From tauqeer9 at gmail.com Wed Nov 22 21:24:12 2017 From: tauqeer9 at gmail.com (Tauqeer Alam) Date: Wed, 22 Nov 2017 20:24:12 -0600 Subject: [Bio-linux-list] Update error Red icon Message-ID: Hi All I was trying to install python 3.6, which I think was installed without problem. Now I get a "red circle with horizontal white line" in the taskbar at the top, and the error message "An error occurred when checking for updates". My computer works fine otherwise without a problem, except that the little red circle is always there on the top. I tried ?sudo apt-get -f install, sudo apt-get update, sudo apt-get upgrade? commands without any success. I also removed python 3.6, still the error exists. Could anyone guide me how to fix this error. Here is the output of the upgrade command- $ sudo apt-get upgrade Reading package lists... Done Building dependency tree Reading state information... Done Calculating upgrade... Done The following packages have been kept back: linux-generic-lts-xenial linux-headers-generic-lts-xenial linux-image-generic-lts-xenial 0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded. Thanks Tauqeer -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Thu Nov 23 07:09:21 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Thu, 23 Nov 2017 12:09:21 +0000 Subject: [Bio-linux-list] Update error Red icon In-Reply-To: References: Message-ID: <89e11a54-1cb7-6d87-c076-0b50f6f35d72@minke-informatics.co.uk> On 23/11/17 02:24, Tauqeer Alam wrote: > Hi All > > I was trying to install python 3.6, which I think was installed without > problem. Now I get a "red circle with horizontal white line" in the > taskbar at the top, and the error message "An error occurred when > checking for updates". My computer works fine otherwise without a > problem, except that the little red circle is always there on the top. I > tried ?sudo apt-get -f install, sudo apt-get update, sudo apt-get > upgrade? commands without any success. I also removed python 3.6, still > the error exists. Could anyone guide me how to fix this error. Here is > the output of the upgrade command- Hi, Tauqeer. How did you install Python 3.6? This is what you should see in Bio-linux 8 (Ubuntu 14.04.5 LTS): > apt list 'python[0-9].[0-9]' > Listing... Done > python2.7/trusty-updates,trusty-security,now 2.7.6-8ubuntu0.3 amd64 [installed,automatic] > python3.4/trusty-updates,trusty-security,now 3.4.3-1ubuntu1~14.04.5 amd64 [installed] Please post the output from: > sudo apt-cache policy 'python3' > sudo apt -f install I suspect that you have packages with dependencies that can't be installed, which gives you the red warning that mean "fix it manually". HTH, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From tauqeer9 at gmail.com Thu Nov 23 10:50:33 2017 From: tauqeer9 at gmail.com (Tauqeer Alam) Date: Thu, 23 Nov 2017 09:50:33 -0600 Subject: [Bio-linux-list] Update error Red icon In-Reply-To: <89e11a54-1cb7-6d87-c076-0b50f6f35d72@minke-informatics.co.uk> References: <89e11a54-1cb7-6d87-c076-0b50f6f35d72@minke-informatics.co.uk> Message-ID: Hi Tony Thanks for your help. It seems like the problem is more complex than I thought. I was trying to fix the problem, but actually I messed up lot of things it seems. The Ubuntu Software Center icon from the side bar also disappeared. Please see the output attached with this e-mail. Thanks Tauqeer On Thu, Nov 23, 2017 at 6:09 AM, Tony Travis < tony.travis at minke-informatics.co.uk> wrote: > On 23/11/17 02:24, Tauqeer Alam wrote: > > Hi All > > > > I was trying to install python 3.6, which I think was installed without > > problem. Now I get a "red circle with horizontal white line" in the > > taskbar at the top, and the error message "An error occurred when > > checking for updates". My computer works fine otherwise without a > > problem, except that the little red circle is always there on the top. I > > tried ?sudo apt-get -f install, sudo apt-get update, sudo apt-get > > upgrade? commands without any success. I also removed python 3.6, still > > the error exists. Could anyone guide me how to fix this error. Here is > > the output of the upgrade command- > > Hi, Tauqeer. > > How did you install Python 3.6? > > This is what you should see in Bio-linux 8 (Ubuntu 14.04.5 LTS): > > > apt list 'python[0-9].