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...

Thank you in advance.

Sebastien


2009/8/26 Sébastien Laigre <sebastien.laigre@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@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@fhcrc.org <mailto:mtmorgan@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@stat.math.ethz.ch
>> >         <mailto:Bioc-devel@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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