R devel - Apr 2024 - read.csv

The build system rolled up R-4.3.3.tar.gz and .xz (codename "Angel Food
Cake") this morning.

This is a minor update, intended as the wrap-up release for the 4.3.x series. 

This also marks the 6th anniversary of R-1.0.0. (2000-02-29)

The list below details the changes in this release. 

You can get the source code from

https://cran.r-project.org/src/base/R-4/R-4.3.3.tar.gz
https://cran.r-project.org/src/base/R-4/R-4.3.3.tar.xz

or wait for it to be mirrored at a CRAN site nearer to you.

Binaries for various platforms will appear in due course.


For the R Core Team,

Peter Dalgaard


These are the checksums (md5 and SHA-256) for the freshly created files, in case
you wish
to check that they are uncorrupted:

MD5 (AUTHORS) = 320967884b547734d6279dedbc739dd4
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = 97a3ddc25aab502a70bfb1a79ab6f862
MD5 (INSTALL) = 7893f754308ca31f1ccf62055090ad7b
MD5 (NEWS) = 0aa4babeb5349c3abc6fb02700e8cf53
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = 4108ab429e768e29b1c3b418c224246e
MD5 (NEWS.2) = b38d94569700664205a76a7de836ba83
MD5 (NEWS.3) = e55ed2c8a547b827b46e08eb7137ba23
MD5 (R-latest.tar.gz) = 4de100b35e3614c19df5e95e483cc3c3
MD5 (R-latest.tar.xz) = 5602f5996107c346dba12a16e866d2e2
MD5 (README) = f468f281c919665e276a1b691decbbe6
MD5 (RESOURCES) = a79b9b338cab09bd665f6b62ac6f455b
MD5 (THANKS) = 45b6d2e88a6ecb5b24fa33a781351cd5
MD5 (VERSION-INFO.dcf) = becc8fce6e97db1703f9ca6d80e36c9d
MD5 (R-4/R-4.3.3.tar.gz) = 4de100b35e3614c19df5e95e483cc3c3
MD5 (R-4/R-4.3.3.tar.xz) = 5602f5996107c346dba12a16e866d2e2

60a0d150e6fc1f424be76ad7b645d236b56e747692a4679f81ce6536c550e949  AUTHORS
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6095e9ffa777dd22839f7801aa845b31c9ed07f3d6bf8a26dc5d2dec8ccc0ef3  COPYING.LIB
3a47bca1e2a7db27c0ca12be388c238e2608ff2f768e627650a71a0ffc826038  FAQ
f87461be6cbaecc4dce44ac58e5bd52364b0491ccdadaf846cb9b452e9550f31  INSTALL
f28b88bf20aa2a0078214b89353985680c53092d55f83e59b8295e61ad1150e0  NEWS
4e21b62f515b749f80997063fceab626d7258c7d650e81a662ba8e0640f12f62  NEWS.0
5de7657c5e58e481403c0dd1a74a5c090b3ef481ce75a91dfe05d4b03f63163f  NEWS.1
cde079b6beab7d700d3d4ecda494e2681ad3b7f8fab13b68be090f949393ec62  NEWS.2
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80851231393b85bf3877ee9e39b282e750ed864c5ec60cbd68e6e139f0520330 
R-latest.tar.gz
9b4c5f4cabab23f38e72fee36d98772c640a97305d06ce6e1a6a73e82b850954 
R-latest.tar.xz
2fdd3e90f23f32692d4b3a0c0452f2c219a10882033d1774f8cadf25886c3ddc  README
8b7d3856100220f4555d4d57140829f2e81c27eccec5b441f5dce616e9ec9061  RESOURCES
8319c5415de58ee10d4bc058d79c370fd8e6b2ad09e25d7a1e04b74ca5f380a6  THANKS
b8c2534c643ffcd942e8df370a4970c913be5dfc24e687bb12d609e974308aef 
VERSION-INFO.dcf
80851231393b85bf3877ee9e39b282e750ed864c5ec60cbd68e6e139f0520330 
R-4/R-4.3.3.tar.gz
9b4c5f4cabab23f38e72fee36d98772c640a97305d06ce6e1a6a73e82b850954 
R-4/R-4.3.3.tar.xz

This is the relevant part of the NEWS file

CHANGES IN R 4.3.3:

  NEW FEATURES:

    * iconv() now fixes up variant encoding names such as "utf8"
      case-insensitively.

