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

From: Spencer Graves <spencer.graves_at_prodsyse.com>
Date: Wed, 05 Dec 2012 15:59:50 -0800

On 12/5/2012 1:12 PM, Duncan Murdoch wrote:

> 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?


       I don't know how it was being set.  I couldn't find the second 
path in environment variables or Rprofile.site. However, when I physically deleted it, restarted R, Emacs, and the Windows Command Prompt, it went away. Now .libPaths() contains only the first path. After I installed zoo in that, this error went away.
       Thanks again for your help.
       Spencer

>
> 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
>


-- 
Spencer Graves, PE, PhD
President and Chief Technology Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San Josť, CA 95126
ph:  408-655-4567
web:  www.structuremonitoring.com

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