Pkg Install Error


#1

Hi, I tried to install pysolfc today, but got the following error message with both the App Cafe and pkg install in a terminal:

[1/4] Installing py27-setuptools-36.5.0…
pkg-static: sqlite error while executing iterator in file pkgdb_iterator.c:1035: database disk image is malformed
pkg-static: sqlite error while executing INSERT OR REPLACE INTO files (path, sha256, package_id) VALUES (?1, ?2, ?3) in file pkgdb.c:1788: database disk image is malformed

Sysinfo gives the following:

Operating system information

Operating system release: FreeBSD 12.0-CURRENT
OS architecture: amd64
Hostname: beastieboy
Kernel build dir location: /usr/obj/usr/src/amd64.amd64/sys/GENERIC
Currently booted kernel: /boot/kernel/kernel

Currently loaded kernel modules (kldstat(8)):
zfs.ko
opensolaris.ko
geom_eli.ko
tmpfs.ko
aesni.ko
linux.ko
linux_common.ko
linux64.ko
libiconv.ko
libmchain.ko
msdosfs_iconv.ko
if_bwn.ko
siba_bwn.ko
gpiobus.ko
bhnd.ko
if_bwi.ko
runfw.ko
if_run.ko
if_rum.ko
if_iwm.ko
cuse.ko
geom_uzip.ko
fdescfs.ko
iwn4965fw.ko
iwn1000fw.ko
iwn5000fw.ko
iwn5150fw.ko
iwn6000fw.ko
iwn6000g2afw.ko
iwn6000g2bfw.ko
iwn6050fw.ko
if_urtw.ko
rtwn.ko
acpi_video.ko
fuse.ko
ums.ko
atp.ko
nvidia.ko
linprocfs.ko
ipfw.ko
autofs.ko
WARNING: The opensolaris.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The tmpfs.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The linux.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The linux_common.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The linux64.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The libiconv.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The libmchain.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The msdosfs_iconv.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The if_bwn.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf. Operating system information

Operating system release: FreeBSD 12.0-CURRENT
OS architecture: amd64
Hostname: beastieboy
Kernel build dir location: /usr/obj/usr/src/amd64.amd64/sys/GENERIC
Currently booted kernel: /boot/kernel/kernel

Currently loaded kernel modules (kldstat(8)):
zfs.ko
opensolaris.ko
geom_eli.ko
tmpfs.ko
aesni.ko
linux.ko
linux_common.ko
linux64.ko
libiconv.ko
libmchain.ko
msdosfs_iconv.ko
if_bwn.ko
siba_bwn.ko
gpiobus.ko
bhnd.ko
if_bwi.ko
runfw.ko
if_run.ko
if_rum.ko
if_iwm.ko
cuse.ko
geom_uzip.ko
fdescfs.ko
iwn4965fw.ko
iwn1000fw.ko
iwn5000fw.ko
iwn5150fw.ko
iwn6000fw.ko
iwn6000g2afw.ko
iwn6000g2bfw.ko
iwn6050fw.ko
if_urtw.ko
rtwn.ko
acpi_video.ko
fuse.ko
ums.ko
atp.ko
nvidia.ko
linprocfs.ko
ipfw.ko
autofs.ko
WARNING: The opensolaris.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The tmpfs.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The linux.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The linux_common.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The linux64.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The libiconv.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The libmchain.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The msdosfs_iconv.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The if_bwn.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The siba_bwn.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The gpiobus.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The bhnd.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The if_bwi.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The runfw.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The if_run.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The if_rum.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The if_iwm.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The cuse.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The geom_uzip.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The fdescfs.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The iwn4965fw.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The iwn1000fw.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The iwn5000fw.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The iwn5150fw.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The iwn6000fw.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The iwn6000g2afw.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The iwn6000g2bfw.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The iwn6050fw.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The if_urtw.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The rtwn.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The acpi_video.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The fuse.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The ums.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The atp.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The nvidia.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The linprocfs.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The ipfw.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The autofs.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.

INFO: For security recommendations see the security(7) man page.
INFO: For system tuning advice, see the tuning(7) man page.
INFO: To view various system statistics use the systat(1) tool.

Bootloader settings
The /boot/loader.conf has the following contents:
crypto_load="YES"
aesni_load="YES"
geom_eli_load="YES"
vfs.zfs.arc_max="512M"
zfs_load=“YES”

WARNING: The siba_bwn.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The gpiobus.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The bhnd.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The if_bwi.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The runfw.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The if_run.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The if_rum.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The if_iwm.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The cuse.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The geom_uzip.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The fdescfs.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The iwn4965fw.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The iwn1000fw.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The iwn5000fw.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The iwn5150fw.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The iwn6000fw.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The iwn6000g2afw.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The iwn6000g2bfw.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The iwn6050fw.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The if_urtw.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The rtwn.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The acpi_video.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The fuse.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The ums.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The atp.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The nvidia.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The linprocfs.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The ipfw.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.
WARNING: The autofs.ko module is loaded, however it is not being loaded upon the system boot time from /boot/loader.conf.

INFO: For security recommendations see the security(7) man page.
INFO: For system tuning advice, see the tuning(7) man page.
INFO: To view various system statistics use the systat(1) tool.

Bootloader settings
The /boot/loader.conf has the following contents:
crypto_load="YES"
aesni_load="YES"
geom_eli_load="YES"
vfs.zfs.arc_max="512M"
zfs_load=“YES”

Not sure what all the warnings are about. Does anyone have any suggestions?
Thanks in advance.


