - I was able to make > > an audio test call. Now can't reproduce anything any more, as I always > > get a segfault after starting up. Could you package 2.1.1, so we can > > test if it works any better? > > > > I'm working on it, but I'm quite busy until tomorrow. Good to hear! Looking forward to doing some more testing. Thanks, Johannes > > I'll upload it after whis weekend. > > Ciao > > -- > - > |Marco Nenciarini| Debian/GNU Linux Developer - Plug Member | > | [EMAIL PROTECTED] | http://www.prato.linux.it/~mnencia | > ----- > Key fingerprint = FED9 69C7 9E67 21F5 7D95 5270 6864 730D F095 E5E4 > -- Dr. Johannes Ranke [EMAIL PROTECTED] Key ID: F649AF90 UFT Bremen, Leobenerstr. 1 +49 421 218 63373 D-28359 Bremen http://www.uft.uni-bremen.de/chemie/ranke -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Bug#503614: rpy: Missing build dependencies
Package: rpy Version: q Severity: normal Hi Dirk, Building my backport of rpy using pbuilder on amd64 (etch) fails (see below). Two commands are missing: pyversions (available in package python) and tex (available in package texlive-base-bin). I believe these are missing build-dependencies (and please forgive me if I overlooked someting in this late hour...). Kind regards, Johannes Setting up r-base-dev (2.8.0-1~etchcran.0) ... Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... -> Finished parsing the build-deps Reading package lists... Building dependency tree... fakeroot is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Copying back the cached apt archive contents Copying source file -> copying [../rpy_1.0.3-3~etchcran.2.8.0.dsc] -> copying [../rpy_1.0.3.orig.tar.gz] -> copying [../rpy_1.0.3-3~etchcran.2.8.0.diff.gz] Extracting source dpkg-source: warning: extracting unsigned source package (./rpy_1.0.3-3~etchcran.2.8.0.dsc) dpkg-source: extracting rpy in rpy-1.0.3 dpkg-source: unpacking rpy_1.0.3.orig.tar.gz dpkg-source: applying ./rpy_1.0.3-3~etchcran.2.8.0.diff.gz -> Building the package dpkg-buildpackage: source package is rpy dpkg-buildpackage: source version is 1.0.3-3~etchcran.2.8.0 dpkg-buildpackage: source changed by Johannes Ranke <[EMAIL PROTECTED]> dpkg-buildpackage: host architecture amd64 dpkg-buildpackage: source version without epoch 1.0.3-3~etchcran.2.8.0 fakeroot debian/rules clean make: pyversions: Command not found dh_testdir dh_testroot rm -f build-stamp configure-stamp [ ! -f Makefile ] || /usr/bin/make distclean (cd doc/ && make clean && rm -vf manual.pdf manual.info manual.dvi \ && rm -vfr manual_html manual_html.tgz) make[1]: Entering directory `/tmp/buildd/rpy-1.0.3/doc' rm -f rpy.cp rpy.cps rpy.fn rpy.fns rpy.ky rm -f rpy.kys rpy.log rpy.pg rpy.pgs rpy.tmp rm -f rpy.toc rpy.tp rpy.tps rpy.vr rpy.vrs rm -f rpy.aux make[1]: Leaving directory `/tmp/buildd/rpy-1.0.3/doc' for python in ; \ do $python setup.py clean; \ done rm -f `find . -name "*~"` rm -rf debian/tmp debian/files* core debian/substvars rm -f doc/html/function.html doc/html/packages.html rm -f doc/rpy.dvi doc/rpy.pdf doc/rpy_html.tgz rm -f config.cache config.status rm -rf build/* rm -rf rpy_version.pyc rpy_tools.pyc rm -rf doc/rpy_html/*.html doc/rpy.info dh_clean dpkg-source -b rpy-1.0.3 dpkg-source: building rpy using existing rpy_1.0.3.orig.tar.gz dpkg-source: building rpy in rpy_1.0.3-3~etchcran.2.8.0.diff.gz dpkg-source: warning: file debian/overrides has no final newline (either original or modified version) dpkg-source: building rpy in rpy_1.0.3-3~etchcran.2.8.0.dsc debian/rules build make: pyversions: Command not found dh_testdir touch configure-stamp dh_testdir for python in ; \ do CFLAGS="-O2 -Wall" $python setup.py build \ build_ext --include-dirs=/usr/share/R/include ; \ done (cd doc && make all) make[1]: Entering directory `/tmp/buildd/rpy-1.0.3/doc' tex rpy.texi make[1]: tex: Command not found make[1]: *** [rpy.dvi] Error 127 make[1]: Leaving directory `/tmp/buildd/rpy-1.0.3/doc' make: *** [build-stamp] Error 2 pbuilder: Failed autobuilding of package -> Aborting with an error -> unmounting dev/pts filesystem -> unmounting proc filesystem -> cleaning the build env -> removing directory /var/cache/pbuilder/build//17908 and its subdirectories -- System Information: Debian Release: lenny/sid APT prefers testing APT policy: (650, 'testing'), (500, 'unstable') Architecture: amd64 (x86_64) Kernel: Linux 2.6.26-1-amd64 (SMP w/1 CPU core) Locale: [EMAIL PROTECTED], [EMAIL PROTECTED] (charmap=ISO-8859-15) Shell: /bin/sh linked to /bin/bash -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Bug#503614: rpy: Missing build dependencies
* Dirk Eddelbuettel <[EMAIL PROTECTED]> [081027 09:10]: > > On 27 October 2008 at 00:23, Johannes Ranke wrote: > | Package: rpy > | Version: q > | Severity: normal > | > | > | Hi Dirk, > | > | Building my backport of rpy using pbuilder on amd64 (etch) fails (see > below). Two commands are missing: > | pyversions (available in package python) and tex (available in package > texlive-base-bin). I believe > | these are missing build-dependencies (and please forgive me if I overlooked > someting in this late > | hour...). > > Could be, haven't build it in a while. Some tex build-depends changed in > other programs too. > > Michael (CC'ed) discoverd last week that Rpy 1.0.* does not build under R > 2.8.0 because a bunch of internal headers for R are no longer exported. > > Greg (also CC'ed) promised to look into and fix Rpy if possible. Any news > there? Well, I just removed the line that includes Rdevices.h in src/RPy.h, and built a functioning (judged from running http://rpy.sourceforge.net/faithful.py) backport of python-rpy against R 2.8.0 (meanwhile on CRAN, I will announce the availability of the packages on r-sig-debian in a minute). I did the backport in a chroot that has tex installed, but when I wanted to build the amd64 package, pbuilder choked as described in the original report. I use pbuilder to check the build dependencies for all my CRAN packages in that way. > I was out of town and haven't looked into anything. > > Dirk > > PS Is Tyler working with you on testing / stable ports for CRAN ? > > | Kind regards, > | > | Johannes > | > | Setting up r-base-dev (2.8.0-1~etchcran.0) ... > | Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... > | -> Finished parsing the build-deps > | Reading package lists... > | Building dependency tree... > | fakeroot is already the newest version. > | 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. > | Copying back the cached apt archive contents > | Copying source file > | -> copying [../rpy_1.0.3-3~etchcran.2.8.0.dsc] > | -> copying [../rpy_1.0.3.orig.tar.gz] > | -> copying [../rpy_1.0.3-3~etchcran.2.8.0.diff.gz] > | Extracting source > | dpkg-source: warning: extracting unsigned source package > (./rpy_1.0.3-3~etchcran.2.8.0.dsc) > | dpkg-source: extracting rpy in rpy-1.0.3 > | dpkg-source: unpacking rpy_1.0.3.orig.tar.gz > | dpkg-source: applying ./rpy_1.0.3-3~etchcran.2.8.0.diff.gz > | -> Building the package > | dpkg-buildpackage: source package is rpy > | dpkg-buildpackage: source version is 1.0.3-3~etchcran.2.8.0 > | dpkg-buildpackage: source changed by Johannes Ranke <[EMAIL PROTECTED]> > | dpkg-buildpackage: host architecture amd64 > | dpkg-buildpackage: source version without epoch 1.0.3-3~etchcran.2.8.0 > | fakeroot debian/rules clean > | make: pyversions: Command not found > | dh_testdir > | dh_testroot > | rm -f build-stamp configure-stamp > | [ ! -f Makefile ] || /usr/bin/make distclean > | (cd doc/ && make clean && rm -vf manual.pdf manual.info manual.dvi \ > | && rm -vfr manual_html manual_html.tgz) > | make[1]: Entering directory `/tmp/buildd/rpy-1.0.3/doc' > | rm -f rpy.cp rpy.cps rpy.fn rpy.fns rpy.ky > | rm -f rpy.kys rpy.log rpy.pg rpy.pgs rpy.tmp > | rm -f rpy.toc rpy.tp rpy.tps rpy.vr rpy.vrs > | rm -f rpy.aux > | make[1]: Leaving directory `/tmp/buildd/rpy-1.0.3/doc' > | for python in ; \ > | do $python setup.py clean; \ > | done > | rm -f `find . -name "*~"` > | rm -rf debian/tmp debian/files* core debian/substvars > | rm -f doc/html/function.html doc/html/packages.html > | rm -f doc/rpy.dvi doc/rpy.pdf doc/rpy_html.tgz > | rm -f config.cache config.status > | rm -rf build/* > | rm -rf rpy_version.pyc rpy_tools.pyc > | rm -rf doc/rpy_html/*.html doc/rpy.info > | dh_clean > | dpkg-source -b rpy-1.0.3 > | dpkg-source: building rpy using existing rpy_1.0.3.orig.tar.gz > | dpkg-source: building rpy in rpy_1.0.3-3~etchcran.2.8.0.diff.gz > | dpkg-source: warning: file debian/overrides has no final newline (either > original or modified version) > | dpkg-source: building rpy in rpy_1.0.3-3~etchcran.2.8.0.dsc > | debian/rules build > | make: pyversions: Command not found > | dh_testdir > | touch configure-stamp > | dh_testdir > | for python in ; \ > | do CFLAGS="-O2 -Wall" $python setup.py build \ > | build_ext --include-dirs=/usr/share/R/include ; \ > | done > | (cd doc && make all) > | make[1]: Entering directory `/tmp/buildd/rpy-1.0.3/doc' > | tex rpy.texi > | make[1
Bug#503614: rpy: Missing build dependencies
* Dirk Eddelbuettel <[EMAIL PROTECTED]> [081027 16:50]: > > On 27 October 2008 at 16:01, Johannes Ranke wrote: > | * Dirk Eddelbuettel <[EMAIL PROTECTED]> [081027 09:10]: > | > > | > On 27 October 2008 at 00:23, Johannes Ranke wrote: > | > | Package: rpy > | > | Version: q > | > | Severity: normal > | > | > | > | > | > | Hi Dirk, > | > | > | > | Building my backport of rpy using pbuilder on amd64 (etch) fails (see > below). Two commands are missing: > | > | pyversions (available in package python) and tex (available in package > texlive-base-bin). I believe > | > | these are missing build-dependencies (and please forgive me if I > overlooked someting in this late > | > | hour...). > | > > | > Could be, haven't build it in a while. Some tex build-depends changed in > | > other programs too. > | > > | > Michael (CC'ed) discoverd last week that Rpy 1.0.* does not build under R > | > 2.8.0 because a bunch of internal headers for R are no longer exported. > | > > | > Greg (also CC'ed) promised to look into and fix Rpy if possible. Any news > | > there? > | > | Well, I just removed the line that includes Rdevices.h in src/RPy.h, and > built > | a functioning (judged from running http://rpy.sourceforge.net/faithful.py) > | backport of python-rpy against R 2.8.0 (meanwhile on CRAN, I will announce > | the availability of the packages on r-sig-debian in a minute). > > Cool. You're ahead of me. I haven't rebuild rpy for Debian-proper yet for R > 2.8.0. > That said, I am not sure what if any interfaces from Rdevices.h are (were?) > used in Rpy so there may be surprises Greg? > > | I did the backport in a chroot that has tex installed, but when I wanted to > | build the amd64 package, pbuilder choked as described in the original > report. I > | use pbuilder to check the build dependencies for all my CRAN packages in > that > | way. > > That is the way to do and how we all (incl autobuilders) find the sets of > packages we need. But sometimes packages get rearranged and we need to > adjust. > > To safe myself a minute or two: which texlive packages did you add? Well, I did not add any texlive package, as I have only built rpy on i386 in a chroot which had tex installed. I suspect texlive-base-bin would be a good guess as it contains /usr/bin/tex. Hannes -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Bug#503338: Installation of openjdk-6-jre fails in a lenny chroot
Package: openjdk-6-jre Version: 6b11-9.1 Followup-For: Bug #503338 Trying to set up a chroot with openjdk-6-jre I get the following: stiller:~# apt-get install openjdk-6-jre Reading package lists... Done Building dependency tree Reading state information... Done openjdk-6-jre is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 4 not fully installed or removed. After this operation, 0B of additional disk space will be used. Can not write log, openpty() failed (/dev/pts not mounted?) Setting up openjdk-6-jre-headless (6b11-9.1) ... warning: can't open /etc/mtab: No such file or directory /proc is not mounted; some java apps may fail /usr/lib/jvm/java-6-openjdk/bin/java: error while loading shared libraries: libjli.so: cannot open shared object file: No such file or directory dpkg: error processing openjdk-6-jre-headless (--configure): subprocess post-installation script returned error exit status 1 dpkg: dependency problems prevent configuration of openjdk-6-jre: openjdk-6-jre depends on openjdk-6-jre-headless (>= 6b11-9.1); however: Package openjdk-6-jre-headless is not configured yet. dpkg: error processing openjdk-6-jre (--configure): dependency problems - leaving unconfigured dpkg: dependency problems prevent configuration of rhino: rhino depends on default-jre-headless | java1-runtime-headless | java2-runtime-headless | java1-runtime | java2-runtime; however: Package default-jre-headless is not installed. Package java1-runtime-headless is not installed. Package java2-runtime-headless is not installed. Package openjdk-6-jre-headless which provides java2-runtime-headless is not configured yet. Package java1-runtime is not installed. Package java2-runtime is not installed. Package openjdk-6-jre which provides java2-runtime is not configured yet. dpkg: error processing rhino (--configure): dependency problems - leaving unconfigured dpkg: dependency problems prevent configuration of openjdk-6-jdk: openjdk-6-jdk depends on openjdk-6-jre (>= 6b11-9.1); however: Package openjdk-6-jre is not configured yet. dpkg: error processing openjdk-6-jdk (--configure): dependency problems - leaving unconfigured Errors were encountered while processing: openjdk-6-jre-headless openjdk-6-jre rhino openjdk-6-jdk E: Sub-process /usr/bin/dpkg returned an error code (1) Any comments appreciated. Johannes -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Bug#503338: openjdk-6-jre: Mounting /proc in the chroot helps...
