From murdoch.duncan at gmail.com  Wed Dec  5 22:12:35 2012
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Wed, 05 Dec 2012 16:12:35 -0500
Subject: [Rd] NAMESPACE problem: import(zoo) but 'zoo' could not be
	loaded
In-Reply-To: <50BFADF8.6010203@prodsyse.com>
References: <50BEE88E.9080701@prodsyse.com> <50BF9C42.8090506@gmail.com>
	<50BF9E30.1050402@prodsyse.com> <50BFA01D.3080708@gmail.com>
	<50BFADF8.6010203@prodsyse.com>
Message-ID: <50BFB8C3.3020208@gmail.com>

On 12-12-05 3:26 PM, Spencer Graves wrote:
> On 12/5/2012 11:27 AM, Duncan Murdoch wrote:
>> On 12-12-05 2:19 PM, Spencer Graves wrote:
>>> On 12/5/2012 11:10 AM, Duncan Murdoch wrote:
>>>> On 12-12-05 1:24 AM, Spencer Graves wrote:
>>>>> Hello:
>>>>>
>>>>>
>>>>>           I'm having problems creating a real NAMESPACE to replace
>>>>> the pro
>>>>> forma one in the fda package on R-Forge.  "R CMD check" complains,
>>>>> "Error: package 'zoo' could not be loaded ... there is no package
>>>>> called
>>>>> 'zoo'";  see below.  I get this both with and without "import(zoo)" in
>>>>> NAMESPACE.
>>>>>
>>>>>
>>>>>           Suggestions?
>>>>>           Thanks,
>>>>>           Spencer
>>>>>
>>>>>
>>>>> p.s.  The current code including this problem can be obtained through
>>>>> anonymous access via "svn checkout
>>>>> svn://svn.r-forge.r-project.org/svnroot/fda/".
>>>>>
>>>>>
>>>>> C:\Users\sgraves\2012\R_pkgs\fda>R CMD check fda_2.3.3.tar.gz
>>>>> * using log directory 'C:/Users/sgraves/2012/R_pkgs/fda/fda.Rcheck'
>>>>> * using R version 2.15.2 (2012-10-26)
>>>>> * using platform: i386-w64-mingw32 (32-bit)
>>>>>
>>>>> <snip>
>>>>>
>>>>> * checking loading without being on the library search path ...
>>>>> WARNING
>>>>> Loading required package: splines
>>>>> Loading required package: zoo
>>>>> Error: package 'zoo' could not be loaded
>>>>> In addition: Warning message:
>>>>> In library(pkg, character.only = TRUE, logical.return = TRUE,
>>>>> lib.loc =
>>>>> lib.loc)
>>>>>      :
>>>>>       there is no package called 'zoo'
>>>>> Execution halted
>>>>>
>>>>> It looks like this package has a loading problem when not on
>>>>> .libPaths:
>>>>> see the messages for details.
>>>>
>>>> This message is printed by tools when there's an error when it tries
>>>> to load a package (not sure if it's yours or zoo) that is not in the
>>>> .libPaths.  There might be more details in the check log.
>>>>
>>>> What does it say there?
>>>
>>>
>>>          I didn't see any more than the portion copied here. Below please
>>> find the entire 00check.log.  Thanks, Spencer
>>>
>>
>> Do you have more than one library, or do you use the default
>> .libPaths()?  I'm on a slightly old install of R on this Mac, and I
>> see this (starting R from the same place I ran the check):
>>
>>> .libPaths()
>> [1] "/Library/Frameworks/R.framework/Versions/2.15/Resources/library"
>>
>> What do you see?
>
>
>   > .libPaths()
> [1] "C:/Users/sgraves/pgms/R/R-2.15.2/library"
> [2] "C:/Users/sgraves/R/win-library/2.15"

I would guess the problem is that it is using a different .libPaths 
setting for that test, and zoo is in the wrong place.  I don't know 
whether this is something you did or a bug in the check code.