[0-9]' > > Listing... Done > > python2.7/trusty-updates,trusty-security,now 2.7.6-8ubuntu0.3 amd64 > [installed,automatic] > > python3.4/trusty-updates,trusty-security,now 3.4.3-1ubuntu1~14.04.5 > amd64 [installed] > > Please post the output from: > > > sudo apt-cache policy 'python3' > > sudo apt -f install > > I suspect that you have packages with dependencies that can't be > installed, which gives you the red warning that mean "fix it manually". > > HTH, > > Tony. > > -- > Minke Informatics Limited, Registered in Scotland - Company No. SC419028 > Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) > tel. +44(0)19755 63548 http://minke-informatics.co.uk > mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk > _______________________________________________ > Bio-Linux-list mailing list > Bio-Linux-list at bioinformatics.org > http://www.bioinformatics.org/mm/listinfo/bio-linux-list > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- :~$ apt list 'python[0-9].[0-9]' Listing... Done python2.7/trusty-updates,trusty-security,now 2.7.6-8ubuntu0.3 amd64 [installed] python3.4/trusty-updates,trusty-security,now 3.4.3-1ubuntu1~14.04.5 amd64 [installed] :~$ sudo apt-cache policy 'python3' python3: Installed: 3.4.0-0ubuntu2 Candidate: 3.4.0-0ubuntu2 Version table: *** 3.4.0-0ubuntu2 0 500 http://us.archive.ubuntu.com/ubuntu/ trusty/main amd64 Packages 100 /var/lib/dpkg/status :~$ sudo apt -f install Reading package lists... Done Building dependency tree Reading state information... Done 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102 not fully installed or removed. After this operation, 0 B of additional disk space will be used. Setting up python3.4-minimal (3.4.3-1ubuntu1~14.04.5) ... # Empty sitecustomize.py to avoid a dangling symlink Could not find platform independent libraries Could not find platform dependent libraries Consider setting $PYTHONHOME to [:] Fatal Python error: Py_Initialize: Unable to get the locale encoding ImportError: No module named 'encodings' Aborted dpkg: error processing package python3.4-minimal (--configure): subprocess installed post-installation script returned error exit status 134 Setting up libc6-dev-i386 (2.19-0ubuntu6.13) ... Setting up libc6-x32 (2.19-0ubuntu6.13) ... Setting up libc6-dev-x32 (2.19-0ubuntu6.13) ... Setting up libx32gcc1 (1:4.9.3-0ubuntu4) ... Setting up lib32gomp1 (4.8.4-2ubuntu1~14.04.3) ... Setting up libx32gomp1 (4.8.4-2ubuntu1~14.04.3) ... Setting up lib32itm1 (4.8.4-2ubuntu1~14.04.3) ... Setting up libx32itm1 (4.8.4-2ubuntu1~14.04.3) ... Setting up lib32atomic1 (4.8.4-2ubuntu1~14.04.3) ... Setting up libx32atomic1 (4.8.4-2ubuntu1~14.04.3) ... Setting up lib32asan0 (4.8.4-2ubuntu1~14.04.3) ... Setting up libx32asan0 (4.8.4-2ubuntu1~14.04.3) ... Setting up lib32quadmath0 (4.8.4-2ubuntu1~14.04.3) ... Setting up libx32quadmath0 (4.8.4-2ubuntu1~14.04.3) ... Setting up lib32gcc-4.8-dev (4.8.4-2ubuntu1~14.04.3) ... Setting up libx32gcc-4.8-dev (4.8.4-2ubuntu1~14.04.3) ... Setting up gcc-4.8-multilib (4.8.4-2ubuntu1~14.04.3) ... Setting up gcc-multilib (4:4.8.2-1ubuntu6) ... Setting up python3-xkit (0.5.0ubuntu2) ... /var/lib/dpkg/info/python3-xkit.postinst: 6: /var/lib/dpkg/info/python3-xkit.postinst: py3compile: not found dpkg: error processing package python3-xkit (--configure): subprocess installed post-installation script returned error exit status 127 dpkg: dependency problems prevent configuration of ubuntu-drivers-common: ubuntu-drivers-common depends on python3-xkit; however: Package python3-xkit is not configured yet. dpkg: error processing package ubuntu-drivers-common (--configure): dependency problems - leaving unconfigured dpkg: dependency problems prevent configuration of python3.4: python3.4 depends on python3.4-minimal (= 3.4.3-1ubuntu1~14.04.5); however: Package python3.4-minimal is not configured yet. dpkg: error processing package python3.4 (--configure): dependency problems - leaving unconfigured Setting up python3-commandnotfound (0.3ubuntu12) ... /var/lib/dpkg/info/python3-commandnotfound.postinst: 6: /var/lib/dpkg/info/python3-commandnotfound.postinst: py3compile: not found dpkg: error processing package python3-commandnotfound (--configure): subprocess installed post-installation script returned error exit status 127 Setting up ufw (0.34~rc-0ubuntu2) ... /var/lib/dpkg/info/ufw.postinst: 162: /var/lib/dpkg/info/ufw.postinst: py3compile: not found dpkg: error processing package ufw (--configure): subprocess installed post-installation script returned error exit status 127 Setting up apturl-common (0.5.2ubuntu4) ... /var/lib/dpkg/info/apturl-common.postinst: 27: /var/lib/dpkg/info/apturl-common.postinst: py3compile: not found dpkg: error processing package apturl-common (--configure): subprocess installed post-installation script returned error exit status 127 Setting up python3-software-properties (0.92.37.8) ... /var/lib/dpkg/info/python3-software-properties.postinst: 6: /var/lib/dpkg/info/python3-software-properties.postinst: py3compile: not found dpkg: error processing package python3-software-properties (--configure): subprocess installed post-installation script returned error exit status 127 dpkg: dependency problems prevent configuration of software-properties-common: software-properties-common depends on python3-software-properties (= 0.92.37.8); however: Package python3-software-properties is not configured yet. dpkg: error processing package software-properties-common (--configure): dependency problems - leaving unconfigured Setting up python3-aptdaemon.gtk3widgets (1.1.1-1ubuntu5.2) ... /var/lib/dpkg/info/python3-aptdaemon.gtk3widgets.postinst: 6: /var/lib/dpkg/info/python3-aptdaemon.gtk3widgets.postinst: py3compile: not found dpkg: error processing package python3-aptdaemon.gtk3widgets (--configure): subprocess installed post-installation script returned error exit status 127 dpkg: dependency problems prevent configuration of software-properties-gtk: software-properties-gtk depends on python3-software-properties (= 0.92.37.8); however: Package python3-software-properties is not configured yet. software-properties-gtk depends on python3-aptdaemon.gtk3widgets; however: Package python3-aptdaemon.gtk3widgets is not configured yet. software-properties-gtk depends on software-properties-common; however: Package software-properties-common is not configured yet. software-properties-gtk depends on ubuntu-drivers-common (>= 1:0.2.75); however: Package ubuntu-drivers-common is not configured yet. dpkg: error processing package software-properties-gtk (--configure): dependency problems - leaving unconfigured dpkg: dependency problems prevent configuration of apturl: apturl depends on apturl-common (= 0.5.2ubuntu4); however: Package apturl-common is not configured yet. apturl depends on software-properties-gtk; however: Package software-properties-gtk is not configured yet. apturl depends on python3-aptdaemon.gtk3widgets; however: Package python3-aptdaemon.gtk3widgets is not configured yet. dpkg: error processing package apturl (--configure): dependency problems - leaving unconfigured Setting up gedit (3.10.4-0ubuntu4) ... /var/lib/dpkg/info/gedit.postinst: 37: /var/lib/dpkg/info/gedit.postinst: py3compile: not found dpkg: error processing package gedit (--configure): subprocess installed post-installation script returned error exit status 127 Setting up python3-xdg (0.25-4) ... /var/lib/dpkg/info/python3-xdg.postinst: 6: /var/lib/dpkg/info/python3-xdg.postinst: py3compile: not found dpkg: error processing package python3-xdg (--configure): subprocess installed post-installation script returned error exit status 127 dpkg: dependency problems prevent configuration of python3-speechd: python3-speechd depends on python3-xdg; however: Package python3-xdg is not configured yet. dpkg: error processing package python3-speechd (--configure): dependency problems - leaving unconfigured Setting up python3-pyatspi (2.10.0+dfsg-1) ... /var/lib/dpkg/info/python3-pyatspi.postinst: 6: /var/lib/dpkg/info/python3-pyatspi.postinst: py3compile: not found dpkg: error processing package python3-pyatspi (--configure): subprocess installed post-installation script returned error exit status 127 Setting up python3-louis (2.5.3-2ubuntu1.2) ... /var/lib/dpkg/info/python3-louis.postinst: 6: /var/lib/dpkg/info/python3-louis.postinst: py3compile: not found dpkg: error processing package python3-louis (--configure): subprocess installed post-installation script returned error exit status 127 dpkg: dependency problems prevent configuration of gnome-orca: gnome-orca depends on python3-speechd (>= 0.6.2); however: Package python3-speechd is not configured yet. gnome-orca depends on python3-pyatspi (>= 2.6); however: Package python3-pyatspi is not configured yet. gnome-orca depends on python3-louis (>= 1.6.2); however: Package python3-louis is not configured yet. dpkg: error processing package gnome-orca (--configure): dependency problems - leaving unconfigured Setting up python3-cairo (1.10.0+dfsg-3ubuntu2) ... /var/lib/dpkg/info/python3-cairo.postinst: 6: /var/lib/dpkg/info/python3-cairo.postinst: py3compile: not found dpkg: error processing package python3-cairo (--configure): subprocess installed post-installation script returned error exit status 127 dpkg: dependency problems prevent configuration of python3-gi-cairo: python3-gi-cairo depends on python3-cairo (>= 1.10.0+dfsg-3~exp2); however: Package python3-cairo is not configured yet. dpkg: error processing package python3-gi-cairo (--configure): dependency problems - leaving unconfigured