Package: openjdk-6-jre Version: 6b11-9.1 Followup-For: Bug #503338 Sorry for the noise, Johannes -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Bug#465608: education-chemistry: fails to install: err 67: Custom distribution education does not exist
Package: education-chemistry Version: 0.824+svn40294 Severity: grave Justification: renders package unusable Setting up education-chemistry (0.824+svn40294) ... err 67: Custom distribution education does not exist dpkg: error processing education-chemistry (--configure): subprocess post-installation script returned error exit status 67 Errors were encountered while processing: education-chemistry E: Sub-process /usr/bin/dpkg returned an error code (1) -- System Information: Debian Release: lenny/sid Architecture: amd64 (x86_64) Kernel: Linux 2.6.23-1-amd64 (SMP w/1 CPU core) Locale: [EMAIL PROTECTED], [EMAIL PROTECTED] (charmap=ISO-8859-15) Shell: /bin/sh linked to /bin/bash Versions of packages education-chemistry depends on: ii education-tasks 0.824+svn40294 Debian Edu tasks for tasksel Versions of packages education-chemistry recommends: ii chemtool 1.6.10-1 Chemical structures drawing progra ii easychem 0.6-4 Draw high-quality molecules and 2D ii gchempaint0.8.6-12D chemical structures editor for ii gdis 0.89-2 molecular display ii ghemical 2.95-2 A GNOME molecular modelling enviro ii gperiodic 2.0.10-2 periodic table application ii kalzium 4:3.5.8-1 chemistry teaching tool for KDE ii pymol 1.0r2-1An OpenGL Molecular Graphics Syste ii viewmol 2.4.1-12 A graphical front end for computat ii xdrawchem 1.9.9-4+b1 Chemical structures and reactions -- no debconf information -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Bug#465747: openbabel: Some man pages are missing
Package: openbabel Version: 2.1.1-2 Severity: wishlist Man pages are missing for the following executables obenergy obminimize obrotamer roundtrip I am attaching a man page for obminimize that I just generated with doxygen from the obminimize.cpp source files from the debian source (2.1.1). I don't know why doxygen does not want to build the obenergy or obrotamer man pages from the respective .cpp files. BTW, the roundtrip executable gives the following usage information: [EMAIL PROTECTED] roundtrip Usage: roundtest which I find sort of confusing. Sorry for mixing the two things into one bug report. I noticed that in the sourceforge svn the man pages are there, except the one for roundtrip. Maybe time for an upload of an svn version? Best regards, and thanks, Johannes Ranke -- System Information: Debian Release: lenny/sid APT prefers unstable APT policy: (500, 'unstable'), (500, 'stable'), (1, 'experimental') Architecture: amd64 (x86_64) Kernel: Linux 2.6.24-1-amd64 (SMP w/1 CPU core) Locale: [EMAIL PROTECTED], [EMAIL PROTECTED] (charmap=ISO-8859-15) Shell: /bin/sh linked to /bin/bash Versions of packages openbabel depends on: ii libc6 2.7-7 GNU C Library: Shared libraries ii libgcc11:4.3-20080202-1 GCC support library ii libopenbabel2 2.1.1-2 Convert and manipulate chemical da ii libstdc++6 4.3-20080202-1The GNU Standard C++ Library v3 ii zlib1g 1:1.2.3.3.dfsg-11 compression library - runtime openbabel recommends no packages. -- no debconf information ..TH "obminimize" 1 "14 Feb 2008" "Version 2.1" "Open Babel" \" -*- nroff -*- ..ad l ..nh ..SH NAME minimize \- the energy for a molecule ..br ..PP \fBSYNOPSIS\fP ..RE ..PP \fBobminimize\fP [options] ..PP \fBDESCRIPTION\fP ..RE ..PP The obminimize tool can be used to minimize the energy for molecules inside (multi-)molecule files (e.g., MOL2, etc.) ..PP \fBOPTIONS\fP ..RE ..PP If no filename is given, obminimize will give all options including the available forcefields. ..PP \fB-n\fP : Specify the maximum number of steps ..br ..br \fB-ff\fP : Select the forcefield ..br ..br ..PP \fBEXAMPLES\fP ..IP "\(bu" 2 View the possible options, including available forcefields: obminimize ..IP "\(bu" 2 Minimize the energy for the molecule(s) in file test.mol2: obminimize test.mol2 ..IP "\(bu" 2 Minimize the energy for the molecule(s) in file test.mol2 using the Ghemical forcefield: obminimize -ff Ghemical test.mol2 ..IP "\(bu" 2 Minimize the energy for the molecule(s) in file test.mol2 and set the maximum numer of steps to 300: obenergy -n 300 test.mol2 ..PP ..RE ..PP \fBAUTHORS\fP ..RE ..PP The obminimize program was contributed by \fBTim\fP \fBVandermeersch\fP. ..PP Open Babel is currently maintained by \fBGeoff\fP \fBHutchison\fP, \fBChris\fP \fBMorley\fP and \fBMichael\fP \fBBanck\fP. ..PP For more contributors to Open Babel, see http://openbabel.sourceforge.net/THANKS.shtml ..PP \fBCOPYRIGHT\fP Copyright (C) 2007 by Tim Vandermeersch. ..br ..br This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation version 2 of the License. ..br ..br This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ..RE ..PP \fBSEE ALSO\fP The web pages for Open Babel can be found at: http://openbabel.sourceforge.net/ ..br The web pages for Open Babel Molecular Mechanics can be found at: http://openbabel.sourceforge.net/wiki/Molecular_mechanics ..br ..RE ..PP
Bug#485747: bind9: Same problem with kernel 2.6.24 from sid
Package: bind9 Followup-For: Bug #485747 I have the same problem with bind9 1:9.5.0.dfsg-1 using the current 2.6.24 kernel from sid (version 2.6.24-7) # grep CAPABILITIES /boot/config-2.6.24-1-amd64 CONFIG_SECURITY_CAPABILITIES=y CONFIG_SECURITY_FILE_CAPABILITIES=y I downgraded to 1:9.4.2-10, in order to have dns working again, and put the package on hold. -- System Information: Debian Release: lenny/sid APT prefers unstable APT policy: (500, 'unstable'), (1, 'experimental') Architecture: amd64 (x86_64) Kernel: Linux 2.6.24-1-amd64 (SMP w/1 CPU core) Locale: [EMAIL PROTECTED], [EMAIL PROTECTED] (charmap=ISO-8859-15) Shell: /bin/sh linked to /bin/bash Versions of packages bind9 depends on: ii adduser 3.108 add and remove users and groups ii libbind9-30 1:9.4.2-10 BIND9 Shared Library used by BIND ii libc62.7-12 GNU C Library: Shared libraries ii libdns32 1:9.4.2-10 DNS Shared Library used by BIND ii libisc32 1:9.4.2-10 ISC Shared Library used by BIND ii libisccc30 1:9.4.2-10 Command Channel Library used by BI ii libisccfg30 1:9.4.2-10 Config File Handling Library used ii liblwres30 1:9.4.2-10 Lightweight Resolver Library used ii libssl0.9.8 0.9.8g-10.1 SSL shared libraries ii lsb-base 3.2-12 Linux Standard Base 3.2 init scrip ii netbase 4.32Basic TCP/IP networking system bind9 recommends no packages. -- debconf information: bind9/different-configuration-file: bind9/run-resolvconf: true bind9/start-as-user: bind -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Bug#465747: openbabel: Some man pages are missing
* Daniel Leidert <[EMAIL PROTECTED]> [080228 01:40]: > forwarded 465747 > http://sourceforge.net/tracker/index.php?func=detail&aid=1900675&group_id=40728&atid=428740 > thanks > > Am Donnerstag, den 14.02.2008, 15:52 +0100 schrieb Johannes Ranke: > > > Man pages are missing for the following executables > > > > obenergy > > obminimize > > obrotamer > > roundtrip > > We know. lintian tells us often enough. > > > I am attaching a man page for obminimize that I just generated with > > doxygen from the obminimize.cpp source files from the debian source > > (2.1.1). > > Sorry, but this one needs to be edited. Section titles are covered by > the .SH macro, which is not the case in the generated man-page. I only have a vague idea what the different macros do, so I guess I am not the right person to create the man pages. Once I created a man page for a KDE binary using XML - this was rather straightforward. > I already tried (a recent) doxygen, but the generated man-pages look > ugly and contain broken ROFF. In any case (and this also seems to be > done by upstream atm) man-pages need to be edited and fixed by hand. > > > I don't know why doxygen does not want to build the obenergy > > or obrotamer man pages from the respective .cpp files. > > Take a look at doc/Makefile.am. There are simply no rules to create the > man-pages from the doxygen comments in the source - and if I take a look > at the result - this currently is the correct decision. I tried to create them by calling doxygen directly, but to no avail in the cases of obenergy and obrotamer. > > BTW, the roundtrip executable gives the following usage information: > > > > [EMAIL PROTECTED] roundtrip > > Usage: roundtest > > > > which I find sort of confusing. Sorry for mixing the two things into one > > bug report. I noticed that in the sourceforge svn the man pages are > > there, except the one for roundtrip. Maybe time for an upload of an > > svn version? > > I've added a hint to your question to the report at sf.net. Thanks. Regards, Johannes -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Bug#469128: gchempaint: crashes on startup
Package: gchempaint Version: 0.8.7-1 Severity: grave Justification: renders package unusable Hi Daniel, I just wanted to give the freshly updated gchempaint a try: [EMAIL PROTECTED]:~$ gchempaint (process:8241): GLib-GObject-CRITICAL **: /build/buildd/glib2.0-2.14.6/gobject/gtype.c:2242: initialization assertion failed, use IA__g_type_init() prior to this function (process:8241): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (process:8241): GLib-GObject-CRITICAL **: g_object_ref: assertion `G_IS_OBJECT (object)' failed Segmentation fault Hope that the above is helpful to find the problem. Best, Johannes Ranke -- System Information: Debian Release: lenny/sid Architecture: amd64 (x86_64) Kernel: Linux 2.6.20-1-amd64 (SMP w/1 CPU core) Locale: LANG=C, LC_CTYPE=C (charmap=ANSI_X3.4-1968) Shell: /bin/sh linked to /bin/bash Versions of packages gchempaint depends on: ii gconf2 2.20.1-3 GNOME configuration database syste ii libart-2.0-2 2.3.20-1 Library of functions for 2D graphi ii libatk1.0-01.20.0-1 The ATK accessibility toolkit ii libbonobo2-0 2.21.90-1 Bonobo CORBA interfaces library ii libbonoboui2-0 2.21.90-1 The Bonobo UI library ii libc6 2.7-9 GNU C Library: Shared libraries ii libcairo2 1.4.14-1 The Cairo 2D vector graphics libra ii libfontconfig1 2.5.0-2 generic font configuration library ii libfreetype6 2.3.5-1+b1FreeType 2 font engine, shared lib ii libgcc11:4.3.0~rc2-1 GCC support library ii libgconf2-42.20.1-3 GNOME configuration database syste ii libgcu00.8.6-1 GNOME chemistry utils (library) ii libgl1-mesa-glx [libgl 7.0.3~rc2-1 A free implementation of the OpenG ii libglade2-01:2.6.2-1 library to load .glade files at ru ii libglib2.0-0 2.14.6-1 The GLib library of C routines ii libglu1-mesa [libglu1] 7.0.3~rc2-1 The OpenGL utility library (GLU) ii libgnome2-02.20.1.1-1The GNOME 2 library - runtime file ii libgnomecanvas2-0 2.20.1.1-1A powerful object-oriented display ii libgnomeprint2.2-0 2.18.4-1 The GNOME 2.2 print architecture - ii libgnomeprintui2.2-0 2.18.2-1 GNOME 2.2 print architecture User ii libgnomeui-0 2.20.1.1-1The GNOME 2 libraries (User Interf ii libgnomevfs2-0 1:2.20.1-2GNOME Virtual File System (runtime ii libgoffice-0-4 0.4.2-4 Document centric objects library - ii libgsf-1-114 1.14.7-2 Structured File Library - runtime ii libgtk2.0-02.12.8-1 The GTK+ graphical user interface ii libgtkglext1 1.2.0-1 OpenGL Extension to GTK+ (shared l ii libice62:1.0.4-1 X11 Inter-Client Exchange library ii libopenbabel2 2.1.1-2 Convert and manipulate chemical da ii liborbit2 1:2.14.10-0.1 libraries for ORBit2 - a CORBA ORB ii libpango1.0-0 1.18.4-1 Layout and rendering of internatio ii libpng12-0 1.2.15~beta5-3PNG library - runtime ii libpopt0 1.10-3lib for parsing cmdline parameters ii libsm6 2:1.0.3-1+b1 X11 Session Management library ii libstdc++6 4.3.0~rc2-1 The GNU Standard C++ Library v3 ii libx11-6 2:1.0.3-7 X11 client-side library ii libxml22.6.31.dfsg-1 GNOME XML library ii libxmu62:1.0.4-1 X11 miscellaneous utility library ii libxrender11:0.9.4-1 X Rendering Extension client libra ii libxt6 1:1.0.5-3 X11 toolkit intrinsics library ii zlib1g 1:1.2.3.3.dfsg-11 compression library - runtime gchempaint recommends no packages. -- no debconf information -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Bug#360575: openoffice.org-writer: Culprit files
Package: openoffice.org-writer Version: 1:2.4.0-3 Followup-For: Bug #360575 The problem hit me, I think with the upgrade to 2.4.0. I followed hungerburgs instruction, and after that, WebWizard does not appear any more in ~/.openoffice.org2/user/basic/dialog.xlc ~/.openoffice.org2/user/basic/script.xlc so I believe deleting the respective rows in these xml config files would do the trick as well. Best, Johannes -- System Information: Debian Release: lenny/sid APT prefers unstable APT policy: (500, 'unstable'), (500, 'stable'), (1, 'experimental') Architecture: amd64 (x86_64) Kernel: Linux 2.6.24-1-amd64 (SMP w/1 CPU core) Locale: [EMAIL PROTECTED], [EMAIL PROTECTED] (charmap=ISO-8859-15) Shell: /bin/sh linked to /bin/bash Versions of packages openoffice.org-writer depends on: ii libc6 2.7-10GNU C Library: Shared libraries ii libgcc11:4.3.0-2 GCC support library ii libicu38 3.8.1-1 International Components for Unico ii libstdc++6 4.3.0-2 The GNU Standard C++ Library v3 ii libwpd8c2a 0.8.14-1 Library for handling WordPerfect d ii libwps-0.1-1 0.1.2-1 Works text file format import filt ii libxml22.6.31.dfsg-2 GNOME XML library ii openoffice.org-base-co 1:2.4.0-3 OpenOffice.org office suite -- lib ii openoffice.org-core1:2.4.0-3 OpenOffice.org office suite archit ii python-uno 1:2.4.0-3 Python interface for OpenOffice.or ii zlib1g 1:1.2.3.3.dfsg-11 compression library - runtime Versions of packages openoffice.org-writer recommends: ii gij-4.1 [java2-runtime] 4.1.2-19 The GNU Java bytecode interpreter ii java-gcj-compat [java2-runtim 1.0.77-5 Java runtime environment using GIJ ii openoffice.org-filter-binfilt 1:2.4.0-3 Legacy filters (e.g. StarOffice 5. ii openoffice.org-java-common1:2.4.0-3 OpenOffice.org office suite Java s ii openoffice.org-writer2latex 0.5-6 Writer/Calc to LaTeX/XHTML convert ii sun-java6-jre [java2-runtime] 6-05-1 Sun Java(TM) Runtime Environment ( Versions of packages openoffice.org-core depends on: ii fontconfig 2.5.0-2 generic font configuration library ii libc6 2.7-10GNU C Library: Shared libraries ii libcairo2 1.4.14-1 The Cairo 2D vector graphics libra ii libcurl3 7.18.0-1 Multi-protocol file transfer libra ii libdb4.6 4.6.21-7 Berkeley v4.6 Database Libraries [ ii libexpat1 1.95.8-4 XML parsing C library - runtime li ii libfreetype6 2.3.5-1+b1FreeType 2 font engine, shared lib ii libgcc11:4.3.0-2 GCC support library ii libglib2.0-0 2.16.1-2 The GLib library of C routines ii libgstreamer-plugins-b 0.10.18-3 GStreamer libraries from the "base ii libgstreamer0.10-0 0.10.18-4 Core GStreamer libraries and eleme ii libgtk2.0-02.12.9-2 The GTK+ graphical user interface ii libhyphen0 2.3.1-2 ALTLinux hyphenation library - sha ii libice62:1.0.4-1 X11 Inter-Client Exchange library ii libicu38 3.8.1-1 International Components for Unico ii libjpeg62 6b-14 The Independent JPEG Group's JPEG ii libldap-2.4-2 2.4.7-6.1 OpenLDAP libraries ii libneon27 0.28.1-2 An HTTP and WebDAV client library ii libnspr4-0d4.7.0-2 NetScape Portable Runtime Library ii libnss3-1d 3.12.0~beta2-1Network Security Service libraries ii libpam0g 0.99.7.1-6Pluggable Authentication Modules l ii libpango1.0-0 1.20.0-1 Layout and rendering of internatio ii libsm6 2:1.0.3-1+b1 X11 Session Management library ii libssl0.9.80.9.8g-8 SSL shared libraries ii libstdc++6 4.3.0-2 The GNU Standard C++ Library v3 ii libx11-6 2:1.0.3-7 X11 client-side library ii libxaw72:1.0.4-1 X11 Athena Widget library ii libxext6 2:1.0.4-1 X11 miscellaneous extension librar ii libxinerama1 2:1.0.3-1 X11 Xinerama extension library ii libxml22.6.31.dfsg-2 GNOME XML library ii libxrender11:0.9.4-1 X Rendering Extension client libra ii libxslt1.1 1.1.22-1 XSLT processing library - runtime ii libxt6 1:1.0.5-3 X11 toolkit intrinsics library ii libxtst6 2:1.0.3-1 X11 Testing -- Resource extension ii openoffice.org-common 1:2.4.0-3 OpenOffice.org office suite archit ii ttf-opensymbol 1:2.4.0-3 The OpenSymbol TrueType font
Bug#982465: Bug in r-base and r-cran-rcppparallel
Am Mittwoch, 10. Februar 2021, 18:55:57 CET schrieb Bastian Blank: > Control: clone -1 -2 > Control: reassign -1 r-base 4.0.3-1 > Control: retitle -1 r-base: dyn.load not useful for system libraries dyn.load is used in base R to load compiled code from R packages. As far as I understand, system libraries are linked at compile time and generally do not have to be loaded explicitly. ... > This are actually two bugs: > - r-base dyn.load not accepting relative library names on Linux systems The documentation of dyn.load says that it accepts a path to a dynamic shared object. Do we need more than that? Johannes
Bug#982465: Bug in r-base and r-cran-rcppparallel
Am Donnerstag, 11. Februar 2021, 12:20:33 CET schrieb Bastian Blank:
> Hi Johannes
Hello Bastian!
> On Thu, Feb 11, 2021 at 09:26:48AM +0100, Johannes Ranke wrote:
> > dyn.load is used in base R to load compiled code from R packages.
>
> Can you show some examples please? I know C and POSIX, but not much
> about R.
Well, in a nutshell, loading a package in R means calling library [1] which in
turn calls loadNamespace [2] which, if the package uses compiled code, calls
library.dynam [3], which uses dyn.load [4] after normalizing the path to the
DLL.
So if you load e.g. the package MASS in R, dyn.load is called:
R> debug(dyn.load)
R> library(MASS)
debugging in: dyn.load(file, DLLpath = DLLpath, ...)
debug: .Internal(dyn.load(x, as.logical(local), as.logical(now), ""))
Browse[2]> x
[1] "/usr/local/lib/R/site-library/MASS/libs/MASS.so"
...
> > The documentation of dyn.load says that it accepts a path to a dynamic
> > shared object. Do we need more than that?
>
> So my change is no problem, because it only changes the behaviour for
> 'dyn.load("object.so")', but not for
> 'dyn.load("/home/foo/projects/bar/object.so")'.
>
> The documentation does not list a search behaviour for bare library
> names on non-Windows systems. So completely ignoring the system library
> paths is kind of weird.
I can see that it looks weird - but is it a bug?
