---
title: "Encryption and Digital Signatures using GPG"
author: "Jeroen Ooms"
output:
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    mathjax: null
    fig_caption: false
    toc: true
    toc_float:
      collapsed: false
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    toc_depth: 3
vignette: >
  %\VignetteIndexEntry{Encryption and Digital Signatures in R using GPG}
  %\VignetteEngine{knitr::rmarkdown}
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---




**DISCLAIMER**: Author is not an expert in cryptography (he is not an expert in anything really). Use this stuff at your own risk. If you find bugs or inaccuracies, please create an issue or PR on the [github repository](https://github.com/jeroen/gpg).  

## GPG basics

The *GNU Privacy Guard*, also known as *GnuPG* or simply *GPG*, is a popular open source OpenPGP ([RFC4880](https://www.rfc-editor.org/rfc/rfc4880)) implementation. The system is widely trusted for securing integrity and confidentiality of internet communications through various cryptographic methods. GPG is used in [Debian](https://wiki.debian.org/SecureApt) and [Redhat](https://access.redhat.com/security/team/key) to verify downloads from package managers (apt, yum) and people like Edward Snowden and [Glenn Greenwald](https://theintercept.com/staff/glenn-greenwald/) use it to encrypt confidential emails.

### Public key crypto

Like most modern crypto systems, GPG makes use of public key methods. You can easily generate a personal keypair which consists of a private key and corresponding public key. 

![pubkey](https://jeroen.github.io/figures/pubkey-crypto/publickey-comic-m.png)

Your **private key** is to be kept secret and needed to **sign** or **decrypt** messages. The corresponding **public key** should be made available to anyone that needs to **verify** your signature, or **encrypt** messages which can only be decrypted by you.

Once we have someone's public key, we can send them secure messages and verify their signatures. However how do we find and authenticate the public key of a person or server if we have not talked to them before?

### Web of trust

The complexity in public key systems derives from authenticating public keys. If we can not trust our communication channel to be safe, we can only be sure that a public key belongs to given person if it has been signed by someone that we do trust.

The major difference between GPG and PKI systems (such as HTTPS) is how we authenticate public keys. HTTPS is based on a system with Certificate Authorities (CA). Anyone can create a keypair for any domain/personal name, however we only trust public keys which have been signed by an official CA. This CA is typically a commercial vendor which verifies your identity (e.g. via a copy of your passport) and then uses their own keypair to sign a certificate containing your public key and your personal name / email / domain.

![trust](https://jeroen.github.io/figures/pubkey-crypto/trust-m.png)

GPG uses a different system which does not distinguish between peers and authorities. In GPG, anyone can sign another persons key. The GPG user determines which peers they choose to trust in their personal keyring. For new peers, the GPG software helps you figure out which of your current peers has verified the identity of the new peer, perhaps indirectly via a third or fourth peer, and so on: a "web of trust".

The easiest way to exchange public keys and key signatures is via a keyserver. GPG is compatible with existing PGP key servers. These servers mirror each other so most keys are available on either one. This package automatically retrieves keys and signatures via the `gpg_recv` function. 

 - https://pgp.mit.edu
 - https://keyserver.ubuntu.com
 
GPG keyservers do not need HTTPS. One should only trust GPG keys on basis of GPG signatures, regardless of how they were obtained. For this reason it is also valid to share GPG public keys via e.g. a website or email.

## Your keyring

It is important to know which version of GPG you are running and where your home dir is. Your home directory contains your configuration and the keyrings. GPG defaults to your system keyring, which is the same as the `gpg` command line utility and system package manager use.


```r
str(gpg_info())
```

```
List of 5
 $ gpgconf: chr "/usr/local/bin/gpgconf"
 $ gpg    : chr "/usr/local/Cellar/gnupg/2.3.6/bin/gpg"
 $ version:Class 'numeric_version'  hidden list of 1
  ..$ : int [1:3] 2 3 6
 $ home   : chr "/Users/jeroen/.gnupg"
 $ gpgme  :Class 'numeric_version'  hidden list of 1
  ..$ : int [1:3] 1 16 0
```

