This is a text-only version of the following page on https://raymii.org:
---
Title       : 	APT keeps complaining that the HTTPS certificate cannot be validated?
Author      : 	Remy van Elst
Date        : 	11-01-2023 05:31
URL         : 	https://raymii.org/s/blog/Syncthing_apt_repo_keeps_complaining_HTTPS_certificate_could_not_be_validated.html
Format      : 	Markdown/HTML
---



![gnutls logo][15]

> The [GnuTLS][16] logo, the TLS library that apt uses.

Recently a few of my Ubuntu 20.04 and Debian 11 servers failed to run an `apt update` because it insisted that the HTTPS certificate for a repository could not be validated, while `curl` on the same system had no issues connecting. Join me on a deep dive into certificate validation and troubleshooting `apt`, digging into the C++ source code for `apt` and `GnuTLS` and in the end, it turned out to be my own fault due to permission on a folder. However, the error messages were totally unhelpful resolving the mysterious validation problem. This article was written over the period of a few days, chronologically during troubleshooting.

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Syncthing is a wonderful peace of software which syncs files to multiple
servers / computers. I use it to keep a subset of my files synced among
multiple computers and even on my servers sometimes to sync images.

The version in the debian repositories is old and Syncthing provide an
`apt` repository with clear copy and paste-able instructions, so I often
use that and have it as an Ansible playbook so I can roll it out and
add the peers automatically (the configuration is a simple XML file).

The current process to add the syncthing apt repository, as [documented 
on their site][1] is the following, first get the GPG key, then add the apt
repository marking it explicitly signed by the GPG key. Afterwards `update`
and `install`:

    sudo curl -o /usr/share/keyrings/syncthing-archive-keyring.gpg https://syncthing.net/release-key.gpg

    echo "deb [signed-by=/usr/share/keyrings/syncthing-archive-keyring.gpg] https://apt.syncthing.net/ syncthing stable" | sudo tee /etc/apt/sources.list.d/syncthing.list

    sudo apt-get update
    sudo apt-get install syncthing


However, the `apt update` step fails on my Ubuntu 20.04 and Debian 11 servers with the 
following error:

    Err:6 https://apt.syncthing.net syncthing Release Certificate verification failed: The certificate is NOT trusted. The certificate issuer is unknown.  Could not handshake: Error in the certificate verification. [IP: 143.244.196.6 443]

The [guide][1] had a section on that specific error message:

    Server Certificate Verification Failed

    Especially for older distributions, your system TLS certificate store might be outdated. Since October 2021, a newer Let's Encrypt root certificate must be installed, or you may see an error similar to the following when running apt-get:

    E: Failed to fetch https://apt.syncthing.net/dists/syncthing/stable/binary-armhf/Packages
    server certificate verification failed. CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile: none
    E: Some index files failed to download. They have been ignored, or old ones used instead.

    Please make sure you have the latest version of the ca-certificates package and try again:

    sudo apt-get update
    sudo apt-get install ca-certificates

That suggestion was not helping, the `ca-certificates` package is up to date.

Join me into a deep-dive on troubleshooting certificate validation paths for
OpenSSL, curl, apt and GnuTLS on Debian and Ubuntu!


### Comparing the installed certificates

As of writing this article, the certificate is signed by Comodo ZeroSSL, not Lets Encrypt:

    echo | openssl s_client -showcerts -connect apt.syncthing.net:443 2>&1 | grep -E "s:|i:"
     0 s:CN = apt.syncthing.net
       i:C = AT, O = ZeroSSL, CN = ZeroSSL ECC Domain Secure Site CA
     1 s:C = AT, O = ZeroSSL, CN = ZeroSSL ECC Domain Secure Site CA
       i:C = US, ST = New Jersey, L = Jersey City, O = The USERTRUST Network, CN = USERTrust ECC Certification Authority
     2 s:C = US, ST = New Jersey, L = Jersey City, O = The USERTRUST Network, CN = USERTrust ECC Certification Authority
       i:C = GB, ST = Greater Manchester, L = Salford, O = Comodo CA Limited, CN = AAA Certificate Services


