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

From: Duncan Murdoch <murdoch.duncan_at_gmail.com>
Date: Wed, 05 Dec 2012 14:27:25 -0500

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?

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
>>>
>>
>
>

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https://stat.ethz.ch/mailman/listinfo/r-devel Received on Wed 05 Dec 2012 - 19:31:46 GMT

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