Use `gpg_restart` to switch to another home directory, e.g. for a client which uses its own configuration and keyrings. For this example we store keys in a temporary directory.


```r
gpg_restart(home = tempdir())
```

```
gpg (GnuPG) 2.3.6
libgcrypt 1.10.1
Copyright (C) 2021 Free Software Foundation, Inc.
License GNU GPL-3.0-or-later <https://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Home: /Users/jeroen/.gnupg
Supported algorithms:
Pubkey: RSA, ELG, DSA, ECDH, ECDSA, EDDSA
Cipher: IDEA, 3DES, CAST5, BLOWFISH, AES, AES192, AES256, TWOFISH,
        CAMELLIA128, CAMELLIA192, CAMELLIA256
AEAD: EAX, OCB
Hash: SHA1, RIPEMD160, SHA256, SHA384, SHA512, SHA224
Compression: Uncompressed, ZIP, ZLIB, BZIP2
```


Use `gpg_list_keys()` to see the current contents of your keyring. It is empty to start with:


```r
gpg_list_keys()
```

```
[1] id    name  email
<0 rows> (or 0-length row.names)
```

### Generate keys

Use `gpg_keygen()` to generate a new public private keypair:


```r
(mykey <- gpg_keygen(name = "Jerry", email = "jerry@gmail.com"))
```

```
[1] "4873903B49318AEE"
```

```r
gpg_list_keys()
```

```
                id  name           email
1 4873903B49318AEE Jerry jerry@gmail.com
```


### Import from keyserver

Use the `gpg_recv` function to download a given key and all available signatures for this key from a keyserver. For example let's import the public key from Michael Rutter which is used to [sign the Ubuntu r-base packages](https://cran.r-project.org/bin/linux/ubuntu/) from CRAN:


```r
gpg_recv(id ="51716619E084DAB9")
```

```
Searching: https://keyserver.ubuntu.com
```

```
     found   imported    secrets signatures    revoked 
         1          1          0          0          0 
```

```r
(keyring <- gpg_list_keys())
```

```
                id           name              email
1 4873903B49318AEE          Jerry    jerry@gmail.com
2 51716619E084DAB9 Michael Rutter marutter@gmail.com
```

Note that for imported keys, we do not have the private key:


```r
(secring <- gpg_list_keys(secret = TRUE))
```

```
                id  name           email
1 4873903B49318AEE Jerry jerry@gmail.com
```

### Import from file

The `gpg_import` function reads an armored GPG key from a file or URL:


```r
gpg_import("https://stallman.org/rms-pubkey.txt")
```

```
     found   imported    secrets signatures    revoked 
         1          1          0          0          0 
```

However this file does not contain any signatures for this key. If we import it from a keyserver we also get the signatures:


```r
(rms_id <- gpg_list_keys("rms")$id)
```

```
[1] "2C6464AF2A8E4C02"
```

```r
gpg_recv(rms_id)
```

```
Searching: https://keyserver.ubuntu.com
```

```
     found   imported    secrets signatures    revoked 
         1          0          0        213          0 
```

```r
gpg_list_signatures(rms_id)
```

```
                 id           timestamp             name       email success
1  2C6464AF2A8E4C02 2013-07-20 18:32:38 Richard Stallman rms@gnu.org    TRUE
2  624DC565135EA668 2013-07-20 18:37:45                                FALSE
3  F05DDAE40371FCE5 2013-09-15 23:18:46                                FALSE
4  231696C3EAE0078A 2013-09-24 23:15:58                                FALSE
5  7B585B30807C2A87 2013-09-28 22:59:04                                FALSE
6  7CEF29847562C516 2013-09-29 04:59:53                                FALSE
7  520E0C8369B003EF 2013-08-20 12:31:55                                FALSE
8  D56E1B4C135D47A1 2013-08-29 13:36:03                                FALSE
9  31CC32CEF78F3EE4 2013-08-29 13:37:52                                FALSE
10 9439E86389D0AF41 2013-08-29 13:55:01                                FALSE
11 C5CFD08B22247CDF 2013-09-24 15:00:05                                FALSE
12 20B7283AFE254C69 2013-09-28 22:44:02                                FALSE
13 A866D7CCAE087291 2013-09-29 17:59:25                                FALSE
14 6D33FBF5B5E4C71A 2013-09-30 15:52:36                                FALSE
15 8916CADF8ACD372A 2013-10-02 13:17:17                                FALSE
16 8E549D02234CC324 2013-10-03 09:36:24                                FALSE
17 D605848ED7E69871 2013-10-04 11:03:23                                FALSE
18 758EAEC123F62336 2013-10-13 00:53:08                                FALSE
19 7B585B30807C2A87 2013-10-18 21:27:08                                FALSE
20 E4A6D8A25310523C 2013-10-23 02:53:11                                FALSE
 [ reached 'max' / getOption("max.print") -- omitted 199 rows ]
```

The signature only contains the key ID of the signer. You would need to download the corresponding pubkeys to actually verify these signatures.