Johannes
[1] https://github.com/wch/r-source/blob/trunk/src/library/base/R/
library.R#L54
[2] https://github.com/wch/r-source/blob/trunk/src/library/base/R/
namespace.R#L185
[3] https://github.com/wch/r-source/blob/trunk/src/library/base/R/
library.R#L572
Bug#982465: Bug in r-base and r-cran-rcppparallel
> | > The documentation does not list a search behaviour for bare library > | > names on non-Windows systems. So completely ignoring the system library > | > paths is kind of weird. > | > | I can see that it looks weird - but is it a bug? > > Exactly. It has been like that since the 1990s Mhm, I am not sure I am seeing an argument here :) > when R's packaging system was > set up. We have hundreds of per package shared libraries. Even the first > one I packaged for Debian (r-cran-rodbc, in 2003 if memory serves) used > that. > > "A feature not a bug" :) Or a missing feature, given that it was proposed to solve a problem... Johannes
Bug#983012: plasma-desktop: installing plasma-desktop does not pull kmix
Package: plasma-desktop Version: 4:5.20.5-3 Severity: important Dear Debian Qt/KDE maintainers, I had to reinstall plasma-desktop upon the upgrade to bullseye, see #981597. After reinstalling plasma-desktop, I had not sound applet in my task bar, and kmix was not installed. Please add a dependency on kmix to plasma-desktop or to one of the packages it depends on, if this is more suitable. I think users rightfully expect to see a sound volume applet after installing a KDE desktop environment. Thanks, Johannes -- System Information: Debian Release: bullseye/sid APT prefers testing APT policy: (500, 'testing') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.10.0-3-amd64 (SMP w/16 CPU threads) Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages plasma-desktop depends on: ii accountsservice 0.6.55-3 ii breeze 4:5.20.5-2 ii kactivitymanagerd5.20.5-1 ii kde-cli-tools4:5.20.5-2 ii kded55.78.0-2 ii kio 5.78.0-4 ii kpackagetool55.78.0-3 ii libaccounts-qt5-11.16-2 ii libc62.31-9 ii libcrypt11:4.4.17-1 ii libglib2.0-0 2.66.7-1 ii libibus-1.0-51.5.23-2 ii libkaccounts24:20.12.1-1 ii libkf5activities55.78.0-2 ii libkf5activitiesstats1 5.78.0-2 ii libkf5authcore5 5.78.0-2 ii libkf5baloo5 5.78.0-2 ii libkf5codecs55.78.0-2 ii libkf5completion55.78.0-3 ii libkf5configcore55.78.0-4 ii libkf5configgui5 5.78.0-4 ii libkf5configwidgets5 5.78.0-2 ii libkf5coreaddons55.78.0-2 ii libkf5crash5 5.78.0-3 ii libkf5dbusaddons55.78.0-2 ii libkf5declarative5 5.78.0-2 ii libkf5globalaccel-bin5.78.0-2 ii libkf5globalaccel5 5.78.0-2 ii libkf5guiaddons5 5.78.0-3 ii libkf5i18n5 5.78.0-2 ii libkf5iconthemes55.78.0-2 ii libkf5itemviews5 5.78.0-2 ii libkf5kcmutils5 5.78.0-3 ii libkf5kdelibs4support5 5.78.0-2 ii libkf5kiocore5 5.78.0-4 ii libkf5kiofilewidgets55.78.0-4 ii libkf5kiogui55.78.0-4 ii libkf5kiowidgets55.78.0-4 ii libkf5notifications5 5.78.0-2 ii libkf5notifyconfig5 5.78.0-2 ii libkf5package5 5.78.0-3 ii libkf5plasma55.78.0-3 ii libkf5plasmaquick5 5.78.0-3 ii libkf5quickaddons5 5.78.0-2 ii libkf5runner55.78.0-3 ii libkf5service-bin5.78.0-2 ii libkf5service5 5.78.0-2 ii libkf5solid5 5.78.0-2 ii libkf5sonnetcore55.78.0-2 ii libkf5sonnetui5 5.78.0-2 ii libkf5wallet-bin 5.78.0-2 ii libkf5wallet55.78.0-2 ii libkf5widgetsaddons5 5.78.0-2 ii libkf5windowsystem5 5.78.0-2 ii libkf5xmlgui55.78.0-2 ii libkworkspace5-5 4:5.20.5-3 ii libnotificationmanager1 4:5.20.5-3 ii libphonon4qt5-4 4:4.11.1-3 ii libprocesscore9 4:5.20.5-1 ii libqt5concurrent55.15.2+dfsg-4 ii libqt5core5a 5.15.2+dfsg-4 ii libqt5dbus5 5.15.2+dfsg-4 ii libqt5gui5 5.15.2+dfsg-4 ii libqt5network5 5.15.2+dfsg-4 ii libqt5qml5 5.15.2+dfsg-4 ii libqt5quick5 5.15.2+dfsg-4 ii libqt5quickwidgets5 5.15.2+dfsg-4 ii libqt5sql5 5.15.2+dfsg-4 ii libqt5widgets5 5.15.2+dfsg-4 ii libqt5x11extras5 5.15.2-2 ii libqt5xml5 5.15.2+dfsg-4 ii libscim8v5 1.4.18-2.2 ii libstdc++6 10.2.1-6 ii libtaskmanager6abi1
Bug#981597: plasma-desktop: Same problem on a system set up with stretch
Package: plasma-desktop Version: 4:5.20.5-3 Followup-For: Bug #981597 I was recently upgrading my system originally set up as a stretch system, but running buster. I can confirm that I had to completely remove all kde related packages including plasma-desktop to be able to do the upgrade to bullseye. This was a bit frightening, but after the upgrade to bullseye, I was able to install plasma-desktop and got back almost all of the KDE programs I was using. Thanks for maintaining KDE in Debian! -- System Information: Debian Release: bullseye/sid APT prefers testing APT policy: (500, 'testing') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.10.0-3-amd64 (SMP w/16 CPU threads) Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages plasma-desktop depends on: ii accountsservice 0.6.55-3 ii breeze 4:5.20.5-2 ii kactivitymanagerd5.20.5-1 ii kde-cli-tools4:5.20.5-2 ii kded55.78.0-2 ii kio 5.78.0-4 ii kpackagetool55.78.0-3 ii libaccounts-qt5-11.16-2 ii libc62.31-9 ii libcrypt11:4.4.17-1 ii libglib2.0-0 2.66.7-1 ii libibus-1.0-51.5.23-2 ii libkaccounts24:20.12.1-1 ii libkf5activities55.78.0-2 ii libkf5activitiesstats1 5.78.0-2 ii libkf5authcore5 5.78.0-2 ii libkf5baloo5 5.78.0-2 ii libkf5codecs55.78.0-2 ii libkf5completion55.78.0-3 ii libkf5configcore55.78.0-4 ii libkf5configgui5 5.78.0-4 ii libkf5configwidgets5 5.78.0-2 ii libkf5coreaddons55.78.0-2 ii libkf5crash5 5.78.0-3 ii libkf5dbusaddons55.78.0-2 ii libkf5declarative5 5.78.0-2 ii libkf5globalaccel-bin5.78.0-2 ii libkf5globalaccel5 5.78.0-2 ii libkf5guiaddons5 5.78.0-3 ii libkf5i18n5 5.78.0-2 ii libkf5iconthemes55.78.0-2 ii libkf5itemviews5 5.78.0-2 ii libkf5kcmutils5 5.78.0-3 ii libkf5kdelibs4support5 5.78.0-2 ii libkf5kiocore5 5.78.0-4 ii libkf5kiofilewidgets55.78.0-4 ii libkf5kiogui55.78.0-4 ii libkf5kiowidgets55.78.0-4 ii libkf5notifications5 5.78.0-2 ii libkf5notifyconfig5 5.78.0-2 ii libkf5package5 5.78.0-3 ii libkf5plasma55.78.0-3 ii libkf5plasmaquick5 5.78.0-3 ii libkf5quickaddons5 5.78.0-2 ii libkf5runner55.78.0-3 ii libkf5service-bin5.78.0-2 ii libkf5service5 5.78.0-2 ii libkf5solid5 5.78.0-2 ii libkf5sonnetcore55.78.0-2 ii libkf5sonnetui5 5.78.0-2 ii libkf5wallet-bin 5.78.0-2 ii libkf5wallet55.78.0-2 ii libkf5widgetsaddons5 5.78.0-2 ii libkf5windowsystem5 5.78.0-2 ii libkf5xmlgui55.78.0-2 ii libkworkspace5-5 4:5.20.5-3 ii libnotificationmanager1 4:5.20.5-3 ii libphonon4qt5-4 4:4.11.1-3 ii libprocesscore9 4:5.20.5-1 ii libqt5concurrent55.15.2+dfsg-4 ii libqt5core5a 5.15.2+dfsg-4 ii libqt5dbus5 5.15.2+dfsg-4 ii libqt5gui5 5.15.2+dfsg-4 ii libqt5network5 5.15.2+dfsg-4 ii libqt5qml5 5.15.2+dfsg-4 ii libqt5quick5 5.15.2+dfsg-4 ii libqt5quickwidgets5 5.15.2+dfsg-4 ii libqt5sql5 5.15.2+dfsg-4 ii libqt5widgets5 5.15.2+dfsg-4 ii libqt5x11extras5 5.15.2-2 ii libqt5xml5 5.15.2+dfsg-4 ii libscim8v5 1.4.18-2.2 ii libstdc++6 10.2.1-6 ii libtaskmanager6abi1
Bug#983012: plasma-desktop: installing plasma-desktop does not pull kmix
> Maybe it has to do with desktop-file-utils? kmix from bullseye/sid installs, among others: /etc/xdg/autostart/kmix_autostart.desktop /etc/xdg/autostart/restore_kmix_volumes.desktop On my system, I have me@box:/etc/xdg/autostart$ ls -lh .. lrwxrwxrwx 1 root root 43 18. Okt 2016 kmix_autostart.desktop -> /usr/ share/autostart/kmix_autostart.desktop -rw-r--r-- 1 root root 3,0K 11. Nov 10:35 kmix_autostart.desktop.dpkg-new ... lrwxrwxrwx 1 root root 49 18. Okt 2016 restore_kmix_volumes.desktop -> / usr/share/autostart/restore_kmix_volumes.desktop -rw-r--r-- 1 root root 2,6K 11. Nov 10:35 restore_kmix_volumes.desktop.dpkg- new ... The links to /usr/share/autostart are missing their targets. They were originally installed with stretch: https://packages.debian.org/stretch/amd64/kmix/filelist Cheers, Johannes
Bug#981597: plasma-desktop: Same problem on a system set up with stretch
Am Donnerstag, 18. Februar 2021, 08:41:48 CET schrieb Norbert Preining: > Did you do dist-upgrade? I simple upgrade might not find a proper > solution because several packages need to be removed. I do remember that I tried apt full-upgrade and aptitude full-upgrade without success. > It is really hard to debug this, and in general it seems to be an apt > problem not being able to find a solution, while there definitely is > one, as you have shown yourself by installing it afterwards ;-) > > So, without more debugging - and that is not possible since you have > already upgraded your system, it is really hard to say why all this > happened. I agree. I thought it was only my system, but now when I see this bug report, I got the impression that it may be a general problem of stretch -> buster installations upgrading to bullseye. I have a stretch chroot hanging around that I could upgrade to buster to see if I can reproduce it. Cheers, Johannes
Bug#983012: plasma-desktop: installing plasma-desktop does not pull kmix
> Hmmm, I don't have kmix installed either ... but I do have a sound > applet in my systray. Oh, I see... > > Please add a dependency on kmix to plasma-desktop or to one of the > > packages it depends on, if this is more suitable. > > kmix doesn't help here, it must be something else that is missing, since > I don't have kmix and I have a sound applet ;-) The applet came back after installing kmix and calling it from the command line. Also, after logging out and logging in again, I did not have to manually start it any more to have it. I just removed kmix, logged out and logged back in, and the applet is gone again... Maybe it has to do with desktop-file-utils? I noticed when installing kmix it processes a trigger for it: ... Setting up kmix (4:20.12.0-1) ... Processing triggers for desktop-file-utils (0.26-1) ... ... Best, Johannes
Bug#981597: plasma-desktop: Same problem on a system set up with stretch
Am Donnerstag, 18. Februar 2021, 09:58:59 CET schrieb Johannes Ranke: > I have a stretch chroot hanging around that I could upgrade to buster to see > if I can reproduce the problem. I just installed plasma-desktop on stretch and upgraded stretch -> buster -> bullseye without problems in a pbuilder chroot. So it seems there was something more specific on my system preventing the smooth upgrade. Thanks, Johannes
Bug#983012: plasma-desktop: installing plasma-desktop does not pull kmix
> The links to /usr/share/autostart are missing their targets. > OK, the problem with the links is a different bug https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=803523 Regarding the Volume applet, there is a competition between plasma-pa and kmix https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=798504 I had plasma-pm applet deactivated in order to avoid having two mixer applets in the systray. So the origin of the problem on my end was actually that kmix got lost in the upgrade to bullseye, because I had to reinstall KDE, as reported under #981597. Thanks again for maintaining Qt/KDE in Debian! Johannes
Bug#981597: plasma-desktop: Same problem on a system set up with stretch
> I tend to close this bug ... any objections from other participants > here? I'd keep it open, as it is not clear where the problem comes from and it was observed on two independent systems. Maybe someone can figure it out before the official release. Johannes
Bug#981597: plasma-desktop: Same problem on a system set up with stretch
I dug up my upgrade transcript, and it shows, after the first apt-upgrade $ apt full-upgrade Some packages could not be installed... ... Die folgenden Pakete haben unerfüllte Abhängigkeiten: libc6-dev : Beschädigt: libgcc-8-dev (< 8.4.0-2~) aber 8.3.0-6 soll installiert werden ... i.e. the installation candidate for libc6-dev had a "Breaks" on libgcc-8-dev (< 8.4.0-2~) but 8.3.0-6 was to be installed. I just checked and libgcc-8-dev is only present in buster (8.3.0-6), but not in bullseye. I then "solved" it by removing libgcc8-dev which removed almost all of KDE which I then reinstalled without problems. Normally (in my pbuilder chroot with less packages installed) apt full-upgrade will remove libgcc-8-dev. It seems some package on my system still wanted libgcc-8-dev. I assume it was just a temporary problem, maybe caused by an incomplete migration of packages to testing. From my part, the bug can be closed. Johannes
Bug#982465: Debian bug report 982465: dyn.load not useful for system libraries
Hi Dirk, Am Freitag, 19. Februar 2021, 00:27:33 CET schrieb Dirk Eddelbuettel: > severity 982465 wishlist I think the severity of the bug [1] depends on Debian policy - is it mandatory to use system libraries if they are available? Johannes [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=982465
Bug#910054: kmail: Fatal startup error: Could not create collection inbox, resourceId: 3
Package: kmail Version: 4:18.08.3-1 Followup-For: Bug #910054 For what it's worth, I can confirm that this is still happening on a fresh buster install. -- System Information: Debian Release: 10.2 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable') Architecture: amd64 (x86_64) Kernel: Linux 4.19.0-6-amd64 (SMP w/8 CPU cores) Kernel taint flags: TAINT_FIRMWARE_WORKAROUND Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8), LANGUAGE= (charmap=UTF-8) Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages kmail depends on: ii akonadi-server 4:18.08.3-7~deb10u1 ii kdepim-runtime 4:18.08.3-4 ii kio 5.54.1-1 ii libc62.28-10 ii libgcc1 1:8.3.0-6 ii libgpgmepp6 1.12.0-6 ii libkf5akonadiagentbase5 4:18.08.3-7~deb10u1 ii libkf5akonadicontact54:18.08.3-1 ii libkf5akonadicore5abi2 4:18.08.3-7~deb10u1 ii libkf5akonadimime5 4:18.08.3-1 ii libkf5akonadisearch-bin 4:18.08.3-1 ii libkf5akonadisearch-plugins 4:18.08.3-1 ii libkf5akonadisearchdebug54:18.08.3-1 ii libkf5akonadisearchpim5 4:18.08.3-1 ii libkf5akonadiwidgets5abi14:18.08.3-7~deb10u1 ii libkf5bookmarks5 5.54.0-1 ii libkf5calendarcore5abi2 4:18.08.3-1 ii libkf5calendarutils5 4:18.08.3-2 ii libkf5codecs55.54.0-1 ii libkf5completion55.54.0-1 ii libkf5configcore55.54.0-1+deb10u1 ii libkf5configgui5 5.54.0-1+deb10u1 ii libkf5configwidgets5 5.54.0-1 ii libkf5contacts5 4:18.08.3-1 ii libkf5coreaddons55.54.0-1 ii libkf5crash5 5.54.0-1 ii libkf5dbusaddons55.54.0-1 ii libkf5followupreminder5 4:18.08.3-2 ii libkf5grantleetheme-plugins 18.08.3-1 ii libkf5gravatar5abi2 4:18.08.3-1 ii libkf5guiaddons5 5.54.0-1 ii libkf5i18n5 5.54.0-1 ii libkf5iconthemes55.54.0-1 ii libkf5identitymanagement518.08.3-2 ii libkf5itemmodels55.54.0-1 ii libkf5itemviews5 5.54.0-1 ii libkf5jobwidgets55.54.0-1 ii libkf5kcmutils5 5.54.0-1 ii libkf5kiocore5 5.54.1-1 ii libkf5kiofilewidgets55.54.1-1 ii libkf5kiowidgets55.54.1-1 ii libkf5kontactinterface5 18.08.3-1 ii libkf5ksieveui5 4:18.08.3-2 ii libkf5libkdepim-plugins 4:18.08.3-2 ii libkf5libkdepim5 4:18.08.3-2 ii libkf5libkdepimakonadi5 4:18.08.3-2 ii libkf5libkleo5 4:18.08.3-2 ii libkf5mailcommon5abi24:18.08.3-2 ii libkf5mailtransport5 18.08.3-2 ii libkf5mailtransportakonadi5 18.08.3-2 ii libkf5messagecomposer5abi1 4:18.08.3-2 ii libkf5messagecore5abi1 4:18.08.3-2 ii libkf5messagelist5abi1 4:18.08.3-2 ii libkf5messageviewer5abi1 4:18.08.3-2 ii libkf5mime5abi1 18.08.3-1 ii libkf5mimetreeparser5abi14:18.08.3-2 ii libkf5notifications5 5.54.0-1 ii libkf5notifyconfig5 5.54.0-1 ii libkf5parts5 5.54.0-1 ii libkf5pimcommon5abi2 4:18.08.3-2 ii libkf5pimcommonakonadi5abi1 4:18.08.3-2 ii libkf5pimtextedit5abi2 18.08.3-1 ii libkf5sendlater5 4:18.08.3-2 ii libkf5service-bin5.54.0-1 ii libkf5service5 5.54.0-1 ii libkf5sonnetui5 5.54.0-1 ii libkf5templateparser54:18.08.3-2 ii libkf5textwidgets5 5.54.0-1 ii libkf5tnef5 4:18.08.3-1 ii libkf5wallet-bin 5.54.0-1 ii libkf5wallet55.54.0-1 ii libkf5webengineviewer5abi1 4:18.08.3-2 ii libkf5widgetsaddons5 5.54.0-1 ii libkf5windowsystem5 5.54.0-1 ii libkf5xmlgui55.54.0-1 ii libqgpgme7 1.12.0-6 ii libqt5core5a 5.11.3+dfsg1-1+deb10u1 ii libqt5dbus5 5.11.3+dfsg1-1+deb10u1 ii libqt5gui5 5.11.3+dfsg1-1+deb10u1 ii libqt5network5 5.11.3+dfsg1-1+deb10u1 ii libqt5widgets5 5.11.3+dfsg1-1+deb10u1 ii libqt5xml5 5.11.3+dfsg1-1+deb10u1 ii libstdc++6 8.3.0-6 Versions of packages kmail recommends: ii accountwizard 4:18.08.3-1 ii gnupg 2.2.12-1+deb10u1 ii kdepim-addons 18.08.3-2 ii kdepim-themeeditors 4:18.08.3-1 ii mbox-importer 4:18.08.3-1 ii pim-data-exporter 4:18.08.3-1 ii pim-sieve-editor4:18.08.3-1 ii pinentry-qt [pinentry-x11] 1.1.0-2 Versions of packages kmail suggests: pn clamav ii kaddressbook 4:18.08.3-3 pn kleopatra pn
Bug#948663: kdepim-runtime: account wizard cannot show kde widgets like KLineEdit
