kmessinger on "Wordpress 4.5.2 Daily Auto Update Fails"

Hi,

I have my own production low volume virtualized server running PHP 5.6, Mariadb, Nginx 1.9+. Several WP sites are stuck at 4.5 and cannot be updated to 4.5.2. What happens is: clicking the "please update button" in the admin area launches the update routine, and states that it is successful. However, at its conclusion, the site comes right back to v 4.5 (even though I get an email stating that the site has been updated to 4.5.2). In fact, the auto update happens a couple times per day, all with the same problem.

So, here's what I've done to track down the problem on one site as a test:
1) Permissions: User and group set the same
chown -R nginx:nginx /var/www/html/somesite.com/
wp-config = 440, directories = 750, files = 640
2) Disabled all plugins
3) Using WP 2016 default theme
4) Optimized and removed orphans from the database
5) Restarted Nginx
6) Tried removing _site_transient_update_core as some have suggested.
7) Removed and reinstalled latest version of WP via FTP
Nothing works. Wondering if this a Nginx issue.

Below are two code sections for you to inspect, to see if I'm missing something:
a) wp-config (redacted as appropriate, left out the db and salted stuff)

/** WordPress Database Table prefix **/
$table_prefix = 'someprefix_';
/** For developers: WordPress debugging mode **/
define('WP_DEBUG', false);
/** Absolute path to the WordPress directory. **/
if ( !defined('ABSPATH') ) define('ABSPATH', diame(__FILE__) . '/');
/** Change Path to Uploads **/
define( 'UPLOADS', 'assets' );
/** Location to cache file
define( 'RT_WP_NGINX_HELPER_CACHE_PATH','/dev/shm/nginx/' );
**/
/** SSL Parameters
define( 'FORCE_SSL_ADMIN', true );
define( 'WP_HTTP_BLOCK_EXTERNAL', false );
**/
/** Increase Memory Available from PHP **/
define( 'WP_MAX_MEMORY_LIMIT', '256M' );
/** Sets up WordPress vars and included files. */
require_once(ABSPATH . 'wp-settings.php');

b) nginx conf file (I put all the includes together here for convenience).

