[R] Problem with package development
Duncan Murdoch
murdoch.duncan at gmail.com
Fri Jun 3 02:32:51 CEST 2011
On 02/06/2011 2:30 PM, Nipesh Bajaj wrote:
> What else I need to do? In the Read-and-delete-me file following steps
> are asked to perform:
> * Edit the help file skeletons in 'man', possibly combining help files
> for multiple functions.
> * Edit the exports in 'NAMESPACE', and add necessary imports.
> * Put any C/C++/Fortran code in 'src'.
> * If you have compiled code, add a useDynLib() directive to 'NAMESPACE'.
> * Run R CMD build to build the package tarball.
> * Run R CMD check to check the package tarball.
>
> I editied the help page for fn1() function (as I already communicated
> in previous mail) as follows:
This doesn't sound very generous of me, but I'm bowing out now. I don't
think I can help you at all.
Duncan
> \name{fn1}
> \alias{fn1}
>
> \title{
> A function.
> }
>
> \description{
> A function.
> }
>
> \usage{
> A function.
> }
>
> \arguments{
> A function.
> }
>
> \value{
> A function.
> }
>
> \author{
> \bold{Me}
> \cr
> \email{Me at me.com}
> }
>
> And regarding th Namespace file, this time I put
> "package.skeleton("trial1",namespace = FALSE, code_files =
> "f:/trial.r")
> "
>
> I do not have any C/C++ code so I ignored 3rd step.
>
> then Read-and-delete-me file asking me to build the package, so in
> cmd, I run following:
> cd C:\R_PackageBuild
> Rcmd build –binary trial1
>
> What I am missing in this entire process? Do you please point me?
>
> Thanks,
>
>
> On Thu, Jun 2, 2011 at 11:40 PM, Duncan Murdoch
> <murdoch.duncan at gmail.com> wrote:
>> On 02/06/2011 2:03 PM, Nipesh Bajaj wrote:
>>>
>>> Thanks Prof. Ripley and Duncan for your pointers. Noting down your
>>> points I have modified my way of building package and have done
>>> following so far:
>>>
>>> 1. In my C: drive I create one working folder naming "R_PackageBuild"
>>> 2. In R console I have written following codes:
>>>> setwd("c:/R_packageBuild")
>>>> package.skeleton("trial1",namespace = TRUE, code_files = "f:/trial.r")
>>> 3. then I opened cmd and wrote following:
>>> cd C:\R_PackageBuild
>>> Rcmd build –binary trial1
>>>
>>> This process halted with following error:
>>> Error: unexpected symbol in “tools:::.test_load_package(‘trial1′,….)”
>>> Execution halted
>>> ERROR: loading failed
>>>
>>> What I have missed in this process? Can you please help me how to
>>> solve this issue?
>>
>> You haven't done the manual changes required between steps 2 and 3.
>> package.skeleton() creates the skeleton of a package; you run it once as
>> you are starting development, the do a lot of manual updates, described on
>> the ?package.skeleton help page, and in the ‘Read-and-delete-me’ file.
>> Once those are done, step 3 should succeed.
>>
>> Duncan Murdoch
>>
>>> Thanks,
>>>
>>> PS: I am sorry I missplet 'Program Files'. Thanks Prof. Ripley for this
>>> pointer.
>>>
>>> On Wed, Jun 1, 2011 at 11:41 AM, Prof Brian Ripley
>>> <ripley at stats.ox.ac.uk> wrote:
>>>> On Wed, 1 Jun 2011, Nipesh Bajaj wrote:
>>>>
>>>>> I have been struggling for last one hour but not yet any through.
>>>>>
>>>>> However again I recreate the package.skeleton and run R CMD check
>>>>> trial3
>>>>>
>>>>> Here are the errors:
>>>>>
>>>>> warning in dir.create(pkgoutdir, mode = "0755"):
>>>>> cannot create dir 'c:\Program files\R\R-2.13.0\bin\trial3.Rcheck',
>>>>> reason .................
>>>>> Error in printLog(Log, "", text, "\n"): object 'Log' not found
>>>>> Execution haulted
>>>>>
>>>>> Why I am getting this error? what is that "Log". I will really
>>>>> appreciate if somebody please help me to figure out.
>>>>
>>>> R CMD check writes a (in your case) trial3.Rcheck directory, and in
>>>> there in
>>>> file 00check.log a copy of the log. If it cannot create trial3.Rcheck
>>>> it
>>>> cannot write the log.
>>>>
>>>> I would be surprised that even on Windows Vista the message was
>>>> literally
>>>>
>>>>> reason .................
>>>>
>>>> but if it was, blame Microsoft for their error messages.
>>>> But
>>>>>
>>>>> cannot create dir 'c:\Program files\R\R-2.13.0\bin\trial3.Rcheck',
>>>>
>>>> is clear enough. You need to run 'R CMD check' in your user area.
>>>> In case you did this because that is where you though 'R' was, it is
>>>> not the
>>>> correct R.exe. You may need to add
>>>>
>>>> c:\Program Files\R\R-2.13.0\bin\i386
>>>>
>>>> (assuming 32-bit R) to your path.