The strange thing is that `curl` on the same systems has no issues with the certificate:

     curl -vI https://apt.syncthing.net

Output:

    [...]
    * successfully set certificate verify locations:
    *   CAfile: /etc/ssl/certs/ca-certificates.crt
      CApath: /etc/ssl/certs
    [...]
    *  subject: CN=apt.syncthing.net
    *  start date: Dec  1 00:00:00 2022 GMT
    *  expire date: Mar  1 23:59:59 2023 GMT
    *  subjectAltName: host "apt.syncthing.net" matched cert's "apt.syncthing.net"
    *  issuer: C=AT; O=ZeroSSL; CN=ZeroSSL ECC Domain Secure Site CA
    *  SSL certificate verify ok.

Maybe `apt` uses a different root store? In [the apt changelog][6] I find some mentions on
adding HTTPS support to the HTTP backend via GnuTLS and you used to have to install `apt-transport-https` but that is no longer needed since `apt` 1.5 as [the package states][7]:

    This is a dummy transitional package - https support has been moved into the apt package in 1.5. It can be safely removed.

Looking through [the apt source code][8] I can see `GnuTLS` being used as the SSL
backend. Installing `gnutls-bin` for the `certtool` command and using that to
check the certificate using not OpenSSL but GnuTLS, shows it as valid:

    certtool --verify --infile chain.pem 

Output:

    Note that no verification profile was selected. In the future the medium profile will be enabled by default.
    Use --verify-profile low to apply the default verification of NORMAL priority string.
    Loaded system trust (125 CAs available)
            Subject: CN=apt.syncthing.net
            Issuer: CN=ZeroSSL ECC Domain Secure Site CA,O=ZeroSSL,C=AT
            Checked against: CN=ZeroSSL ECC Domain Secure Site CA,O=ZeroSSL,C=AT
            Signature algorithm: ECDSA-SHA384
            Output: Verified. The certificate is trusted. 

    Chain verification output: Verified. The certificate is trusted. 

Using `gnutls-cli apt.syncthing.net --print-cert` to get that cert also shows it being
valid:

    Processed 125 CA certificate(s).
    Resolving 'apt.syncthing.net:443'...
    Connecting to '143.244.196.6:443'...
    - Certificate type: X.509
    - Got a certificate list of 3 certificates.
    - Certificate[0] info:
    [...]
    - Status: The certificate is trusted. 


Just to be sure, let's also test with OpenSSL.

Using [the openssl commands from here][2] I can also print the exact serial number and signatures/key id's of the certificates presented:

    OLDIFS=$IFS; IFS=':' certificates=$(openssl s_client -connect apt.syncthing.net:443 -showcerts -tlsextdebug 2>&1 </dev/null | sed -n '/-----BEGIN/,/-----END/ {/-----BEGIN/ s/^/:/; p}'); for certificate in ${certificates#:}; do echo $certificate | openssl x509 -noout -subject -fingerprint -issuer -ext subjectKeyIdentifier,authorityKeyIdentifier; echo; done; IFS=$OLDIFS

Output:

    subject=CN = apt.syncthing.net
    SHA1 Fingerprint=29:CA:71:94:D0:96:9E:F0:B0:41:A3:B6:12:9A:2C:D9:81:68:9C:06
    issuer=C = AT, O = ZeroSSL, CN = ZeroSSL ECC Domain Secure Site CA
    X509v3 Authority Key Identifier: 
        keyid:0F:6B:E6:4B:CE:39:47:AE:F6:7E:90:1E:79:F0:30:91:92:C8:5F:A3

    X509v3 Subject Key Identifier: 
        E6:56:EC:BD:0E:6F:0C:1E:0E:87:FD:55:18:20:94:21:EE:2B:DB:6E

    subject=C = AT, O = ZeroSSL, CN = ZeroSSL ECC Domain Secure Site CA
    SHA1 Fingerprint=7F:95:27:6D:49:51:49:9F:D7:56:DF:34:4A:A2:4F:B3:8C:EA:F6:78
    issuer=C = US, ST = New Jersey, L = Jersey City, O = The USERTRUST Network, CN = USERTrust ECC Certification Authority
    X509v3 Authority Key Identifier: 
        keyid:3A:E1:09:86:D4:CF:19:C2:96:76:74:49:76:DC:E0:35:C6:63:63:9A