In any case, that's a funny ordering you're using:  normally I'd expect 
the user-specific library to come first (because it would be searched 
first), and that would be followed by the system library installed with 
R.  How are you setting it?

Duncan Murdoch

>   >
>
>         Thanks.  Spencer
>
>>
>> Duncan Murdoch
>>
>>
>>>
>>> * using log directory 'C:/Users/sgraves/2012/R_pkgs/fda/fda.Rcheck'
>>> * using R version 2.15.2 (2012-10-26)
>>> * using platform: i386-w64-mingw32 (32-bit)
>>> * using session charset: ISO8859-1
>>> * checking for file 'fda/DESCRIPTION' ... OK
>>> * this is package 'fda' version '2.3.3'
>>> * checking package namespace information ... OK
>>> * checking package dependencies ... OK
>>> * checking if this is a source package ... OK
>>> * checking if there is a namespace ... OK
>>> * checking for executable files ... OK
>>> * checking whether package 'fda' can be installed ... OK
>>> * checking installed package size ... OK
>>> * checking package directory ... OK
>>> * checking for portable file names ... OK
>>> * checking DESCRIPTION meta-information ... OK
>>> * checking top-level files ... OK
>>> * checking for left-over files ... OK
>>> * checking index information ... OK
>>> * checking package subdirectories ... OK
>>> * checking R files for non-ASCII characters ... OK
>>> * checking R files for syntax errors ... OK
>>> * checking whether the package can be loaded ... OK
>>> * checking whether the package can be loaded with stated dependencies
>>> ... OK
>>> * checking whether the package can be unloaded cleanly ... OK
>>> * checking whether the namespace can be loaded with stated dependencies
>>> ... OK
>>> * checking whether the namespace can be unloaded cleanly ... OK
>>> * checking loading without being on the library search path ... WARNING
>>> Loading required package: splines
>>> Loading required package: zoo
>>> Error: package 'zoo' could not be loaded
>>> In addition: Warning message:
>>> In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc =
>>> lib.loc) :
>>>      there is no package called 'zoo'
>>> Execution halted
>>>
>>> It looks like this package has a loading problem when not on .libPaths:
>>> see the messages for details.
>>> * checking for unstated dependencies in R code ... OK
>>> * checking S3 generic/method consistency ... OK
>>> * checking replacement functions ... OK
>>> * checking foreign function calls ... OK
>>> * checking R code for possible problems ... OK
>>> * checking Rd files ... OK
>>> * checking Rd metadata ... OK
>>> * checking Rd cross-references ... WARNING
>>> Missing link(s) in documentation object
>>> 'C:/Users/sgraves/2012/R_pkgs/fda/fda.Rcheck/00_pkg_src/fda/man/basisfd.Rd':
>>>
>>>      'use.proper.basis' 'is.eqbasis'
>>>
>>> Missing link(s) in documentation object
>>> 'C:/Users/sgraves/2012/R_pkgs/fda/fda.Rcheck/00_pkg_src/fda/man/cca.fd.Rd':
>>>
>>>      'plot.cca.fd'
>>>
>>> Missing link(s) in documentation object
>>> 'C:/Users/sgraves/2012/R_pkgs/fda/fda.Rcheck/00_pkg_src/fda/man/monomial.Rd':
>>>
>>>      'polynom'
>>>
>>> Missing link(s) in documentation object
>>> 'C:/Users/sgraves/2012/R_pkgs/fda/fda.Rcheck/00_pkg_src/fda/man/monomialpen.Rd':
>>>
>>>      'polynompen'
>>>
>>> Missing link(s) in documentation object
>>> 'C:/Users/sgraves/2012/R_pkgs/fda/fda.Rcheck/00_pkg_src/fda/man/readHMD.Rd':
