Bug#759543: fastqc: commons-math3 not found
Package: fastqc Version: 0.11.2+dfsg-2 Severity: important Dear Maintainer, Thank you for supporting fastqc! Please add commons-math3 to class-path in the manifest. --- fastqc-0.11.2+dfsg/debian/manifest 2014-08-26 14:54:22.048426545 +0400 +++ fastqc-0.11.2+dfsg-1/debian/manifest 2014-08-26 14:38:09.196491481 +0400 @@ -1,3 +1,3 @@ /usr/share/fastqc/fastqc.jar: Main-Class: uk.ac.babraham.FastQC.FastQCApplication - Class-Path: /usr/share/java/jbzip2.jar /usr/share/java/sam.jar + Class-Path: /usr/share/java/jbzip2.jar /usr/share/java/sam.jar /usr/share/java/commons-math3.jar Before the suggested change fastqc exposed the following symptoms on any data file: it started analysis, produced exception trace (see below) and then gets stuck. (In UI mode nothing changes after printing the exception trace). Started analysis of Intoshia_ATGTCA_L008_R1.fastq Approx 5% complete for Intoshia_ATGTCA_L008_R1.fastq Approx 10% complete for Intoshia_ATGTCA_L008_R1.fastq Approx 15% complete for Intoshia_ATGTCA_L008_R1.fastq Approx 20% complete for Intoshia_ATGTCA_L008_R1.fastq Approx 25% complete for Intoshia_ATGTCA_L008_R1.fastq Approx 30% complete for Intoshia_ATGTCA_L008_R1.fastq Approx 35% complete for Intoshia_ATGTCA_L008_R1.fastq Approx 40% complete for Intoshia_ATGTCA_L008_R1.fastq Approx 45% complete for Intoshia_ATGTCA_L008_R1.fastq Approx 50% complete for Intoshia_ATGTCA_L008_R1.fastq Approx 55% complete for Intoshia_ATGTCA_L008_R1.fastq Approx 60% complete for Intoshia_ATGTCA_L008_R1.fastq Approx 65% complete for Intoshia_ATGTCA_L008_R1.fastq Approx 70% complete for Intoshia_ATGTCA_L008_R1.fastq Approx 75% complete for Intoshia_ATGTCA_L008_R1.fastq Approx 80% complete for Intoshia_ATGTCA_L008_R1.fastq Approx 85% complete for Intoshia_ATGTCA_L008_R1.fastq Approx 90% complete for Intoshia_ATGTCA_L008_R1.fastq Approx 95% complete for Intoshia_ATGTCA_L008_R1.fastq Approx 100% complete for Intoshia_ATGTCA_L008_R1.fastq Exception in thread Thread-1 java.lang.NoClassDefFoundError: org/apache/commons/math3/distribution/BinomialDistribution at uk.ac.babraham.FastQC.Modules.KmerContent.calculateEnrichment(KmerContent.java:229) at uk.ac.babraham.FastQC.Modules.KmerContent.raisesError(KmerContent.java:390) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:334) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.init(HTMLReportArchive.java:84) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:163) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:110) at java.lang.Thread.run(Thread.java:745) Caused by: java.lang.ClassNotFoundException: org.apache.commons.math3.distribution.BinomialDistribution at java.net.URLClassLoader$1.run(URLClassLoader.java:366) at java.net.URLClassLoader$1.run(URLClassLoader.java:355) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:354) at java.lang.ClassLoader.loadClass(ClassLoader.java:425) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308) at java.lang.ClassLoader.loadClass(ClassLoader.java:358) ... 7 more Cheers, Daniil -- System Information: Debian Release: jessie/sid APT prefers testing APT policy: (990, 'testing'), (500, 'unstable'), (1, 'experimental') Architecture: amd64 (x86_64) Kernel: Linux 3.12-1-amd64 (SMP w/2 CPU cores) Locale: LANG=en_US.utf8, LC_CTYPE=en_US.utf8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Versions of packages fastqc depends on: ii libcommons-math3-java 3.3-1 ii libjbzip2-java 0.9.1-3 ii libsam-java1.113-1 fastqc recommends no packages. fastqc 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#679935: smbldap-tools: smbldap-useradd -P fails with .../smbldap-passwd.cmd not found
Package: smbldap-tools Version: 0.9.7-1 Severity: important Tags: patch The problem is completely described in subject. This is easily fixed by replacing my @passwd_cmd = ($RealBin/smbldap-passwd.cmd); with my @passwd_cmd = ($RealBin/smbldap-passwd); on line 651. Thanks! -- System Information: Debian Release: squeeze/sid APT prefers testing APT policy: (990, 'testing'), (500, 'unstable'), (500, 'stable'), (1, 'experimental') Architecture: amd64 (x86_64) Kernel: Linux 3.1.0-1-amd64 (SMP w/8 CPU cores) Locale: LANG=C, LC_CTYPE=ru_RU.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/bash Versions of packages smbldap-tools depends on: ii libcrypt-smbhash-perl 0.12-3 generate LM/NT hash of a password ii libio-socket-ssl-perl 1.31-1 Perl module implementing object or ii libnet-ldap-perl 1:0.39-1 client interface to LDAP servers ii libunicode-maputf8-perl 1.11-2 Perl module for conversing between ii perl 5.14.2-9 Larry Wall's Practical Extraction smbldap-tools recommends no packages. smbldap-tools 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#679936: smbldap-tools: smbldap-useradd does not work with -M
Package: smbldap-tools
Version: 0.9.7-1
Severity: normal
Tags: patch
smbldap-adduser -M some@email some-user produces an error stating that
it can not add the value for 'mail' attribute to LDAP record, since the
value already exists.