    X509v3 Subject Key Identifier: 
        0F:6B:E6:4B:CE:39:47:AE:F6:7E:90:1E:79:F0:30:91:92:C8:5F:A3

    subject=C = US, ST = New Jersey, L = Jersey City, O = The USERTRUST Network, CN = USERTrust ECC Certification Authority
    SHA1 Fingerprint=CA:77:88:C3:2D:A1:E4:B7:86:3A:4F:B5:7D:00:B5:5D:DA:CB:C7:F9
    issuer=C = GB, ST = Greater Manchester, L = Salford, O = Comodo CA Limited, CN = AAA Certificate Services
    X509v3 Authority Key Identifier: 
        keyid:A0:11:0A:23:3E:96:F1:07:EC:E2:AF:29:EF:82:A5:7F:D0:30:A4:B4

    X509v3 Subject Key Identifier: 
        3A:E1:09:86:D4:CF:19:C2:96:76:74:49:76:DC:E0:35:C6:63:63:9A


If the  `Subject Key Identifier` of the issuer matches the `Authority Key Identifier` of the 
subject, you can easily identify the certificate validation path (via RFC 4158 (Internet X.509 Public Key Infrastructure: Certification Path Building), summarized [here][3]).


On Debian and Ubuntu the certificates are built and combined, but the sources are
stored in `/usr/share/ca-certificates`. Using `/etc/ca-certificates.conf` or 
`dpkg-reconfigure ca-certificates` one can include or exclude root certificates,
and in there I found the certificate for `USERTrust_ECC_Certification_Authority`. 
The same command as above gives different output for this certificate:

    openssl x509 -noout -subject -fingerprint -issuer -ext subjectKeyIdentifier,authorityKeyIdentifier -in /usr/share/ca-certificates/mozilla/USERTrust_ECC_Certification_Authority.crt

Output:

    subject=C = US, ST = New Jersey, L = Jersey City, O = The USERTRUST Network, CN = USERTrust ECC Certification Authority
    SHA1 Fingerprint=D1:CB:CA:5D:B2:D5:2A:7F:69:3B:67:4D:E5:F0:5A:1D:0C:95:7D:F0
    issuer=C = US, ST = New Jersey, L = Jersey City, O = The USERTRUST Network, CN = USERTrust ECC Certification Authority
    X509v3 Subject Key Identifier: 
        3A:E1:09:86:D4:CF:19:C2:96:76:74:49:76:DC:E0:35:C6:63:63:9A

The Subject Key Identifier and the subject are the same so depending on the validation implementation, this should be good enough. The first `curl` command to get the GPG key
worked without issues, so `curl` has no issues with the certificate. 

### Adding the ZeroSSL intermediate certificate

My first guess was to try and add the ZeroSSL intermediate certificate. Should
not be needed since the chain of trust is complete because the system already
knows about the `USERTrust ECC Certification Authority` certificate, but
still worth a try. 

Place the PEM file in `/usr/share/ca-certificates/ZeroSSL.crt`, add that file
to `/etc/ca-certificates.conf` and execute the command
`update-ca-certificates`. 

The command `update-ca-certificates` will compile all certificates into one file,
`/etc/ssl/certs/ca-certificates.crt` which is used by the system.