Package: kdepim-runtime Version: 4:18.08.3-4 Severity: normal Dear Maintainer, on a freshly installed buster system I would like to configure my PIM accounts for use with kontact. Upon the first start of kontact, the account wizard starts. When I select kolab as the account type I would like to set up, I get a window for entering personal settings which is incomplete. On the command line where I started kontact I get org.kde.pim.kidentitymanagement: IdentityManager: There was no default identity. Marking first one as default. No text-to-speech plug-ins were found. kf5.kxmlgui: cannot find .rc file "kontactsummary_part.rc" for component "kontact" No such XML file "/home/jranke/.local/share/kontact/default-.rc" org.kde.pim.akonadiplugin_indexer: unknown term "birthday" org.kde.pim.akonadiplugin_indexer: unknown term "birthday" "https://dot.kde.org/rss.xml"; "https://www.linux.com/feeds/rss"; "https://planetkde.org/rss20.xml"; "https://store.kde.org/content.rdf"; "https://planetkde.org/pt-br/rss20.xml"; "https://planet.kde-espana.org/atom.xml"; "http://planet.debian.org/rss20.xml"; "http://www.debian.org/News/news"; org.kde.pim.akonadiplugin_indexer: unknown term "birthday" org.kde.pim.akonadiplugin_indexer: unknown term "birthday" org.kde.pim.akonadiplugin_indexer: unknown term "birthday" org.kde.pim.akonadiplugin_indexer: unknown term "birthday" "QFormBuilder was unable to create a widget of the class 'KLineEdit'." "Empty widget item in QFormLayout 'formLayout'." "QFormBuilder was unable to create a widget of the class 'KLineEdit'." "Empty widget item in QFormLayout 'formLayout'." "QFormBuilder was unable to create a custom widget of the class 'KPasswordLineEdit'; defaulting to base class 'QWidget'." Kross: "Error error=TypeError: Result of expression 'page.widget().nameEdit' [undefined] is not an object. lineno=27 trace=\n() at /usr/share/akonadi/accountwizard/kolab/kolabwizard.es:27" I was trying to find a missing dependency, but libkf5completion5 where KLineEdit is defined is installed as can be seen below. Also, libkf5widgetsaddons is installed, which should have KPasswordLineEdit. Thanks for maintaining KDE PIM software! Johannes -- System Information: Debian Release: 10.2 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable') Architecture: amd64 (x86_64) Kernel: Linux 4.19.0-6-amd64 (SMP w/8 CPU cores) Kernel taint flags: TAINT_FIRMWARE_WORKAROUND Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8), LANGUAGE= (charmap=UTF-8) Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages kdepim-runtime depends on: ii akonadi-server 4:18.08.3-7~deb10u1 ii kio 5.54.1-1 ii kio-ldap 18.08.3-1 ii libc62.28-10 ii libgcc1 1:8.3.0-6 ii libkf5akonadiagentbase5 4:18.08.3-7~deb10u1 ii libkf5akonadicalendar5abi1 4:18.08.3-1 ii libkf5akonadicontact54:18.08.3-1 ii libkf5akonadicore5abi2 4:18.08.3-7~deb10u1 ii libkf5akonadimime5 4:18.08.3-1 ii libkf5akonadinotes5 4:18.08.3-1 ii libkf5akonadiwidgets5abi14:18.08.3-7~deb10u1 ii libkf5alarmcalendar5abi1 4:18.08.3-2 ii libkf5calendarcore5abi2 4:18.08.3-1 ii libkf5codecs55.54.0-1 ii libkf5completion55.54.0-1 ii libkf5configcore55.54.0-1+deb10u1 ii libkf5configgui5 5.54.0-1+deb10u1 ii libkf5configwidgets5 5.54.0-1 ii libkf5contacts5 4:18.08.3-1 ii libkf5coreaddons55.54.0-1 ii libkf5dbusaddons55.54.0-1 ii libkf5i18n5 5.54.0-1 ii libkf5identitymanagement518.08.3-2 ii libkf5imap5 18.08.3-1 ii libkf5itemmodels55.54.0-1 ii libkf5jobwidgets55.54.0-1 ii libkf5kdelibs4support5 5.54.0-1 ii libkf5kiocore5 5.54.1-1 ii libkf5kiowidgets55.54.1-1 ii libkf5mailtransport5 18.08.3-2 ii libkf5mailtransportakonadi5 18.08.3-2 ii libkf5mbox5 18.08.3-1 ii libkf5mime5abi1 18.08.3-1 ii libkf5notifications5 5.54.0-1 ii libkf5notifyconfig5 5.54.0-1 ii libkf5service-bin5.54.0-1 ii libkf5service5 5.54.0-1 ii libkf5textwidgets5 5.54.0-1 ii libkf5wallet-bin 5.54.0-1 ii libkf5wallet55.54.0-1 ii libkf5widgetsaddons5 5.54.0-1 ii libkf5windowsystem5 5.54.0-1 ii libkf5xmlgui55.54.0-1 ii libkolabxml1v5 1.1.6-4 ii libkpimgapicalendar5 18.08.3-2 ii libkpimgapicontacts5 18.08.3-2 ii libkpimgapicore5abi1 18.08.3-2 ii libkpim
Bug#986186: postgresql-common: pg_dump does not talk to the last major version (11): Error: PostgreSQL version 9.6 is not installed
Am Mittwoch, 14. April 2021, 17:36:19 CEST schrieb Christoph Berg: > Re: Johannes Ranke > > > > Everything should be detailed in > > > /usr/share/doc/postgresql-common/README.Debian.gz. > > > > How about inserting a pointer to this (very helpful and carefully > > prepared) > > document in the release notes under 5.3? I think it is important for > > administrators to be aware that psql and the commands handled by > > pg_wrapper > > will not "just work" after the upgrade. > > If you run pg_upgradecluster properly, it will flip the ports used so > "psql" will continue to work for the upgraded cluster on port 5432. For me, a sentence in the bullseye release notes that I need to run pg_upgradecluster and a pointer to the README would have been very helpful in the upgrade process, as I did not anticipate that I need to do something regarding postgres. Anyways, many thanks for your excellent work on this, Johannes > > Christoph
Bug#986186: postgresql-common: pg_dump does not talk to the last major version (11): Error: PostgreSQL version 9.6 is not installed
Package: postgresql-common Version: 225 Severity: normal Dear Maintainer, I have upgraded this buster system to bullseye. I did not do anything postgresql related during the upgrade and phppgadmin kept working, so I kept entering data with that. I think both clusters (11 and 13) were running at the same time, and phppgadmin connected to 11. Now I would like to make a database dump before I upgrade the cluster. The postgresql 9.6 directory is still present, and postgresql-11 is still installed and running: $ pg_lsclusters Ver Cluster Port StatusOwnerData directory Log file 9.6 main5432 down,binaries_missing postgres /var/lib/postgresql/9.6/main /var/log/postgresql/postgresql-9.6-main.log 11 main5433 onlinepostgres /var/lib/postgresql/11/main /var/log/postgresql/postgresql-11-main.log 13 main5434 onlinepostgres /var/lib/postgresql/13/main /var/log/postgresql/postgresql-13-main.log I can connect to the version 11 cluster with psql -p 5433 my_database, but when I run pg_dump -p 5433 my_database, I get Error: PostgreSQL version 9.6 is not installed After dropping 9.6 with pg_dropcluster this works as expected, but I think it would be preferable if this would not be necessary. BTW, is there work underway to provide a postgresql specific paragraph in the bullseye release notes? I am not very experienced with postgresql, but would be willing to help writing/proof reading/testing. Johannes -- System Information: Debian Release: bullseye/sid APT prefers testing APT policy: (500, 'testing'), (500, 'stable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.10.0-3-amd64 (SMP w/16 CPU threads) Kernel taint flags: TAINT_WARN Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages postgresql-common depends on: ii adduser 3.118 ii debconf [debconf-2.0] 1.5.75 ii lsb-base 11.1.0 ii perl 5.32.1-3 ii postgresql-client-common 225 ii ssl-cert 1.1.0 ii ucf 3.0043 Versions of packages postgresql-common recommends: ii e2fsprogs 1.46.2-1 ii logrotate 3.18.0-2 Versions of packages postgresql-common suggests: ii libjson-perl 4.03000-1 -- Configuration Files: /etc/apt/apt.conf.d/01autoremove-postgresql changed [not included] -- debconf information: * postgresql-common/obsolete-major: postgresql-common/catversion-bump: postgresql-common/ssl: true
Bug#986186: postgresql-common: pg_dump works after dropping the upgraded cluster
Package: postgresql-common Version: 225 Followup-For: Bug #986186 OK, after I dropped the upgraded version 11 cluster, pg_dump works as expected. It still seems to me that that pg_dump/pg_wrapper needs a way to select the cluster it should talk to. Thanks, Johannes
Bug#986186: postgresql-common: pg_dump in bullseye does not talk to version 13
Package: postgresql-common Version: 225 Followup-For: Bug #986186 After successfully dumping my database as described above, I upgraded the cluster to version 13 which worked nicely. However, when I run pg_dump with the upgraded cluster running on port 5433, I get LANG=C pg_dump -p 5433 my_database pg_dump: server version: 13.2 (Debian 13.2-1); pg_dump version: 11.6 (Debian 11.6-0+deb10u1) pg_dump: aborting because of server version mismatch I thought this may be due to the buster packages still being installed, so I removed postgresql-11. After that, I get Error: PostgreSQL version 11 is not installed Is it possible that pg_dump in bullseye does not work at all with the default postgresql package in bullseye? Cheers, Johannes -- System Information: Debian Release: bullseye/sid APT prefers testing APT policy: (500, 'testing') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.10.0-3-amd64 (SMP w/16 CPU threads) Kernel taint flags: TAINT_WARN Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages postgresql-common depends on: ii adduser 3.118 ii debconf [debconf-2.0] 1.5.75 ii lsb-base 11.1.0 ii perl 5.32.1-3 ii postgresql-client-common 225 ii ssl-cert 1.1.0 ii ucf 3.0043 Versions of packages postgresql-common recommends: ii e2fsprogs 1.46.2-1 ii logrotate 3.18.0-2 Versions of packages postgresql-common suggests: ii libjson-perl 4.03000-1 -- Configuration Files: /etc/apt/apt.conf.d/01autoremove-postgresql changed [not included] -- debconf information: postgresql-common/ssl: true * postgresql-common/obsolete-major: postgresql-common/catversion-bump:
Bug#986186: postgresql-common: pg_dump does not talk to the last major version (11): Error: PostgreSQL version 9.6 is not installed
... > It would probably be a good idea to include the "-p 5433" argument in > the cluster selection algorithm - so far I refrained from doing that > in order not to create more corner cases, but I guess it just makes > sense. (And granted, -p 54NN is also how I select my local version NN > cluster here.) It's too late to do that for bullseye, though. I'm glad you like the idea. This will make it more intuitive, as it will be consistent with psql in this respect. > > BTW, is there work underway to provide a postgresql specific paragraph > > in the bullseye release notes? I am not very experienced with > > postgresql, but would be willing to help writing/proof reading/testing. > > Everything should be detailed in > /usr/share/doc/postgresql-common/README.Debian.gz. How about inserting a pointer to this (very helpful and carefully prepared) document in the release notes under 5.3? I think it is important for administrators to be aware that psql and the commands handled by pg_wrapper will not "just work" after the upgrade. Johannes
Bug#751414: [Debichem-devel] Bug#751414: rdkit: postgresql cartridge not built
Hi Michael, thanks for addressing this! I am still using rdkit, so it is very good to have the option to use the database functionality in the future. Cheers, Johannes Am Mittwoch, 9. Januar 2019, 10:52:51 CET schrieb Michael Banck: > Version: 201803.4+dfsg-1 > > On Thu, Jun 12, 2014 at 05:22:06PM +0200, Johannes Ranke wrote: > > Source: rdkit > > Severity: wishlist > > > > Dear Maintainer, > > > > It would be great to have access to the postgresql cartridge. Currently, > > it seems it is not being installed: > > > > postgres@mybox:~$ createdb test_rdkit > > postgres@mybox:~$ psql -c 'create extension rdkit' test_rdkit > > ERROR: could not open extension control file > > "/usr/share/postgresql/9.3/extension/rdkit.control": Datei oder > > Verzeichnis nicht gefunden > > The PostgreSQL cartridge is now finally shipped in Debian as of > rdkit_201803.4+dfsg-1. Sorry if that is too late for you :-/ > > > Michael
Bug#942431: akonadi-backend-mysql: Error during TagSync/ItemFetch faile: "Failed to store tag"
Package: akonadi-backend-mysql Version: 4:18.08.3-5 Severity: normal Dear Maintainer, Since the upgrade to buster, I get error messages when starting akonadi from the command line. I am including the complete output below: me@box:~$ LANG=C akonadictl start Connecting to deprecated signal QDBusConnectionInterface::serviceOwnerChanged(QString,QString,QString) me@box:~$ akonadi.collectionattributetable OK akonadi.collectionmimetyperelation OK akonadi.collectionpimitemrelation OK akonadi.collectiontableOK akonadi.flagtable OK akonadi.mimetypetable OK akonadi.parttable OK akonadi.parttypetable OK akonadi.pimitemflagrelationOK akonadi.pimitemtable OK akonadi.pimitemtagrelation OK akonadi.relationtable OK akonadi.relationtypetable OK akonadi.resourcetable OK akonadi.schemaversiontable OK akonadi.tagattributetable OK akonadi.tagremoteidresourcerelationtable OK akonadi.tagtable OK akonadi.tagtypetable OK Connecting to deprecated signal QDBusConnectionInterface::serviceOwnerChanged(QString,QString,QString) org.kde.pim.akonadiserver: "Cannot connect to agent instance with identifier 'akonadi_kolab_resource_0', error message: ''" org.kde.pim.akonadiserver: "Cannot connect to agent instance with identifier 'akonadi_kolab_resource_0', error message: ''" org.kde.pim.akonadiserver: "Cannot connect to agent instance with identifier 'akonadi_kolab_resource_0', error message: ''" org.kde.pim.akonadiserver: "Cannot connect to agent instance with identifier 'akonadi_kolab_resource_0', error message: ''" org.kde.pim.akonadiserver: DATABASE ERROR: org.kde.pim.akonadiserver: Error code: "1452" org.kde.pim.akonadiserver: DB error: "Cannot add or update a child row: a foreign key constraint fails (`akonadi`.`tagtable`, CONSTRAINT `tagtable_ibfk_1` FOREIGN KEY (`parentId`) REFERENCES `tagtable` (`id`) ON DELETE CASCADE ON UPDATE CASCADE)" org.kde.pim.akonadiserver: Error text: "Cannot add or update a child row: a foreign key constraint fails (`akonadi`.`tagtable`, CONSTRAINT `tagtable_ibfk_1` FOREIGN KEY (`parentId`) REFERENCES `tagtable` (`id`) ON DELETE CASCADE ON UPDATE CASCADE) QMYSQL3: Unable to execute statement" org.kde.pim.akonadiserver: Query: "INSERT INTO TagTable (gid, typeId) VALUES (:0, :1)" org.kde.pim.akonadiserver: Error during insertion into table "TagTable" "Cannot add or update a child row: a foreign key constraint fails (`akonadi`.`tagtable`, CONSTRAINT `tagtable_ibfk_1` FOREIGN KEY (`parentId`) REFERENCES `tagtable` (`id`) ON DELETE CASCADE ON UPDATE CASCADE) QMYSQL3: Unable to execute statement" org.kde.pim.akonadicore: Error during TagSync: "Failed to store tag" Akonadi::TagCreateJob org.kde.pim.akonadicore: ItemFetch failed: "Failed to store tag" org.kde.pim.akonadiserver: DATABASE ERROR: org.kde.pim.akonadiserver: Error code: "1452" org.kde.pim.akonadiserver: DB error: "Cannot add or update a child row: a foreign key constraint fails (`akonadi`.`tagtable`, CONSTRAINT `tagtable_ibfk_1` FOREIGN KEY (`parentId`) REFERENCES `tagtable` (`id`) ON DELETE CASCADE ON UPDATE CASCADE)" org.kde.pim.akonadiserver: Error text: "Cannot add or update a child row: a foreign key constraint fails (`akonadi`.`tagtable`, CONSTRAINT `tagtable_ibfk_1` FOREIGN KEY (`parentId`) REFERENCES `tagtable` (`id`) ON DELETE CASCADE ON UPDATE CASCADE) QMYSQL3: Unable to execute statement" org.kde.pim.akonadiserver: Query: "INSERT INTO TagTable (gid, typeId) VALUES (:0, :1)" org.kde.pim.akonadiserver: Error during insertion into table "TagTable" "Cannot add or update a child row: a foreign key constraint fails (`akonadi`.`tagtable`, CONSTRAINT `tagtable_ibfk_1` FOREIGN KEY (`parentId`) REFERENCES `tagtable` (`id`) ON DELETE CASCADE ON UPDATE CASCADE) QMYSQL3: Unable to execute statement" org.kde.pim.akonadicore: Error during TagSync: "Failed to store tag" Akonadi::TagCreateJob org.kde.pim.akonadicore: ItemFetch failed: "Failed to store tag" I am not having problems that I think would be caused by this, but I am afraid something is not working correctly which may have detrimental effects that I am not aware of. Kind regards, Johannes -- System Information: Debian Release: 10.1 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable'), (15, 'unstable'), (1, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.19.0-6-amd64 (SMP w/16 CPU cores) Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UT
Bug#930059: kmail: Fails to connect to IMAP server using starttls: "plain login is disabled by the server"