>>>
>>>      'getURL'
>>>
>>> See the information in section 'Cross-references' of the 'Writing R
>>> Extensions' manual.
>>>
>>> * checking for missing documentation entries ... OK
>>> * checking for code/documentation mismatches ... OK
>>> * checking Rd \usage sections ... OK
>>> * checking Rd contents ... OK
>>> * checking for unstated dependencies in examples ... OK
>>> * checking contents of 'data' directory ... OK
>>> * checking data for non-ASCII characters ... OK
>>> * checking data for ASCII and uncompressed saves ... OK
>>> * checking installed files from 'inst/doc' ... OK
>>> * checking examples ... ERROR
>>> Running examples in 'fda-Ex.R' failed
>>> The error most likely occurred in:
>>>
>>>    > ### Name: CanadianWeather
>>>    > ### Title: Canadian average annual weather cycle
>>>    > ### Aliases: CanadianWeather daily
>>>    > ### Keywords: datasets
>>>    >
>>>    > ### ** Examples
>>>    >
>>>    > ##
>>>    > ## 1.  Plot (latitude & longitude) of stations by region
>>>    > ##
>>>    > with(CanadianWeather, plot(-coordinates[, 2], coordinates[, 1],
>>> type='n',
>>> +                            xlab="West Longitude", ylab="North
>>> Latitude",
>>> +                            axes=FALSE) )
>>>    > Wlon <- pretty(CanadianWeather$coordinates[, 2])
>>>    > axis(1, -Wlon, Wlon)
>>>    > axis(2)
>>>    >
>>>    > rgns <- 1:4
>>>    > names(rgns) <- c('Arctic', 'Atlantic', 'Continental', 'Pacific')
>>>    > Rgns <- rgns[CanadianWeather$region]
>>>    > with(CanadianWeather, points(-coordinates[, 2], coordinates[, 1],
>>> +                              col=Rgns, pch=Rgns) )
>>>    > legend('topright', legend=names(rgns), col=rgns, pch=rgns)
>>>    >
>>>    > ##
>>>    > ## 2.  Plot dailyAv[, 'Temperature.C'] for 4 stations
>>>    > ##
>>>    > data(CanadianWeather)
>>>    > # Expand the left margin to allow space for place names
>>>    > op <- par(mar=c(5, 4, 4, 5)+.1)
>>>    > # Plot
>>>    > stations <- c("Pr. Rupert", "Montreal", "Edmonton", "Resolute")
>>>    > matplot(day.5, CanadianWeather$dailyAv[, stations, "Temperature.C"],
>>> +         type="l", axes=FALSE, xlab="", ylab="Mean Temperature (deg
>>> C)")
>>> Error in UseMethod("matplot") :
>>>      no applicable method for 'matplot' applied to an object of class
>>> "c('double', 'numeric')"
>>> Calls: matplot
>>> Execution halted
>>>
>>>>
>>>> Duncan Murdoch
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>     > sessionInfo()
>>>>> R version 2.15.2 (2012-10-26)
>>>>> Platform: i386-w64-mingw32/i386 (32-bit)
>>>>>
>>>>> locale:
>>>>> [1] LC_COLLATE=English_United States.1252
>>>>> [2] LC_CTYPE=English_United States.1252
>>>>> [3] LC_MONETARY=English_United States.1252
>>>>> [4] LC_NUMERIC=C
>>>>> [5] LC_TIME=English_United States.1252
>>>>>
>>>>> attached base packages:
>>>>> [1] stats     graphics  grDevices utils     datasets methods base
>>>>>
>>>>> other attached packages:
>>>>> [1] zoo_1.7-9
>>>>>
>>>>> loaded via a namespace (and not attached):
>>>>> [1] grid_2.15.2     lattice_0.20-10
>>>>>
>>>>> ______________________________________________
>>>>> R-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>>
>>>>
>>>
>>>
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>
>



[Rd] NAMESPACE problem: import(zoo) but 'zoo' could not be loaded
Duncan Murdoch