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[Bioc-devel] Creating a package, Error in match.arg(units)
10 messages · Sébastien Laigre, Martin Morgan, Patrick Aboyoun
S?bastien 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 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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Hi S?bastien --
S?bastien 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 n?cessit? le package : tcltk
Chargement de Tcl/Tk... termin?
Le chargement a n?cessit? 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 n?cessit? le package : R2HTML
Le chargement a n?cessit? le package : svMisc
*** 'hhc.exe' introuvable : l'aide CHM ne peut ?tre g?n?r?e
* 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.
S?bastien
2009/8/25 Martin Morgan <mtmorgan at fhcrc.org <mailto:mtmorgan at fhcrc.org>>
S?bastien 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> 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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S?bastien 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 S?bastien 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 ?tre 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 ?chou? pour 'MyApp'
Ex?cution arr?t?e
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 S?bastien --
S?bastien 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 n?cessit? le package : tcltk
> Chargement de Tcl/Tk... termin?
> Le chargement a n?cessit? 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 n?cessit? le package : R2HTML
> Le chargement a n?cessit? le package : svMisc
>
> *** 'hhc.exe' introuvable : l'aide CHM ne peut ?tre g?n?r?e
>
> * 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.
>
>
>
> S?bastien
>
>
>
> 2009/8/25 Martin Morgan <mtmorgan at fhcrc.org
<mailto:mtmorgan at fhcrc.org> <mailto:mtmorgan at fhcrc.org
<mailto:mtmorgan at fhcrc.org>>>
>
> S?bastien 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 > >
4 days later
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S?bastien Laigre wrote:
Hi Martin, Thank you for answering. I managed to solved my problem. In fact, it was a conflict between Hmisc and xtable. Hmisc overrided units from base package, and xtable needed it, so there was a problem. I used only 2 functions, so I copied/pasted these 2 functions in my package, and do not use Hmisc. So the problem disapeared !
A better solution is to use a name space and 'importsFrom', for instance in the DESCRIPTION file: Imports: Hmisc and in the NAMESPACE file importFrom(Hmisc, someFunction, anotherFunction) if you are not already using a name space, then I'd strongly encourage you to use one. It'll help avoid conflicts like this in the future. Use is documented in the 'Writing R extensions' manual. Martin
Thank you very much for your help.
2009/8/27 Martin Morgan <mtmorgan at fhcrc.org <mailto:mtmorgan at fhcrc.org>>
S?bastien 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 S?bastien Laigre <sebastien.laigre at gmail.com
<mailto:sebastien.laigre at gmail.com>
> <mailto: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 ?tre 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 ?chou?
pour 'MyApp'
> Ex?cution arr?t?e
>
> 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> <mailto:mtmorgan at fhcrc.org
<mailto:mtmorgan at fhcrc.org>>>
>
> Hi S?bastien --
>
> S?bastien 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 n?cessit? le package : tcltk
> > Chargement de Tcl/Tk... termin?
> > Le chargement a n?cessit? 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 n?cessit? le package : R2HTML
> > Le chargement a n?cessit? le package : svMisc
> >
> > *** 'hhc.exe' introuvable : l'aide CHM ne peut ?tre g?n?r?e
> >
> > * 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.
> >
> >
> >
> > S?bastien
> >
> >
> >
> > 2009/8/25 Martin Morgan <mtmorgan at fhcrc.org
<mailto:mtmorgan at fhcrc.org>
> <mailto:mtmorgan at fhcrc.org <mailto:mtmorgan at fhcrc.org>>
<mailto:mtmorgan at fhcrc.org <mailto:mtmorgan at fhcrc.org>
> <mailto:mtmorgan at fhcrc.org <mailto:mtmorgan at fhcrc.org>>>>
> >
> > S?bastien 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>>
> > <mailto: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
> >
> >
>
>
>
S?bastien, In addition to Martin's comments, copying code from Hmisc to your package could be a violation of Hmisc's license. As Martin's e-mail shows, importing symbols is a straight-forward process and is the recommended method in this situation. Patrick
Martin Morgan wrote:
S?bastien Laigre wrote:
Hi Martin,
Thank you for answering. I managed to solved my problem. In fact, it was
a conflict between Hmisc and xtable. Hmisc overrided units from base
package, and xtable needed it, so there was a problem. I used only 2
functions, so I copied/pasted these 2 functions in my package, and do
not use Hmisc. So the problem disapeared !
A better solution is to use a name space and 'importsFrom', for instance in the DESCRIPTION file: Imports: Hmisc and in the NAMESPACE file importFrom(Hmisc, someFunction, anotherFunction) if you are not already using a name space, then I'd strongly encourage you to use one. It'll help avoid conflicts like this in the future. Use is documented in the 'Writing R extensions' manual. Martin
Thank you very much for your help.
2009/8/27 Martin Morgan <mtmorgan at fhcrc.org <mailto:mtmorgan at fhcrc.org>>
S?bastien 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 S?bastien Laigre <sebastien.laigre at gmail.com
<mailto:sebastien.laigre at gmail.com>
> <mailto: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 ?tre 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 ?chou?
pour 'MyApp'
> Ex?cution arr?t?e
>
> 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> <mailto:mtmorgan at fhcrc.org
<mailto:mtmorgan at fhcrc.org>>>
>
> Hi S?bastien --
>
> S?bastien 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 n?cessit? le package : tcltk
> > Chargement de Tcl/Tk... termin?
> > Le chargement a n?cessit? 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 n?cessit? le package : R2HTML
> > Le chargement a n?cessit? le package : svMisc
> >
> > *** 'hhc.exe' introuvable : l'aide CHM ne peut ?tre g?n?r?e
> >
> > * 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.
> >
> >
> >
> > S?bastien
> >
> >
> >
> > 2009/8/25 Martin Morgan <mtmorgan at fhcrc.org
<mailto:mtmorgan at fhcrc.org>
> <mailto:mtmorgan at fhcrc.org <mailto:mtmorgan at fhcrc.org>>
<mailto:mtmorgan at fhcrc.org <mailto:mtmorgan at fhcrc.org>
> <mailto:mtmorgan at fhcrc.org <mailto:mtmorgan at fhcrc.org>>>>
> >
> > S?bastien 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>>
> > <mailto: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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