  DEPRECATED AND DEFUNCT:

    * The legacy encoding = "MacRoman" is deprecated in pdf() and
      postscript(): support was incomplete in earlier versions of R.

  BUG FIXES:

    * Arguments are now properly forwarded to methods on S4 generics
      with ... in the middle of their formal arguments. This was broken
      for the case when a method introduced an argument but did not
      include ... in its own formals. Thanks to Herv'e Pag`es for the
      report PR#18538.

    * Some invalid file arguments to pictex(), postscript() and xfig()
      opened a file called NA rather than throw an error.  These
      included postscript(NULL) (which some people expected to work
      like pdf(NULL)).

    * Passing filename = NA to svg(), cairo_pdf(), cairo_ps() or the
      Cairo-based bitmap devices opened a file called NA: it now throws
      an error.

    * quartz(file = NA) opened a file called NA, including when used as
      a Quartz-based bitmap device.  It now gives an error.

    * rank(<long vector>) now works, fixing PR#18617, thanks to Ilia
      Kats.

    * seq.int() did not adequately check its length.out argument.

    * match(<POSIXct>, .) is correct again for differing time zones,
      ditto for "POSIXlt", fixing PR#18618 reported by Bastian Klein.

    * drop.terms(*, dropx = <0-length>) now works, fixing PR#18563 as
      proposed by Mikael Jagan.

    * drop.terms(*) keeps + offset(.) terms when it should, PR#18565,
      and drop.terms() no longer makes up a response, PR#18566, fixing
      both bugs thanks to Mikael Jagan.

    * getS3method("t", "test") no longer finds the t.test()
function,
      fixing PR#18627.

    * pdf() and postscript() support for the documented Adobe encodings
      "Greek" and "Cyrilllic" was missing (although the
corresponding
      Windows' codepages could be used).

    * Computations of glyph metric information for pdf() and
      postscript() did not take into account that transliteration could
      replace one character by two or more (only seen on macOS 14) and
      typically warned that the information was not known.

    * rank(x) no longer overflows during integer addition, when
      computing rank average for largish but not-yet long vector x,
      fixing PR#18630, thanks to Ilia Kats.

    * list.files() on Windows now returns also files with names longer
      that 260 bytes (the Windows limit is 260 characters).
      Previously, some file names particularly with 'East Asian'
      characters were omitted.

    * cov2cor(<0 x 0>) now works, fixing PR#18423 thanks to Mikael
      Jagan and Elin Waring.

    * cov2cor(<negative diagonal>) and similar now give one warning
      instead of two, with better wording, fixing PR#18424 thanks to
      Mikael Jagan.

    * tools:: startDynamicHelp() now ensures port is in proper range,
      fixing PR#18645.

    * pbeta(x, a,b) is correct now for x=0 or 1 in the boundary cases
      where a or b or both are 0, fixing PR#18672 thanks to Michael
      Fay.

    * pmatch(x, table) for large table, also called for data frame row
      selection, dfrm[nm, ], is now interruptible, fixing PR#18656.

    * predict(<rank-deficient lm>, newdata=*) fix computing of nbasis,
      see Russ Lenth's comment 29 in PR#16158.

    * Added a work-around for a bug in macOS 14.3.1 and higher which
      prevents R plots in the Quartz Cocoa device from updating on
      screen.


-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com

Dear R-developers,

I came to a somewhat unexpected behaviour of read.csv() which is trivial but
worthwhile to note -- my data involves a protein named "1433E" but to
save space I drop the quote so it becomes,

Gene,SNP,prot,log10p
YWHAE,13:62129097_C_T,1433E,7.35
YWHAE,4:72617557_T_TA,1433E,7.73

Both read.cv() and readr::read_csv() consider prot(ein) name as (possibly
confused by scientific notation) numeric 1433 which only alerts me when I tried
to combine data,

all_data <- data.frame()
for (protein in proteins[1:7])
{
   cat(protein,":\n")
   f <- paste0(protein,".csv")
   if(file.exists(f))
   {
     p <- read.csv(f)
     print(p)
     if(nrow(p)>0) all_data  <- bind_rows(all_data,p)
   }
}

proteins[1:7]
[1] "1433B" "1433E" "1433F" "1433G"
"1433S" "1433T" "1433Z"

dplyr::bind_rows() failed to work due to incompatible types nevertheless rbind()
went ahead without warnings.

Best wishes,


Jing Hua