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.
On Fri, 11 Dec 2015, William Dunlap wrote:> 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, Okay. I intended to update R after the packages. Will run version upgrade, then see how the package update goes. Result will be reported here. Thanks, Rich
On Fri, 11 Dec 2015, Rich Shepard wrote:> On Fri, 11 Dec 2015, William Dunlap wrote: > >> stats::sigma was added to R recently. It is is R-devel now, I don't know >> about yesterday's R-3.2.3.> Okay. I intended to update R after the packages. Will run version upgrade, > then see how the package update goes. Result will be reported here.Well, R-3.2.3 does not include stats::sigma. An upgraded version of stats is apparently not yet released. I'll wait to upgrade pbkrtes until next Friday. Thanks Duncan and Bill, Rich
Duncan Murdoch
2015-Dec-11 20:40 UTC
[R] Updating Package Fails: Help on How to Fix Needed
On 11/12/2015 2:36 PM, William Dunlap wrote:> stats::sigma was added to R recently. It is is R-devel now, I don't know > about yesterday's R-3.2.3.As Rich saw, it's not. pbkrtest should have "Depends: R (>= 3.3.0)" instead of "Depends: R (>= 3.0.0)" in its DESCRIPTION. You can see it failed tests on CRAN. Duncan Murdoch> 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.
> On Dec 11, 2015, at 2:40 PM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote: > > On 11/12/2015 2:36 PM, William Dunlap wrote: >> stats::sigma was added to R recently. It is is R-devel now, I don't know >> about yesterday's R-3.2.3. > > As Rich saw, it's not. pbkrtest should have "Depends: R (>= 3.3.0)" instead of "Depends: R (>= 3.0.0)" in its DESCRIPTION. > You can see it failed tests on CRAN. > > Duncan MurdochJust to confirm, having installed 3.2.3 this morning, stats::sigma is not present. FWIW, it may, in some fashion, be related to the dependency of pbkrtest on lme4. The ?sigma for lme4 shows the following in Examples: methods(sigma)# from R 3.3.0 on, shows methods from pkgs 'stats' *and* 'lme4' So there may be a package namespace/export issue at play here... Regards, Marc Schwartz>> 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. > > ______________________________________________ > 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.