Failure in performing update and upgrade on Raspbian Jessie

Question

I am new to Raspbian. I have a Raspberry Pi3 Model B.

I am trying to interface RTC DS1307 with it.

The steps outlined in the documentation are:

1. sudo apt-get update
2. sudo apt-get upgrade

When I perform the step 1., I get the following errors:

Get:1 http://repo.mysql.com stretch InRelease
Get:2 http://mirrordirector.raspbian.org jessie InRelease
99% [1 InRelease gpgv 197 B] [Connecting to archive.raspberrypi.org]Splitting up /var/lib/apt/lists/partial/repo.mysql.com_apt_debian_dists_stretch_InRelease into data Err http://repo.mysql.com stretch InRelease

99% [2 InRelease gpgv 197 B] [Connecting to archive.raspberrypi.org]Splitting up /var/lib/apt/lists/partial/mirrordirector.raspbian.org_raspbian_dists_jessie_InRelease Err http://mirrordirector.raspbian.org jessie InRelease

Get:3 http://archive.raspberrypi.org jessie InRelease
Err http://archive.raspberrypi.org jessie InReleasept/lists/partial/archive.raspberrypi.org_debian_dists_jessie_InRelease into data and signature failed

Fetched 591 B in 5s (112 B/s)
Reading package lists... Done
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http://repo.mysql.com stretch InRelease: Clearsigned file isn't valid, got 'NODATA' (does the network require authentication?)

W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http//mirrordirector.raspbian.org jessie InRelease: Clearsigned file isn't valid, got 'NODATA' (does the network require authentication?)

W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http://archive.raspberrypi.org jessie InRelease: Clearsigned file isn't valid, got 'NODATA' (does the network require authentication?)

W: Failed to fetch http://mirrordirector.raspbian.org/rasp ... /InRelease

W: Failed to fetch http://repo.mysql.com/apt/debian/dists/ ... /InRelease

W: Failed to fetch http://archive.raspberrypi.org/debian/d ... /InRelease

W: Some index files failed to download. They have been ignored, or old ones used instead.

When I perform step 2., I get the following errors:

Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
3 not fully installed or removed.
After this operation, 0 B of additional disk space will be used.
Do you want to continue? [Y/n] Y
Setting up python3 (3.4.2-2) ...
running python rtupdate hooks for python3.4...
dpkg-query: package 'gdebi-core' is not installed
Use dpkg --info (= dpkg-deb --info) to examine archive files,
and dpkg --contents (= dpkg-deb --contents) to list their contents.
Traceback (most recent call last):
File "/usr/bin/py3clean", line 210, in <module>
main()
File "/usr/bin/py3clean", line 196, in main
pfiles = set(dpf.from_package(options.package))
File "/usr/share/python3/debpython/files.py", line 53, in from_package
raise Exception("cannot get content of %s" % package_name)
Exception: cannot get content of gdebi-core
error running python rtupdate hook gdebi-core
dpkg-query: package 'python3-uno' is not installed
Use dpkg --info (= dpkg-deb --info) to examine archive files,
and dpkg --contents (= dpkg-deb --contents) to list their contents.
Traceback (most recent call last):
File "/usr/bin/py3clean", line 210, in <module>
main()
File "/usr/bin/py3clean", line 196, in main
pfiles = set(dpf.from_package(options.package))
File "/usr/share/python3/debpython/files.py", line 53, in from_package
raise Exception("cannot get content of %s" % package_name)
Exception: cannot get content of python3-uno
error running python rtupdate hook python3-uno
dpkg: error processing package python3 (--configure):
subprocess installed post-installation script returned error exit status 4
dpkg: dependency problems prevent configuration of python3-dev:
python3-dev depends on python3 (= 3.4.2-2); however:
Package python3 is not configured yet.

dpkg: error processing package python3-dev (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of dh-python:
dh-python depends on python3:any (>= 3.3.2-2~); however:
Package python3 is not configured yet.

dpkg: error processing package dh-python (--configure):
dependency problems - leaving unconfigured
Errors were encountered while processing:
python3
python3-dev
dh-python
E: Sub-process /usr/bin/dpkg returned an error code (1)

May I know where I am going wrong? Or what needs to be done?

Answer 1

Seems there is something broken with your apt list files. You can try to reinitialize them. Edit this two files:

/etc/apt/sources.list
/etc/apt/sources.list.d/raspi.list

Note what lines does not have a # at first character. Set it and save the files. Then do:

rpi ~$ sudo apt update

Because there are no entries in sources.list and raspi.list (they are all commented), all list files for the repositories will be removed. Now edit the two files again and remove the # you have set, but only that. Now do:

rpi ~$ sudo apt update
rpi ~$ sudo apt full-upgrade

Don't know if that helps but it is worth a try.