Package: kmail Version: 4:18.08.3-1 Severity: normal After upgrading from stretch to buster, one IMAP resource stopped working. Long story short, it turned out that it worked again when switching from STARTTLS (port 143) to SSL/TLS (port 993). Unfortunately STARTTLS (port 143) is selected after pressing the button "Auto Detect". I confirmed the problem with a fresh user account. The full error message when configuring with STARTTLS claims that the server refused the supplied username and password, and says: "login failed, plain login is disabled", which is misleading, as it makes the user a) entering the username and password again, thinking it may have been incorrectly entered and b) trying other connection settings than "PLAIN" or "Cleartext". The configuration with STARTTLS (port 143) has been working and still works on stretch systems. Thanks for maintaining kdepim packages! Johannes -- System Information: Debian Release: 10.0 APT prefers testing APT policy: (500, 'testing'), (15, 'unstable'), (1, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.19.0-5-amd64 (SMP w/16 CPU cores) Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8), LANGUAGE= (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages kmail depends on: ii akonadi-server 4:18.08.3-5 ii kdepim-runtime 4:18.08.3-4 ii kio 5.54.1-1 ii libc62.28-10 ii libgcc1 1:8.3.0-6 ii libgpgmepp6 1.12.0-6 ii libkf5akonadiagentbase5 4:18.08.3-5 ii libkf5akonadicontact54:18.08.3-1 ii libkf5akonadicore5abi2 4:18.08.3-5 ii libkf5akonadimime5 4:18.08.3-1 ii libkf5akonadisearch-bin 4:18.08.3-1 ii libkf5akonadisearch-plugins 4:18.08.3-1 ii libkf5akonadisearchdebug54:18.08.3-1 ii libkf5akonadisearchpim5 4:18.08.3-1 ii libkf5akonadiwidgets5abi14:18.08.3-5 ii libkf5bookmarks5 5.54.0-1 ii libkf5calendarcore5abi2 4:18.08.3-1 ii libkf5calendarutils5 4:18.08.3-2 ii libkf5codecs55.54.0-1 ii libkf5completion55.54.0-1 ii libkf5configcore55.54.0-1 ii libkf5configgui5 5.54.0-1 ii libkf5configwidgets5 5.54.0-1 ii libkf5contacts5 4:18.08.3-1 ii libkf5coreaddons55.54.0-1 ii libkf5crash5 5.54.0-1 ii libkf5dbusaddons55.54.0-1 ii libkf5followupreminder5 4:18.08.3-2 ii libkf5grantleetheme-plugins 18.08.3-1 ii libkf5gravatar5abi2 4:18.08.3-1 ii libkf5guiaddons5 5.54.0-1 ii libkf5i18n5 5.54.0-1 ii libkf5iconthemes55.54.0-1 ii libkf5identitymanagement518.08.3-2 ii libkf5itemmodels55.54.0-1 ii libkf5itemviews5 5.54.0-1 ii libkf5jobwidgets55.54.0-1 ii libkf5kcmutils5 5.54.0-1 ii libkf5kiocore5 5.54.1-1 ii libkf5kiofilewidgets55.54.1-1 ii libkf5kiowidgets55.54.1-1 ii libkf5kontactinterface5 18.08.3-1 ii libkf5ksieveui5 4:18.08.3-2 ii libkf5libkdepim-plugins 4:18.08.3-2 ii libkf5libkdepim5 4:18.08.3-2 ii libkf5libkdepimakonadi5 4:18.08.3-2 ii libkf5libkleo5 4:18.08.3-2 ii libkf5mailcommon5abi24:18.08.3-2 ii libkf5mailtransport5 18.08.3-2 ii libkf5mailtransportakonadi5 18.08.3-2 ii libkf5messagecomposer5abi1 4:18.08.3-2 ii libkf5messagecore5abi1 4:18.08.3-2 ii libkf5messagelist5abi1 4:18.08.3-2 ii libkf5messageviewer5abi1 4:18.08.3-2 ii libkf5mime5abi1 18.08.3-1 ii libkf5mimetreeparser5abi14:18.08.3-2 ii libkf5notifications5 5.54.0-1 ii libkf5notifyconfig5 5.54.0-1 ii libkf5parts5 5.54.0-1 ii libkf5pimcommon5abi2 4:18.08.3-2 ii libkf5pimcommonakonadi5abi1 4:18.08.3-2 ii libkf5pimtextedit5abi2 18.08.3-1 ii libkf5sendlater5 4:18.08.3-2 ii libkf5service-bin5.54.0-1 ii libkf5service5 5.54.0-1 ii libkf5sonnetui5 5.54.0-1 ii libkf5templateparser54:18.08.3-2 ii libkf5textwidgets5 5.54.0-1 ii libkf5tnef5 4:18.08.3-1 ii libkf5wallet-bin 5.54.0-1 ii libkf5wallet55.54.0-1 ii libkf5webengineviewer5abi1 4:18.08.3-2 ii libkf5widgetsaddons5 5.54.0-1 ii libkf5windowsystem5 5.54.0-1 ii libkf5xmlgui55.54.0-1 ii libqgpgme7 1.12.0-6 ii libqt5core5a 5.11.3+dfsg1-1 ii libqt5dbus5 5.11.3+dfsg1-1 ii libqt5gui5 5.11.3+dfsg1-1 ii libqt5network5 5.11.3+dfsg1-1 ii libqt5widgets5 5.11.3+dfsg1-1 ii libqt5xml5
Bug#961141: antimony: q
Package: antimony Version: 0.9.3-1+b1 Followup-For: Bug #961141 Dear Maintainer, The package is currently unusable in Debian stable. I compiled my own package from the sources in unstable and was able to test antimony. Thanks for packaging antimony. Johannes -- System Information: Debian Release: 10.4 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable'), (15, 'unstable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.19.0-9-amd64 (SMP w/16 CPU cores) Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8), LANGUAGE= (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages antimony depends on: ii libboost-python1.67.0 1.67.0-13+deb10u1 ii libc6 2.28-10 ii libgcc11:8.3.0-6 ii libpng16-161.6.36-6 ii libpython3.7 3.7.3-2+deb10u1 ii libqt5concurrent5 5.11.3+dfsg1-1+deb10u3 ii libqt5core5a 5.11.3+dfsg1-1+deb10u3 ii libqt5gui5 5.11.3+dfsg1-1+deb10u3 ii libqt5network5 5.11.3+dfsg1-1+deb10u3 ii libqt5opengl5 5.11.3+dfsg1-1+deb10u3 ii libqt5widgets5 5.11.3+dfsg1-1+deb10u3 ii libstdc++6 8.3.0-6 ii python33.7.3-1 ii zlib1g 1:1.2.11.dfsg-1 antimony recommends no packages. antimony suggests no packages. -- no debconf information
Bug#1039926: Will file bug report for complete R transition (Was: Bug#1039926: svglite requires rebuild under R 4.3.*)
Hi, I think option 1 from [1] is the way to go, i.e. make r-base provide a graphics API version according to the R changelog, and have the relevant packages depend on that graphics API version. How to identify them was discussed previously on this list [2]. Using the codesearch and github URLS provided in that email, the list given there could be updated. Somehow Dirk is hesitant to do this, I think it is just a matter of "is this really necessary"? To me, it seems there is ample evidence by now that it is indeed necessary, for the mental sanity of everyone involved, and to avoid future discussions about a full R API bump just because of the graphics API on the one hand, and to avoid breaking things by just ignoring the issue on the other hand. Kind regards, Johannes Am Freitag, 30. Juni 2023, 14:01:55 CEST schrieb Andreas Tille: > Hi Dirk, > > Am Thu, Jun 29, 2023 at 05:52:34PM -0500 schrieb Dirk Eddelbuettel: > > This accidentally omitted > > > > library(svglite) > > > > The package loads fine, but like the others will not create a graphics > > device as it was built under the previous R 4.2.* series. > > Thanks a lot for your specific bug reports to somehow heal the R > graphics ABI change issue. I've got the impression there is no good > simple rule to detect the right set of packages that need rebuilt > against r-base 4.3.1 to fix this issue. I also spotted that vdiffr > needs to be rebuilt to let ggplot2 passing its test suite (and so I > did). > > Thus I think it is the best solution to ask the release team for > a full r-base transition (option 2 I suggested in [1]). > > BTW, when I was running the autopkgtest of svglite I've spotted an issue > which was solved by Nilesh Patra and reported as #1039955. I'd like to > make you remind this kind of situation if you might fall back into your > "do not test Debian packages, rather trust CRAN" pattern in future. We > do not run tests against CRAN code (despite we had spotted mistakes even > there in the past) but we are testing Debian packages which is a > different thing. > > I also spotted vdiffr because of the autopkgtest in ggplot2. It makes > simply sense to test what we are shipping before we ship it to our > users (specifically if we as Debian maintainers like I am are not at > all R experts as I expressed several times). > > Kind regards > Andreas. > [1] https://lists.debian.org/debian-r/2023/06/msg00025.html [2] https://lists.debian.org/debian-r/2022/04/msg00018.html
Bug#782764: r-base-dev: Make it possible for maintainers to set builttimeStamp in d/rules
Am Samstag, 18. April 2015, 06:27:03 schrieb Dirk Eddelbuettel: > On 18 April 2015 at 11:15, Philip Rinn wrote: > | Hi, > | > | I think this patch is more what I wanted. > | It now sets the build-timestamp to the time of the last changelog entry if > | the maintainer does not set builttimeStamp explicitly. > | With this change almost all GNU R packages in Debian would automatically > | build reproducible. > > And I presume that is what we want? I never heard from the reproducibility > group after I made the two patches (cf old bug report) to R itself and > r-cran.mk. Without having further background information I would say that the build- timestamp should be either set to the build time (to carry correct information) or not at all (to have reproducible builds). Johannes > Too bad you sent me this today. I just made four uploads of R in the last > few days leading up to R 3.2.0. > > Dirk > > | Best, > | Philip > | > | x[DELETED ATTACHMENT usable_builttimeStamp2.patch, text/x-patch] > | x[DELETED ATTACHMENT signature.asc, application/pgp-signature] -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Bug#861333: r-base: R packages uploaded to Debian before 14 April 2017 that use .C or .Fortran fail to find objects
Nice. Amazing work. So buster should be covered then. Now (correct me if I am wrong) if we could adapt your scripts to create versioned Breaks: relationships with these packages, this would open the possibility to create backports for stretch-backports and jessie-backports- sloppy, taking advantage of the Debian infrastructure for builds on all architectures. Side note: Regarding backports on CRAN, I have chosen to create a separate repository for R >= 3.4.0, so people should be conscious about the issue for R package debs when they install it.
Bug#863864: release-notes: Document that nagios is not in stretch and how to switch to icinga (if that is possible)
Package: release-notes Severity: normal I assume that switching to icinga is possible, but I am missing a hint in the release notes. Will icinga use nagios configuration files? -- System Information: Debian Release: 9.0 APT prefers testing APT policy: (500, 'testing') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.9.0-3-amd64 (SMP w/8 CPU cores) Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system)
Bug#863864: [Pkg-nagios-devel] Bug#863864: release-notes: Document that nagios is not in stretch and how to switch to icinga (if that is possible)
Am Donnerstag, 1. Juni 2017, 11:52:24 CEST schrieb Baptiste Jammet: > Control: tags -1 moreinfo > > Hello all, > > Le 01/06/2017 09:26, Alexander Wirt a écrit : > > No, and those files are not fully compatible. > > Le 01/06/2017 10:00, Bas Couwenberg a écrit : > > Icinga 1.x uses the same configuration syntax as Nagios 3.x, so > > switching from Nagios 3 to Icinga 1 should be as simple as copying the > > configuration files to the appropriate directory > > (/etc/icinga/objects). > > Could you provide some text we will include in the release notes ? > And since there is 2 different answers (and I know nothing about Nagios > nor incinga), ideally find a shared answer/solution ! > > Thanks > > Baptiste I just would like to add that I had a dangling symlink in /etc/apache2/conf- enabled/nagios3.conf after the upgrade, keeping apache2 from starting. Should I file a bug against the jessie package of nagios3? The good news is that I was indeed able to easily migrate from nagios3 from jessie to icinga1.x from stretch by copying the contents of /etc/nagios3 and /etc/nagios3/conf.d that I had modified over to /etc/icinga and /etc/icinga/ objects, plus some renaming of files named *_nagios2.cfg to *_icinga.cfg. Cheers, Johannes
Bug#682232: Failed upgrade of mysql from squeeze to wheezy
Just for the record, maybe there are more people out there that are late upgrading their servers from squeeze to wheezy... When /etc/init.d/mysql start fails as described in this report, the command mysqld gives information on the command line what is going on. In my case, I had several errors, including the hint that I should run mysql_upgrade (which did not work, as it needs a running mysql server): 160307 21:49:22 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it. 160307 21:49:22 [ERROR] mysqld: unknown option '--skip-bdb' 160307 21:49:22 [ERROR] Aborting So in the end, in addition to using default-storage-engine=myisam I had to comment out the line #skip-bdb Johannes
Bug#682232: Failed upgrade of mysql from squeeze to wheezy
The skip-bdb option could be a leftover from much earlier times, as the box has started with Debian sarge in 2007...
Bug#682232: [debian-mysql] Bug#682232: Failed upgrade of mysql from squeeze to wheezy
> Hi Johannes! Thanks for taking the time to reach out. I'm struggling > to understand what the "bug" is. Config files that have been customized > have to be manually updated in any major upgrade. I don't think that's > specific to MySQL. Hi Clint, good question. It bugged me, because I did not get any log entries under /var/log/mysql*, so I had to start mysqld in a way I usually don't, in order to get a diagnostic message about what was going on. Also, as far as I can remember I never introduced the option skip-bdb manually. For me, if a previously valid configuration option makes a service fail to start after the upgrade, this is unexpected. But I do not want to complain, I added this information to help others to solve the problem! If the maintainers get something out of it, even better.
Bug#877283: rkward should depend on r-api-3.4
Package: rkward Severity: normal Dear Maintainer, In order to get picked up by future transitions of the r-api such as the one planned for next year (R 3.5.0), I believe rkward should depend on r-api-3.4 which is currently provided by r-base in unstable. Johannes
Bug#868558: Would you please not upload new r-* packages until transition is finalised (Re: r-api-3.4)
Am Donnerstag, 12. Oktober 2017, 12:01:14 CEST schrieb Dirk Eddelbuettel: > So we did this 71 times, but stopped 4+ years ago. Not sure what got the > toolchain coughing, but I guess we could try again. texi2dvi used to trip over ~ in path names, so for locally building backports we used to rename the directory that the source was extracted to, substituting "~" by "-" before building. But I don't know if that was the reason for Dirk to change the scheme. It seems that this was fixed in texi2dvi upstream http://svn.savannah.gnu.org/viewvc/texinfo/trunk/util/texi2dvi? r1=7199&r2=7200 Johannes
Bug#861333: r-base: R packages uploaded to Debian before 14 April 2017 that use .C or .Fortran fail to find objects
Package: r-base Version: 3.4.0-1 Severity: normal With current R, R packages built for Debian before the upload of R 3.3.3.20170413-1 on 14 April that use .C or .Fortran do no work properly, because the functions calling .C or .Fortran do not find the compiled objects. Example packages are r-cran-spatial and r-cran-kernsmooth. An example session in a fresh Debian sid chroot: > library(spatial) > example(surf.gls) srf.gl> library(MASS) # for eqscplot srf.gl> data(topo, package="MASS") srf.gl> topo.kr <- surf.gls(2, expcov, topo, d=0.7) Error in surf.gls(2, expcov, topo, d = 0.7) : object 'VR_frset' not found The relevant NEWS entry from R is * Packages which register native routines for .C or .Fortran need to be re-installed for this version (unless installed with R-devel SVN revision r72375 or later). Packages compiled locally can simply be rebuilt using update.packages(lib.loc="/usr/local/lib/R/site-library", checkBuilt=TRUE) However the packages provided by Debian packages are installed in a directory only writable by privileged users. Cheers, Johannes -- System Information: Debian Release: 9.0 APT prefers unstable APT policy: (500, 'unstable') Architecture: amd64 (x86_64) Kernel: Linux 4.9.0-0.bpo.2-amd64 (SMP w/8 CPU cores) Locale: LANG=C, LC_CTYPE=C (charmap=ANSI_X3.4-1968) Shell: /bin/sh linked to /usr/bin/dash Init: unable to detect Versions of packages r-base depends on: ii r-base-core3.4.0-1 ii r-recommended 3.4.0-1 Versions of packages r-base recommends: ii r-base-html 3.4.0-1 ii r-doc-html 3.4.0-1 Versions of packages r-base suggests: pn ess pn r-doc-info | r-doc-pdf -- no debconf information
Bug#861333: r-base: R packages uploaded to Debian before 14 April 2017 that use .C or .Fortran fail to find objects
> | Packages compiled locally can simply be rebuilt using > | > | update.packages(lib.loc="/usr/local/lib/R/site-library", > | checkBuilt=TRUE) > | > | However the packages provided by Debian packages are installed in a > | directory only writable by privileged users. > > That's irrelevant. You also need to be "privileged" to install a .deb > package. Not quite irrelevant, as it was recommended on r-help to Göran, who first reported this for Debian, to just use update.packages(checkBuilt=TRUE) which tries to reinstall also the packages in /usr/lib/R/site-library, which should be left to the Debian package management.
