Problems with source() function
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Does source(textConnection(readLines(url(http://...))) give the correct answer. If not, what is being dropped when you just use readLines() and look at the contents of the download. And how long is the longest line? The RCurl package (http://www.omegahat.org/RCurl) gives you a lot of control in perform and processing HTTP requests, allowing you to control the request, and read the body and the header of the response. It may be worth a try if things are getting frustrating. D.
Al wrote:
Hello list members! I'm trying to enter some data in an R session using source() function with an URL as argument. The data source is a PHP script located in an apache web server and the data is a long list generated on-the-fly, these are the initial lines: groups<-list() groups[['ENSMUST00000000001']]=c(52611,483683,147952,132170,297514,469248,291525,364037,469915,55472,280220,314688,415650,486875,440898,6781,497785) groups[['ENSMUST00000000003']]=c(416911,327120,425495,72272,297529,101933,371418,139034,318872,367204,237702) groups[['ENSMUST00000000028']]=c(199311,325400,184761,241988,376845,75052,67724,404240,439543,391057,393816) groups[['ENSMUST00000000031']]=c(402587,352900,139030,186068,463553,328881,74942,277085,301431,256149,410846) groups[['ENSMUST00000000033']]=c(12700,23908,11140,122358,389908,390084,383903,354007,457965,106395,131876) groups[['ENSMUST00000000049']]=c(59336,203239,101077,382882,327374,281549,212042,275594,361523,490934,240275) groups[['ENSMUST00000000056']]=c(409571,304584,394332,379699,13785,4260,288889,42538,304075,47734,485512,52501,328509,504846,334607,82566,250088,150240,16422,446551,314484,91878,124752,341638,379512,379890,319764,8019,59221,156508,362524,74001,149400) groups[['ENSMUST00000000058']]=c(26511,4
5!
5190,466368,358528,268486,315461,149260,422804,137641,163718,352555) The problem: When I execute the command it apparently finish ok, without printed errors but when I test the consistency of the data entered using the command length() I always obtain different figures. More facts: When I source the data from a static file instead an url, the data is fully entered and the length is always the same (20346 list elements). It delays 30 secs to load. When I source the data from the dynamic way, from an url, it delays 2 min. and always data is truncated. Tried and miserably failed: - Changed .Options$timeout from 60 to 300 - Using R --verbose is of no help, the data is silently truncated. - Changed the expression in which data is entered: groups<-list( 'ENSMUST00000000001'=c(52611,483683,147952,132170,297514,469248,291525,364037,469915,55472,280220,314688,415650,486875,440898,6781,497785), 'ENSMUST00000000003'=c(416911,327120,425495,72272,297529,101933,371418,139034,318872,367204,237702) ... ) Kind list members, is there some timeout I am missing? Some way to debug the process? Some suggestion? Sincerely, thank you! Alberto de Luis www.cicancer.org
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- -- Duncan Temple Lang duncan at wald.ucdavis.edu Department of Statistics work: (530) 752-4782 371 Kerr Hall fax: (530) 752-7099 One Shields Ave. University of California at Davis Davis, CA 95616, USA -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2 (Darwin) Comment: Using GnuPG with Thunderbird - http://enigmail.mozdev.org iD8DBQFDYSvk9p/Jzwa2QP4RAsqfAJ98RNScQ7ea1/MAnt72R0VGZoXaEQCfZvyl WNNN/HT1hx/Kix3KSp15XwM= =VsDG -----END PGP SIGNATURE-----