Not sure whether the "bug" (undocumented behavior) I encountered is common to other people, but this comment might save hours of painful debug:
If you can't generate a new private key using openssl_pkey_new() or openssl_csr_new(), your script hangs during the call of these functions and in case you specified a "private_key_bits" parameter, ensure that you cast the variable to an int. Took me ages to notice that.

<?php
$SSLcnf = array('config' => '/usr/local/nessy2/share/ssl/openssl.cnf',
        'encrypt_key' => true,
        'private_key_type' => OPENSSL_KEYTYPE_RSA,
        'digest_alg' => 'sha1',
        'x509_extensions' => 'v3_ca',
        'private_key_bits' => $someVariable // ---> bad
        'private_key_bits' => (int)$someVariable // ---> good
        'private_key_bits' => 512 // ---> obviously good
        );
?>

When in doubt, read the source code to PHP!

$configargs is fairly opaque as to what is going on behind the scenes.  That is, until you actually look at php_openssl_parse_config() in '/ext/openssl/openssl.c':

    SET_OPTIONAL_STRING_ARG("digest_alg", req->digest_name,
        CONF_get_string(req->req_config, req->section_name, "default_md"));
    SET_OPTIONAL_STRING_ARG("x509_extensions", req->extensions_section,
        CONF_get_string(req->req_config, req->section_name, "x509_extensions"));
    SET_OPTIONAL_STRING_ARG("req_extensions", req->request_extensions_section,
        CONF_get_string(req->req_config, req->section_name, "req_extensions"));
    SET_OPTIONAL_LONG_ARG("private_key_bits", req->priv_key_bits,
        CONF_get_number(req->req_config, req->section_name, "default_bits"));

    SET_OPTIONAL_LONG_ARG("private_key_type", req->priv_key_type, OPENSSL_KEYTYPE_DEFAULT);

Here we can see that SET_OPTIONAL_STRING_ARG() is called for most inputs but for 'private_key_bits' SET_OPTIONAL_LONG_ARG() is called.  Both calls are C macros that expand to code that enforces the expected input type.  The generated code ignores the input without warning/notice if an unexpected type is used and just uses the default from the configuration file.  This is why using a string with 'private_key_bits' will result in unexpected behavior.

Further inspection of the earlier initialization in the same function:

    SET_OPTIONAL_STRING_ARG("config", req->config_filename, default_ssl_conf_filename);
    SET_OPTIONAL_STRING_ARG("config_section_name", req->section_name, "req");
    req->global_config = CONF_load(NULL, default_ssl_conf_filename, NULL);
    req->req_config = CONF_load(NULL, req->config_filename, NULL);

    if (req->req_config == NULL) {
        return FAILURE;
    }

And elsewhere in another function:

    /* default to 'openssl.cnf' if no environment variable is set */
    if (config_filename == NULL) {
        snprintf(default_ssl_conf_filename, sizeof(default_ssl_conf_filename), "%s/%s",
                X509_get_default_cert_area(),
                "openssl.cnf");
    } else {
        strlcpy(default_ssl_conf_filename, config_filename, sizeof(default_ssl_conf_filename));
    }

Reveals that 'config' in $configargs is an override for any default setting elsewhere.  This actually negates the comment in the documentation that says "Note: You need to have a valid openssl.cnf installed for this function to operate correctly. See the notes under the installation section for more information."  A more correct sentence would be "Note:  You need to either have a valid openssl.cnf set up or use $configargs to point at a valid openssl.cnf file for this function to operate correctly."

All of that goes to show that looking at the PHP source code is the only real way to figure out what is actually happening.  Doing so saves time and effort.

For those of you using Debian-based systems, the openssl configuration file is at: /etc/ssl/openssl.cnf

To set the "basicConstraints" to  "critical,CA:TRUE", you have to define configargs, but in the openssl_csr_sign() function !

That's my example of code to sign a "child" certificate :

$CAcrt = "file://ca.crt";
$CAkey = array("file://ca.key", "myPassWord");

$clientKeys = openssl_pkey_new();
$dn = array(
    "countryName" => "FR",
    "stateOrProvinceName" => "Finistere",
    "localityName" => "Plouzane",
    "organizationName" => "Ecole Nationale d'Ingenieurs de Brest",
    "organizationalUnitName" => "Enib Students",
    "commonName" => "www.enib.fr",
    "emailAddress" => "[email protected]"
);
$csr = openssl_csr_new($dn, $clientPrivKey);

$configArgs = array("x509_extensions" => "v3_req");
$cert = openssl_csr_sign($csr, $CAcrt, $CAkey, 100, $configArgs);

openssl_x509_export_to_file($cert, "childCert.crt");

Then if you want to add some more options, you can edit the "/etc/ssl/openssl.cnf" ssl config' file (debian path), and add these after the [ v3_req ] tag.

In the PHP example above it uses "UK" as the country name which is incorrect, the country name must be "GB"

When using `openssl_csr_new()` or `openssl_csr_sign()` for X25519 or Ed25519 certs, you have to set the `["digest_alg" => ""]` or if you use the `"config"` option to `null`, like so:

<?php
// Setting the "digest_alg" option:
$csr = openssl_csr_new(
    $distinguished_names,
    $private_key,
    ["digest_alg" => ""]
);

// Setting with "config":
$csr = openssl_csr_new(
    $distinguished_names,
    $private_key,
    ["config" => "/path/to/openssl.conf"]
);
?>

openssl.conf
```
[req]
default_md = null
// ...
```

If you get the error:

error:0D11A086:asn1 encoding routines:ASN1_mbstring_copy:string too short

then look at your key:value pairs in the $dn (distinguished name) array.

If you have one value (like "organizationalUnitName" = "") set to an empty string, it will throw the above error.

Fix the error by either eliminating that array element from $dn completely, or using a space " " instead of an empty string.

I am using PHP-4.3.11.
The type of configargs--private_key_bits is a INTEGER, not a string.
An example of configration:
<?php
$config = array(
  "digest_alg" => "sha1",
  "private_key_bits" => 2048,
  "private_key_type" => OPENSSL_KEYTYPE_DSA,
  "encrypt_key" => false
);
?>

As you probably guessed from the example, the documentation is misinforming.  openssl_csr_new returns a CSR resource or FALSE on failure.

mixed openssl_csr_new (assoc_array dn, resource_privkey, [...])

There appears to be no openssl_csr_free function.

At least not here.

If it's in the source, one might be able to just call it.

If it's not in the source, it probably should be.

One command to create modern certificate request with 4 SAN subdomain.
According to RFC you can change CN (common name) and subjectAltName. When cert validated searching in CN and subjectAltName.

openssl req -new -nodes -config <( cat <<-EOF
[req]
default_bits = 2048
prompt = no
default_md = sha256
req_extensions = re
distinguished_name = dn
[ dn ]
CN = my.tld
C = country
ST = state
L = location
O = ORGANISATION
[ re ]
subjectAltName = DNS.1: www.my.tld, DNS.2: www2.my.tld, DNS.3: www3.my.tld, DNS.4: www4.my.tld
EOF
) -keyout secret.key -out req.csr