Third seed Wawrinka did book his place in the second round, although his path to victory against straight-hitting Lukas Rosol was equally tortuous.
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The two-time quarterfinalist from Spain struggled early but rallied to beat Anna Karolina Schmiedlova 3-6, 6-3, 6-3.
It was the eighth time in his grand slam career and ninth time overall that Murray has recovered from two sets down to win a match.
He polished that set off easily, but the fifth brought the Scot to the brink of defeat, with Stepanek two points away from victory at one point.
Australian Open champion Angelique Kerber, the No. 3 seed in the women’s tournament, was beaten 6-2, 3-6, 6-3 by 58th-ranked Kiki Bertens of the Netherlands.
Romania’s Halep, runner-up to Maria Sharapova in 2014, took a while to tame Kazakhstan’s Zarina Diyas to win 7-6 (5), 6-2. The second-seeded Murray acknowledged he can’t keep getting pushed to the limit if he has designs on adding a third Grand Slam title to his collection. I was missing a lot of balls long, and his ball was jumping up a lot.
The world No.2, who was also pushed the distance by veteran Radek Stepanek in the opening round, suffered an alarming mid-match dip before coming through 6-2 2-6 4-6 6-2 6-3.
Stepanek is well known for his ability to wind up opponents both with his canny play and on-court antics, and after withstanding Murray pressure in the opening game of the decider he whipped up the crowd.
Second seed Agnieszka Radwanska will come up against another home player, Caroline Garcia, while fourth seed Garbine Muguruza and the sixth-seeded Simona Halep will be trying to continue their progress on the clay.
Wearing a fluorescent yellow shirt and shoes, defending champion Stan Wawrinka is up against Lukas Rosol on Court Philippe Chatrier.
The 21-year-old Yorkshireman battled to a a 7-6 (7/4) 6-7 (9/7) 7-5 6-1 victory that lasted two hours and 47 minutes. He has opted for a pair of black shorts this year.
Andy Murray has reached the third round of the French Open after defeating Mathias Bourgue at Roland Garros. Murray hasn’t been eliminated before the fourth round of a grand slam since the 2010 US Open. A retractable roof is expected to be delivered by 2018.
Schiavone was surprised to receive a standing ovation after her loss, and was annoyed at tournament organizers for prematurely announcing this was her last French Open. I had some momentum when I came out but I know that in a fifth set that anything can happen.
Murray conceded there had been little margin for error once play resumed in more overcast conditions on Tuesday, barely more than 12 hours later.
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It might have been because of the weather, or his opponent’s gamesmanship, but Andy Murray has become temperamental on his match against Radek Stepanek on the 2nd day of French Open 2016.
