[Rd] cannot connect to an FTP server with long HELLO message

Hervé Pagès hpages at fhcrc.org
Fri Oct 22 08:02:05 CEST 2010


Trying to access files on the ftp server at ftp.ncbi.nih.gov
will either give a time out or sometimes even a segfault on Linux.
The 2 following methods give the same results:

   f <- 
url("ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS10.soft.gz", open="r")


I've tried one or the other method with all release versions >= 2.8
and with current R devel and they always fail to connect to this
FTP server.

What's particular about this FTP server is that it sends a long HELLO
message before it finally sends the 220 control code.
Using the Unix ftp client:

hpages at latitude:~$ ftp ftp.ncbi.nih.gov
Connected to ftp.ncbi.nih.gov.
  Warning Notice!

  This is a U.S. Government computer system, which may be accessed and used
  only for authorized Government business by authorized personnel.
  Unauthorized access or use of this computer system may subject 
violators to
  criminal, civil, and/or administrative action.

  All information on this computer system may be intercepted, recorded, 
  copied, and disclosed by and to authorized personnel for official 
  including criminal investigations. Such information includes sensitive 
  encrypted to comply with confidentiality and privacy requirements. Access
  or use of this computer system by any person, whether authorized or
  unauthorized, constitutes consent to these terms. There is no right of
  privacy in this system.
  Welcome to the NCBI ftp server! The official anonymous access URL is 

  Public data may be downloaded by logging in as "anonymous" using your 
E-mail address as a password.

  Please see ftp://ftp.ncbi.nih.gov/README.ftp for hints on large file 
220 FTP Server ready.

This seems to cause problems to the nanoftp module
(src/modules/internet/nanoftp.c) used by url() and download.file()
as it doesn't seem to be able to catch the 220 control code.

I'm not familiar with the nanoftp module, or with socket programming in
general, or with RFC 959 (FTP protocal), so I'm not really in a position
to say what's going wrong exactly in the module but it seems that
increasing the value of FTP_BUF_SIZE (size of the buffer for data
received from the control connection) fixes the problem.
Currently this is:

#define FTP_BUF_SIZE            1024

but, interestingly, *any* value > 1024 seems to fix the problem (even
though the long HELLO message above is 1091 bytes).

Any idea what's going on?


Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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