Bug#861333: r-base: R packages uploaded to Debian before 14 April 2017 that use .C or .Fortran fail to find objects
Am Montag, 1. Mai 2017, 14:53:49 schrieb Charles Plessy: ... > At this point I see 3 options: > > - For each rebuild, insert a "Breaks" relationship in r-base's control > file; This is the solution favoured by me as the maintainer of the backports on CRAN (I know, this is the Debian BTS, but nonetheless), as it would just cause rebuilds/reinstalls of the packages really affected, assuming that we manage to have a versioned Breaks relationship for those packages (e.g. r-cran-spatial <= xy). > - Increment r-api-3 to r-api-4 (or r-api-3.4, etc.) in order to not have to > maintain a long list of "Breaks" declarations. In that case, we have to > rebuild everything. Would be OK for me, but seems to cause a lot of work for r-cran-* and r-bioc* maintainers > - Just rebuild what has to be rebuilt, and do not support partial upgrades, > which is what has been done until now. In this case, I would create a new repository on CRAN (again, I know that this is not really Debians business), so people would consciously install R 3.4.0 and not be surprised by packages suddenly failing to find their objects. > Not supporting partial upgrades puts the maintainers of the r-cran and > r-bioc packages between the hammer and the anvil. I do not understand this sentence. > This said, I think that > we have made constant progresses over the years, so I do not feel shy > saying "not yet" to the Release team again if needed.
Bug#891968: texlive-base should depend on xzdec as it is needed to initialise tlmgr
> So maybe it is indirectly called via some other R function .. hard to
> say. In any case, *this*should*not*be*done*.
>
> It would be nice to find out who actually called tlmgr. If you could
> manage to find this it would help a lot. Thanks
After many hours of digging (sigh):
It is the function tinytex::latexmk. Long story (unfortunately not so) short,
if a user calls
Rscript -e 'rmarkdown::render("test.rmd", "pdf_document")'
on some R markdown file (it is enough to have just the word "Test" in it)
on stretch system with the necessary texlive packages installed, except e.g.
for the package lmodern, then he gets
user@box:~/tmp/test$ Rscript -e 'rmarkdown::render("test.rmd",
"pdf_document")'
processing file: test.rmd
|.| 100%
ordinary text without R code
output file: test.knit.md
/usr/bin/pandoc +RTS -K512m -RTS test.utf8.md --to latex --from markdown
+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output
test.tex --template /usr/local/lib/R/site-library/rmarkdown/rmd/latex/
default-1.17.0.2.tex --highlight-style tango --latex-engine pdflatex --variable
graphics=yes --variable 'geometry:margin=1in'
You are recommended to install the tinytex package to build PDF.FALSE
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian)
(preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
! LaTeX Error: File `lmodern.sty' not found.
...
So at this point the user can
a) find out e.g. using apt-file which Debian package provides lmodern.sty
(which
is what I have done in earlier times), or
b) install the R package tinytex as recommended above [1,2]
If the user chooses b), and then tries again, he gets
...
/usr/bin/pandoc +RTS -K512m -RTS test.utf8.md --to latex --from markdown
+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output
test.tex --template /usr/local/lib/R/site-library/rmarkdown/rmd/latex/
default-1.17.0.2.tex --highlight-style tango --latex-engine pdflatex --variable
graphics=yes --variable 'geometry:margin=1in'
tlmgr search --file --global '/lmodern.sty'
Cannot determine type of tlpdb from /home/user/texmf!
cannot setup TLPDB in /home/user/texmf at /usr/bin/tlmgr line 5713.
! LaTeX Error: File `lmodern.sty' not found.
! Emergency stop.
Error: Failed to compile test.tex. See test.log for more info.
In addition: Warning messages:
1: running command ''tlmgr' search --file --global '/lmodern.sty'' had status 2
2: In parse_packages(logfile, quiet = c(TRUE, FALSE, FALSE)) :
Failed to find a package that contains lmodern.sty
Execution halted
So when a user than goes on to try to get tlmgr to do the work, and issues
user@box: tlmgr init-usertree
he gets:
(running on Debian, switching to user mode!)
Cannot determine type of tlpdb from /home/user/texmf!
Then the user scratches his head. Either he will consult a commonly used
search engine, and read through some stackoverflow postings, or just try the
rendering again, which will yield:
...
/usr/bin/pandoc +RTS -K512m -RTS test.utf8.md --to latex --from markdown
+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output
test.tex --template /usr/local/lib/R/site-library/rmarkdown/rmd/latex/
default-1.17.0.2.tex --highlight-style tango --latex-engine pdflatex --variable
graphics=yes --variable 'geometry:margin=1in'
tlmgr search --file --global '/lmodern.sty'
/usr/bin/tlmgr: Initialization failed (in setup_unix_one):
/usr/bin/tlmgr: could not find a usable xzdec.
/usr/bin/tlmgr: Please install xzdec and try again.
tlmgr: Couldn't set up the necessary programs.
Installation of packages is not supported.
Please report to texl...@tug.org.
tlmgr: Continuing anyway ...
Use of uninitialized value $r in split at /usr/bin/tlmgr line 3899.
tlmgr: Cannot find main repository, you have to tag one as main!
! LaTeX Error: File `lmodern.sty' not found.
...
So he thinks, yay, I will just install xzdec and all will be good, which will
then yield:
...
/usr/bin/pandoc +RTS -K512m -RTS test.utf8.md --to latex --from markdown
+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output
test.tex --template /usr/local/lib/R/site-library/rmarkdown/rmd/latex/
default-1.17.0.2.tex --highlight-style tango --latex-engine pdflatex --variable
graphics=yes --variable 'geometry:margin=1in'
tlmgr search --file --global '/lmodern.sty'
Trying to automatically install missing LaTeX packages...
tlmgr install lm
(running on Debian, switching to user mode!)
tlmgr: package repository http://ftp.fau.de/ctan/systems/texlive/tlnet
(verified)
[1/1, ??:??/??:??] install: lm [11651k]
tlmgr: package log updated: /home/jranke/texmf/web2c/tlmgr.log
running mktexlsr ...
done running mktexlsr.
running updmap ...
done running updmap.
tlmgr path add
(running on Debian, switching to user mode!)
tlmgr: action `path' not supported in usermode!
Output created: test.pdf
Side remark: I do share Yihui's wi
Bug#898419: Fixed by installing okular-extra-backends
When reading my own bug report I noticed that okular suggests okular-extra- backends. After installing this, I can correctly view multipage tiff files again. I am not sure if the packaging could be improved so that the user opening such a file would get a hint about the availability of this package.
Bug#891554: okular: Desktop freezes when resizing the okular window
Package: okular Version: 4:16.08.2-1+b1 Severity: important When I resize an okular window with or without a file opened, the whole desktop freezes. The mouse pointer still shows the resize symbol and I can move it around, but clicking does not do anything, and I can not select e.g. a konsole to enter text. This happens either on the first resize action (making the window bigger or smaller) or on a later resize action. In some cases I was able to get a terminal by pressing . htop did not show anything abnormal, just low CPU and memory usage. In /var/log/syslog I find entries like this -syslog case 1- Feb 26 15:50:56 ryz kernel: [13936.882860] nouveau :06:00.0: gr: TRAP ch 7 [003fa1f000 kwin_x11[1691]] Feb 26 15:50:56 ryz kernel: [13936.882875] nouveau :06:00.0: gr: GPC0/TPC0/TEX: 8049 Feb 26 15:50:56 ryz kernel: [13936.882892] nouveau :06:00.0: fifo: read fault at 0005f32000 engine 00 [GR] client 01 [GPC0/T1_0] reason 02 [PTE] on channel 7 [003fa1f000 kwin_x11[1691]] Feb 26 15:50:56 ryz kernel: [13936.882908] nouveau :06:00.0: fifo: channel 7: killed Feb 26 15:50:56 ryz kernel: [13936.882911] nouveau :06:00.0: fifo: runlist 0: scheduled for recovery Feb 26 15:50:56 ryz kernel: [13936.882916] nouveau :06:00.0: fifo: engine 0: scheduled for recovery Feb 26 15:50:56 ryz kernel: [13936.882944] nouveau :06:00.0: kwin_x11[1691]: channel 7 killed! -end case 1- -syslog case 2- Feb 26 16:29:11 ryz kernel: [ 1745.904036] nouveau :06:00.0: gr: TRAP ch 2 [003fc0a000 Xorg[863]] Feb 26 16:29:11 ryz kernel: [ 1745.904047] nouveau :06:00.0: gr: GPC0/TPC0/TEX: 8049 Feb 26 16:29:11 ryz kernel: [ 1745.904057] nouveau :06:00.0: fifo: read fault at 000d64 engine 00 [GR] client 01 [GPC0/T1_0] reason 02 [PTE] on channel 2 [003fc0a000 Xorg[863]] Feb 26 16:29:11 ryz kernel: [ 1745.904067] nouveau :06:00.0: fifo: channel 2: killed Feb 26 16:29:11 ryz kernel: [ 1745.904069] nouveau :06:00.0: fifo: runlist 0: scheduled for recovery Feb 26 16:29:11 ryz kernel: [ 1745.904072] nouveau :06:00.0: fifo: engine 0: scheduled for recovery Feb 26 16:29:11 ryz kernel: [ 1745.904080] nouveau :06:00.0: fifo: engine 6: scheduled for recovery Feb 26 16:29:11 ryz kernel: [ 1745.904145] nouveau :06:00.0: Xorg[863]: channel 2 killed! -end case 2- -syslog case 3- Feb 26 16:48:14 ryz kernel: [ 1026.261644] nouveau :06:00.0: gr: TRAP ch 7 [003fa1f000 kwin_x11[1692]] Feb 26 16:48:14 ryz kernel: [ 1026.261657] nouveau :06:00.0: gr: GPC0/TPC0/TEX: 8049 Feb 26 16:48:14 ryz kernel: [ 1026.261673] nouveau :06:00.0: fifo: read fault at 00059a4000 engine 00 [GR] client 01 [GPC0/T1_0] reason 02 [PTE] on channel 7 [003fa1f000 kwin_x11[1692]] Feb 26 16:48:14 ryz kernel: [ 1026.261685] nouveau :06:00.0: fifo: channel 7: killed Feb 26 16:48:14 ryz kernel: [ 1026.261688] nouveau :06:00.0: fifo: runlist 0: scheduled for recovery Feb 26 16:48:14 ryz kernel: [ 1026.261693] nouveau :06:00.0: fifo: engine 0: scheduled for recovery Feb 26 16:48:14 ryz kernel: [ 1026.261705] nouveau :06:00.0: kwin_x11[1692]: channel 7 killed! -end case 3- I have not observed similar freezes with other kde or non-kde programs, so I am reporting this against the okular package. Any hints welcome, Johannes -- System Information: Debian Release: 9.3 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable'), (15, 'testing'), (1, 'experimental') Architecture: amd64 (x86_64) Kernel: Linux 4.14.0-0.bpo.3-amd64 (SMP w/16 CPU cores) Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8), LANGUAGE= (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages okular depends on: ii kde-runtime 4:16.08.3-2 ii libc6 2.24-11+deb9u1 ii libfreetype62.6.3-3.2 ii libjpeg62-turbo 1:1.5.1-2 ii libkdecore5 4:4.14.26-2 ii libkdeui5 4:4.14.26-2 ii libkexiv2-114:15.04.3-1 ii libkio5 4:4.14.26-2 ii libkparts4 4:4.14.26-2 ii libkprintutils4 4:4.14.26-2 ii libkpty44:4.14.26-2 ii libokularcore7 4:16.08.2-1+b1 ii libphonon4 4:4.9.0-4 ii libpoppler-qt4-40.48.0-2+deb9u2 ii libqca2 2.1.1-4+b2 ii libqimageblitz4 1:0.0.6-4+b2 ii libqmobipocket1 4:16.08.0-1 ii libqt4-dbus 4:4.8.7+dfsg-11 ii libqt4-declarative 4:4.8.7+dfsg-11 ii libqt4-svg 4:4.8.7+dfsg-11 ii libqt4-xml 4:4.8.7+dfsg-11 ii libqtcore4 4:4.8.7+dfsg-11 ii libqtgui4 4:4.8.7+dfsg-11 ii libsolid4 4:4.14.26-2 ii libspectre1 0.2.8-1 ii libstdc++6 6.3.0-18+deb9u1 ii phonon 4:4.9.0-4 ii zlib1g 1:1.2.8.dfsg-5 Versions of packages okular recommends: ii cups-bsd 2.2.1-8 Versions of packages okular suggests: ii ghostscript9
Bug#891554: Additional info
It seems that the nouveau driver is not fit for modern KDEs use of OpenGL [1] as suggested in a comment to a different bug [2]. In my case the affected card is a GeForce GT 710 (MSI 1 GB D3 X GT710 LP passive). [1] https://bugs.freedesktop.org/show_bug.cgi?id=98039#c3 [2] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=851416#10
Bug#889150: Confirmation
Just a quick note from an affected user that installing apparmor and apparmor- profiles from stetch-proposed-updates and running sudo systemctl reload apparmor fixes the issue for me.
Bug#891968: texlive-base should depend on xzdec as it is needed to initialise tlmgr
Package: texlive-base Version: 2016.20170123-5 Severity: normal Dear Maintainer, On a fresh Debian stretch installation, when trying to process a tex document tlmgr could not be initialized because xzdec was not installed: /usr/bin/tlmgr: Initialization failed (in setup_unix_one): /usr/bin/tlmgr: could not find a usable xzdec. /usr/bin/tlmgr: Please install xzdec and try again. tlmgr: Couldn't set up the necessary programs. Installation of packages is not supported. Please report to texl...@tug.org. tlmgr: Continuing anyway ... Use of uninitialized value $r in split at /usr/bin/tlmgr line 3899. tlmgr: Cannot find main repository, you have to tag one as main! ... After installing the xzdec package the compile succeeded. I checked the texlive-base package in unstable (2017.20180225-1) and it also does not depend on xzdec. As the tlmgr binary is in texlive-base, I think texlive-base should depend on xzdec. Cheers, Johannes ## List of ls-R files -rw-r--r-- 1 username username 1354 Feb 20 02:38 /home/username/texmf/ls-R -rw-r--r-- 1 root root 1200 Feb 20 02:43 /var/lib/texmf/ls-R -rw-rw-r-- 1 username staff 80 Mar 3 11:46 /usr/local/share/texmf/ls-R lrwxrwxrwx 1 root root 29 Jan 17 2017 /usr/share/texmf/ls-R -> /var/lib/texmf/ls-R-TEXMFMAIN lrwxrwxrwx 1 root root 31 Mar 4 2017 /usr/share/texlive/texmf-dist/ls-R -> /var/lib/texmf/ls-R-TEXLIVEDIST lrwxrwxrwx 1 root root 31 Mar 4 2017 /usr/share/texlive/texmf-dist/ls-R -> /var/lib/texmf/ls-R-TEXLIVEDIST ## Config files -rw-r--r-- 1 root root 475 Feb 20 02:43 /etc/texmf/web2c/texmf.cnf lrwxrwxrwx 1 root root 33 Mar 4 2017 /usr/share/texmf/web2c/fmtutil.cnf -> /var/lib/texmf/fmtutil.cnf-DEBIAN -rw-r--r-- 1 username username 154 Mar 3 11:46 /home/username/texmf/web2c/updmap.cfg -rw-r--r-- 1 root root 2763 Feb 20 02:43 /var/lib/texmf/tex/generic/config/language.dat ## Files in /etc/texmf/web2c/ total 8 -rw-r--r-- 1 root root 283 Jan 17 2017 mktex.cnf -rw-r--r-- 1 root root 475 Feb 20 02:43 texmf.cnf ## md5sums of texmf.d ca40c66f144b4bafc3e59a2dd32ecb9c /etc/texmf/texmf.d/00debian.cnf -- System Information: Debian Release: 9.3 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable'), (15, 'proposed-updates'), (15, 'testing'), (1, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.15.0-1-amd64 (SMP w/16 CPU cores) Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8), LANGUAGE= (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages texlive-base depends on: ii debconf [debconf-2.0] 1.5.61 ii libpaper-utils 1.1.24+nmu5 ii tex-common 6.06 ii texlive-binaries 2016.20160513.41080.dfsg-2 ii ucf3.0036 ii xdg-utils 1.1.1-1 Versions of packages texlive-base recommends: pn lmodern Versions of packages texlive-base suggests: ii ghostscript [postscript-viewer] 9.20~dfsg-3.2+deb9u1 ii okular [postscript-viewer] 4:16.08.2-1+b1 pn perl-tk ii xpdf [pdf-viewer]3.04-4 Versions of packages tex-common depends on: ii dpkg 1.18.24 ii ucf 3.0036 Versions of packages tex-common suggests: ii debhelper 10.2.5 Versions of packages texlive-base is related to: ii tex-common6.06 ii texlive-binaries 2016.20160513.41080.dfsg-2 -- debconf information: texlive-base/texconfig_ignorant: texlive-base/binary_chooser: pdftex, dvips, dvipdfmx, xdvi
Bug#891995: kaffeine: qInstant recording does not record anything
Package: kaffeine Version: 2.0.5-1 Severity: normal Dear Maintainer, when I watch TV and press "Instant Recording", the message "Instant Record Started" gets displayed. When I stop it then, I get the message "Instant Record Stopped". However, no file appears in the directory configured for recording. Recording from the Program Guide works fine and a file appears in the recording directory. I started kaffeine with the --debug option, but found no hint in the output, only lots info about EPG, and many lines with "EPG channel invalid" which is probably not related. Cheers, Johannes -- System Information: Debian Release: 9.3 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable') Architecture: amd64 (x86_64) Kernel: Linux 4.9.0-5-amd64 (SMP w/8 CPU cores) Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8), LANGUAGE= (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages kaffeine depends on: ii kio 5.28.0-2 ii libc62.24-11+deb9u1 ii libdvbv5-0 1.12.3-1 ii libkf5configcore55.28.0-2 ii libkf5configwidgets5 5.28.0-2 ii libkf5coreaddons55.28.0-2 ii libkf5dbusaddons55.28.0-1 ii libkf5i18n5 5.28.0-2 ii libkf5kiocore5 5.28.0-2 ii libkf5kiofilewidgets55.28.0-2 ii libkf5solid5 5.28.0-3 ii libkf5widgetsaddons5 5.28.0-3 ii libkf5xmlgui55.28.0-1 ii libqt5core5a 5.7.1+dfsg-3+b1 ii libqt5dbus5 5.7.1+dfsg-3+b1 ii libqt5gui5 5.7.1+dfsg-3+b1 ii libqt5network5 5.7.1+dfsg-3+b1 ii libqt5sql5 5.7.1+dfsg-3+b1 ii libqt5sql5-sqlite5.7.1+dfsg-3+b1 ii libqt5widgets5 5.7.1+dfsg-3+b1 ii libqt5x11extras5 5.7.1~20161021-2 ii libqt5xml5 5.7.1+dfsg-3+b1 ii libstdc++6 6.3.0-18+deb9u1 ii libvlc5 2.2.7-1~deb9u1 ii libxss1 1:1.2.2-1 ii vlc-plugin-base 2.2.7-1~deb9u1 ii vlc-plugin-video-output 2.2.7-1~deb9u1 kaffeine recommends no packages. Versions of packages kaffeine suggests: ii libdvdcss2 1.2.13-0 -- no debconf information
Bug#891968: texlive-base should depend on xzdec as it is needed to initialise tlmgr
Am Sonntag, 4. März 2018, 16:17:27 CET schrieb Norbert Preining: > Hi > > > On a fresh Debian stretch installation, when trying to process a tex > > > document tlmgr could not be initialized because xzdec was not installed: > Very unlikely, because tlmgr is not used for processing *any* tex file. > tlmgr should not be used and I ship it only in Debian in the restricted > USER MODE (see man page), all system wide actions are prohibited because > they interfere with the package manager (apt/dpkg) system. > > What kind of tex document did you try to process? Let's see: I called the RMakeRmd function of the Nvim-R plugin on an R markdown document. This vim function calls some R functions that prepare a markdown document with embedded tex code. This is then processed by pandoc -- latex-engine pdflatex --output document.tex --template my_template.tex. This is the reason why I said I tried to processed a tex document - I think what happens is that pandoc uses pdflatex internally on some document.tex to produce the pdf that is the result of the process. I should also mention that I had run tlmgr init-usertree presumably because I am using a private tex style from /home/user/texmf. I'll happily dig further if you need more details.