We can then use the following `awk` command to check all installed certificates and print
their subject (or fingerprint):

    awk -v cmd='openssl x509 -noout -subject -fingerprint -issuer -ext subjectKeyIdentifier,authorityKeyIdentifier; echo' '/BEGIN/{close(cmd)};{print | cmd}' < /etc/ssl/certs/ca-certificates.crt 

This output, at the bottom, includes the new ZeroSSL intermediate issuer:

    subject=C = AT, O = ZeroSSL, CN = ZeroSSL ECC Domain Secure Site CA
    SHA1 Fingerprint=7F:95:27:6D:49:51:49:9F:D7:56:DF:34:4A:A2:4F:B3:8C:EA:F6:78
    issuer=C = US, ST = New Jersey, L = Jersey City, O = The USERTRUST Network, CN = USERTrust ECC Certification Authority
    X509v3 Authority Key Identifier: 
        keyid:3A:E1:09:86:D4:CF:19:C2:96:76:74:49:76:DC:E0:35:C6:63:63:9A

    X509v3 Subject Key Identifier: 
        0F:6B:E6:4B:CE:39:47:AE:F6:7E:90:1E:79:F0:30:91:92:C8:5F:A3

However, `apt update` was still giving the same error.

### Going into the source code

Since my manual attempts to add the certificate failed and the debug information
is lacking, let's look deeper, starting in the apt source code. Grepping
for `GnuTLS` and the error message `Certificate verification failed` 
brought me to [line 850 of][9] `methods/connect.cc`:

     if (err == GNUTLS_E_CERTIFICATE_VERIFICATION_ERROR) {
        gnutls_datum_t txt;
        auto type = gnutls_certificate_type_get(session);
        auto status = gnutls_session_get_verify_cert_status(session);
        if (gnutls_certificate_verification_status_print(status, type, &txt, 0) == 0) {
           _error->Error("Certificate verification failed: %s", txt.data);
        }

That [error code][10] says little:

    -348    GNUTLS_E_CERTIFICATE_VERIFICATION_ERROR Error in the certificate verification.

But looking further in the apt source code, in `UnwrapTLS`, I can see another error
message, `No system certificates available. Try installing ca-certificates`:

   
    // No CaInfo specified, use system trust store.
    err = gnutls_certificate_set_x509_system_trust(tlsFd->credentials);
    if (err == 0)
    Owner->Warning("No system certificates available. Try installing ca-certificates.");

Maybe GnuTLS has trouble finding our system certificates. Lets figure out
which file is used by default as a root trust store.

The method `gnutls_certificate_set_x509_system_trust`, returns the number of
certificates processed or a negative error code on error. Since we get
exactly zero (0), it seems to be that GnuTLS is unable to load the system
certificate store. I wonder where it tries to load them from. 

This method [seems to call][10] `gnutls_x509_trust_list_add_system_trust`,
which in turn calls `add_system_trust`. The latter one is conditional
`#ifdef`, but the implementation I'm looking at checks for
`DEFAULT_TRUST_STORE_FILE`. That is not defined in code but is a
`./configure` option, wonderful syntax but at least it has default
filenames:

    dnl auto detect https://lists.gnu.org/archive/html/help-gnutls/2012-05/msg00004.html
    AC_ARG_WITH([default-trust-store-file],
      [AS_HELP_STRING([--with-default-trust-store-file=FILE],
        [use the given file default trust store])], with_default_trust_store_file="$withval",
      [if test "$build" = "$host" && test x$with_default_trust_store_pkcs11 = x && test x$with_default_trust_store_dir = x && test x$have_macosx = x;then
      for i in \
        /etc/ssl/ca-bundle.pem \
        /etc/ssl/certs/ca-certificates.crt \
        /etc/pki/tls/cert.pem \
        /usr/local/share/certs/ca-root-nss.crt \
        /etc/ssl/cert.pem
        do
        if test -e "$i"; then
          with_default_trust_store_file="$i"
          break
        fi
      done
      fi]
    )


I'm not sure which compile option was used for the Debian packages, but I only
have the file `/etc/ssl/certs/ca-certificates.crt` on my servers. Downloading
the [source package][14] and looking at the `rules` file I can see that that
is also the file used during compilation:

    CONFIGUREARGS = \
        [...]
        --with-default-trust-store-file=/etc/ssl/certs/ca-certificates.crt \
        [...]

After all that searching through code we're still not any further. The files
exist, another GnuTLS using-program can validate the certificate, so now
what?