### Export a key

To export our newly created public key:


```r
str <- gpg_export(id = mykey)
cat(str)
```

```
-----BEGIN PGP PUBLIC KEY BLOCK-----
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=KRml
-----END PGP PUBLIC KEY BLOCK-----
```

If you also own the private key you can export this as well:


```r
str <- gpg_export(id = mykey, secret = TRUE)
cat(str)
```

```
-----BEGIN PGP PRIVATE KEY BLOCK-----

lFgEYoyt6BYJKwYBBAHaRw8BAQdA1aJPM7jRZaeBjSc2cQUdCYqPFDkgLXdz1lGi
tC374W0AAQCDUd2YMbw49Asfh0xCidRcKwdyhRGVbX7/NQD7RgJDfA1LtBdKZXJy
eSA8amVycnlAZ21haWwuY29tPoiZBBMWCgBBFiEE8vmL45ASiPSYn8yISHOQO0kx
iu4FAmKMregCGwMFCQPCZwAFCwkIBwICIgIGFQoJCAsCBBYCAwECHgcCF4AACgkQ
SHOQO0kxiu5tnwEA1+YnAo5SF+IhvvsFT16+e4mGwz/yF7HaklpLh3oVubMA+gOr
LIhMchJcbDsZzR7UrrLYems69UfCrSjKEFa0GckJnF0EYoyt6BIKKwYBBAGXVQEF
AQEHQEmHqcVwXBbQ2TQF7Vqr2lP0NP+iHuH4IE+X1NA9t21UAwEIBwAA/0W2MldJ
mgyIeOE5Ynq0If10SNPtBlCuAdmxEzYTow24DwmIeAQYFgoAIBYhBPL5i+OQEoj0
mJ/MiEhzkDtJMYruBQJijK3oAhsMAAoJEEhzkDtJMYrul0IBANUF8TPx1HPGak3J
IMSvU4cKy2SPiRr+SP+yQMVnDeBtAQC32X4aUSFYuroKY6Roud+yp4hl78cUxo/t
b18CFrTECg==
=77cU
-----END PGP PRIVATE KEY BLOCK-----
```

### Delete a key

Delete a key from its ID or fingerprint. Let's delete the RMS key:


```r
gpg_delete('2C6464AF2A8E4C02')
```

```
[1] "2C6464AF2A8E4C02"
```

```r
gpg_list_keys()
```

```
                id           name              email
1 4873903B49318AEE          Jerry    jerry@gmail.com
2 51716619E084DAB9 Michael Rutter marutter@gmail.com
```


## Digital Signatures

A digital signature is a mathematical scheme for demonstrating the authenticity of a digital message or document. If you sign a file using your personal secret key, anyone can verify that this file has not been modified (i.e. the hash matches the one in your signature) via your public key.

GPG signatures are widely used by Linux package managers such as `apt` to verify the integrity of downloaded files. Typically the public key is shipped with the OS, and the private key is owned by the repository maintainers. This way we can safely install software from any mirror or network.

### Sign a file

Let's use the private key we generated earlier to sign a file:


```r
myfile <- tempfile()
writeLines("This is a signed message", con = myfile)
sig <- gpg_sign(myfile)
writeLines(sig, "sig.gpg")
cat(sig)
```

```
-----BEGIN PGP SIGNATURE-----

iHUEABYKAB0WIQTy+YvjkBKI9JifzIhIc5A7STGK7gUCYoyt6gAKCRBIc5A7STGK
7thMAP9W4h8p8whnhPVPn+9CPNJDRC6t7WsLpLay7EQMbJ9xJgD/W7/X094mCfag
K2SLC+k9N/HueL0YfgtUuDFAp63d8gw=
=9pnc
-----END PGP SIGNATURE-----
```

