Hi,
Eric, thanks for the report; we are investigating.
(I don't know how to investigate attachments, but i know that an am-dev
message with a 6MB attachment went through on july 9.)
scott
On Tue, Jul 13, 2021 at 01:13:40PM -0700, Eric Pettersen wrote:
> Anyway, here's the patch as straight text, if the remailer doesn't mangle it...
>
> --- AmberTools/src/antechamber/common.c 2020-04-27 18:19:42.000000000 -0700
> +++ AmberTools/src/antechamber/common.c.new 2021-07-13 11:32:49.000000000 -0700
> .. -21,14 +21,22 ..
> 'for_system' indicates if the path will be used in a 'system'
> command and therefore needs quotes if there are spaces in the
> AMBERHOME variable.
> - dac change: code to handle spaces in AMBERHOME is wrong! remove earlier refs to quote
> */
> size_t build_path(char *path, const char *subdir, const char *fname, size_t sizeof_path,
> int for_system)
> {
> /* number of chars copied plus 1; on overflow > sizeof_path */
> + char *quote = NULL;
> size_t c = 1;
> path[0] = '\0';
> + if (for_system && index(amberhome, ' ') != NULL) {
> + if (index(amberhome, '"') == NULL)
> + quote = "\"";
> + else
> + quote = "'";
> + strncat(path, quote, sizeof_path - c);
> + c += 1;
> + }
>
> strncat(path, amberhome, sizeof_path - c);
> c += strlen(amberhome);
> .. -36,6 +44,10 ..
> c += strlen(subdir);
> strncat(path, fname, sizeof_path - c);
> c += strlen(fname);
> + if (quote != NULL) {
> + strncat(path, quote, sizeof_path - c);
> + c += 1;
> + }
> if (c > sizeof_path) {
> eprintf("Insufficient string size.\n"
> "Increase MAXCHAR in define.h and rebuild.\n"
>
>
> > On Jul 13, 2021, at 1:12 PM, Eric Pettersen <pett.cgl.ucsf.edu> wrote:
> >
> > Does the list strip attachments? The mail I originally sent had the attachment...
> >
> >> On Jul 13, 2021, at 1:09 PM, Eric Pettersen <pett.cgl.ucsf.edu> wrote:
> >>
> >> Hi All,
> >> Somewhere between AmberTools 18 and 20, the code in antechamber that quoted executable paths with spaces in them before being sent to a system() call got removed. Consequently, antechamber can't execute its subprograms (e.g. bondtype) in such situations and bombs out (since the system() call interprets the path up to the first space as the "executable"). So antechamber will fail if AmberTools is installed into a folder/directory with a space anywhere in the path leading to it.
> >> I have attached a patch file for AmberTools/src/antechamber/common.c that restores the quote-if-necessary functionality. I hope it can be incorporated, or some other code added that produces the same result.
> >>
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Received on Wed Jul 14 2021 - 15:00:02 PDT
