Notes of a Programmer: October 2021

I want to mount a NSF share exported on a FreeNAS/TrueNAS/FreeBSD system on a Fedora Linux system. These two systems have their own independent user IDs and domains. To display the user name of the NSF share as a user name on the client, I figure that I need to use nfsidmap. For this, I need to solve the following problems.

Map the Linux client's NSF domain to that of the FreeNAS/TrueNAS/FreeBSD server. For this, I need to find out the domain name of the FreeNAS/TrueNAS/FreeBSD server. On the server, open a console/terminal, issue the following command
```
hostname -d        
```
Assume the output is local. We can check whether this matches the NSF domain on the Linux client side, by running the following command on the client side,
```
sudo nfsidmap -d 
```
Map the Linux client's user to that of the FreeNAS/TrueNAS/FreeBSD server. For this, I update /etc/idmapd.conf

Finally, I update the Linux client's /etc/idmapd.conf configuration file. Below is an example.

[General]
Domain = local # use the output of "hostname -d" on the server side

[Mapping]
Nobody-User = nobody
Nobody-Group = nobody
        
[Translation]

[Static]
server_user1@local=client_user1

I am upgrading a Fedora Linux system. A necessary step is to bring the system up-to-date. For this, I issue the command,

sudo dnf upgrade --refresh

However, the upgrade fails with an error message that complains about "unpacking of archive failed ... cpio: File from package already exists as a directory in system". Below is an exerpt of the error message,


$ sudo dnf upgrade --refresh
Docker CE Stable - x86_64                       110 kB/s | 3.5 kB     00:00
Fedora 32 openh264 (From Cisco) - x86_64        3.4 kB/s | 990  B     00:00
Fedora Modular 32 - x86_64                      146 kB/s |  12 kB     00:00
Fedora Modular 32 - x86_64 - Updates             69 kB/s |  12 kB     00:00
Fedora 32 - x86_64 - Updates                    122 kB/s |  12 kB     00:00
Fedora 32 - x86_64                              120 kB/s |  12 kB     00:00
Dependencies resolved.
================================================================================
 Package                 Arch     Version                       Repo       Size
================================================================================
Upgrading:
 filesystem              x86_64   3.14-2.fc32                   fedora    1.1 M
 gawk                    x86_64   5.0.1-7.fc32                  fedora    1.2 M
 npm                     x86_64   1:6.14.12-1.12.22.1.1.fc32    updates   3.3 M
 python3-numpy           x86_64   1:1.18.4-2.fc32               updates   4.4 M
 texlive-texlive.infra   noarch   7:20200327-21.fc32            updates   279 k

Transaction Summary
================================================================================
Upgrade  5 Packages

Total download size: 10 M
Is this ok [y/N]: y
Downloading Packages:
(1/5): texlive-texlive.infra-20200327-21.fc32.n 630 kB/s | 279 kB     00:00
(2/5): npm-6.14.12-1.12.22.1.1.fc32.x86_64.rpm  4.7 MB/s | 3.3 MB     00:00
(3/5): filesystem-3.14-2.fc32.x86_64.rpm        3.1 MB/s | 1.1 MB     00:00
(4/5): python3-numpy-1.18.4-2.fc32.x86_64.rpm   3.6 MB/s | 4.4 MB     00:01
(5/5): gawk-5.0.1-7.fc32.x86_64.rpm             2.0 MB/s | 1.2 MB     00:00
--------------------------------------------------------------------------------
Total                                           6.6 MB/s |  10 MB     00:01
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Running scriptlet: filesystem-3.14-2.fc32.x86_64                          1/1
  Preparing        :                                                        1/1
  Upgrading        : filesystem-3.14-2.fc32.x86_64                         1/10
Error unpacking rpm package filesystem-3.14-2.fc32.x86_64
  Upgrading        : gawk-5.0.1-7.fc32.x86_64                              2/10
error: unpacking of archive failed on file /usr/tmp: cpio: File from package already exists as a directory in system
error: filesystem-3.14-2.fc32.x86_64: install failed

Error unpacking rpm package gawk-5.0.1-7.fc32.x86_64
  Upgrading        : texlive-texlive.infra-7:20200327-21.fc32.noarch       3/10
error: unpacking of archive failed on file /usr/libexec/gawk: cpio: File from package already exists as a directory in system
error: gawk-5.0.1-7.fc32.x86_64: install failed