dpkg: dependency problems prevent configuration of gnome-sudoku: gnome-sudoku depends on python3-gi-cairo (>= 2.90.1); however: Package python3-gi-cairo is not configured yet. gnome-sudoku depends on python3-cairo; however: Package python3-cairo is not configured yet. dpkg: error processing package gnome-sudoku (--configure): dependency problems - leaving unconfigured dpkg: dependency problems prevent configuration of language-selector-gnome: language-selector-gnome depends on python3-aptdaemon.gtk3widgets; however: Package python3-aptdaemon.gtk3widgets is not configured yet. dpkg: error processing package language-selector-gnome (--configure): dependency problems - leaving unconfigured Setting up libc6-pic:amd64 (2.19-0ubuntu6.13) ... dpkg: dependency problems prevent configuration of onboard: onboard depends on python3-cairo; however: Package python3-cairo is not configured yet. onboard depends on python3-gi-cairo; however: Package python3-gi-cairo is not configured yet. dpkg: error processing package onboard (--configure): dependency problems - leaving unconfigured Setting up python3-chardet (2.2.1-2~ubuntu1) ... /var/lib/dpkg/info/python3-chardet.postinst: 6: /var/lib/dpkg/info/python3-chardet.postinst: py3compile: not found dpkg: error processing package python3-chardet (--configure): subprocess installed post-installation script returned error exit status 127 Setting up python3-lxml (3.3.3-1ubuntu0.1) ... /var/lib/dpkg/info/python3-lxml.postinst: 6: /var/lib/dpkg/info/python3-lxml.postinst: py3compile: not found dpkg: error processing package python3-lxml (--configure): subprocess installed post-installation script returned error exit status 127 dpkg: dependency problems prevent configuration of python3-plainbox: python3-plainbox depends on python3-lxml; however: Package python3-lxml is not configured yet. dpkg: error processing package python3-plainbox (--configure): dependency problems - leaving unconfigured Setting up python3-six (1.5.2-1ubuntu1) ... /var/lib/dpkg/info/python3-six.postinst: 6: /var/lib/dpkg/info/python3-six.postinst: py3compile: not found dpkg: error processing package python3-six (--configure): subprocess installed post-installation script returned error exit status 127 dpkg: dependency problems prevent configuration of python3-urllib3: python3-urllib3 depends on python3-six; however: Package python3-six is not configured yet. dpkg: error processing package python3-urllib3 (--configure): dependency problems - leaving unconfigured dpkg: dependency problems prevent configuration of python3-requests: python3-requests depends on python3-chardet; however: Package python3-chardet is not configured yet. python3-requests depends on python3-urllib3 (>= 1.5); however: Package python3-urllib3 is not configured yet. dpkg: error processing package python3-requests (--configure): dependency problems - leaving unconfigured Setting up python3-pyparsing (2.0.1+dfsg1-1build1) ... /var/lib/dpkg/info/python3-pyparsing.postinst: 6: /var/lib/dpkg/info/python3-pyparsing.postinst: py3compile: not found dpkg: error processing package python3-pyparsing (--configure): subprocess installed post-installation script returned error exit status 127 dpkg: dependency problems prevent configuration of python3-checkbox-support: python3-checkbox-support depends on python3-pyparsing; however: Package python3-pyparsing is not configured yet. dpkg: error processing package python3-checkbox-support (--configure): dependency problems - leaving unconfigured dpkg: dependency problems prevent configuration of python3-checkbox-ng: python3-checkbox-ng depends on python3-plainbox (>= 0.5.3); however: Package python3-plainbox is not configured yet. python3-checkbox-ng depends on python3-requests (>= 1.0); however: Package python3-requests is not configured yet. python3-checkbox-ng depends on python3-checkbox-support; however: Package python3-checkbox-support is not configured yet. dpkg: error processing package python3-checkbox-ng (--configure): dependency problems - leaving unconfigured Setting up python3-crypto (2.6.1-4ubuntu0.2) ... /var/lib/dpkg/info/python3-crypto.postinst: 6: /var/lib/dpkg/info/python3-crypto.postinst: py3compile: not found dpkg: error processing package python3-crypto (--configure): subprocess installed post-installation script returned error exit status 127 dpkg: dependency problems prevent configuration of python3-debian: python3-debian depends on python3-chardet; however: Package python3-chardet is not configured yet. python3-debian depends on python3-six; however: Package python3-six is not configured yet. dpkg: error processing