### My trusty old friend, strace

As a last resort I tried `strace`. It shows you all the syscalls that are
made. Lots of noise, but with a bit of filtering we can get useful
information:

    strace -f -e stat,read,write,execve,openat -s 2048 apt update 2>&1 | less

In that massive list of output I see this which seems relevant:

    [pid 2522130] execve("/usr/lib/apt/methods/https", ["/usr/lib/apt/methods/https"], 0x7fff668e0300 /* 23 vars */) = 0

This seems to be a URI handler for getting files from repositories. APT supports multiple schemes, methods as APT calls it, for repositories, such as http, ftp and cd-rom. It turns out that
it did not have any options to tweak. Other strace output didn't have much to go on either.


### Disabling SSL, bad idea!

Just disabling SSL certificate validation for this specific hostname is an
option, since the packages are signed by a specific GPG key (mentioned in
`sources.list`) and the `curl` command gave no certificate warning, and all
manual troubleshooting shows me that, at this moment, the repository is
signed by a trusted issuer.

I don't like disabling verification, but since I was out of options, I added
the [following options][5] to the specific `apt.conf.d` file:

    cat /etc/apt/apt.conf.d/80-ssl-exceptions 

File contents:

    Acquire::https::apt.syncthing.net::Verify-Peer "false";
    Acquire::https::apt.syncthing.net::Verify-Host "false";

This results in no more errors during an `apt update`. But that was simply not
an option for the long run. One more attempt, starting over a few days later.
Sometimes it helps to take a step back and let it rest when you're knee-deep
in a problem.

### Manually adding the entire chain for Apt

Reading the manual page again for this config file I saw the `CaInfo` option.
Earlier I tried that, by adding just the intermediate ZeroSSL CA file:

    # file: /etc/apt/apt.conf.d/80-ssl-exceptions
    Acquire::https::apt.syncthing.net::CaInfo "/etc/ssl/certs/apt.syncthing.net.chain.pem";

This failed with the following error:

      Could not load certificates from /etc/ssl/certs/apt.syncthing.net.chain.pem (CaInfo option): Error while reading file. [IP: 143.244.196.6 443]

Trying the default system certificate store (`/etc/ssl/certs/ca-certificates.crt`) explicitly
configured as `CaInfo` gave the same error. **Then it dawned on me**, another ansible playbook
recently, a few weeks earlier, did stuff with the `/etc/ssl/` folder regarding certificate synchronization. 

Look at the permissions from a working server:

    remy@workingserver:~$ ls -lah /etc/ssl/
    total 40K
    drwxr-xr-x  4 root root     4.0K Oct 26  2021 .
    drwxr-xr-x 94 root root     4.0K Jan 10 06:51 ..
    drwxr-xr-x  2 root root      16K Feb 15  2022 certs
    -rw-r--r--  1 root root      11K Aug 24  2021 openssl.cnf
    drwx--x---  2 root ssl-cert 4.0K Nov 26  2021 private

Now compare that to all the non-working servers:

    root@non-working-server:~# ls -lah /etc/ssl/
    total 48K
    drw-r--r--  5 root root     4.0K Jan  8 13:00 .
    drwxr-xr-x 90 root root     4.0K Jan  8 12:25 ..
    drwxr-xr-x  2 root root      20K Jan  8 12:25 certs
    -rw-r--r--  1 root root      11K May 30  2019 openssl.cnf
    drwx--x---  2 root ssl-cert 4.0K Mar 19  2021 private

Do you see it?

    # /etc/ssl/
    drw-r--r--  5 root root     4.0K Jan  8 13:00 .
    drwxr-xr-x  4 root root     4.0K Oct 26  2021 .


Dropping to the user that `apt` uses shows me the error in more detail:

    su - _apt -s /bin/bash
    _apt@server:/$ ls -lah /etc/ssl/
    ls: cannot access '/etc/ssl/certs': Permission denied
    ls: cannot access '/etc/ssl/.': Permission denied
        
    total 0
    d????????? ? ? ? ?            ? .
    d????????? ? ? ? ?            ? certs