You can also create a signed message which includes the data itself by setting `mode` to `normal` or `clear`, which is useful for email:


```r
clearsig <- gpg_sign(myfile, mode = "clear")
writeLines(clearsig, "clearsig.gpg")
cat(clearsig)
```

```
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

This is a signed message
-----BEGIN PGP SIGNATURE-----

iHUEARYKAB0WIQTy+YvjkBKI9JifzIhIc5A7STGK7gUCYoyt6gAKCRBIc5A7STGK
7ozyAP0c/Aaakyx4VSxVgP4iULVd1x/AbNqRCjSlXfaL9TgHUQEA2mUP3Ek8/hoX
d57V6yfOg7ywdzuOSqHscvhqqBVX0AE=
=ODvd
-----END PGP SIGNATURE-----
```

### Verify a signature

The `gpg_verify` function will see if a signature is valid for any of the keys in the keyring:


```r
gpg_verify("sig.gpg", data = myfile)
```

```
                               fingerprint           timestamp   hash pubkey success
1 F2F98BE3901288F4989FCC884873903B49318AEE 2022-05-24 12:05:30 SHA512  EdDSA    TRUE
```

If the signature is in `clear` or `normal` mode, the signature file contains both the message and signature: 


```r
gpg_verify("clearsig.gpg")
```

```
                               fingerprint           timestamp   hash pubkey success
1 F2F98BE3901288F4989FCC884873903B49318AEE 2022-05-24 12:05:30 SHA512  EdDSA    TRUE
```




### Debian example

Let's verify a Debian file. The [Debian page on CRAN](https://cran.r-project.org/bin/linux/debian/) says the following:


*Since 16th of November 2021, the buster40 and bullseye40 repositories are signed with a new key with the key ID 0xB8F25A8A73EACF41, fingerprint 95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7 and user ID Johannes Ranke <johannes.ranke@jrwb.de>.*

Let's import his key so that we can verify the [Release](https://cran.r-project.org/bin/linux/debian/bullseye-cran40/Release) file, which contains checksums for all files in the repository:


```r
# take out the spaces
johannes <- "0xB8F25A8A73EACF41"
gpg_recv(johannes)
```

```
     found   imported    secrets signatures    revoked 
         1          1          0          0          0 
```

If you don't trust the CRAN homepage, you could check who has signed this key. You'd need to import the corresponding peer keys for more information.


```r
gpg_list_signatures(johannes)
```

```
                id           timestamp           name                  email success
1 DC78B2DDEABC47B7 2021-11-16 11:17:18 Johannes Ranke johannes.ranke@jrwb.de    TRUE
```

Now lets verify the release files:


```r
# Verify the file
library(curl)
```

```
Using libcurl 7.64.1 with LibreSSL/2.8.3
```

```r
curl_download('https://cran.r-project.org/bin/linux/debian/bullseye-cran40/Release', 'Release')
curl_download('https://cran.r-project.org/bin/linux/debian/bullseye-cran40/Release.gpg','Release.gpg')
gpg_verify('Release.gpg', 'Release')
```

```
                               fingerprint           timestamp   hash pubkey success
1 7BA040A510E4E66ED3743EC1B8F25A8A73EACF41 2022-04-26 06:51:50 SHA512    RSA    TRUE
```

Looking good! We can trust the checksums in the `Release` file to be legitimate.



## Anonymous Encryption

GPG uses public key encryption. You can use someone's public key to encrypt a message or document, in a way that only the owner of the corresponding private key will be able to decrypt. This is a great way to send somebody highly confidential data.

