Duncan Murdoch
2017-Apr-28 10:08 UTC
[R] Error with installed.packages with R 3.4.0 on Windows
On 28/04/2017 4:45 AM, Thierry Onkelinx wrote:> Dear Peter, > > It actually breaks install.packages(). So it is not that innocent.I don't think he meant that it is harmless, he meant that the fix is easy, and is in place in R-patched and R-devel. You should use R-patched and you won't have the problem. More generally, there's a lot more variety of systems in the wild than on our test machines, so we really do rely on people testing things in the alpha/beta/rc phase. In this case we saw the error too late to fix it (as I recall, it was very late in rc). If more people had tested, we might have found it earlier. Duncan Murdoch> > Best regards, > > Thierry > > > Op 28 apr. 2017 10:36 a.m. schreef "peter dalgaard" <pdalgd at gmail.com>: > > Yes, we noticed this in the last days of the code freeze before release and > shied away from inserting a workaround, partly because we couldn't see what > the root of the problem might be. > > For the purposes of installed.packages it is relatively harmless to treat > the NA condition as FALSE, since it is just a matter of whether a cache is > valid. I.e., it might cause an unnecessary cache rebuild. For other > situations it might be more of an issue. > > The workaround (NA -> FALSE, basically) is in place in R-patched and > R-devel. > > -pd > >> On 28 Apr 2017, at 07:47 , Thierry Onkelinx <thierry.onkelinx at inbo.be> > wrote: >> >> We have several computers with the same problem. >> >> Op 28 apr. 2017 7:25 a.m. schreef "Jean-Claude Arbaut" <arbautjc at gmail.com >> : >> >> Hello, >> >> I am currently getting a strange error when I call installed.packages(): >> >> Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) && : >> missing value where TRUE/FALSE needed >> Calls: installed.packages >> >> >> I am working with R 3.4.0 on Windows. I didn't get this error with R > 3.3.3. >> Apparently, file.mtime() is returning NA well applied to a directory, and >> this causes the entire && expression to be NA, then the "if" fails because >> it needs either T or F. >> The source of "installed.packages" seems to be roughly the same as in R >> 3.3.3, so I wonder if there have been other changes in R, maybe the > logical >> operators, that would make this function fail. >> >> Any idea? >> >> Best regards, >> >> Jean-Claude Arbaut >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> 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. >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> 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. > > -- > 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 > > [[alternative HTML version deleted]] > > ______________________________________________ > 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. >
peter dalgaard
2017-Apr-28 17:04 UTC
[R] Error with installed.packages with R 3.4.0 on Windows
> On 28 Apr 2017, at 12:08 , Duncan Murdoch <murdoch.duncan at gmail.com> wrote: > > On 28/04/2017 4:45 AM, Thierry Onkelinx wrote: >> Dear Peter, >> >> It actually breaks install.packages(). So it is not that innocent. > > I don't think he meant that it is harmless, he meant that the fix is easy, and is in place in R-patched and R-devel. You should use R-patched and you won't have the problem.Read more carefully: I said that the _fix_ is harmless for this case, but might not be so in general. -pd> > More generally, there's a lot more variety of systems in the wild than on our test machines, so we really do rely on people testing things in the alpha/beta/rc phase. In this case we saw the error too late to fix it (as I recall, it was very late in rc). If more people had tested, we might have found it earlier. > > Duncan Murdoch > >> >> Best regards, >> >> Thierry >> >> >> Op 28 apr. 2017 10:36 a.m. schreef "peter dalgaard" <pdalgd at gmail.com>: >> >> Yes, we noticed this in the last days of the code freeze before release and >> shied away from inserting a workaround, partly because we couldn't see what >> the root of the problem might be. >> >> For the purposes of installed.packages it is relatively harmless to treat >> the NA condition as FALSE, since it is just a matter of whether a cache is >> valid. I.e., it might cause an unnecessary cache rebuild. For other >> situations it might be more of an issue. >> >> The workaround (NA -> FALSE, basically) is in place in R-patched and >> R-devel. >> >> -pd >> >>> On 28 Apr 2017, at 07:47 , Thierry Onkelinx <thierry.onkelinx at inbo.be> >> wrote: >>> >>> We have several computers with the same problem. >>> >>> Op 28 apr. 2017 7:25 a.m. schreef "Jean-Claude Arbaut" <arbautjc at gmail.com >>> : >>> >>> Hello, >>> >>> I am currently getting a strange error when I call installed.packages(): >>> >>> Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) && : >>> missing value where TRUE/FALSE needed >>> Calls: installed.packages >>> >>> >>> I am working with R 3.4.0 on Windows. I didn't get this error with R >> 3.3.3. >>> Apparently, file.mtime() is returning NA well applied to a directory, and >>> this causes the entire && expression to be NA, then the "if" fails because >>> it needs either T or F. >>> The source of "installed.packages" seems to be roughly the same as in R >>> 3.3.3, so I wonder if there have been other changes in R, maybe the >> logical >>> operators, that would make this function fail. >>> >>> Any idea? >>> >>> Best regards, >>> >>> Jean-Claude Arbaut >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________________________ >>> 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. >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________________________ >>> 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. >> >> -- >> 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 >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> 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.-- 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
Patrick Connolly
2017-May-22 09:10 UTC
[R] Error with installed.packages with R 3.4.0 on Windows
On Fri, 28-Apr-2017 at 07:04PM +0200, peter dalgaard wrote: |> |> > On 28 Apr 2017, at 12:08 , Duncan Murdoch <murdoch.duncan at gmail.com> wrote: |> > |> > On 28/04/2017 4:45 AM, Thierry Onkelinx wrote: |> >> Dear Peter, |> >> |> >> It actually breaks install.packages(). So it is not that innocent. |> > |> > I don't think he meant that it is harmless, he meant that the fix is easy, and is in place in R-patched and R-devel. You should use R-patched and you won't have the problem. |> |> Read more carefully: I said that the _fix_ is harmless for this case, but might not be so in general. |> |> -pd Apparently it isn't harmless.> install.packages("withr")Error in readRDS(dest) : error reading from connection>> > sessionInfo()R version 3.4.0 Patched (2017-05-19 r72713) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS Matrix products: default BLAS: /home/hrapgc/local/R-patched/lib/libRblas.so LAPACK: /home/hrapgc/local/R-patched/lib/libRlapack.so locale: [1] LC_CTYPE=en_NZ.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_NZ.UTF-8 LC_COLLATE=en_NZ.UTF-8 [5] LC_MONETARY=en_NZ.UTF-8 LC_MESSAGES=en_NZ.UTF-8 [7] LC_PAPER=en_NZ.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grDevices utils stats graphics methods base other attached packages: [1] lattice_0.20-35 loaded via a namespace (and not attached): [1] compiler_3.4.0 tools_3.4.0 grid_3.4.0>Has anyone a workaround? -- ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~. ___ Patrick Connolly {~._.~} Great minds discuss ideas _( Y )_ Average minds discuss events (:_~*~_:) Small minds discuss people (_)-(_) ..... Eleanor Roosevelt ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.