[R] Updating Package Fails: Help on How to Fix Needed

[Rich Shepard]

On Fri, 11 Dec 2015, Duncan Murdoch wrote:

> I don't see that.  You need to give more details:  I'd start with
> sessionInfo(), and the version number of the pbkrtest package that you're
> trying to install. (If R is downloading it for you,
> available.packages()["pbkrtest",] will give lots of useful information.)

Duncan,

   Started R and the update.packages() function. Selected the Seattle, WA
one.

pbkrtest :
  Version 0.4-2 installed in /usr/lib/R/library
  Version 0.4-3 available at https://cran.fhcrc.org
Update (y/N/c)?  y
trying URL 'https://cran.fhcrc.org/src/contrib/pbkrtest_0.4-3.tar.gz'
Content type 'application/x-gzip' length 164415 bytes (160 KB)
==================================================
downloaded 160 KB

* installing *source* package ‘pbkrtest’ ...
** package ‘pbkrtest’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘stats::sigma’ when loading ‘pbkrtest’
Error : object ‘sigma’ is not exported by 'namespace:stats'
ERROR: lazy loading failed for package ‘pbkrtest’
* removing ‘/usr/lib/R/library/pbkrtest’
* restoring previous ‘/usr/lib/R/library/pbkrtest’

The downloaded source packages are in
 	‘/tmp/RtmpQGb2HS/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(update[instlib == l, "Package"], l, contriburl =
contriburl,  :
   installation of package ‘pbkrtest’ had non-zero exit status

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: i486-slackware-linux-gnu (32-bit)
Running under: Slackware 14.1

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C 
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tools_3.2.2 tcltk_3.2.2

> available.packages()["pbkrtest",]
                                      Package
                                   "pbkrtest"
                                      Version
                                      "0.4-3"
                                     Priority
                                           NA
                                      Depends
             "R (>= 3.0.2), lme4 (>= 1.1.10)"
                                      Imports 
"Matrix (>= 1.1.1), parallel, MASS, methods"
                                    LinkingTo
                                           NA
                                     Suggests
                                     "gplots"
                                     Enhances
                                           NA
                                      License
                                 "GPL (>= 2)"
                              License_is_FOSS
                                           NA
                        License_restricts_use
                                           NA
                                      OS_type
                                           NA
                                        Archs
                                           NA
                                       MD5sum
                                           NA
                             NeedsCompilation
                                         "no"
                                         File
                                           NA
                                   Repository
          "https://cran.fhcrc.org/src/contrib"

   Installed is lme4 Version: 1.1-10.

Rich