Wow, I completely forgot about Rockman VS, the mini-manga inspired by Rockman EXE Operate Shooting Star. According this Japanese blog, the comic saw its final chapter in last month's issue of Coro Coro Special, sister magazine of Coro Coro Comics.
Rockman VS, originally marketed as a one-shot to promote the release of OSS, went on for an additional four chapters spread out throughout the remainder of 2009 and February, April 2010 respectively. The story revolved around Raito Amino and his Navi Rockman.EXE on their quest to become strong enough to defeat a childhood rival and his Navi, Shooting Star Rockman.
At this time, there are no plans to compile the manga into a single collected volume.