[Solved] yum update, no module named sqlite

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Fufu
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Joined: 2014/07/08 09:35:44

[Solved] yum update, no module named sqlite

Post by Fufu » 2014/07/10 03:49:04

I am trying this route to get the yum groupinstall "Development Tools" for the nVidia drivers.

yum update

stops here...

Code: Select all

 Updating   : 1:java-1.7.0-openjdk-headless-1.7.0.55-2.4.7.2.el7_0.x    35/113 
warning: /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.55-2.4.7.2.el7_0.x86_64/jre/lib/security/US_export_policy.jar created as /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.55-2.4.7.2.el7_0.x86_64/jre/lib/security/US_export_policy.jar.rpmnew
warning: /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.55-2.4.7.2.el7_0.x86_64/jre/lib/security/local_policy.jar created as /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.55-2.4.7.2.el7_0.x86_64/jre/lib/security/local_policy.jar.rpmnew
  Updating   : selinux-policy-3.12.1-153.el7_0.10.noarch                 36/113 
/var/tmp/rpm-tmp.efJcBa: line 1: 16677 Bus error               semodule -nB
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/yum/rpmtrans.py", line 482, in callback
    self._scriptStop(bytes, total, h);
  File "/usr/lib/python2.7/site-packages/yum/rpmtrans.py", line 647, in _scriptStop
    self._scriptout(txmbr or name)
  File "/usr/lib/python2.7/site-packages/yum/rpmtrans.py", line 258, in _scriptout
    self.base.history.log_scriptlet_output(data, msgs)
  File "/usr/lib/python2.7/site-packages/yum/history.py", line 981, in log_scriptlet_output
    self._commit()
  File "/usr/lib/python2.7/site-packages/yum/history.py", line 740, in _commit
    return self._conn.commit()
sqlite3.OperationalError: disk I/O error
FATAL ERROR: python callback <bound method RPMTransaction.callback of <yum.rpmtrans.RPMTransaction instance at 0x1950b48>> failed, aborting!

[root@localhost liveuser]# yum update
There was a problem importing one of the Python modules
required to run yum. The error leading to this problem was:

   No module named sqlite

Please install a package which provides this module, or
verify that the module is installed correctly.

It's possible that the above module doesn't match the
current version of Python, which is:
2.7.5 (default, Jun 17 2014, 18:11:42) 
[GCC 4.8.2 20140120 (Red Hat 4.8.2-16)]

If you cannot solve this problem yourself, please go to 
the yum faq at:
  http://yum.baseurl.org/wiki/Faq
Last edited by Fufu on 2014/07/10 07:02:25, edited 2 times in total.
KDE | 3.10.0-123.4.2.el7.x86_64 | Fujitsu T901 | nVidia NVS 4200M | Intel i7-2640M 2.8GHz | 16GB | SSD
CentOS 7: Step-by-step solution for nVidia NVS Optimus drivers

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avij
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Re: yum update, no module named sqlite

Post by avij » 2014/07/10 04:00:19

Fufu wrote:sqlite3.OperationalError: disk I/O error
Sounds like a hardware failure to me (hard disk failure). Do you get any "read errors" or such in the output of dmesg?

gerald_clark
Posts: 10642
Joined: 2005/08/05 15:19:54
Location: Northern Illinois, USA

Re: yum update, no module named sqlite

Post by gerald_clark » 2014/07/10 04:00:56

sqlite3.OperationalError: disk I/O error
Replace the bad drive and start over.

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Fufu
Posts: 16
Joined: 2014/07/08 09:35:44

Re: yum update, no module named sqlite

Post by Fufu » 2014/07/10 05:12:45

Thank you @avij and @gerald_clark. It was the drive.

I changed the SSD then ran: yum update then received these warnings, while installing:

Code: Select all

Updating   : 1:java-1.7.0-openjdk-headless-1.7.0.55-2.4.7.2.el7_0.x    35/115 
warning: /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.55-2.4.7.2.el7_0.x86_64/jre/lib/security/US_export_policy.jar created as /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.55-2.4.7.2.el7_0.x86_64/jre/lib/security/US_export_policy.jar.rpmnew
warning: /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.55-2.4.7.2.el7_0.x86_64/jre/lib/security/local_policy.jar created as /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.55-2.4.7.2.el7_0.x86_64/jre/lib/security/local_policy.jar.rpmnew
installation completed

then ran dmesg that threw:

