diff --git a/phpseclib/Crypt/RSA/PKCS.php b/phpseclib/Crypt/RSA/PKCS.php
index f25e20b0..f56e6a85 100644
--- a/phpseclib/Crypt/RSA/PKCS.php
+++ b/phpseclib/Crypt/RSA/PKCS.php
@@ -408,7 +408,7 @@ abstract class PKCS
          * subject=/O=organization/OU=org unit/CN=common name
          * issuer=/O=organization/CN=common name
          */
-        $temp = preg_replace('#.*?^-+[^-]+-+#ms', '', $str, 1);
+        $temp = preg_replace('#.*?^-+[^-]+-+[\r\n ]*$#ms', '', $str, 1);
         // remove the -----BEGIN CERTIFICATE----- and -----END CERTIFICATE----- stuff
         $temp = preg_replace('#-+[^-]+-+#', '', $temp);
         // remove new lines
diff --git a/phpseclib/File/X509.php b/phpseclib/File/X509.php
index 2ee9300d..47e723b2 100644
--- a/phpseclib/File/X509.php
+++ b/phpseclib/File/X509.php
@@ -104,6 +104,12 @@ class X509
      * Only works on CSRs. Not currently supported.
      */
     const FORMAT_SPKAC = 2;
+    /**
+     * Auto-detect the format
+     *
+     * Used only by the load*() functions
+     */
+    const FORMAT_AUTO_DETECT = 3;
     /**#@-*/
 
     /**
@@ -1404,10 +1410,11 @@ class X509
      * Returns an associative array describing the X.509 cert or a false if the cert failed to load
      *
      * @param string $cert
+     * @param int $mode
      * @access public
      * @return mixed
      */
-    function loadX509($cert)
+    function loadX509($cert, $mode = self::FORMAT_AUTO_DETECT)
     {
         if (is_array($cert) && isset($cert['tbsCertificate'])) {
             unset($this->currentCert);
@@ -1428,7 +1435,13 @@ class X509
 
         $asn1 = new ASN1();
 
-        $cert = $this->_extractBER($cert);
+        if ($mode != self::FORMAT_DER) {
+            $newcert = $this->_extractBER($cert);
+            if ($mode == self::FORMAT_PEM && $cert == $newcert) {
+                return false;
+            }
+            $cert = $newcert;
+        }
 
         if ($cert === false) {
             $this->currentCert = false;
@@ -2820,7 +2833,7 @@ class X509
      * @access public
      * @return mixed
      */
-    function loadCSR($csr)
+    function loadCSR($csr, $mode = self::FORMAT_AUTO_DETECT)
     {
         if (is_array($csr) && isset($csr['certificationRequestInfo'])) {
             unset($this->currentCert);
@@ -2839,7 +2852,13 @@ class X509
 
         $asn1 = new ASN1();
 
-        $csr = $this->_extractBER($csr);
+        if ($mode != self::FORMAT_DER) {
+            $newcsr = $this->_extractBER($csr);
+            if ($mode == self::FORMAT_PEM && $csr == $newcsr) {
+                return false;
+            }
+            $csr = $newcsr;
+        }
         $orig = $csr;
 
         if ($csr === false) {
@@ -3059,7 +3078,7 @@ class X509
      * @access public
      * @return mixed
      */
-    function loadCRL($crl)
+    function loadCRL($crl, $mode = self::FORMAT_AUTO_DETECT)
     {
         if (is_array($crl) && isset($crl['tbsCertList'])) {
             $this->currentCert = $crl;
@@ -3069,7 +3088,13 @@ class X509
 
         $asn1 = new ASN1();
 
-        $crl = $this->_extractBER($crl);
+        if ($mode != self::FORMAT_DER) {
+            $newcrl = $this->_extractBER($crl);
+            if ($mode == self::FORMAT_PEM && $crl == $newcrl) {
+                return false;
+            }
+            $crl = $newcrl;
+        }
         $orig = $crl;
 
         if ($crl === false) {
@@ -4560,7 +4585,7 @@ class X509
          * subject=/O=organization/OU=org unit/CN=common name
          * issuer=/O=organization/CN=common name
          */
-        $temp = preg_replace('#.*?^-+[^-]+-+#ms', '', $str, 1);
+        $temp = preg_replace('#.*?^-+[^-]+-+[\r\n ]*$#ms', '', $str, 1);
         // remove the -----BEGIN CERTIFICATE----- and -----END CERTIFICATE----- stuff
         $temp = preg_replace('#-+[^-]+-+#', '', $temp);
         // remove new lines
diff --git a/phpseclib/Net/SFTP.php b/phpseclib/Net/SFTP.php
index 09362c50..3c92ae3d 100644
--- a/phpseclib/Net/SFTP.php
+++ b/phpseclib/Net/SFTP.php
@@ -1416,6 +1416,7 @@ class SFTP extends SSH2
             return true;
         }
 
