seeming simple rpubchem interactive function produces error

Question

The following lines of R code produces the errors in italics. It would seem to be a rpubchem error, unless I'm doing something stupid:

    require(rpubchem);
    get.aid.by.cid(614467, type="raw")

Output:

***Warning messages:
1: In readLines(icon, n = 100) :
  seek on a gzfile connection returned an internal error
2: In readLines(icon, n = 100) :
  seek on a gzfile connection returned an internal error
3: In file.remove(iname) :
  cannot remove file 'C:\Users\bkoch\AppData\Local\Temp\RtmpSs77GM\abycbdc276782.gz', reason 'Permission denied'***

Anyone know what is going on here?

this is not an error message. it is a warning message, which are different than error messages. An error means your command was not applied successfully. A warning on the other hand suggests the command was executed (but with caveats) — Cyrus Mohammadian, Aug 23 '16 at 23:33

score 0 · Answer 1 · answered Aug 23 '16 at 22:05

In the folder mentioned by the warning are temporary files creating during your data pull via this package. The file name mentioned by the warning exists but lacks the .gz extension, which is probably part of the problem.

I verified this by running your code and inspecting the files. Apparently the issue is a minor bug and I would suggest to file a bug report on GitHub.

However please note it's only a warning not an error and the function seems to still work.

Thanks to both for the clarifications. – B Koch Aug 25 '16 at 15:42 — B Koch, Aug 25 '16 at 15:42

seeming simple rpubchem interactive function produces error

1 Answers1