#2

What does the “about” command say? That tells us if you are runnng TrueOS STABLE or UNSTABLE. If UNSTABLE, did you recently update? If so back out to the previous BE because there were issues with the last UNSTABLE (right before Christmas); I don’t know if they got fixed yet.

Edit:
The warnings don’t mean anything more than “there are modules loaded that are not loaded from /boot/loader.conf”. Non issue since by design modules can be loaded at any time, and on TrueOS, they are loaded from the “modules” OpenRC service (runlevel boot). Nothing to do with your real problem of “database disk image is malformed”.


#3

mer: Sorry, we were called out of town to help with grandkids. Thanks for your explanation about all those warnings! The “about” command yields:

number of cores ……………… 2
host ……………………………………………………… beastieboy
memory ………………………………………………… 4096 MB available, 3311 MB free
OS git branch ……………………………………………………………………………………… trueos-stable-17.12
OS git revision ………………………………………………………………………………… d26791952
OS kernel build time ………………………………………………………… Sat 2017 Dec 9 18:10:09 UTC
OS kernel identity …………………………………………… (uname -i) GENERIC
OS platform (architecture) ……………………… (uname -m) amd64
OS release level ………………………………………………… (uname -r) 12.0-CURRENT
OS version and patch level …… (freebsd-version) 12.0-CURRENT
TrueOS package set ………………… STABLE
TrueOS version …………………………… TrueOS-Desktop-201712111405
uptime ………………………………………………… 1 min
user …………………………………………………… mikeb

More (TrueOS Desktop):

desktop environment …… Lumina
sound card driver ………… pcm0: <Analog Devices AD1986A (Analog 6ch/2.0)> (play/rec) default
wireless driver ……………… 
X11 drivers ………………………… nvidia_drv.so 

IIRC, I’ve received and installed one update since installation.


#4

Just attempted to install on my STABLE box

I must have the dependencies already, as I can install pysolfc no issues.


#5

Rod: I still get

[1/4] Installing py27-setuptools-36.5.0…
pkg-static: sqlite error while executing iterator in file pkgdb_iterator.c:1035: database disk image is malformed
pkg-static: sqlite error while executing INSERT OR REPLACE INTO files (path, sha256, package_id) VALUES (?1, ?2, ?3) in file pkgdb.c:1788: database disk image is malformed

Given that I’m running ZFS on a single disk, what might be the next step, if I in fact have some corrupted data? Thanks in advance.


#6

I’ll grab my test machine in a little while, do a fresh STABLE install and try to install then


#7

just did a clean install, and all 4 packages installed just fine


#8

Rod: Obviously a reinstall is in order (grumble).
1.) Just to be careful, I procured a new-in-the-packaging 1TB HD.
2.) I downloaded the latest and greatest stable version (17.12-x64) instead of using the DVD I had and upgrading again.
3.) I checked the download’s md5 hash, and it matched what was published on the web site.
4.) I burned a DVD and checked that; it was fine. I then did a fresh install on to the new HD.
5.) I rebooted after the install, and everything looked fine. I shut off the screen saver and power manager as I usually do. Then I opened the update client, and seeing that the update was over 700MB, I just let it run while I attended to dinner and an errand.
6.) When I returned, the screen was blank. I hit the space bar, and got the log in dialog box. So I entered the password, but all I got was the background and a featureless black bar across the bottom.
7.) I waited for a few minutes, and then forced a power switch reboot. All seemed to go normally, but after the log in screen, I was returned to the same background, black bar, and cursor. I clicked on the screen for several minutes, and then finally the desktop filled in the bar color and icons and worked. To explore this delay further, I rebooted a third time; it took 45 seconds from entering the password to opening Lumina. This time, Lumina turned on fully functional. ???
8.) I opened the AppCafe, and downloaded Pysolfc. It installed
and ran normally.

I don’t know if my pysolfc problem was caused by HD corruption or the system update that I did from 17-05, but the initial problems with the fresh install seem to have healed themselves. My next step is to install the additional software that I had and go on from there.
Thanks for your time on my behalf!


#9

‘pkg-static’ seems wrong.
According to FreeBSD documentation, the first activity of package-managent after fresh installation should be replacement of ‘pkg-static’ by ‘pkg’. Then, after completing this, everything else has to be installed by ‘pkg’, and never again by ‘pkg-static’.


#10

pc-updatemanger should take care of syncing the repos, if I read your comment correctly.

I’ve only ever had to ever use pkg-static in the case I screwed up the system.

So, yes. pkg is the standard way to install programs, and pc-updatemanger is used to update the system.

working on first cuppa, so hopefully this makes sense


#11

Quote man pkg-static(8):

pkg-static is a statically linked variant of pkg typically only used for the initial installation of pkg. There are some differences in functionality.

Quote man pkg(7):

To avoid backwards incompatibility issues, the actual pkg(8) tool is not installed in the base system. The first time invoked, pkg will bootstrap the real pkg(8) from a remote repository.

Final remark:

If this is relevant, the developers know better than I do.

But pkg-static doesn’t seem to be standard default behavior.

If it is permanent default in TrueOS, then I didn’t know it.


#12

Yes they know.

They try to keep as mush FreeBSD as possible, but make changes when necessary.