package python3-debian (--configure): dependency problems - leaving unconfigured Setting up python3-feedparser (5.1.3-2) ... /var/lib/dpkg/info/python3-feedparser.postinst: 6: /var/lib/dpkg/info/python3-feedparser.postinst: py3compile: not found dpkg: error processing package python3-feedparser (--configure): subprocess installed post-installation script returned error exit status 127 Setting up python3-httplib2 (0.8-2build1) ... /var/lib/dpkg/info/python3-httplib2.postinst: 6: /var/lib/dpkg/info/python3-httplib2.postinst: py3compile: not found dpkg: error processing package python3-httplib2 (--configure): subprocess installed post-installation script returned error exit status 127 Setting up python3-markupsafe (0.18-1build2) ... /var/lib/dpkg/info/python3-markupsafe.postinst: 6: /var/lib/dpkg/info/python3-markupsafe.postinst: py3compile: not found dpkg: error processing package python3-markupsafe (--configure): subprocess installed post-installation script returned error exit status 127 dpkg: dependency problems prevent configuration of python3-mako: python3-mako depends on python3-markupsafe; however: Package python3-markupsafe is not configured yet. dpkg: error processing package python3-mako (--configure): dependency problems - leaving unconfigured Setting up python3-natsort (3.5.1-1ubuntu1) ... /var/lib/dpkg/info/python3-natsort.postinst: 6: /var/lib/dpkg/info/python3-natsort.postinst: py3compile: not found dpkg: error processing package python3-natsort (--configure): subprocess installed post-installation script returned error exit status 127 dpkg: dependency problems prevent configuration of python3-oauthlib: python3-oauthlib depends on python3-crypto; however: Package python3-crypto is not configured yet. dpkg: error processing package python3-oauthlib (--configure): dependency problems - leaving unconfigured Setting up python3-problem-report (2.14.1-0ubuntu3.27) ... /var/lib/dpkg/info/python3-problem-report.postinst: 6: /var/lib/dpkg/info/python3-problem-report.postinst: py3compile: not found dpkg: error processing package python3-problem-report (--configure): subprocess installed post-installation script returned error exit status 127 Setting up python3-uno (1:4.2.8-0ubuntu5.2) ... /var/lib/dpkg/info/python3-uno.postinst: 6: /var/lib/dpkg/info/python3-uno.postinst: py3compile: not found dpkg: error processing package python3-uno (--configure): subprocess installed post-installation script returned error exit status 127 dpkg: dependency problems prevent configuration of rhythmbox: rhythmbox depends on python3.4; however: Package python3.4 is not configured yet. dpkg: error processing package rhythmbox (--configure): dependency problems - leaving unconfigured dpkg: dependency problems prevent configuration of rhythmbox-plugin-magnatune: rhythmbox-plugin-magnatune depends on rhythmbox (= 3.0.2-0ubuntu2); however: Package rhythmbox is not configured yet. dpkg: error processing package rhythmbox-plugin-magnatune (--configure): dependency problems - leaving unconfigured dpkg: dependency problems prevent configuration of rhythmbox-plugins: rhythmbox-plugins depends on python3.4; however: Package python3.4 is not configured yet. rhythmbox-plugins depends on rhythmbox (= 3.0.2-0ubuntu2); however: Package rhythmbox is not configured yet. rhythmbox-plugins depends on python3-mako; however: Package python3-mako is not configured yet. dpkg: error processing package rhythmbox-plugins (--configure): dependency problems - leaving unconfigured dpkg: dependency problems prevent configuration of rhythmbox-plugin-zeitgeist: rhythmbox-plugin-zeitgeist depends on rhythmbox (>= 3.0); however: Package rhythmbox is not configured yet. rhythmbox-plugin-zeitgeist depends on rhythmbox (<< 3.1); however: Package rhythmbox is not configured yet. dpkg: error processing package rhythmbox-plugin-zeitgeist (--configure): dependency problems - leaving unconfigured Setting up software-center-aptdaemon-plugins (0.1.6build1) ... /var/lib/dpkg/info/software-center-aptdaemon-plugins.postinst: 13: /var/lib/dpkg/info/software-center-aptdaemon-plugins.postinst: py3compile: not found dpkg: error processing package software-center-aptdaemon-plugins (--configure): subprocess installed post-installation script returned error exit status 127 dpkg: dependency problems prevent configuration of usb-creator-common: usb-creator-common depends on python3-debian; however: Package python3-debian is not configured yet. dpkg: error processing package usb-creator-common (--configure): dependency problems - leaving unconfigured dpkg: dependency problems prevent configuration of usb-creator-gtk: usb-creator-gtk depends on usb-creator-common (= 0.2.56.3ubuntu0.1); however: Package usb-creator-common is not configured yet. dpkg: error processing package usb-creator-gtk (--configure): dependency problems - leaving unconfigured dpkg: dependency problems prevent configuration of friends-dispatcher: friends-dispatcher depends on python3-oauthlib; however: Package python3-oauthlib is not configured yet. dpkg: error processing package friends-dispatcher (--configure): dependency problems - leaving unconfigured dpkg: dependency problems prevent configuration of friends: friends depends on friends-dispatcher; however: Package friends-dispatcher is not configured yet. dpkg: error processing package friends (--configure): dependency problems - leaving unconfigured dpkg: too many errors, stopping Processing triggers for libc-bin (2.19-0ubuntu6.13) ... Processing triggers for menu (2.1.46ubuntu1) ... Errors were encountered while processing: python3.4-minimal python3-xkit ubuntu-drivers-common python3.4 python3-commandnotfound ufw apturl-common python3-software-properties software-properties-common python3-aptdaemon.gtk3widgets software-properties-gtk apturl gedit python3-xdg python3-speechd python3-pyatspi python3-louis gnome-orca python3-cairo python3-gi-cairo gnome-sudoku language-selector-gnome onboard python3-chardet python3-lxml python3-plainbox python3-six python3-urllib3 python3-requests python3-pyparsing python3-checkbox-support python3-checkbox-ng python3-crypto python3-debian python3-feedparser python3-httplib2 python3-markupsafe python3-mako python3-natsort python3-oauthlib python3-problem-report python3-uno rhythmbox rhythmbox-plugin-magnatune rhythmbox-plugins rhythmbox-plugin-zeitgeist software-center-aptdaemon-plugins usb-creator-common usb-creator-gtk friends-dispatcher friends Processing was halted because there were too many errors. E: Sub-process /usr/bin/dpkg returned an error code (1) From tony.travis at minke-informatics.co.uk Thu Nov 23 11:04:35 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Thu, 23 Nov 2017 16:04:35 +0000 Subject: [Bio-linux-list] Update error Red icon In-Reply-To: References: <89e11a54-1cb7-6d87-c076-0b50f6f35d72@minke-informatics.co.uk> Message-ID: On 23/11/17 15:50, Tauqeer Alam wrote: > Hi Tony > Thanks for your help. It seems like the problem is more complex than I > thought. I was trying to fix the problem, but actually I messed up lot > of things it seems. The Ubuntu Software Center icon from the side bar > also disappeared. Please see the output attached with this e-mail. Hi, Tauqeer. How did you install Python 3.6? Bye, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From tauqeer9 at gmail.com Thu Nov 23 11:20:13 2017 From: tauqeer9 at gmail.com (Tauqeer Alam) Date: Thu, 23 Nov 2017 10:20:13 -0600 Subject: [Bio-linux-list] Update error Red icon In-Reply-To: References: <89e11a54-1cb7-6d87-c076-0b50f6f35d72@minke-informatics.co.uk> Message-ID: Hi Tony I followed this link- https://askubuntu.com/questions/865554/how-do-i-install-python-3-6-using-apt-get sudo add-apt-repository ppa:jonathonf/python-3.6 sudo apt-get update sudo apt-get install python3.6 Tauqeer On Thu, Nov 23, 2017 at 10:04 AM, Tony Travis < tony.travis at minke-informatics.co.uk> wrote: > On 23/11/17 15:50, Tauqeer Alam wrote: > > Hi Tony > > Thanks for your help. It seems like the problem is more complex than I > > thought. I was trying to fix the problem, but actually I messed up lot > > of things it seems. The Ubuntu Software Center icon from the side bar > > also disappeared. Please see the output attached with this e-mail. > > Hi, Tauqeer. > > How did you install Python 3.6? > > Bye, > > Tony. > > -- > Minke Informatics Limited, Registered in Scotland - Company No. SC419028 > Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) > tel. +44(0)19755 63548 http://minke-informatics.co.uk > mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk > _______________________________________________ > Bio-Linux-list mailing list > Bio-Linux-list at bioinformatics.org > http://www.bioinformatics.org/mm/listinfo/bio-linux-list > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Thu Nov 23 11:27:50 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Thu, 23 Nov 2017 16:27:50 +0000 Subject: [Bio-linux-list] Update error Red icon In-Reply-To: References: <89e11a54-1cb7-6d87-c076-0b50f6f35d72@minke-informatics.co.uk> Message-ID: <4e0ed0d7-a523-d85c-29a0-e62be2fff6bb@minke-informatics.co.uk> On 23/11/17 16:20, Tauqeer Alam wrote: > Hi Tony > I followed this link- > > https://askubuntu.com/questions/865554/how-do-i-install-python-3-6-using-apt-get > > sudo add-apt-repository ppa:jonathonf/python-3.6 > sudo apt-get update > sudo apt-get install python3.6 Hi, Tauqeer. You need to remove the PPA repository that you installed from: /etc/apt/sources.list.d/ Then: sudo apt update sudo apt -f install sudo apt full-upgrade Let me know how you get on? Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From tony.travis at minke-informatics.co.uk Thu Nov 23 11:31:45 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Thu, 23 Nov 2017 16:31:45 +0000 Subject: [Bio-linux-list] Update error Red icon In-Reply-To: <4e0ed0d7-a523-d85c-29a0-e62be2fff6bb@minke-informatics.co.uk> References: <89e11a54-1cb7-6d87-c076-0b50f6f35d72@minke-informatics.co.uk> <4e0ed0d7-a523-d85c-29a0-e62be2fff6bb@minke-informatics.co.uk> Message-ID: On 23/11/17 16:27, Tony Travis wrote: > On 23/11/17 16:20, Tauqeer Alam wrote: >> Hi Tony >> I followed this link- >> >> https://askubuntu.com/questions/865554/how-do-i-install-python-3-6-using-apt-get >> >> sudo add-apt-repository ppa:jonathonf/python-3.6 >> sudo apt-get update >> sudo apt-get install python3.6 Hi, Tauqeer. In case you don't know, use: sudo add-apt-repository --remove ppa:jonathonf/python-3.6 HTH, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From tauqeer9 at gmail.com Thu Nov 23 11:40:05 2017 From: tauqeer9 at gmail.com (Tauqeer Alam) Date: Thu, 23 Nov 2017 10:40:05 -0600 Subject: [Bio-linux-list] Update error Red icon In-Reply-To: References: <89e11a54-1cb7-6d87-c076-0b50f6f35d72@minke-informatics.co.uk> <4e0ed0d7-a523-d85c-29a0-e62be2fff6bb@minke-informatics.co.uk> Message-ID: Hi Tony It is not working. :~$ sudo add-apt-repository --remove ppa:jonathonf/python-3.6 sudo: unable to execute /usr/bin/add-apt-repository: No such file or directory On Thu, Nov 23, 2017 at 10:31 AM, Tony Travis < tony.travis at minke-informatics.co.uk> wrote: > On 23/11/17 16:27, Tony Travis wrote: > > On 23/11/17 16:20, Tauqeer Alam wrote: > >> Hi Tony > >> I followed this link- > >> > >> https://askubuntu.com/questions/865554/how-do-i- > install-python-3-6-using-apt-get > >> > >> sudo add-apt-repository ppa:jonathonf/python-3.6 > >> sudo apt-get update > >> sudo apt-get install python3.6 > > Hi, Tauqeer. > > In case you don't know, use: > > sudo add-apt-repository --remove ppa:jonathonf/python-3.6 > > HTH, > > Tony. > > -- > Minke Informatics Limited, Registered in Scotland - Company No. SC419028 > Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) > tel. +44(0)19755 63548 http://minke-informatics.co.uk > mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk > _______________________________________________ > Bio-Linux-list mailing list > Bio-Linux-list at bioinformatics.org > http://www.bioinformatics.org/mm/listinfo/bio-linux-list > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tauqeer9 at gmail.com Thu Nov 23 11:45:19 2017 From: tauqeer9 at gmail.com (Tauqeer Alam) Date: Thu, 23 Nov 2017 10:45:19 -0600 Subject: [Bio-linux-list] Update error Red icon In-Reply-To: References: <89e11a54-1cb7-6d87-c076-0b50f6f35d72@minke-informatics.co.uk> <4e0ed0d7-a523-d85c-29a0-e62be2fff6bb@minke-informatics.co.uk> Message-ID: Hi Tony I just deleted "/etc/apt/sources.list.d/" directory by mistake. That's why it is not working I guess. Tauqeer On Thu, Nov 23, 2017 at 10:40 AM, Tauqeer Alam wrote: > Hi Tony > It is not working. > > :~$ sudo add-apt-repository --remove ppa:jonathonf/python-3.6 > > sudo: unable to execute /usr/bin/add-apt-repository: No such file or > directory > > On Thu, Nov 23, 2017 at 10:31 AM, Tony Travis informatics.co.uk> wrote: > >> On 23/11/17 16:27, Tony Travis wrote: >> > On 23/11/17 16:20, Tauqeer Alam wrote: >> >> Hi Tony >> >> I followed this link- >> >> >> >> https://askubuntu.com/questions/865554/how-do-i-install- >> python-3-6-using-apt-get >> >> >> >> sudo add-apt-repository ppa:jonathonf/python-3.6 >> >> sudo apt-get update >> >> sudo apt-get install python3.6 >> >> Hi, Tauqeer. >> >> In case you don't know, use: >> >> sudo add-apt-repository --remove ppa:jonathonf/python-3.6 >> >> HTH, >> >> Tony. >> >> -- >> Minke Informatics Limited, Registered in Scotland - Company No. SC419028 >> Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) >> tel. +44(0)19755 63548 http://minke-informatics.co.uk >> mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk >> _______________________________________________ >> Bio-Linux-list mailing list >> Bio-Linux-list at bioinformatics.org >> http://www.bioinformatics.org/mm/listinfo/bio-linux-list >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Thu Nov 23 11:56:36 