# For more information on configuration, see:
# * Official English Documentation: http://nginx.org/en/docs/
# * Official Russian Documentation: http://nginx.org/ru/docs/
user nginx;
worker_processes 4;
error_log /var/log/nginx/error.log;
pid /run/nginx.pid;
events { worker_connections 1024;
}
http { # Fast CGI Caching # fastcgi_cache_path /dev/shm/nginx levels=1:2 keys_zone=stupidfast:16m max_size=1024m inactive=60m; # fastcgi_cache_key "$scheme$request_method$host$request_uri"; #fastcgi_cache_use_stale error timeout invalid_header http_500; add_header rt-Fastcgi-Cache $upstream_cache_status; charset UTF-8; # hide some server information server_tokens off; server_name_in_redirect off; include /etc/nginx/mime.types; default_type application/octet-stream; log_format main '$remote_addr - $remote_user [$time_local] "$request" ' '$status $body_bytes_sent "$http_referer" ' '"$http_user_agent" "$http_x_forwarded_for"'; # access_log /var/log/nginx/access.log main; access_log off; sendfile on; #tcp_nopush on; tcp_nodelay on; client_header_buffer_size 1k; client_max_body_size 20m; client_body_buffer_size 128K; large_client_header_buffers 4 16k; client_body_timeout 12; client_header_timeout 12; keepalive_timeout 10s; send_timeout 10; types_hash_max_size 2048; server_names_hash_bucket_size 64; # Enable Gzip compressed. gzip on; # Compression level (1-9). # 5 is a perfect compromise between size and cpu usage, offering about # 75% reduction for most ascii files (almost identical to level 9). gzip_comp_level 6; # Don't compress anything that's already small and unlikely to shrink much # if at all (the default is 20 bytes, which is bad as that usually leads to # larger files after gzipping). gzip_min_length 256; # Compress data even for clients that are connecting to us via proxies, # identified by the "Via" header (required for CloudFront). gzip_proxied any; gzip_buffers 16 8k; # Tell proxies to cache both the gzipped and regular version of a resource # whenever the client's Accept-Encoding capabilities header varies; # Avoids the issue where a non-gzip capable client (which is extremely rare # today) would display gibberish if their proxy gave them the gzipped version. gzip_vary on; # Compress all output labeled with one of the following MIME-types. gzip_types application/atom+xml application/font-otf application/font-ttf application/json application/ld+json application/manifest+json application/rss+xml application/vnd.geo+json application/vnd.ms-fontobject application/x-font-ttf application/x-javascript application/x-web-app-manifest+json application/xhtml+xml application/xml font/opentype image/bmp image/svg+xml image/x-icon text/cache-manifest text/css text/javascript text/xml text/plain text/vcard text/vnd.rim.location.xloc text/vtt text/x-component text/x-cross-domain-policy; # text/html is always compressed by HttpGzipModule server { listen [::]:80; listen 80; server_name somesite.com www.somesite.com; root /var/www/html/somesite.com/wwwroot; access_log /var/log/nginx/somesite.access.log main; error_log /var/log/nginx/somesite.error.log wa; # -- Error Pages # show "Not Found" 404 errors in place of "Forbidden" 403 errors, # because forbidden errors allow attackers potential insight into your server's layout and contents error_page 403 = 404; error_page 404 /404.html; location = /40x.html { } error_page 500 502 503 504 /50x.html; location = /50x.html { } # -- Security and Location location = /robots.txt { allow all; access_log off; log_not_found off; } location = /favicon.ico { access_log off; log_not_found off; } # prevent browsing hidden files (beginning with a period) from being served location ~ /. { access_log off; log_not_found off; deny all; } # prevent access to any files starting with a $ (usually temp files) location ~ ~$ { access_log off; log_not_found off; deny all; } # prevent browsing to certain wordpress files location ~* /wp-includes/.*.php$ { deny all; access_log off; log_not_found off; } location ~* /wp-content/.*.php$ { deny all; access_log off; log_not_found off; } location ~* /(?:uploads|files)/.*.php$ { deny all; access_log off; log_not_found off; } location = /xmlrpc.php { deny all; access_log off; log_not_found off; } # add trailing slash to */wp-admin requests so the admin interface works correctly rewrite /wp-admin$ $scheme://$host$uri/ permanent; # -- Prevent Caching of Static Resources set $no_cache 0; if ($request_method = POST) { set $no_cache 1; } if ($query_string != "") { set $no_cache 1; } if ($request_uri ~* "(/wp-admin/|/xmlrpc.php|/wp-(app|cron|login|register|mail).php|wp-.*.php|/feed/|index.php|wp-Idea-popup.php|wp-links-opml.php|wp-locations.php|sitemap(_index)?.xml|[a-z0-9_-]+-sitemap([0-9]+)?.xml)") { set $no_cache 1; } if ($http_cookie ~* "comment_author|wordpress_[a-f0-9]+|wp-postpass|wordpress_no_cache|wordpress_logged_in") { set $no_cache 1; } # -- Caching Controls # keep images, CSS and other static files around in browser cache for as long as possible, to cut down on server load location ~* .(ogg|ogv|svg|svgz|eot|otf|woff|mp4|ttf|css|rss|atom|js|jpg|jpeg|gif|png|ico|zip|tgz|gz|rar|bz2|doc|xls|exe|ppt|tar|mid|midi|wav|bmp|rtf)$ { access_log off; log_not_found off; expires max; # 360d; add_header Pragma public; add_header Cache-Control "public, must-revalidate, proxy-revalidate"; } #location ~* .(php|html)$ { #access_log off; #log_not_found off; #add_header Pragma public; #add_header Cache-Control "public"; #expires 14d; #} # -- General Directives location / { # First attempt to serve request as file, then as directory, then fall back to index.html # This is cool because no php is touched for static content. # include the "?$args" part so non-default permalinks doesn't break when using query string # if you're just using wordpress and don't want extra rewrites # then replace the word @rewrites with /index.php # try_files $uri $uri/ @rewrites; index index.php index.html index.htm; try_files $uri $uri/ /index.html /index.php?$args; } location @rewrites { # Can put some of your own rewrite rules in here # for example rewrite ^/~(.*)/(.*)/? /users/$1/$2 last; # If nothing matches we'll just send it to /index.php rewrite ^ /index.php last; } location ~ .php$ { #fastcgi_pass_header Set-Cookie; #fastcgi_pass_header Cookie; #fastcgi_ignore_headers Cache-Control Expires Set-Cookie; fastcgi_index index.php; fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name; fastcgi_split_path_info ^(.+.php)(/.+)$; fastcgi_param PATH_INFO $fastcgi_path_info; fastcgi_param PATH_TRANSLATED $document_root$fastcgi_path_info; fastcgi_intercept_errors on; fastcgi_pass unix:/var/run/php5.6-fpm/php5.6-fpm.sock; fastcgi_param GATEWAY_INTERFACE CGI/1.1; fastcgi_param SERVER_SOFTWARE nginx/$nginx_version; fastcgi_param QUERY_STRING $query_string; fastcgi_param REQUEST_METHOD $request_method; fastcgi_param CONTENT_TYPE $content_type; fastcgi_param CONTENT_LENGTH $content_length; fastcgi_param SCRIPT_NAME $fastcgi_script_name; fastcgi_param REQUEST_URI $request_uri; fastcgi_param DOCUMENT_URI $document_uri; fastcgi_param DOCUMENT_ROOT $document_root; fastcgi_param SERVER_PROTOCOL $server_protocol; fastcgi_param HTTPS $https if_not_empty; fastcgi_param REMOTE_ADDR $remote_addr; fastcgi_param REMOTE_PORT $remote_port; fastcgi_param SERVER_ADDR $server_addr; fastcgi_param SERVER_PORT $server_port; fastcgi_param SERVER_NAME $server_name; # PHP only, required if PHP was built with --enable-force-cgi-redirect fastcgi_param REDIRECT_STATUS 200; # Caching Bypasses #fastcgi_no_cache $no_cache; #fastcgi_cache_bypass $no_cache; #fastcgi_cache stupidfast; #fastcgi_cache_key $server_name|$request_uri; # Caching Expiration and Headers #fastcgi_cache_valid 404 60m; #fastcgi_cache_valid 200 60m; #fastcgi_max_temp_file_size 4m; #fastcgi_max_temp_file_size 0; #fastcgi_cache_use_stale updating; #fastcgi_cache_valid 200 302 1h; #fastcgi_cache_valid 301 1h; #fastcgi_cache_valid any 1h; #fastcgi_cache_min_uses 2; fastcgi_buffer_size 4K; #fastcgi_buffer_size 128K; fastcgi_buffers 64 4k; #fastcgi_buffers 4 256k; #fastcgi_ignore_client_abort off; #fastcgi_connect_timeout 60; #fastcgi_send_timeout 90; #fastcgi_read_timeout 90; #fastcgi_busy_buffers_size 256k; #fastcgi_temp_file_write_size 256k; #fastcgi_pass localhost:9000; fastcgi_param WP_NGINX_CONFIG done; }
}
}