Version Upgrade and Packages

Hi Rich,

Immediately after you see one of those messages, do, e.g.,

  find('cor')

It should tell you that you have more than one object named 'cor' in your
search path, and where they all are. Then you can decide if it's what you
want (probably not, but can't say from here).

-Don

Don MacQueen

Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062





On 3/4/13 7:38 AM, "Rich Shepard" <rshepard at appl-ecosys.com> wrote:

   I just upgraded from 2.15.2 to 2.15.3 on our Slackware systems and see
the
following when testing that the new version properly loads:

"The following object(s) are masked from 'package:stats':
     cor

"The following object(s) are masked from 'package:base':
     as.Date, as.Date.numeric"

   What, exactly, does this mean?

   Also, I assume that if I see no errors about loading packages that means
they do not need to be upgraded to work with this low level upgrade.

Rich

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Immediately after you see one of those messages, do, e.g.,

 find('cor')

It should tell you that you have more than one object named 'cor' in your
search path, and where they all are. Then you can decide if it's what you
want (probably not, but can't say from here).

Don,

   find doesn't because these are apparently not individual files. So I run
egrep -R 'cor' * or egrep -R 'as.Date' * within /usr/lib/R/library and see
many instances of where these strings are used. Many are in help files.
Others are used in different libraries; for example:

gdata/unitTests/runit.getDateTimeParts.R:cDate <- as.Date(tDate)

plyr/tests/test-rbind.r:    d = as.Date(c("2008-01-01", "2009-01-01",
"2010-01-01")))

spacetime/demo/gvis.R:	rural_PM10$time == as.Date("2003-12-31"))

timeDate/unitTests/runit.SpecialDates.R:    dts <- as.Date(ch.dts)

zoo/NAMESPACE:   "as.Date",

   I'm not seeing code for as.Date, as.Date.numeric, or cor in multiple
libraries.

Thanks,

Rich

On Mon, 4 Mar 2013, MacQueen, Don wrote:

Immediately after you see one of those messages, do, e.g.,

find('cor')

It should tell you that you have more than one object named 'cor' in your
search path, and where they all are. Then you can decide if it's what you
want (probably not, but can't say from here).

Don,

 find doesn't because these are apparently not individual files. So I run
egrep -R 'cor' * or egrep -R 'as.Date' * within /usr/lib/R/library and see
many instances of where these strings are used. Many are in help files.
Others are used in different libraries; for example:

Don assumed you were in an R session. The `find` function in R takes a character argument. You did not produce the entire message because you should have seen immediately above that message the name of  a package being loaded (in this case most likely as part of the startup process)

?Startup

In my ,Rprofile I load both package:sos and package:utils and I see this at startupo:
-------
Attaching package: ?utils?

The following object(s) are masked from ?package:sos?:

    ?
------------

So the sos function '?' is masked by the utils function named '?'

gdata/unitTests/runit.getDateTimeParts.R:cDate <- as.Date(tDate)

plyr/tests/test-rbind.r:    d = as.Date(c("2008-01-01", "2009-01-01",
"2010-01-01")))

spacetime/demo/gvis.R:	rural_PM10$time == as.Date("2003-12-31"))

timeDate/unitTests/runit.SpecialDates.R:    dts <- as.Date(ch.dts)

zoo/NAMESPACE:   "as.Date",

 I'm not seeing code for as.Date, as.Date.numeric, or cor in multiple
libraries.

Please read Uwe Ligges' excellent article regarding finding R code:

http://cran.r-project.org/doc/Rnews/Rnews_2006-4.pdf

David Winsemius
Alameda, CA, USA