### Encrypt a message

For example we want to send an email [Jeroen](https://launchpad.net/~opencpu) containing top secret information that may not be snooped by our ISP or email provider. First we import Jeroen's public key using the ID as listed e.g. [here](https://launchpad.net/~opencpu):


```r
jeroen <- '16C019F96112961CEB4F38B76094FC5BDA955A42'
gpg_recv(jeroen)
```

```
     found   imported    secrets signatures    revoked 
         1          1          0          0          0 
```

```r
writeLines("Pizza delivery is on it's way!", "secret.txt")
msg <- gpg_encrypt("secret.txt", receiver = jeroen)
writeLines(msg, "msg.gpg")
unlink("secret.txt")
cat(msg)
```

```
-----BEGIN PGP MESSAGE-----

hQEMA4BQ/mdnc2saAQf/S7x4bnWPte7ryuJLg0Sf320qDoqurY++pIXBqXH8pxjs
6ZVux0B+QD04Oc9MmmxrqNs7srv4pExBDTFIq7kLR9jVaP4I7VbBqL33JrwqvmmE
jeoQRYvyB33KKoLSE9G8aNyxe9JAAjYxmx9zWGaDhDPV790sJS9hMGpRzTv14N8r
Wq5XeDjPR7mIWC484LgYv/U4B8CIweVXli4YkmiBAuZTRVv7SDLnmyjXGh+ssfTU
wY+b0WJ4AYL+r+6vmHDaCK5qysfabhIDVqWY7dh3V88B2i9mmYn3JH3yl0orUR5T
39iPiBTcacGKN5/GYweZ1Dh2JLch4vWuHN7Xnc32nNJaARxqLyDv4sH1MxFEWkp3
uJn9YN/49AJXU+8rEX84eYlCqatKDf8QnPB99vVa1X2/YLa/eksA1XphrdOT9/yR
2y8KGoPA+4QDSB+1laU3QzPF1kv2r2oe5mZv
=xbeq
-----END PGP MESSAGE-----
```

Now you can safely send this message over any channel (email, twitter, etc). Nobody in the world besides Jeroen will be able to decipher this message (not even you).

### Decrypt a message

Decrypting a message is just as easy. GPG will automatically find the correct private key from your keyring, or raise an error if you don't have it. For example we will not be able to decrypt the message we created above for Jeroen


```r
# This will error, we do not have this private key
gpg_decrypt("msg.gpg")
```

```
Error: GnuPG verify signatures and decrypt message error: No secret key
```

To demonstrate decryption, we encrypt a message using our own keypair (for which we own the private key).


```r
writeLines("This is a test!", "secret.txt")
msg <- gpg_encrypt("secret.txt", receiver = mykey)
writeLines(msg, "msg.gpg")
cat(msg)
```

```
-----BEGIN PGP MESSAGE-----

hF4DskhirNAetCQSAQdAlZa9W98XMeSWUJmyAr0rvSJjnOb+BgAnUWxXhoKO2lAw
7VaxBMQkUGiuqAcX/Aut/yYXa+FVQcRQwHBhEyDrQE/vO7nqtAFzIpatNt6qmQ/i
1FQBCQIQBAlqsccwm9Ezbz5gAx/ZuI3jz8Ee3Atjm9otwZTnGNQ2dkQRsmjumJO6
mMqxy53U8cSc0jRXlbYocbYgSHltvFobo0ncz6Zf6r1147Ghkw0=
=jc2h
-----END PGP MESSAGE-----
```

Decryption is simple, given that we own the secret key for the message:


```r
gpg_decrypt("msg.gpg")
```

```
[1] "This is a test!\n"
```

## Authenticated Encryption

So we showed how to encrypt a message so that it can only be read by the receiver. But how does Jeroen verify the sender identity?

### Sign and Encrypt

In signed encryption, also known as authenticated encryption, uses combined encryption and signing. The public key of the receiver is used to encrypt the message, and the private key of the sender to sign the message. This way the message is both confidential and the integrity of the sender can be checked and verified, only by the receiver.


```r
msg <- gpg_encrypt("secret.txt", receiver = jeroen, signer = mykey)
writeLines(msg, "msg.gpg")
cat(msg)
```

```
-----BEGIN PGP MESSAGE-----
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=beBb
-----END PGP MESSAGE-----
```

### Decrypt and Verify

If the encrypted message contains a signature, it will automatically be verified when the message is decrypted. The function raises an error otherwise.

For purpose of illustrating authenticated decryption, we encrypt and sign using our own key (which usually does not make sense):


```r
msg <- gpg_encrypt("secret.txt", receiver = mykey, signer = mykey)
writeLines(msg, "msg.gpg")
gpg_decrypt("msg.gpg")
```

```
[1] "This is a test!\n"
attr(,"signer")
[1] "F2F98BE3901288F4989FCC884873903B49318AEE"
```

The signer fingerprint (if any) will be added as an attribute to the decrypted message.