The error is produced from duplication of code block:
if (@adds) {
my $modify =
$ldap_master-modify( uid=$userName,$config{usersdn}, add = {@adds} );
$modify-code die failed to add entry: , $modify-error;
}
on lines 624 and 510.
To fix this one needs to either remove one of these blocks, or add
@adds = ();
on line 512.
Thanks!
PS. Sorry for not giving the exact error messages / properly formatted
patches, I already have no unfixed versions on my hands and it seems not
too big deal to fetch another copy to make a better description of the
patch.
-- System Information:
Debian Release: squeeze/sid
APT prefers testing
APT policy: (990, 'testing'), (500, 'unstable'), (500, 'stable'), (1,
'experimental')
Architecture: amd64 (x86_64)
Kernel: Linux 3.1.0-1-amd64 (SMP w/8 CPU cores)
Locale: LANG=C, LC_CTYPE=ru_RU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/bash
Versions of packages smbldap-tools depends on:
ii libcrypt-smbhash-perl 0.12-3 generate LM/NT hash of a password
ii libio-socket-ssl-perl 1.31-1 Perl module implementing object or
ii libnet-ldap-perl 1:0.39-1 client interface to LDAP servers
ii libunicode-maputf8-perl 1.11-2 Perl module for conversing between
ii perl 5.14.2-9 Larry Wall's Practical Extraction
smbldap-tools recommends no packages.
smbldap-tools suggests no packages.
-- no debconf information
--
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Bug#610316: Please update tmux to version 1.4
Squeeze freeze is over. Please push tmux 1.4 to sid. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#610316: Please update tmux to version 1.4
Package: tmux Version: 1.3-2 Severity: wishlist subj. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#610316: Please update tmux to version 1.4
Of course, as soon as the squeeze freeze ends. Good! (Sorry, I did not keep up to date with Debian news). -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#571023: /usr/bin/xsetwacom: xsetwacom --set|--get TwinView does not support leftof aboveof
Package: xserver-xorg-input-wacom Version: 0.10.3+20100109-1 Severity: normal File: /usr/bin/xsetwacom Tags: patch The problem is completely described in subject. Additional minor bug is that xsetwacom --set TwinView gives errnoeous error message if given wrong arguments. The attached patch seems to solve both problems for me. Cheers, -- Danya. -- System Information: Debian Release: squeeze/sid APT prefers testing APT policy: (990, 'testing'), (500, 'unstable'), (500, 'stable') Architecture: amd64 (x86_64) Kernel: Linux 2.6.30-1-amd64 (SMP w/4 CPU cores) Locale: LANG=C, LC_CTYPE=ru_RU.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/bash Versions of packages xserver-xorg-input-wacom depends on: ii libc6 2.10.2-2 GNU C Library: Shared libraries ii libx11-6 2:1.3.3-1 X11 client-side library ii libxi62:1.3-2X11 Input extension library ii xserver-xorg-core 2:1.7.4-2 Xorg X server - core server xserver-xorg-input-wacom recommends no packages. Versions of packages xserver-xorg-input-wacom suggests: ii xinput1.4.2-1Runtime configuration and test of -- no debconf information diff -u -r xf86-input-wacom-0.10.3+20100109.my/tools/xsetwacom.c xf86-input-wacom-0.10.3+20100109/tools/xsetwacom.c --- xf86-input-wacom-0.10.3+20100109.my/tools/xsetwacom.c 2010-02-22 20:40:47.221083896 +0300 +++ xf86-input-wacom-0.10.3+20100109/tools/xsetwacom.c 2010-01-09 10:40:54.0 +0300 @@ -1495,14 +1495,10 @@ if (strcasecmp(argv[0], none) == 0) twinview = TV_NONE; - else if (strcasecmp(argv[0], horizontal) == 0 || strcasecmp(argv[0], rightof) == 0) + else if (strcasecmp(argv[0], horizontal) == 0) twinview = TV_LEFT_RIGHT; - else if (strcasecmp(argv[0], vertical) == 0 || strcasecmp(argv[0], belowof) == 0) + else if (strcasecmp(argv[0], vertical) == 