Re: [Rd] [BioC] Suppress output from getGEO

some time ago i communicated the same issue to sean, and i'm very glad he has improved the package -- thanks! i'm purposefully posting to r-devel rather than to bioconductor. i think that download.file could be improved to avoid this sort of spamming output seen previously with getGEO.

[Rd] Bug in so_strsplit (PR#13742)

Full_Name: Wacek Kusnierczyk Version: 2.10.0 r48689 OS: Ubuntu 8.04 Linux 32b Submission from: (NULL) (129.241.199.78) src/main/character.c:435-438 (do_strsplit) contains the following code: for (i = 0; i tlen; i++) if (getCharCE(STRING_ELT(tok, 0)) == CE_UTF8) use_UTF8 = TRUE;

[Rd] incorrect output and segfaults from sprintf with %*d (PR#13667)

Full_Name: Wacek Kusnierczyk Version: 2.10.0 r48365 OS: Ubuntu 8.04 Linux 32bit Submission from: (NULL) (129.241.110.141) sprintf has a documented limit on strings included in the output using the format '%s'. It appears that there is a limit on the length of strings included with, e.g., the

[Rd] actual argument matching does not conform to the definition (PR#13634)

Full_Name: Wacek Kusnierczyk Version: 2.10.0 r48269 OS: Ubuntu 8.04 Linux 32 bit Submission from: (NULL) (129.241.199.164) In the following example (and many other cases): quote(a=1) # 1 the argument matching is apparently incorrect wrt. the documentation (The R Language Definition, v

[Rd] duplicated fails to rise correct errors (PR#13632)

Full_Name: Wacek Kusnierczyk Version: 2.8.0 and 2.10.0 r48242 OS: Ubuntu 8.04 Linux 32 bit Submission from: (NULL) (129.241.110.161) In the following code: duplicated(data.frame(), incomparables=NA) # Error in if (!is.logical(incomparables) || incomparables) .NotYetUsed(incomparables !=

[Rd] Incorrect behaviour of [.data.frame (PR#13628)

Full_Name: Wacek Kusnierczyk Version: 2.8.0 and 2.10.0 r48231 OS: Ubuntu 8.04 Linux 32 bit Submission from: (NULL) (80.202.30.36) According to the R Language definition (sec. 3.4.3), [.data.frame has the following properties: if two indices are supplied (even if one is empty) it creates

[Rd] Another incorrect behaviour of [.data.frame (PR#13629)

Full_Name: Wacek Kusnierczyk Version: 2.8.0 and 2.10.0 r48231 OS: Ubuntu 8.04 Linux 32 bit Submission from: (NULL) (129.241.198.65) In a previous report (Incorrect behaviour of [.data.frame (PR#13628), awaiting approval) I showed that [.data.frame behaves incorrectly (i.e., in contradiction to

[Rd] if does not covert raw to logical (PR#13630)

Full_Name: Wacek Kusnierczyk Version: 2.8.0 and 2.10.0 r48242 OS: Ubuntu 8.04 Linux 32 bit Submission from: (NULL) (80.202.30.36) The following raises an error: if (as.raw(1)) 1 # error: unimplemented type 'raw' in 'asLogical' However, ?'if' says: Arguments: cond: A length-one

[Rd] gsub('(.).(.)(.)', '\\3\\2\\1', 'gsub') (PR#13617)

Full_Name: Wacek Kusnierczyk Version: 2.10.0 r48181 OS: Ubuntu 8.04 Linux 32bit Submission from: (NULL) (129.241.199.135) there seems to be something wrong with r's regexing. consider the following example: gregexpr('a*|b', 'ab') # positions: 1 2 # lengths: 1 1 gsub('a*|b',

[Rd] sprintf causes a segfault (PR#13613)

Full_Name: Wacek Kusnierczyk Version: 2.8.0 and 2.10.0 r48163 OS: Ubuntu 8.04 Linux 32bit Submission from: (NULL) (129.241.198.172) the following code illustrates a problem with sprintf which consistently causes a segfault when applied to certain type of arguments. it also shows inconsistent