Code: Select all

[    0.979086] ACPI Warning: \_SB_.PCI0.GFX0._DSM: Argument #4 type mismatch - Found [Integer], ACPI requires [Package] (20130517/nsarguments-95)
[    0.979141] ACPI Warning: \_SB_.PCI0.GFX0._DSM: Argument #4 type mismatch - Found [Buffer], ACPI requires [Package] (20130517/nsarguments-95)
[    0.979243] ACPI Warning: \_SB_.PCI0.GFX0._DSM: Argument #4 type mismatch - Found [Buffer], ACPI requires [Package] (20130517/nsarguments-95)
[    0.979340] pci 0000:00:02.0: optimus capabilities: enabled, status dynamic power, 
[    0.979348] ACPI Warning: \_SB_.PCI0.P0P2.PEGP._DSM: Argument #4 type mismatch - Found [Integer], ACPI requires [Package] (20130517/nsarguments-95)
[    0.979365] ACPI Warning: \_SB_.PCI0.P0P2.PEGP._DSM: Argument #4 type mismatch - Found [Buffer], ACPI requires [Package] (20130517/nsarguments-95)
[    0.979448] ACPI Warning: \_SB_.PCI0.P0P2.PEGP._DSM: Argument #4 type mismatch - Found [Buffer], ACPI requires [Package] (20130517/nsarguments-95)
[    0.979530] pci 0000:01:00.0: optimus capabilities: enabled, status dynamic power, 
[    0.979534] VGA switcheroo: detected Optimus DSM method \_SB_.PCI0.P0P2.PEGP handle
[    0.979550] checking generic (e0000000 300000) vs hw (c0000000 10000000)
[    0.979551] checking generic (e0000000 300000) vs hw (d0000000 2000000)
[    0.979561] nouveau 0000:01:00.0: enabling device (0006 -> 0007)
[    0.979712] [drm] hdmi device  not found 1 0 1
...
[    4.593352] ACPI Warning: SystemIO range 0x0000000000000428-0x000000000000042f conflicts with OpRegion 0x0000000000000400-0x000000000000047f (\_SB_.PCI0.LPCB.PMIO) (20130517/utaddress-254)
[    4.593360] ACPI: If an ACPI driver is available for this device, you should use it instead of the native driver
[    4.593364] ACPI Warning: SystemIO range 0x0000000000000540-0x000000000000054f conflicts with OpRegion 0x0000000000000500-0x000000000000054b (\_SB_.PCI0.LPCB.OGIO) (20130517/utaddress-254)
[    4.593368] ACPI Warning: SystemIO range 0x0000000000000540-0x000000000000054f conflicts with OpRegion 0x0000000000000500-0x000000000000055f (\_SB_.PCI0.P0P2.PEGP.GPIO) (20130517/utaddress-254)
[    4.593371] ACPI: If an ACPI driver is available for this device, you should use it instead of the native driver
[    4.593372] ACPI Warning: SystemIO range 0x0000000000000530-0x000000000000053f conflicts with OpRegion 0x0000000000000500-0x000000000000054b (\_SB_.PCI0.LPCB.OGIO) (20130517/utaddress-254)
[    4.593375] ACPI Warning: SystemIO range 0x0000000000000530-0x000000000000053f conflicts with OpRegion 0x0000000000000500-0x000000000000055f (\_SB_.PCI0.P0P2.PEGP.GPIO) (20130517/utaddress-254)
[    4.593378] ACPI: If an ACPI driver is available for this device, you should use it instead of the native driver
[    4.593379] ACPI Warning: SystemIO range 0x0000000000000500-0x000000000000052f conflicts with OpRegion 0x0000000000000500-0x000000000000054b (\_SB_.PCI0.LPCB.OGIO) (20130517/utaddress-254)
[    4.593382] ACPI Warning: SystemIO range 0x0000000000000500-0x000000000000052f conflicts with OpRegion 0x0000000000000500-0x000000000000055f (\_SB_.PCI0.P0P2.PEGP.GPIO) (20130517/utaddress-254)
[    4.593385] ACPI: If an ACPI driver is available for this device, you should use it instead of the native driver
...
[  300.630784] mce: [Hardware Error]: Machine check events logged
[  303.853483] SELinux: initialized (dev binfmt_misc, type binfmt_misc), uses genfs_contexts
[  305.405550] xor: automatically using best checksumming function:
[  305.414934]    avx       : 25248.000 MB/sec
[  305.432954] raid6: sse2x1    9023 MB/s
[  305.449982] raid6: sse2x2    9503 MB/s
[  305.466992] raid6: sse2x4   11695 MB/s
[  305.466995] raid6: using algorithm sse2x4 (11695 MB/s)
[  305.466996] raid6: using ssse3x2 recovery algorithm
[  305.483350] bio: create slab <bio-2> at 2
[  305.483688] Btrfs loaded
[  305.489242] fuse init (API version 7.22)
[  305.497489] SELinux: initialized (dev fusectl, type fusectl), uses genfs_contexts
[  305.716530] XFS (sdb1): Mounting Filesystem
[  305.853454] XFS (sdb1): recovery required on read-only device.
[  305.853464] XFS (sdb1): write access unavailable, cannot proceed.
[  305.853469] XFS (sdb1): log mount/recovery failed: error 30
[  305.853526] XFS (sdb1): log mount failed
[  306.283745] nr_pdflush_threads exported in /proc is scheduled for removal