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Thu, 23 Nov 2017 16:56:36 +0000 Subject: [Bio-linux-list] Update error Red icon In-Reply-To: References: <89e11a54-1cb7-6d87-c076-0b50f6f35d72@minke-informatics.co.uk> <4e0ed0d7-a523-d85c-29a0-e62be2fff6bb@minke-informatics.co.uk> Message-ID: <351a8020-789a-6d45-8381-8ef2e16a0dad@minke-informatics.co.uk> On 23/11/17 16:40, Tauqeer Alam wrote: > Hi Tony > It is not working. > > :~$ sudo add-apt-repository --remove ppa:jonathonf/python-3.6 > > sudo: unable to execute /usr/bin/add-apt-repository: No such file or > directory Hi, Tauqeer. Looks like your system has deeper problems :-( I use Python 3.6 under Bio-Linux with "Bioconda": > https://bioconda.github.io/ I wrote a wrapper that runs Python 3.6 under "Bioconda" in a chroot to avoid precisely the type of Ubuntu 14.04 system conflicts that you have encountered: > rwt017 at wildcat:~$ cat /usr/local/bin/bioconda3 > #!/bin/bash > #@(#)bioconda3.sh 2017-08-08 A.J.Travis > # > # Wrapper for Bioconda Python environment > # > > # check if already in Bioconda environment > export BIOCONDA_HOME=/usr/local/miniconda3 > if [[ "$PATH" != *$BIOCONDA_HOME* ]]; then > > # added by Miniconda3 4.3.11 installer > export PATH="$BIOCONDA_HOME/bin:$PATH" > debian_chroot=bioconda3 exec /bin/bash > fi > rwt017 at wildcat:~$ bioconda3 > (bioconda3)rwt017 at wildcat:~$ python -V > Python 3.6.0 :: Continuum Analytics, Inc. Contact me directly via Skype if you want help to fix your problems: Skype name "ajtravis" HTH, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From tony.travis at minke-informatics.co.uk Thu Nov 23 11:59:46 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Thu, 23 Nov 2017 16:59:46 +0000 Subject: [Bio-linux-list] Update error Red icon In-Reply-To: References: <89e11a54-1cb7-6d87-c076-0b50f6f35d72@minke-informatics.co.uk> <4e0ed0d7-a523-d85c-29a0-e62be2fff6bb@minke-informatics.co.uk> Message-ID: <182c8b06-cb1a-ec99-cc46-2f9d8c18c93b@minke-informatics.co.uk> On 23/11/17 16:45, Tauqeer Alam wrote: > Hi Tony > I just deleted?"/etc/apt/sources.list.d/" directory by mistake. That's > why it is not working I guess.? Hi, Tauqeer. No problem, just restore it from your backup... You did a backup, didn't you? People never take backups seriously until things go wrong! [We created "bio-linux-backups" to make it easy to do them] Bye, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From tauqeer9 at gmail.com Thu Nov 23 12:07:09 2017 From: tauqeer9 at gmail.com (Tauqeer Alam) Date: Thu, 23 Nov 2017 11:07:09 -0600 Subject: [Bio-linux-list] Update error Red icon In-Reply-To: <182c8b06-cb1a-ec99-cc46-2f9d8c18c93b@minke-informatics.co.uk> References: <89e11a54-1cb7-6d87-c076-0b50f6f35d72@minke-informatics.co.uk> <4e0ed0d7-a523-d85c-29a0-e62be2fff6bb@minke-informatics.co.uk> <182c8b06-cb1a-ec99-cc46-2f9d8c18c93b@minke-informatics.co.uk> Message-ID: Unfortunately I do not have a backup. Please let me know a good day/time to skype. Thanks Tauqeer On Thu, Nov 23, 2017 at 10:59 AM, Tony Travis < tony.travis at minke-informatics.co.uk> wrote: > On 23/11/17 16:45, Tauqeer Alam wrote: > > Hi Tony > > I just deleted "/etc/apt/sources.list.d/" directory by mistake. That's > > why it is not working I guess. > > Hi, Tauqeer. > > No problem, just restore it from your backup... > > You did a backup, didn't you? > > People never take backups seriously until things go wrong! > > [We created "bio-linux-backups" to make it easy to do them] > > Bye, > > Tony. > > -- > Minke Informatics Limited, Registered in Scotland - Company No. SC419028 > Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) > tel. +44(0)19755 63548 http://minke-informatics.co.uk > mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk > _______________________________________________ > Bio-Linux-list mailing list > Bio-Linux-list at bioinformatics.org > http://www.bioinformatics.org/mm/listinfo/bio-linux-list > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Thu Nov 23 12:09:01 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Thu, 23 Nov 2017 17:09:01 +0000 Subject: [Bio-linux-list] Update error Red icon In-Reply-To: References: <89e11a54-1cb7-6d87-c076-0b50f6f35d72@minke-informatics.co.uk> <4e0ed0d7-a523-d85c-29a0-e62be2fff6bb@minke-informatics.co.uk> <182c8b06-cb1a-ec99-cc46-2f9d8c18c93b@minke-informatics.co.uk> Message-ID: <0719a2a6-d536-4711-dab4-5a665821196f@minke-informatics.co.uk> On 23/11/17 17:07, Tauqeer Alam wrote: > Unfortunately I do not have a backup. Please let me know a good day/time > to skype. Hi, Tauqeer. OK, I'll email you off-list. Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk