Trying to update package pbkrtest failed because of a missing object in another namespace. Not having experienced this issue before now I don't know what to do to fix the problem. Here's the story: * 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/RtmppHtiuJ/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 Advice needed. Rich
Duncan Murdoch
2015-Dec-11 19:05 UTC
[R] Updating Package Fails: Help on How to Fix Needed
On 11/12/2015 1:44 PM, Rich Shepard wrote:> Trying to update package pbkrtest failed because of a missing object in > another namespace. Not having experienced this issue before now I don't know > what to do to fix the problem. Here's the story: > > * 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/RtmppHtiuJ/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 > > Advice needed.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 Murdoch
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
William Dunlap
2015-Dec-11 19:36 UTC
[R] Updating Package Fails: Help on How to Fix Needed
stats::sigma was added to R recently. It is is R-devel now, I don't know about yesterday's R-3.2.3. Bill Dunlap TIBCO Software wdunlap tibco.com On Fri, Dec 11, 2015 at 11:05 AM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:> On 11/12/2015 1:44 PM, Rich Shepard wrote: >> >> Trying to update package pbkrtest failed because of a missing object >> in >> another namespace. Not having experienced this issue before now I don't >> know >> what to do to fix the problem. Here's the story: >> >> * 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/RtmppHtiuJ/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 >> >> Advice needed. > > > 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 Murdoch > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.