>>>>
>>>> However, your use of e.g. 'Program files' suggests you are not
>>>> accurately
>>>> transmitting the messages you got.
>>>>
>>>>
>>>>>
>>>>> Thanks,
>>>>>
>>>>> On Wed, Jun 1, 2011 at 1:20 AM, Nipesh Bajaj<bajaj141003 at gmail.com>
>>>>> wrote:
>>>>>>
>>>>>> Actually partly I followed. Here is the more details what I have done
>>>>>> so
>>>>>> far:
>>>>>>
>>>>>> 1. Edit the help file skeletons in 'man', possibly combining help
>>>>>> files for multiple functions.
>>>>>> I have modified with following:
>>>>>> \name{fn1}
>>>>>> \alias{fn1}
>>>>>>
>>>>>> \title{
>>>>>> A function.
>>>>>> }
>>>>>>
>>>>>> \description{
>>>>>> A function.
>>>>>> }
>>>>>>
>>>>>> \usage{
>>>>>> A function.
>>>>>> }
>>>>>>
>>>>>> \arguments{
>>>>>> A function.
>>>>>> }
>>>>>>
>>>>>> \value{
>>>>>> A function.
>>>>>> }
>>>>>>
>>>>>> \author{
>>>>>> \bold{Me}
>>>>>> \cr
>>>>>> \email{Me at me.com}
>>>>>> }
>>>>>>
>>>>>> 2. Edit the exports in 'NAMESPACE', and add necessary imports.
>>>>>> Actually I really do not know what I would do here. In the
>>>>>> corresponding file, only "exportPattern("^[[:alpha:]]+")" is there.
>>>>>> Therefore I put that unaltered.
>>>>>>
>>>>>> 3. Put any C/C++/Fortran code in 'src'.
>>>>>> I do not have any such code
>>>>>>
>>>>>> 4. If you have compiled code, add a useDynLib() directive to
>>>>>> 'NAMESPACE'.
>>>>>> Again I do not know what to do, so ingored this step.
>>>>>>
>>>>>> 5. Run R CMD build to build the package tarball.
>>>>>> * Run R CMD check to check the package tarball.
>>>>>>
>>>>>> I did not follow this step exactly. What I done is, put 'trial3'
>>>>>> folder in R/R-2.13.0bin folder (after above modification), from the
>>>>>> R-working folder. Then just run R CMD INSTALL trial3. However
>>>>>> previously with this job, I could create package effectively. After
>>>>>> updating R to the current version my problem starts.
>>>>>>
>>>>>> Those are not sufficient?
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> On Wed, Jun 1, 2011 at 1:09 AM, Duncan
>>>>>> Murdoch<murdoch.duncan at gmail.com>
>>>>>> wrote:
>>>>>>>
>>>>>>> On 11-05-31 3:36 PM, Nipesh Bajaj wrote:
>>>>>>>>
>>>>>>>> Dear all, I am having a strage problem while I was trying to build
>>>>>>>> a
>>>>>>>> package. Here is my package skeleton:
>>>>>>>>
>>>>>>>> fn1<- Vectorize(function(x,y,z) {
>>>>>>>> return(x + y +z)
>>>>>>>> }, vectorize.args = c("x"), SIMPLIFY = TRUE)
>>>>>>>> package.skeleton("trial3",namespace = TRUE)
>>>>>>>
>>>>>>> Did you follow the instructions that package.skeleton printed?
>>>>>>>
>>>>>>> Duncan Murdoch
>>>>>>>
>>>>>>>>
>>>>>>>> However when I tun "R CMD INSTALL trial3" in CMD, the execution
>>>>>>>> stopped with following message:
>>>>>>>>
>>>>>>>> *** installing help indices
>>>>>>>> ** building package indices...
>>>>>>>> ** testing if install package can be loaded
>>>>>>>> Error: unexpected symbol in
>>>>>>>> "tools:::test_load_package(.............."
>>>>>>>> Execution haulted
>>>>>>>> ERROR: loading failed.............
>>>>>>>>
>>>>>>>> I am using R 2.13.0 in Vista with latest Rtools installed. Can
>>>>>>>> somebody guide me where I have done wrong?
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> ______________________________________________
>>>>>>>> R-help at r-project.org mailing list
>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>>>>> PLEASE do read the posting guide
>>>>>>>> http://www.R-project.org/posting-guide.html
>>>>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>> ______________________________________________
>>>>> R-help at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>> PLEASE do read the posting guide
>>>>> http://www.R-project.org/posting-guide.html
>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>>
>>>>
>>>> --
>>>> Brian D. Ripley, ripley at stats.ox.ac.uk
>>>> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
>>>> University of Oxford, Tel: +44 1865 272861 (self)
>>>> 1 South Parks Road, +44 1865 272866 (PA)
>>>> Oxford OX1 3TG, UK Fax: +44 1865 272595
>>
>>
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