[Bioc-devel] Creating a package, Error in match.arg(units)
Martin Morgan
mtmorgan at fhcrc.org
Thu Aug 27 15:15:31 CEST 2009
Sébastien Laigre wrote:
> Hi Martin,
>
> I just saw that in install.out, there are the following lines :
>
>> Attachement du package : 'Hmisc'
>>
>> The following object(s) are masked from package:base :
>>
>> format.pval,
>> round.POSIXt,
>> trunc.POSIXt,
>> units
>
> Then an error occurs with match.arg(units)...
>
> So, could it be a conflict between "units" of Hmisc package and "units"
> of base package ?
> It sounds that units is taken from Hmisc instead of base, how can tell
> the compiler to take it into base package ? I tried with importFrom in
> NAMESPACE but it sounds it is not allowed...
Your own package should have a name space, and if you use functions from
Hmisc you should import just those
importFrom(Hmisc, foo, bar, baz)
If you are importing from Hmisc, then the DESCRIPTION file should have
Imports: Hmisc. If there are still problems, you can fully qualify the
symbols that you want
base::units
It might be that there is still a problem, e.g., a third package that
does not have a name space but uses units, and so must find 'units' on
the search() path. In this case you must work around this by convincing
the third party author to use a name space, not use the third package,
or not use Hmisc.
Martin
>
> Thank you in advance.
>
> Sebastien
>
>
> 2009/8/26 Sébastien Laigre <sebastien.laigre at gmail.com
> <mailto:sebastien.laigre at gmail.com>>
>
> Hi Martin,
>
> Thank you for your suggestions. I tried once again with LazyLoad =
> no (in DESCRIPTION file), and now, it tells me :
>
> ...
> Attachement du package : 'xtable'
>
>
>
> The following object(s) are masked from package:Hmisc :
>
> label,
> label<-
>
> Error in match.arg(units) :
> 'arg' doit Ûtre un de "secs", "mins", "hours", "days"
> Error : impossible de charger le code R depuis le package 'MyApp'
> Erreur : le chargement du package / espace de noms a ÚchouÚ pour 'MyApp'
> ExÚcution arrÛtÚe
>
> It looks like this package has a loading problem: see the messages for
> details.
>
> It sounds that a package could not be loaded correctly, but I can
> not find which one. Is it the latest loaded (xtable) ? How can I
> "load it correctly" ?
> Thank you.
>
> Sebastien
>
>
>
>
> 2009/8/26 Martin Morgan <mtmorgan at fhcrc.org <mailto:mtmorgan at fhcrc.org>>
>
> Hi Sébastien --
>
> Sébastien Laigre wrote:
> > Hi Martin,
> >
> > Thank you for helping me.
> > I just tried to create a new R session, but it doesn't work so
> much. I
> > also tried to load files one by one using your 2 code lines,
> but there
> > are dependancies problems including files files ar not loaded
> in the
> > right order.
>
> it is not too hard to figure out how to load all the packages, e.g.,
> following the sequence listed in the 00install.out output, below.
>
> > In fact, I managed to check & build the package a few time
> ago, but it
> > doesn't work now. I had the right methodology, but I can't
> know what has
> > changed (sorry). My methodolgy is :
> > 1. Create the package skeleton with package.build(...) in R
> console.
>
> Perhaps it would help to review the manual 'Writing R Extensions' so
> that you can get an understanding of what various files are?
>
> > 2. Fill R documentation files in the man folder in skeleton,
> NAMESPACE
> > and DESCRIPTION files
> > 3. Execute "Rcmd check c:/base/MyApp" with cmd.exe (located in
> R/bin folder)
> > 4. Execute "Rcmd build c:/base/MyApp" with cmd.exe (located in
> R/bin folder)
>
> Usually you want to do Rcmd build ... and then Rcmd check ....
>
> Make sure that there are no 'hidden' files (starting with a '.')
> in any
> of the folders in c:/base/MyApp/.
>
> I don't really have other suggestions, other than to try to
> narrow down
> where in your package the error occurs, e.g., by temporarily
> renaming
> one file after the other in the MyApp/R directory.