Error unpacking rpm package texlive-texlive.infra-7:20200327-21.fc32.noarch
  Upgrading        : python3-numpy-1:1.18.4-2.fc32.x86_64                  4/10
error: unpacking of archive failed on file /usr/share/perl5/TeXLive: cpio: File from package already exists as a directory in system
error: texlive-texlive.infra-7:20200327-21.fc32.noarch: install failed

Error unpacking rpm package python3-numpy-1:1.18.4-2.fc32.x86_64
  Upgrading        : npm-1:6.14.12-1.12.22.1.1.fc32.x86_64                 5/10
error: unpacking of archive failed on file /usr/include/numpy: cpio: File from package already exists as a directory in system
error: python3-numpy-1:1.18.4-2.fc32.x86_64: install failed

Error unpacking rpm package npm-1:6.14.12-1.12.22.1.1.fc32.x86_64
  Verifying        : npm-1:6.14.12-1.12.22.1.1.fc32.x86_64                 1/10
  Verifying        : npm-1:6.14.8-1.12.19.0.1.fc31.x86_64                  2/10
  Verifying        : python3-numpy-1:1.18.4-2.fc32.x86_64                  3/10
  Verifying        : python3-numpy-1:1.17.4-2.fc31.x86_64                  4/10
  Verifying        : texlive-texlive.infra-7:20200327-21.fc32.noarch       5/10
  Verifying        : texlive-texlive.infra-7:20190410-8.fc31.noarch        6/10
  Verifying        : filesystem-3.14-2.fc32.x86_64                         7/10
  Verifying        : filesystem-3.12-2.fc31.x86_64                         8/10
  Verifying        : gawk-5.0.1-7.fc32.x86_64                              9/10
  Verifying        : gawk-5.0.1-5.fc31.x86_64                             10/10

Failed:
  filesystem-3.12-2.fc31.x86_64
  filesystem-3.14-2.fc32.x86_64
  gawk-5.0.1-5.fc31.x86_64
  gawk-5.0.1-7.fc32.x86_64
  npm-1:6.14.8-1.12.19.0.1.fc31.x86_64
  npm-1:6.14.12-1.12.22.1.1.fc32.x86_64
  python3-numpy-1:1.17.4-2.fc31.x86_64
  python3-numpy-1:1.18.4-2.fc32.x86_64
  texlive-texlive.infra-7:20190410-8.fc31.noarch
  texlive-texlive.infra-7:20200327-21.fc32.noarch

Error: Transaction failed
$

As it complains that it can not write to the path indicated in the error message, such as, /usr/include/numpy because the directory already exists. To address this, I come out the following solution, i.e., to rename the directory or file that the error message complains about. For instance, we do these,


sudo mv /usr/tmp /usr/tmp.bu
sudo mv /usr/libexec/gawk /usr/libexec/gawk.bu
sudo mv /usr/share/perl5/TeXLive /usr/share/perl5/TeXLive.bu
sudo mv /usr/include/numpy /usr/include/numpy.bu

Then do upgrade again, as in,

sudo dnf upgrade --refresh

After this, don't forget to remove the backup files or directories, such as,


sudo rm -rf /usr/tmp.bu
sudo rm -rf /usr/libexec/gawk.bu
sudo rm -rf /usr/share/perl5/TeXLive.bu
sudo rm -rf /usr/include/numpy.bu

Dealing with Complexities

The above solutions work for some packages. However, there are two complexities.

Some packages has more than one or two files or directories that cause cpio to fail. The sympotom is that we would encounter the similar error. The solution is obvious, just to rename the file or the directory that causes the problem until we can successfully upgrade the package.
Sometimes, the error message does not indicate which file or the directory causes the problem, such as, the example below,