[  306.283864] sysctl: The scan_unevictable_pages sysctl/node-interface has been disabled for lack of a legitimate use case.  If you have one, please send an email to linux-mm@kvack.org.
[  582.924002] CPU2: Core temperature above threshold, cpu clock throttled (total events = 3000)
[  582.924003] CPU3: Core temperature above threshold, cpu clock throttled (total events = 2999)
[  582.924005] CPU1: Package temperature above threshold, cpu clock throttled (total events = 3198)
[  582.924006] CPU0: Package temperature above threshold, cpu clock throttled (total events = 3197)
[  582.924007] CPU3: Package temperature above threshold, cpu clock throttled (total events = 3198)
[  582.924013] CPU2: Package temperature above threshold, cpu clock throttled (total events = 3199)
[  582.929994] CPU0: Package temperature/speed normal
[  582.929995] CPU3: Core temperature/speed normal
[  582.929996] CPU2: Core temperature/speed normal
[  582.929997] CPU1: Package temperature/speed normal
[  582.929997] CPU3: Package temperature/speed normal
[  582.929998] CPU2: Package temperature/speed normal
[  600.995928] mce: [Hardware Error]: Machine check events logged
[  606.771867] XFS (sdb1): Mounting Filesystem
[  606.936135] XFS (sdb1): recovery required on read-only device.
[  606.936140] XFS (sdb1): write access unavailable, cannot proceed.
[  606.936142] XFS (sdb1): log mount/recovery failed: error 30
[  606.936202] XFS (sdb1): log mount failed
[ 1174.687092] CPU3: Core temperature above threshold, cpu clock throttled (total events = 7100)
[ 1174.687094] CPU0: Package temperature above threshold, cpu clock throttled (total events = 7506)
[ 1174.687095] CPU1: Package temperature above threshold, cpu clock throttled (total events = 7507)
[ 1174.687096] CPU2: Core temperature above threshold, cpu clock throttled (total events = 7101)
[ 1174.687098] CPU2: Package temperature above threshold, cpu clock throttled (total events = 7508)
[ 1174.687102] CPU3: Package temperature above threshold, cpu clock throttled (total events = 7507)
[ 1174.688128] CPU3: Core temperature/speed normal
[ 1174.688128] CPU2: Core temperature/speed normal
[ 1174.688130] CPU2: Package temperature/speed normal
[ 1174.688133] CPU3: Package temperature/speed normal
[ 1174.688158] CPU0: Package temperature/speed normal
[ 1174.688159] CPU1: Package temperature/speed normal
[ 1197.941024] SELinux: 2048 avtab hash slots, 100030 rules.
[ 1197.950566] SELinux: 2048 avtab hash slots, 100030 rules.
[ 1197.964223] SELinux:  8 users, 86 roles, 4808 types, 281 bools, 1 sens, 1024 cats
[ 1197.964227] SELinux:  83 classes, 100030 rules
[ 1198.189782] SELinux:  Context root:staff_r:sandbox_t:s0-s0:c0.c1023 became invalid (unmapped).
[ 1198.599362] SELinux:  Context system_u:unconfined_r:sandbox_t:s0-s0:c0.c1023 became invalid (unmapped).
[ 1198.824038] SELinux:  Context root:sysadm_r:sandbox_t:s0-s0:c0.c1023 became invalid (unmapped).
[ 1198.990684] SELinux:  Context root:unconfined_r:sandbox_t:s0-s0:c0.c1023 became invalid (unmapped).
[ 1199.049696] SELinux:  Context unconfined_u:unconfined_r:sandbox_t:s0-s0:c0.c1023 became invalid (unmapped).
[ 1201.820248] mce: [Hardware Error]: Machine check events logged
[ 1208.044836] XFS (sdb1): Mounting Filesystem
[ 1208.225550] XFS (sdb1): recovery required on read-only device.
[ 1208.225554] XFS (sdb1): write access unavailable, cannot proceed.
[ 1208.225556] XFS (sdb1): log mount/recovery failed: error 30
[ 1208.225622] XFS (sdb1): log mount failed
I am not sure where to update the ACPI drivers or what failed in the logs as I am not sure what to look for.

ran yum groupinstall "Development Tools", which was successful!
KDE | 3.10.0-123.4.2.el7.x86_64 | Fujitsu T901 | nVidia NVS 4200M | Intel i7-2640M 2.8GHz | 16GB | SSD
CentOS 7: Step-by-step solution for nVidia NVS Optimus drivers

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avij
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Re: [Solved] yum update, no module named sqlite

Post by avij » 2014/07/10 08:52:18

The Java message is harmless. And dmesg only shows messages for your current session. If you replaced your hard disk and rebooted, the dmesg message buffer got emptied. It is possible that some of those disk I/O errors ended up getting recorded to /var/log/messages, though. But if your system is working now after the hard disk replacement, perhaps there's no need to dig further.

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