0) twinview = TV_ABOVE_BELOW; - else if (strcasecmp(argv[0], aboveof) == 0) - twinview = TV_BELOW_ABOVE; - else if (strcasecmp(argv[0], leftof) == 0) - twinview = TV_RIGHT_LEFT; else goto error; @@ -1532,9 +1528,7 @@ return; error: - fprintf(stderr, - Usage: xsetwacom TwinView device name -[none|horizontal|vertical|leftof|aboveof]\n); + fprintf(stderr, Usage: xsetwacom rotate device name [NONE | CW | CCW | HALF]\n); return; } @@ -1770,8 +1764,6 @@ case TV_NONE: twinview = none; break; case TV_ABOVE_BELOW: twinview = vertical; break; case TV_LEFT_RIGHT: twinview = horizontal; break; - case TV_BELOW_ABOVE: twinview = aboveof; break; - case TV_RIGHT_LEFT: twinview = leftof; break; default: break; }
Bug#571025: xserver-xorg-input-wacom: Impossible to set TVResolutions
Package: xserver-xorg-input-wacom
Version: 0.10.3+20100109-1
Severity: normal
Tags: patch
Hi,
it appears that setting tvResolutions through either of 'xsetwacom' or
'xinput set-int-prop' is impossible for any TwinView value. Any such
attempt returns BadInt error.
The problem appears to be in sanity checks for the received values in
wacom drivers: it was required for both sums of widths and heights of
monitors to be equal to xinerama screen size. This permits for only very
strange screen layouts, like this:
+---++
| 1 ||
+---++
| | 2 |
+---++
The attached patch fixes the checks to a more reasonable behaviour
(which depends on whether monitors are reported to be arranged
horizontally or vertically).
This led to a second problem in xsetwacom: initially tvResolutions is
set to [0,0,0,0], which means autodetect. Thus, sending either
TVResolution0, or TVResolution1 would yield values that will not pass
the checks. (One can bypass this bug by giving 4 values to xsetwacom
set ... TVResolution0). I assume a reasonable bypass would be to remove
parameter TVResolution1 from xsetwacom altogether and rename
TVResolution0 to TVResolutions. I assume that changing interface is
possible, since I see no way this parameter could be used before.
This suggested change is also in the attached patch.
Cheers,
-- Danya.
-- System Information:
Debian Release: squeeze/sid
APT prefers testing
APT policy: (990, 'testing'), (500, 'unstable'), (500, 'stable')
Architecture: amd64 (x86_64)
Kernel: Linux 2.6.30-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=C, LC_CTYPE=ru_RU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/bash
Versions of packages xserver-xorg-input-wacom depends on:
ii libc6 2.10.2-2 GNU C Library: Shared libraries
ii libx11-6 2:1.3.3-1 X11 client-side library
ii libxi62:1.3-2X11 Input extension library
ii xserver-xorg-core 2:1.7.4-2 Xorg X server - core server
xserver-xorg-input-wacom recommends no packages.
Versions of packages xserver-xorg-input-wacom suggests:
ii xinput1.4.2-1Runtime configuration and test of
-- no debconf information
diff -u -r xf86-input-wacom-0.10.3+20100109/src/wcmXCommand.c xf86-input-wacom-0.10.3+20100109.my/src/wcmXCommand.c
--- xf86-input-wacom-0.10.3+20100109/src/wcmXCommand.c 2010-01-09 10:40:54.0 +0300
+++ xf86-input-wacom-0.10.3+20100109.my/src/wcmXCommand.c 2010-02-22 23:45:54.165461382 +0300
@@ -585,13 +585,26 @@
values = (CARD32*)prop-data;
+ DBG(0, priv, (PROP_TV_RESOLUTIONS) values=[%d, %d, %d, %d]\n,
+ values[0], values[1], values[2], values[3]);
+
/* non-TwinView settings can not set TwinView RESOLUTION */
if ((priv-twinview == TV_NONE) || (values[0] 0) ||
-(values[1] 0) || (values[2] 0) || (values[3] 0) ||
-((values[0] + values[2]) != screenInfo.screens[0]-width) ||
-((values[1] + values[3]) != screenInfo.screens[0]-height))
+(values[1] 0) || (values[2] 0) || (values[3] 0))
return BadValue;
+ if ((priv-twinview == TV_LEFT_RIGHT) ||
+(priv-twinview == TV_RIGHT_LEFT))
+ if (((values[0] + values[2]) != screenInfo.screens[0]-width) ||
+ max(values[1], values[3]) != screenInfo.screens[0]-height)
+return BadValue;
+
+ if ((priv-twinview == TV_ABOVE_BELOW) ||
+(priv-twinview == TV_BELOW_ABOVE))
+ if (((values[1] + values[3]) != screenInfo.screens[0]-height) ||
+ max(values[0], values[2]) != screenInfo.screens[0]-width)
+return BadValue;
+
if (!checkonly)
{
priv-tvResolution[0] = values[0];
diff -u -r xf86-input-wacom-0.10.3+20100109/tools/xsetwacom.c xf86-input-wacom-0.10.3+20100109.my/tools/xsetwacom.c
--- xf86-input-wacom-0.10.3+20100109/tools/xsetwacom.c 2010-01-09 10:40:54.0 +0300
+++ xf86-input-wacom-0.10.3+20100109.my/tools/xsetwacom.c 2010-02-23 00:05:46.702573807 +0300
@@ -471,20 +471,13 @@
.prop_offset = 3,
},
{
- .name = TVResolution0,
- .desc = Sets MetaModes option for TwinView Screen 0. ,
+ .name = TVResolutions,
+ .desc = Sets MetaModes option for TwinView. Format: W0 H0 W1 H1. ,
.prop_name = WACOM_PROP_TWINVIEW_RES,
.prop_format = 32,
.prop_offset = 0,
},
{
- .name = TVResolution1,
- .desc = Sets MetaModes option for TwinView Screen 1. ,
- .prop_name = WACOM_PROP_TWINVIEW_RES,
- .prop_format = 32,
- .prop_offset = 1,
- },
- {
.name = RawFilter,
.desc = Enables and disables filtering of raw data,
default is true/on.,
Bug#539747: nut: Driver patch for Ippon BCP800 (06da/0003) to work with blazer_usb
Package: nut
Version: 2.4.1-3
Severity: normal
Tags: patch
Attached patch makes phoenix subdriver of blazer_usb useable for Ippon BCP800
I also sent the patch directly to upstream mailing list:
http://lists.alioth.debian.org/pipermail/nut-upsdev/2009-August/003976.html
Cheers,
-- Danya
-- System Information:
Debian Release: squeeze/sid
APT prefers testing
APT policy: (990, 'testing'), (500, 'unstable'), (500, 'stable')
Architecture: amd64 (x86_64)
Kernel: Linux 2.6.30-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=C, LC_CTYPE=ru_RU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/bash
Versions of packages nut depends on:
ii adduser 3.110 add and remove users and groups
ii debconf 1.5.27 Debian configuration management sy
ii libc62.9-12 GNU C Library: Shared libraries
ii libupsclient12.4.1-3 network UPS tools - client library
ii libusb-0.1-4 2:0.1.12-13 userspace USB programming library
ii libwrap0 7.6.q-18Wietse Venema's TCP wrappers libra
ii lsb-base 3.2-22 Linux Standard Base 3.2 init scrip
ii udev 0.141-1 /dev/ and hotplug management daemo
Versions of packages nut recommends:
ii bash-completion 1:1.0-3programmable completion for the ba
Versions of packages nut suggests:
pn nut-cgi none (no description available)
pn nut-dev none (no description available)
pn nut-snmp none (no description available)
pn nut-xml none (no description available)
-- debconf information:
nut/major_upstream_changes:
--- nut-2.4.1.orig/drivers/blazer_usb.c 2009-02-17 12:20:48.0 +0300
+++ nut-2.4.1/drivers/blazer_usb.c 2009-08-01 20:39:46.128727718 +0400
@@ -47,6 +47,23 @@
static int (*subdriver_command)(const char *cmd, char *buf, size_t buflen) = NULL;
+static int phoenix_flush_io()
+{
+ static
+ char buf[SMALLBUF+1];
+ int i, ret;
+ upsdebugx(3, phoenix_flush_io);
+ for(i = 0; i 10; i++) {
+ memset(buf, 0, sizeof(buf));
+ /* ret = usb-get_interrupt(udev, (unsigned char *)buf, 8, 1000); */
+ ret = usb_interrupt_read(udev, 0x81, buf, SMALLBUF, 1000);
+ upsdebugx(4, flush(%d,%d) - '%s', ret, strlen(buf), buf);
+ if (ret 1)
+ break;
+ }
+ return 0;
+}
+
static int phoenix_command(const char *cmd, char *buf, size_t buflen)
{
char tmp[SMALLBUF];
@@ -56,6 +73,7 @@
memset(tmp, 0, sizeof(tmp));
snprintf(tmp, sizeof(tmp), %s, cmd);
+ phoenix_flush_io();
for (i = 0; i strlen(tmp); i += ret) {
/* Write data in 8-byte chunks */