>
> Martin
>
> > 5. Execute "Rcmd INSTALL MyApp.tar.gz" with cmd.exe (located
> in R/bin
> > folder)
> >
> > The error occurs when executing check command, here it is the full
> > install00.out :
> >
> > Le chargement a nécessité le package : tcltk
> > Chargement de Tcl/Tk... terminé
> > Le chargement a nécessité le package : Hmisc
> > Attachement du package : 'Hmisc'
> >
> > The following object(s) are masked from package:base :
> >
> > format.pval,
> > round.POSIXt,
> > trunc.POSIXt,
> > units
>
> > Le chargement a nécessité le package : R2HTML
> > Le chargement a nécessité le package : svMisc
> >
> > *** 'hhc.exe' introuvable : l'aide CHM ne peut être générée
> >
> > * Installing *source* package 'MyApp' ...
> > ** R
> > ** preparing package for lazy loading
> > Loading required package: grid
> > Loading required package: reshape
> > Loading required package: plyr
> >
> > Attaching package: 'plyr'
> >
> > The following object(s) are masked from package:Hmisc :
> >
> > is.discrete,
> > summarize
> >
> >
> > Attaching package: 'ggplot2'
> >
> > The following object(s) are masked from package:grid :
> >
> > nullGrob
> >
> >
> > Attaching package: 'xtable'
> >
> > The following object(s) are masked from package:Hmisc :
> >
> > label,
> > label<-
> >
> > Error in match.arg(units) :
> > 'arg' should be one of "secs", "mins", "hours", "days"
> > Error : unable to load R code in package 'MyApp'
> > ERREUR : lazy loading failed pour le package 'MyApp'
> > * Removing 'C:/PROGRA~1/R/R-29~1.1/bin/MYAPP~1.RCH/MyApp'
> >
> >
> >
> > Thank you again for you help.
> >
> >
> >
> > Sébastien
> >
> >
> >
> > 2009/8/25 Martin Morgan <mtmorgan at fhcrc.org
> <mailto:mtmorgan at fhcrc.org> <mailto:mtmorgan at fhcrc.org
> <mailto:mtmorgan at fhcrc.org>>>
> >
> > Sébastien Laigre wrote:
> >
> > Hello everybody,
> >
> > I have got several S4 classes for my R application,
> and I'm
> > trying to create
> > a package to deal it easier. It runs on windows XP.
> >
> > So I make :
> >
> > - a package.build(........) to build the skeleton of
> the package.
> > - Rcmd check c:/base/MyApp
> >
> > But, checking whether package 'MyApp' can be
> installed, I have
> > the following
> > error (in the install.out file) :
> > Error in match.arg(units) :
> > 'arg' should be one of "secs", "mins", "hours", "days"
> >
> > I already encountered this kind error, and adding
> > "importFrom("package",
> > "function") " in the NAMESPACE file solved it.
> > But the match.arg function is in the base package and
> I can not
> > do that.
> >
> > Can anyone help me please ? Does anybody knows what
> can it be
> > due to ?
> >
> >
> > Have you tried to start a new R session
> >
> > R --vanilla
> >
> > and then source each of the files in the 'R' directory of the
> > package, along the lines of
> >
> > fls = list.files("c:/base/MyApp/R", full=TRUE)
> > for (f in fls) { cat(f, "\n"); source(f) }
> >
> > ? Or can you provide more information about where during the
> > installation the error message is generated? Please also
> include
> > sessionInfo().
> >
> > Martin
> >
> >
> > Thank you in advance.
> >
> >
> > Sebastien
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at stat.math.ethz.ch
> <mailto:Bioc-devel at stat.math.ethz.ch>
> > <mailto:Bioc-devel at stat.math.ethz.ch
> <mailto:Bioc-devel at stat.math.ethz.ch>> mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
> >
> > --
> > Martin Morgan
> > Computational Biology / Fred Hutchinson Cancer Research Center
> > 1100 Fairview Ave. N.
> > PO Box 19024 Seattle, WA 98109
> >
> > Location: Arnold Building M1 B861
> > Phone: (206) 667-2793
> >
> >
>
>
>
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