Bug#843534: akonadi-server: Workarounds don't work
Package: akonadi-server Version: 1.13.0-2+deb8u1 Followup-For: Bug #843534 I have added "secure_file_priv=" to ~/.local/share/akonadi/mysql.conf as suggested in the original bug report. This did not help. I also added this instruction to /etc/akonadi/mysql-global.conf. Finally, I have created the directory in question manually using these commands mkdir -m700 /var/lib/mysql-files chown mysql:mysql /var/lib/mysql-files Nevertheless, akonadi still crashes when starting kmail or when issuing akonadictl start, so kmail is unusable on this machine at the moment while it was fully functional two days ago. The report given by the akonadi selftest follows after the system information. Any hints are welcome. -- System Information: Debian Release: 8.6 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable') Architecture: amd64 (x86_64) Kernel: Linux 3.16.0-4-amd64 (SMP w/8 CPU cores) Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages akonadi-server depends on: ii akonadi-backend-mysql 1.13.0-2+deb8u1 ii libakonadiprotocolinternals11.13.0-2+deb8u1 ii libboost-program-options1.55.0 1.55.0+dfsg-3 ii libc6 2.19-18+deb8u6 ii libgcc1 1:4.9.2-10 ii libqt4-dbus 4:4.8.6+git64-g5dc8b2b+dfsg-3+deb8u1 ii libqt4-network 4:4.8.6+git64-g5dc8b2b+dfsg-3+deb8u1 ii libqt4-sql 4:4.8.6+git64-g5dc8b2b+dfsg-3+deb8u1 ii libqt4-xml 4:4.8.6+git64-g5dc8b2b+dfsg-3+deb8u1 ii libqtcore4 4:4.8.6+git64-g5dc8b2b+dfsg-3+deb8u1 ii libqtgui4 4:4.8.6+git64-g5dc8b2b+dfsg-3+deb8u1 ii libstdc++6 4.9.2-10 akonadi-server recommends no packages. Versions of packages akonadi-server suggests: ii akonadi-backend-mysql 1.13.0-2+deb8u1 pn akonadi-backend-postgresql pn akonadi-backend-sqlite -- no debconf information -- Akonadi Server Self-Test Report === Test 1: SUCCESS Database driver found. Details: The QtSQL driver 'QMYSQL' is required by your current Akonadi server configuration and was found on your system. File content of '/home/USERNAME/.config/akonadi/akonadiserverrc': [%General] Driver=QMYSQL [QMYSQL] Name=akonadi Host= Options="UNIX_SOCKET=/tmp/akonadi-USERNAME.gzrNgH/mysql.socket" ServerPath=/usr/sbin/mysqld StartServer=true [Debug] Tracer=null Test 2: SUCCESS Akonadi is not running as root Details: Akonadi is not running as a root/administrator user, which is the recommended setup for a secure system. Test 3: SUCCESS MySQL server found. Details: You have currently configured Akonadi to use the MySQL server '/usr/sbin/mysqld'. Make sure you have the MySQL server installed, set the correct path and ensure you have the necessary read and execution rights on the server executable. The server executable is typically called 'mysqld'; its location varies depending on the distribution. Test 4: SUCCESS MySQL server is executable. Details: MySQL server found: 161109 18:42:51 [Warning] Using unique option prefix key_buffer instead of key_buffer_size is deprecated and will be removed in a future release. Please use the full name instead. /usr/sbin/mysqld Ver 5.5.53-0+deb8u1 for debian-linux-gnu on x86_64 ((Debian)) Test 5: SUCCESS No current MySQL error log found. Details: The MySQL server did not report any errors during this startup. The log can be found in '/home/USERNAME/.local/share/akonadi/db_data/mysql.err'. Test 6: SUCCESS MySQL server default configuration found. Details: The default configuration for the MySQL server was found and is readable at /etc/akonadi/mysql-global.conf. File content of '/etc/akonadi/mysql-global.conf': # # Global Akonadi MySQL server settings, # These settings can be adjusted using $HOME/.config/akonadi/mysql-local.conf # # Based on advice by Kris Köhntopp # [mysqld] # strict query parsing/interpretation # TODO: make Akonadi work with those settings enabled # sql_mode=strict_trans_tables,strict_all_tables,strict_error_for_division_by_zero,no_auto_create_user,no_auto_value_on_zero,no_engine_substitution,no_zero_date,no_zero_in_date,only_full_group_by,pipes_as_concat # sql_mode=strict_trans_tables # DEBUGGING: # log all queries, useful for debugging but generates an enormous amount of data # log=mysql.full # log queries slower than n seconds, log file name relative to datadir (for debugging only) # log_slow_queries=mysql.slow # long_query_time=1 # log queries not using indices, debug only, disable for production use # log_queries_not_using_indexes=1 # # mesure database size and adjust innodb_buffer_pool_size # SELECT sum(data_length) as bla, sum(index_length) as blub FROM information_sch
Bug#843534: akonadi-server: Workarounds don't work
Also, when I do su mysql I can read the file without problems, e.g. cat mysql.conf works. signature.asc Description: This is a digitally signed message part.
Bug#843534: akonadi-server: Workarounds don't work
When I run the same command using strace, I get
...
getcwd("/home/USERNAME/.local/share/akonadi", 510) = 34
stat("/home/USERNAME/.local/share/akonadi/mysql.conf", {st_mode=S_IFREG|0644,
st_size=3486, ...}) = 0
open("/home/USERNAME/.local/share/akonadi/mysql.conf", O_RDONLY) = -1 EACCES
(Permission denied)
write(2, "Could not open required defaults"..., 84Could not open required
defaults file: /home/USERNAME/.local/share/akonadi/mysql.conf
) = 84
write(2, "Fatal error in defaults handling"..., 50Fatal error in defaults
handling. Program aborted
) = 50
exit_group(1) = ?
+++ exited with 1 +++
signature.asc
Description: This is a digitally signed message part.
Bug#843534: akonadi-server: Workarounds don't work
OK, good idea, this gets me a bit further:
USERNAME@HOST:~/.local/share/akonadi$ /usr/sbin/mysqld --defaults-
file=/tmp/mysql.conf --datadir=/home/USERNAME/.local/share/akonadi/db_data/ --
socket=/tmp/akonadi-USERNAME.gzrNgH/mysql.socket
161110 13:28:37 [Warning] Insecure configuration for --secure-file-priv:
Current
value does not restrict location of generated files. Consider setting it to a
valid, non-empty path.
161110 13:28:37 [Note] /usr/sbin/mysqld (mysqld 5.5.53-0+deb8u1) starting as
process 2783 ...
161110 13:28:37 [Warning] Can't create test file
/home/USERNAME/.local/share/akonadi/db_data/HOST.lower-test
161110 13:28:37 [Warning] Can't create test file
/home/USERNAME/.local/share/akonadi/db_data/HOST.lower-test
161110 13:28:37 [Note] Plugin 'FEDERATED' is disabled.
161110 13:28:37 InnoDB: The InnoDB memory heap is disabled
161110 13:28:37 InnoDB: Mutexes and rw_locks use GCC atomic builtins
161110 13:28:37 InnoDB: Compressed tables use zlib 1.2.8
161110 13:28:37 InnoDB: Using Linux native AIO
161110 13:28:37 InnoDB: Initializing buffer pool, size = 80.0M
161110 13:28:37 InnoDB: Completed initialization of buffer pool
161110 13:28:37 InnoDB: Operating system error number 13 in a file operation.
InnoDB: The error means mysqld does not have the access rights to
InnoDB: the directory.
InnoDB: File name ./ibdata1
InnoDB: File operation call: 'open'.
InnoDB: Cannot continue operation.
It seems that the path to the datadir is also restricted, as this directory is
also writeable by USERNAME...
I see this as a bug in mysql, especially as it is not described in the
changelog, any other opinions on that?
Cheers, Johannes
Am Donnerstag, 10. November 2016, 13:07:40 schrieb Sandro Knauß:
> Hey,
>
> just try tp copy the file to /tmp/ and than try to start the server?
>
> /usr/sbin/mysqld --defaults-file=/tmp/mysql.conf --datadir=[...]
>
> maybe you have strange permission in one folder?
>
> But mysqld is runas normal so if this user can read the file this
> should be enough. Does 5.5.23 somehow also limit the paths to load
> defaults- file from? Doesn't seems so from changelog
>
> https://dev.mysql.com/doc/relnotes/mysql/5.5/en/news-5-5-53.html
>
> Best regards,
>
> sandro
>
> --
>
> Am Donnerstag, 10. November 2016, 12:51:59 CET schrieb Johannes Ranke:
> > When I run the same command using strace, I get
> >
> > ...
> >
> > getcwd("/home/USERNAME/.local/share/akonadi", 510) = 34
> > stat("/home/USERNAME/.local/share/akonadi/mysql.conf",
> > {st_mode=S_IFREG|0644, st_size=3486, ...}) = 0
> > open("/home/USERNAME/.local/share/akonadi/mysql.conf", O_RDONLY) = -1
> > EACCES (Permission denied)
> > write(2, "Could not open required defaults"..., 84Could not open required
> > defaults file: /home/USERNAME/.local/share/akonadi/mysql.conf
> > ) = 84
> > write(2, "Fatal error in defaults handling"..., 50Fatal error in defaults
> > handling. Program aborted
> > ) = 50
> > exit_group(1) = ?
> > +++ exited with 1 +++
--
PD Dr. Johannes Ranke
Kronacher Str. 12
79639 Grenzach-Wyhlen
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Bug#843534: (no subject)
spot on! I was using apparmor on this machine without knowing it. I know I have looked into it one or two years ago... Removing apparmor and rebooting fixed my problem. Thanks everybody, happy hacking, Johannes
Bug#829190: /usr/share/texlive/texmf-dist/scripts/texlive/tlmgr.pl: tlmgr install fails: Unknown directive ...containerchecksum ...