+        $filename = $this->_realPath($filename);
         // rather than return what the permissions *should* be, we'll return what they actually are.  this will also
         // tell us if the file actually exists.
         // incidentally, SFTPv4+ adds an additional 32-bit integer field - flags - to the following:
diff --git a/tests/Functional/Net/SFTPUserStoryTest.php b/tests/Functional/Net/SFTPUserStoryTest.php
index fcc41eda..963ead41 100644
--- a/tests/Functional/Net/SFTPUserStoryTest.php
+++ b/tests/Functional/Net/SFTPUserStoryTest.php
@@ -240,6 +240,20 @@ class Functional_Net_SFTPUserStoryTest extends PhpseclibFunctionalTestCase
 
     /**
      * @depends testTruncate
+     * @group github850
+     */
+    public function testChModOnFile($sftp)
+    {
+        $this->assertNotFalse(
+            $sftp->chmod(0755, 'file1.txt'),
+            'Failed asserting that chmod() was successful.'
+        );
+
+        return $sftp;
+    }
+
+    /**
+     * @depends testChModOnFile
      */
     public function testChDirOnFile($sftp)
     {
diff --git a/tests/Unit/File/X509/CSRTest.php b/tests/Unit/File/X509/CSRTest.php
index 7a91262b..6e4b827d 100644
--- a/tests/Unit/File/X509/CSRTest.php
+++ b/tests/Unit/File/X509/CSRTest.php
@@ -68,4 +68,29 @@ draiRBZruwMPwPIP
 
         $this->assertInternalType('array', $csr);
     }
+
+    public function testCSRDER()
+    {
+        $csr = 'MIICdzCCAV8CAQEwDDEKMAgGA1UEAwwBeDCCASIwDQYJKoZIhvcNAQEBBQADggEP' .
+               'ADCCAQoCggEBALtcrFDD2AHe3x2bR00wPDsPH6FJLxr5uc1ybb+ldDB5xNVImC8P' .
+               'LU6VXDZ5z68KjSovs1q0OWJWfCjlAuGLzqO35s86LI1CFuTFdkScVHMwh8zUVFoP' .
+               'pG7/9rKaNxCgaHs4evxjxQP2+Ny7tBqPLb/KV0exm6Twocf963jC/Tyn57G5erRf' .
+               'zpFrfK7DozhxY7znumJ4FuSn0TVkD6PPwZFn9VoTjv2ZoJmacGK+0r5yNKG799F5' .
+               'K8EgDrOCfbzCZjX6GJctyn2SNPTeBuXS9piH21FGnJAryv80zG+zUqFdEyoLUGJt' .
+               '4Vy6+tDP9cW68fiwTZS1Oc1VeFdL1G/CrjkCAwEAAaAmMCQGCSqGSIb3DQEJDjEX' .
+               'MBUwEwYKKwYBBAGCqlsBCQQFMAOCAQEwDQYJKoZIhvcNAQELBQADggEBAF4XOd+1' .
+               'jkJOYRInNpHfhzSD/ktDY50gpLPuDvl4f/ZBlKrb1eDYQG5F3bnYzoZWHN4n+6Zs' .
+               'CkljXs5ZPUZ5LuVpASumoG/aHXGz8c8NC3asJ1V73ljEPAfIXwqoIUoaP9jLL+Ee' .
+               'zy/ZCi2NKWVo2D7ocnn79oblAem9ksSeQl4z3Gvhuug6MsMqn96NU/ZY/vjYzAjb' .
+               'MAvJIVRY0rbCxbFa0K+XNJtF7GLyBxyPNFWCvADhvm9C4uPmoypYg7MY6EewJInN' .
+               'xzMH7I4xDLjNu0VBa6lAxTvflp0joQHKlTYX0SDIKPbQivjZMuObPuxDtkVZ0rQl' .
+               'AjmgMowaN5otTXM=';
+        $csr = base64_decode($csr);
+
+        $x509 = new X509();
+
+        $csr = $x509->loadCSR($csr);
+
+        $this->assertInternalType('array', $csr);
+    }
 }