$ sudo dnf upgrade --refresh
[sudo] password for hchen:
Docker CE Stable - x86_64                        38 kB/s |  13 kB     00:00
Fedora 33 - x86_64                               11 MB/s |  72 MB     00:06
Fedora 33 openh264 (From Cisco) - x86_64        1.4 kB/s | 2.5 kB     00:01
Fedora Modular 33 - x86_64                      3.1 MB/s | 3.3 MB     00:01
Fedora 33 - x86_64 - Updates                     12 MB/s |  30 MB     00:02
Fedora Modular 33 - x86_64 - Updates            2.8 MB/s | 3.2 MB     00:01
Last metadata expiration check: 0:00:01 ago on Sat 02 Oct 2021 09:14:19 PM EDT.
Dependencies resolved.
================================================================================
 Package   Architecture Version                             Repository     Size
================================================================================
Upgrading:
 npm       x86_64       1:6.14.15-1.14.17.6.1.fc33          updates       3.3 M

Transaction Summary
================================================================================
Upgrade  1 Package

Total download size: 3.3 M
Is this ok [y/N]: y
Downloading Packages:
npm-6.14.15-1.14.17.6.1.fc33.x86_64.rpm         6.2 MB/s | 3.3 MB     00:00
--------------------------------------------------------------------------------
Total                                           4.0 MB/s | 3.3 MB     00:00
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Running scriptlet: npm-1:6.14.15-1.14.17.6.1.fc33.x86_64                  1/1
  Preparing        :                                                        1/1
  Upgrading        : npm-1:6.14.15-1.14.17.6.1.fc33.x86_64                  1/2
Error unpacking rpm package npm-1:6.14.15-1.14.17.6.1.fc33.x86_64
  Verifying        : npm-1:6.14.15-1.14.17.6.1.fc33.x86_64                  1/2
  Verifying        : npm-1:6.14.8-1.12.19.0.1.fc31.x86_64                   2/2

Failed:
  npm-1:6.14.8-1.12.19.0.1.fc31.x86_64   npm-1:6.14.15-1.14.17.6.1.fc33.x86_64

Error: Transaction failed
$

One solution is to download the rpm package, and attempt to upgrade it using rpm. In this way we can observe which file and directory that have caused the problem. For instance, we first download the npmpackage,


sudo dnf download npm

Then we attempt to install it,


$ sudo rpm -U -i -v -h npm-6.14.15-1.14.17.6.1.fc33.x86_64.rpm
Verifying...                          ################################# [100%]
Preparing...                          ################################# [100%]
Updating / installing...
   1:npm-1:6.14.15-1.14.17.6.1.fc33   ################################# [ 50%]
error: unpacking of archive failed on file /usr/lib/node_modules/npm/docs: cpio: File from package already exists as a directory in system
error: npm-1:6.14.15-1.14.17.6.1.fc33.x86_64: install failed
error: npm-1:6.14.8-1.12.19.0.1.fc31.x86_64: erase skipped
$

which shows that the /usr/lib/node_modules/npm/docs directory is the culprit. We need to rename it following the approach discussed in the above


sudo mv /usr/lib/node_modules/npm/docs /usr/lib/node_modules/npm/docs.bu

After that, we can upgrade the package, for instance,


$ sudo rpm -U -i -v -h npm-6.14.15-1.14.17.6.1.fc33.x86_64.rpm
Verifying...                          ################################# [100%]
Preparing...                          ################################# [100%]
Updating / installing...
   1:npm-1:6.14.15-1.14.17.6.1.fc33   ################################# [ 50%]
Cleaning up / removing...
   2:npm-1:6.14.8-1.12.19.0.1.fc31    ################################# [100%]
$ sudo dnf upgrade --refresh
Docker CE Stable - x86_64                        22 kB/s | 3.5 kB     00:00
Fedora 33 - x86_64                               47 kB/s |  13 kB     00:00
Fedora 33 openh264 (From Cisco) - x86_64        9.7 kB/s | 990  B     00:00
Fedora Modular 33 - x86_64                      121 kB/s |  12 kB     00:00
Fedora 33 - x86_64 - Updates                     95 kB/s |  11 kB     00:00
Fedora 33 - x86_64 - Updates                    496 kB/s | 430 kB     00:00
Fedora Modular 33 - x86_64 - Updates             49 kB/s |  11 kB     00:00
Dependencies resolved.
Nothing to do.
Complete!
$

Notes of a Programmer

Saturday, October 9, 2021

Mapping NFS User ID between Linux and FreeNAS/TrueNAS/FreeBSD

Saturday, October 2, 2021

Dealing with "error: unpacking of archive failed" when upgrading Fedora Linux

Dealing with Complexities