Package: texlive-base Version: 2014.20141024-2 Severity: normal File: /usr/share/texlive/texmf-dist/scripts/texlive/tlmgr.pl Dear Maintainer, I would like to install the most recent version of the metropolis package on Debian stable. So I did tlmgr init-usertree which created a fresh user tree under ~/texmf, but then tlmgr install metropolis gives me (running on Debian, switching to user mode!) Unknown directive ...containerchecksum c59200574a316416a23695c258edf3a32531fbda43ccdc09360ee105c3f07f9fb77df17c4ba4c2ea4f3a5ea6667e064b51e3d8c2fe6c984ba3e71b4e32716955... , please fix it! at /usr/share/texlive/tlpkg/TeXLive/TLPOBJ.pm line 210, <$retfh> line 5579. I had a look at the file TLPOBJ.pm but am not able to see what is going wrong. Thanks, Johannes ## List of ls-R files -rw-r--r-- 1 jranke jranke 599 Feb 4 2015 /home/jranke/texmf/ls-R -rw-r--r-- 1 root root 1251 Jun 24 12:38 /var/lib/texmf/ls-R -rw-rw-r-- 1 jranke staff 80 Mar 24 2015 /usr/local/share/texmf/ls-R lrwxrwxrwx 1 root root 29 Oct 21 2014 /usr/share/texmf/ls-R -> /var/lib/texmf/ls-R-TEXMFMAIN lrwxrwxrwx 1 root root 31 Dec 2 2014 /usr/share/texlive/texmf-dist/ls-R -> /var/lib/texmf/ls-R-TEXLIVEDIST lrwxrwxrwx 1 root root 31 Dec 2 2014 /usr/share/texlive/texmf-dist/ls-R -> /var/lib/texmf/ls-R-TEXLIVEDIST ## Config files -rw-r--r-- 1 root root 945 Nov 13 2015 /etc/texmf/web2c/texmf.cnf -rw-r--r-- 1 root root 4897 Jun 24 12:38 /var/lib/texmf/web2c/fmtutil.cnf lrwxrwxrwx 1 root root 32 Dec 2 2014 /usr/share/texmf/web2c/updmap.cfg -> /var/lib/texmf/updmap.cfg-DEBIAN -rw-r--r-- 1 root root 4429 Jun 24 12:38 /var/lib/texmf/tex/generic/config/language.dat ## Files in /etc/texmf/web2c/ total 8 -rw-r--r-- 1 root root 283 Oct 21 2014 mktex.cnf -rw-r--r-- 1 root root 945 Nov 13 2015 texmf.cnf ## md5sums of texmf.d ca40c66f144b4bafc3e59a2dd32ecb9c /etc/texmf/texmf.d/00debian.cnf 1df66bc319cec731e202eaf39f5d85e1 /etc/texmf/texmf.d/96JadeTeX.cnf c95cb926cc5d0b758ade26598679a2a1 /etc/texmf/texmf.d/local.cnf -- System Information: Debian Release: 8.5 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable'), (15, 'testing'), (10, 'unstable'), (5, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.5.0-trunk-amd64 (SMP w/8 CPU cores) Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages texlive-base depends on: ii debconf [debconf-2.0] 1.5.56 ii dpkg 1.17.27 ii libpaper-utils 1.1.24+nmu4 ii tex-common 5.03 ii texlive-binaries 2014.20140926.35254-6 ii ucf3.0030 ii xdg-utils 1.1.0~rc1+git20111210-7.4 Versions of packages texlive-base recommends: ii lmodern 2.004.4-5 Versions of packages texlive-base suggests: ii evince [postscript-viewer] 3.14.1-2+deb8u1 ii ghostscript [postscript-viewer] 9.06~dfsg-2+deb8u1 ii okular [postscript-viewer] 4:4.14.2-2 pn perl-tk ii xpdf [pdf-viewer]3.03-17+b1 Versions of packages tex-common depends on: ii debconf [debconf-2.0] 1.5.56 ii dpkg 1.17.27 ii ucf3.0030 Versions of packages tex-common suggests: ii debhelper 9.20150101 Versions of packages texlive-base is related to: ii tex-common5.03 ii texlive-binaries 2014.20140926.35254-6 -- debconf information excluded
Bug#740707: okular: full-screen hangs depending on printer configuration
Package: okular Version: 4:4.14.2-2 Followup-For: Bug #740707 Dear Maintainer, In my case, okular did not really freeze, but it showed me a grey screen for a long time (> 15 seconds) when I entered full-screen mode. This depends on the printer configuration. When the network is disabled, it does not occur, i.e. okular enters full-screen model quickly. It seems this behaviour started when some printers were automatically configured that are now unavailable. Now I discovered another case (different default network printer) where it showed me the grey screen for more than 1 minute, so I assume it would never return. Okular stopped to disbehave in this way when I selected a certain printer as default that is also not available. However, this "good" printer differs from the other unavailable printers, as its configuration opens immediately in the CUPS configuration, so CUPS obviously knows it's not available and does not try to talk to it. Hope this is helpful for someone in a similar situation... Cheers, Johannes -- System Information: Debian Release: 8.5 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable'), (15, 'testing'), (10, 'unstable'), (5, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.5.0-trunk-amd64 (SMP w/8 CPU cores) Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages okular depends on: ii kde-runtime 4:4.14.2-2 ii libc6 2.19-18+deb8u4 ii libfreetype62.5.2-3+deb8u1 ii libjpeg62-turbo 1:1.3.1-12 ii libkactivities6 4:4.13.3-1 ii libkdecore5 4:4.14.2-5+deb8u1 ii libkdeui5 4:4.14.2-5+deb8u1 ii libkexiv2-114:4.14.2-1 ii libkio5 4:4.14.2-5+deb8u1 ii libkparts4 4:4.14.2-5+deb8u1 ii libkprintutils4 4:4.14.2-5+deb8u1 ii libkpty44:4.14.2-5+deb8u1 ii libokularcore5 4:4.14.2-2 ii libphonon4 4:4.8.0-4 ii libpoppler-qt4-40.26.5-2+deb8u1 ii libqca2 2.0.3-6 ii libqimageblitz4 1:0.0.6-4 ii libqmobipocket1 4:4.14.2-1 ii libqt4-dbus 4:4.8.6+git64-g5dc8b2b+dfsg-3+deb8u1 ii libqt4-declarative 4:4.8.6+git64-g5dc8b2b+dfsg-3+deb8u1 ii libqt4-svg 4:4.8.6+git64-g5dc8b2b+dfsg-3+deb8u1 ii libqt4-xml 4:4.8.6+git64-g5dc8b2b+dfsg-3+deb8u1 ii libqtcore4 4:4.8.6+git64-g5dc8b2b+dfsg-3+deb8u1 ii libqtgui4 4:4.8.6+git64-g5dc8b2b+dfsg-3+deb8u1 ii libsolid4 4:4.14.2-5+deb8u1 ii libspectre1 0.2.7-3 ii libstdc++6 4.9.2-10 ii phonon 4:4.8.0-4 ii zlib1g 1:1.2.8.dfsg-2+b1 okular recommends no packages. Versions of packages okular suggests: ii ghostscript9.06~dfsg-2+deb8u1 ii jovie 4:4.14.2-1 ii okular-extra-backends 4:4.14.2-2 ii poppler-data 0.4.7-1 ii texlive-binaries 2014.20140926.35254-6 ii unrar 1:5.2.7-0.1 -- no debconf information
Bug#781266: r-base-core: Package fails to install when there is no group names "staff" on the system
Am Donnerstag, 26. März 2015, 12:48:37 schrieb Dirk Eddelbuettel: > On 26 March 2015 at 18:03, Alexander Schlarb wrote: > | Package: r-base-core > | Version: 3.1.1-1+b2 > | Severity: grave > | Justification: renders package unusable > | > | When installing the package `r-base-core` (or anything that depends on it) > | on a clean jessie install (not upgraded) then the depricated "staff" > | group will not > Uh-oh. When did 'staff' get deprecated? > > Do we have a list of still-supported groups? [Ok, went looking via a quick > docker image for 'jessie'.] > > I'll change it to a group I create, something like rpkgs. > > | exist and the calls to `chown root:staff /usr/local/lib/R` and `chown > | root:staff /usr/local/lib/R/site-library` will fail. This prevents the > | package (and any dependant packages) from being configured correctly. > > The package is used to widely (eg by all r-cran-* packages) that I am a > little surprised it has not come up earlier. For what it's worth, I do not recall having problems with my jessie pbuilder chroot (i386) and manually debootstrapped chroots (for amd64 and armel) that I used for the recent backport of R 3.1.3 to jessie. I think if I would have had to manually add the "staff" group I would remember... I suspect it is not really gone yet. I did not find anything in the draft release notes either, just some transition plan in #29007. Alexander, could we be educated further? Even if /usr/local were not to be owned by root:staff any more, does this mean the group will be gone in jessie? Johannes > > Dirk > > | -- System Information: > | Debian Release: 8.0 > | > | APT prefers testing > | APT policy: (500, 'testing') > | > | Architecture: amd64 (x86_64) > | Foreign Architectures: i386 > | > | Kernel: Linux 4.0.0-999-lowlatency (SMP w/8 CPU cores; PREEMPT) > | Locale: LANG=de_AT.UTF-8, LC_CTYPE=de_AT.UTF-8 (charmap=UTF-8) > | Shell: /bin/sh linked to /bin/dash > | Init: systemd (via /run/systemd/system) > | > | Versions of packages r-base-core depends on: > | ii libblas3 [libblas.so.3]1.2.20110419-10 > | ii libbz2-1.0 1.0.6-7+b2 > | ii libc6 2.19-15 > | ii libcairo2 1.14.0-2.1 > | ii libgfortran3 4.9.2-10 > | ii libglib2.0-0 2.42.1-1 > | ii libgomp1 4.9.2-10 > | ii libice62:1.0.9-1+b1 > | ii libjpeg62-turbo1:1.3.1-12 > | ii liblapack3 [liblapack.so.3]3.5.0-4 > | ii liblzma5 5.1.1alpha+20120614-2+b3 > | ii libopenblas-base [liblapack.so.3] 0.2.12-1 > | ii libpango-1.0-0 1.36.8-3 > | ii libpangocairo-1.0-01.36.8-3 > | ii libpaper-utils 1.1.24+nmu4 > | ii libpcre3 2:8.35-3.3 > | ii libpng12-0 1.2.50-2+b2 > | ii libquadmath0 4.9.2-10 > | ii libreadline6 6.3-8+b3 > | ii libsm6 2:1.2.2-1+b1 > | ii libtcl8.5 8.5.17-1 > | ii libtiff5 4.0.3-12.2 > | ii libtk8.5 8.5.17-1 > | ii libx11-6 2:1.6.2-3 > | ii libxext6 2:1.3.3-1 > | ii libxss11:1.2.2-1 > | ii libxt6 1:1.1.4-1+b1 > | ii ucf3.0030 > | ii unzip 6.0-16 > | ii xdg-utils 1.1.0~rc1+git20111210-7.4 > | ii zip3.0-8 > | ii zlib1g 1:1.2.8.dfsg-2+b1 > | > | Versions of packages r-base-core recommends: > | iu r-base-dev 3.1.1-1 > | ii r-doc-html 3.1.1-1 > | iu r-recommended 3.1.1-1 > | > | Versions of packages r-base-core suggests: > | pn ess > | iu r-base-html 3.1.1-1 > | pn r-doc-info | r-doc-pdf > | pn r-mathlib > | > | -- no debconf information -- PD Dr. Johannes Ranke Kronacher Str. 8 79639 Grenzach-Wyhlen -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Bug#804217: virt-viewer: Please package version 2.0
Package: virt-viewer Version: 1.0-1 Severity: normal Dear Maintainer, As the changelog for version 2.0 lists some fixes for various crashes and memory leaks https://virt-manager.org/download/ I think the new version should be provided in Debian. Unfortunately, this involves packaging new versions of spice-gtk and spice-protocol as well. Kind regards, Johannes Ranke -- System Information: Debian Release: 8.2 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable'), (10, 'unstable'), (5, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 3.16.0-4-amd64 (SMP w/8 CPU cores) Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages virt-viewer depends on: ii libatk1.0-0 2.14.0-1 ii libc6 2.19-18+deb8u1 ii libcairo-gobject2 1.14.0-2.1 ii libcairo2 1.14.0-2.1 ii libgdk-pixbuf2.0-0 2.31.1-2+deb8u3 ii libglib2.0-02.42.1-1 ii libgtk-3-0 3.14.5-1+deb8u1 ii libgtk-vnc-2.0-00.5.3-1.3 ii libgvnc-1.0-0 0.5.3-1.3 ii libpango-1.0-0 1.36.8-3 ii libpangocairo-1.0-0 1.36.8-3 ii libspice-client-glib-2.0-8 0.29-1 ii libspice-client-gtk-3.0-4 0.29-1 ii libvirt01.2.9-9+deb8u1 ii libxml2 2.9.1+dfsg1-5 virt-viewer recommends no packages. Versions of packages virt-viewer suggests: ii netcat-openbsd [netcat] 1.105-7 ii netcat-traditional [netcat] 1.10-41 -- no debconf information
Bug#804823: kreversi: crashes on start
Package: kreversi
Version: 4:4.13.1-1
Severity: grave
Justification: renders package unusable
Dear Maintainer,
When I try to start kreversi on jessie, I get
file:///usr/share/kde4/apps/kreversi/qml/Table.qml:107:5: Type CanvasItem
unavailable
CanvasItem {
^
file:///usr/share/kde4/apps/kreversi/qml/CanvasItem.qml:25:1: module
"org.kde.games.core" is not installed
import org.kde.games.core 0.1 as KgCore
^
QObject::connect: Cannot connect (null)::cellClicked(int,int) to
KReversiView::onPlayerMove(int,int)
KCrash: Application 'kreversi' crashing...
KCrash: Attempting to start /usr/lib/kde4/libexec/drkonqi from kdeinit
KCrash: Connect sock_file=/home/myuser/.kde/socket-myhost/kdeinit4__0
Kind regards,
Johannes
-- System Information:
Debian Release: 8.2
APT prefers stable-updates
APT policy: (500, 'stable-updates'), (500, 'stable'), (10, 'unstable'), (5,
'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 4.2.0-1-amd64 (SMP w/8 CPU cores)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
Versions of packages kreversi depends on:
ii kde-runtime 4:4.14.2-2
ii libc6 2.19-18+deb8u1
ii libkdecore5 4:4.14.2-5
ii libkdegames6abi14:4.14.2-1
ii libkdeui5 4:4.14.2-5
ii libqt4-declarative 4:4.8.6+git64-g5dc8b2b+dfsg-3+deb8u1
ii libqt4-svg 4:4.8.6+git64-g5dc8b2b+dfsg-3+deb8u1
ii libqtcore4 4:4.8.6+git64-g5dc8b2b+dfsg-3+deb8u1
ii libqtgui4 4:4.8.6+git64-g5dc8b2b+dfsg-3+deb8u1
ii libstdc++6 4.9.2-10
Versions of packages kreversi recommends:
ii khelpcenter4 4:4.14.2-2
kreversi suggests no packages.
-- no debconf information
Bug#804823: Only a dependency missing
I just discovered that it runs fine after installation of kde-games-core-declarative Cheers, Johannes
Bug#804823: Severity and title
Package: kreversi Version: 4:4.13.1-1 Followup-For: Bug #804823 Control: severity -1 important Maybe other games are affected as well.
Bug#804823: kreversi: crashes on start
Package: kreversi Version: 4:4.13.1-1 Followup-For: Bug #804823 Control: retitle -1 Fails to start due to missing dependency
Bug#857446: gitolite3: The user 'gitolite' mentioned in README.Debian is not the default user
Package: gitolite3 Version: 3.6.1-2+deb8u1 Severity: minor Dear Maintainer, When cloning from a fresh default gitolite3 setup using git clone gitol...@mydomain.org:testing I was asked for a password. So I consulted the README.Debian to see if there are any Debian specifics, and found a hint that the typical gitolite hosting user is 'gitolite'. However, for gitolite3 the default hosting user is 'gitolite3'. This should be corrected in the README.Debian. Also, it would be good to be made aware of the username of the hosting user during setup. Johannes -- System Information: Debian Release: 8.7 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable') Architecture: amd64 (x86_64) Kernel: Linux 3.16.0-4-amd64 (SMP w/1 CPU core) Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages gitolite3 depends on: ii adduser 3.113+nmu3 ii debconf [debconf-2.0]1.5.56 ii git [git-core] 1:2.1.4-2.1+deb8u2 ii openssh-server [ssh-server] 1:6.7p1-5+deb8u3 ii perl 5.20.2-3+deb8u6 gitolite3 recommends no packages. Versions of packages gitolite3 suggests: pn git-daemon-run pn gitweb -- debconf information: * gitolite3/adminkey: gitolite3/gituser: gitolite3 gitolite3/gitdir: /var/lib/gitolite3
Bug#857446: gitolite3: The user 'gitolite' mentioned in README.Debian is not the default user
Am Samstag, 11. März 2017, 13:11:16 schrieb David Bremner: ... > I agree that the documentation should mention the name of the default > user, but note that the mention of the user 'gitolite' is under the > "upgrading from gitolite v2', where it is indeed the default. Since v2 > is only present in oldstable, those instructions can probably just be > deleted now. OK. Yes. Thanks! Johannes
Bug#338020: nvidia-kernel-source: Not fixed for amd64, please reopen
Package: nvidia-kernel-source Version: 1.0.7174-3 Followup-For: Bug #338020 On amd64, the latest nvidia-kernel-source version is 1.0.7174-3 and therefore on this architecture, this bug is still bugging (not me any more, because I applied the patch mentioned in #338020) -- System Information: Debian Release: testing/unstable APT prefers unstable APT policy: (500, 'unstable'), (500, 'testing') Architecture: amd64 (x86_64) Shell: /bin/sh linked to /bin/bash Kernel: Linux 2.6.15.4-stiller1 Locale: [EMAIL PROTECTED], [EMAIL PROTECTED] (charmap=ISO-8859-15) Versions of packages nvidia-kernel-source depends on: ii debhelper5.0.24 helper programs for debian/rules ii dpatch 2.0.18 patch maintenance system for Debia ii make 3.80+3.81.rc1-1 The GNU version of the "make" util ii sed 4.1.4-5 The GNU sed stream editor Versions of packages nvidia-kernel-source recommends: ii devscripts2.9.15 Scripts to make the life of a Debi ii kernel-package10.035 A utility for building Linux kerne ii nvidia-glx1.0.7174-3 NVIDIA binary XFree86 4.x driver -- no debconf information -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Bug#354723: unixodbc: fails to retrieve data from ODBC connection
Package: unixodbc
Version: 2.2.11-9
Severity: important
The combination of unixodbc, libmyodbc and r-cran-rodbc works nicely on
a couple of i386 (debian unstable) and one amd64 (debian stable) boxes.
On this machine, I am running pure amd64 unstable, and I get a very
strange behavior with ODBC connections to my local mysql database:
A php test script
just segfaults. strace ends with
a_family=AF_INET, sin_port=htons(3306),
sin_addr=inet_addr("127.0.0.1")}, 16) = 0
setsockopt(3, SOL_IP, IP_TOS, [53983375223947272], 4) = 0
setsockopt(3, SOL_TCP, TCP_NODELAY, [53983375223947265], 4) = 0
setsockopt(3, SOL_SOCKET, SO_KEEPALIVE, [-6000514326958440447], 4) = 0
read(3, "A\0\0\0\n5.0.18-Debian_8-log\0,\0\0\0>?b"..., 16384) = 69
stat("/usr/share/mysql/charsets/Index.xml", {st_mode=S_IFREG|0644,
st_size=18171, ...}) = 0
open("/usr/share/mysql/charsets/Index.xml", O_RDONLY) = 4
read(4, " tables <- sqlQuery(channel,query,errors=TRUE)
> tables
[1] "[RODBC] ERROR: Could not SQLExecDirect"
[2] "S0022 1054 [unixODBC][MySQL][ODBC 3.51
Driver][mysqld-5.0.18-Debian_8-log]Unknown column 'plates' in 'field
list'"
but if I use the correct column name, it returns an empty set
> query <- "select plate from plates"
> tables <- sqlQuery(channel,query,errors=TRUE)
> tables
character(0)
> odbcGetErrMsg(channel)
character(0)
although the same query issued with the mysql command line client (and
same username and password) gives 1202 rows.
I don't know how to debug this. Any comments welcome!
Johannes Ranke
-- System Information:
Debian Release: testing/unstable
APT prefers unstable
APT policy: (500, 'unstable'), (500, 'testing')
Architecture: amd64 (x86_64)
Shell: /bin/sh linked to /bin/bash
Kernel: Linux 2.6.13.4-stiller1
Locale: [EMAIL PROTECTED], [EMAIL PROTECTED] (charmap=ISO-8859-15)
Versions of packages unixodbc depends on:
ii libc6 2.3.6-1GNU C Library: Shared libraries an
ii libltdl3 1.5.22-2 A system independent dlopen wrappe
ii libreadline5 5.1-6 GNU readline and history libraries
ii odbcinst1debian1 2.2.11-9 Support library and helper program
unixodbc recommends no packages.
-- no debconf information
--
To UNSUBSCRIBE, email to [EMAIL PROTECTED]
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Bug#354723: unixodbc: fails to retrieve data from ODBC connection
> strace is useless for debugging a segfault. Please run your test script > under gdb and forward the backtrace. > > http://wiki.debian.org/HowToGetABacktrace OK, thanks for the hint! I just wanted to install the build-deps for php5-odbc but then it wanted to deinstall a couple of things: stiller:~/tmp# LANG=en_EN apt-get build-dep php5-odbc Reading package lists... Done Building dependency tree... Done The following packages will be REMOVED: flex-old libdb3-dev libgnome-dev libmysqlclient12-dev flex-old and libmysqlclient12-dev were build-deps of unixodbc which I rebuilt earlier today. I guess that's the problem. So I would like to focus on RODBC: > > but if I use the correct column name, it returns an empty set > > > > query <- "select plate from plates" > > > tables <- sqlQuery(channel,query,errors=TRUE) > > > tables > > character(0) > > > odbcGetErrMsg(channel) > > character(0) > > > although the same query issued with the mysql command line client (and > > same username and password) gives 1202 rows. > > And what happens if you issue the query using the isql commandline tool? Then it also gives 1202 rows! So it seems to be a coincidence that both RODBC and php5-odbc are messed up on my system. I didn't know isql so far, although I was looking for something like this - it's great! I am just rebuilding R with the nostrip option because this is what I am really interested in. -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