    _apt@server:/$ ls -lah /etc/ssl/certs
    ls: cannot access '/etc/ssl/certs': Permission denied

The execute (`x`) bit for the folder `/etc/ssl/` was missing. Since you can't
`execute` a directory, the execute bit has been put to better use. The
execute bit on a directory allows you to access items that are inside the
directory, even if you cannot list the directories contents. From the manpage:

    The letters rwxXst select file mode bits for the affected users: read (r), write (w), execute (or search for directories) (x), 


The folder on the broken servers has permission `644` and the working server has 
`755`. (The command `stat -c %a /path` shows you the permissions in octal form). 
The playbook I talked about earlier from a few weeks ago had given the `/etc/ssl`
folder the wrong permissions.

Lets try what happens with the correct permissions:

    chmod 755 /etc/ssl/
    apt update

Output:

    Hit:1 https://apt.syncthing.net syncthing InRelease
    Reading package lists... Done
    Building dependency tree       
    Reading state information... Done
    All packages are up to date.

No more errors!

Re-doing the `strace` part and grepping for `Permission Denied` also showed the error:

    [pid 2526028] openat(AT_FDCWD, "/etc/ssl/certs/ca-certificates.crt", O_RDONLY) = -1 EACCES (Permission denied)

I missed it due to there being so much other output. Knowing what to look for
makes troubleshooting so much easier.

### Conclusion

The error message `The certificate issuer is unknown` put me on the wrong track,
going down a rabbit hole of SSL certificate validation and SSL library code,
even into which SSL backend `apt` uses and how they validate certificates. 

Only after a few days and re-reading the man page, trying out a different option,
I got a more clear error message: `Error while reading file`. After that it was 
an easy fix. 


Since I was running as `root` and was unaware `apt` drops privileges
(to `_apt:nogroup`), I didn't look into the permissions right away. If the
error message had been `permission denied while reading ca issuer file /etc/ssl/certs/ca-certificates.crt`, it would have been way more clear and easier to fix.

But hey, I learned a bit more about how recent versions of `apt` handle 
SSL, took a look at the `apt` `c++` code and in the end banged my head
against my desk since the issue was my fault all along. But that doesn't
really matter since the journey towards the solution was valuable.



[1]: https://web.archive.org/web/20221231011933/https://apt.syncthing.net/ 
[2]: /s/articles/OpenSSL_-_Get_all_certificates_from_a_website_in_plain_text.html
[3]: https://web.archive.org/web/20230108204354/https://stackoverflow.com/questions/38899286/how-to-get-the-root-ca-certificate-fingerprint-using-openssl
[4]: https://web.archive.org/web/20230108203241/https://manpages.ubuntu.com/manpages/focal/man5/apt.conf.5.html
[5]: https://web.archive.org/web/20220516183420/https://manpages.ubuntu.com/manpages/focal/man1/apt-transport-https.1.html
[6]: https://raw.githubusercontent.com/Debian/apt/main/debian/changelog
[7]: https://web.archive.org/web/20230110062913/https://packages.debian.org/bullseye/apt-transport-https
[8]: https://github.com/Debian/apt/blob/5919d2d18eac6e445a59da23246df94258e103eb/methods/connect.cc#L808
[9]: https://salsa.debian.org/apt-team/apt/-/blob/main/methods/connect.cc#L850
[10]: https://github.com/gnutls/gnutls/blob/4e5afffcba3e5f898eca7c450408605969135d48/lib/cert-cred-x509.c#L1281
[11]: https://gnutls.org/reference/gnutls-gnutls.html#gnutls-certificate-set-x509-system-trust
[12]: https://github.com/gnutls/gnutls/blob/4e5afffcba3e5f898eca7c450408605969135d48/lib/system/certs.c#L372
[13]: https://github.com/gnutls/gnutls/blob/4e5afffcba3e5f898eca7c450408605969135d48/configure.ac#L1097
[14]: https://packages.ubuntu.com/source/focal/gnutls28
[15]: /s/inc/img/gnutls-logo-nobackground.png
[16]: https://gnutls.org/gnutls-logo.html


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