[R] Problem with package development
Nipesh Bajaj
bajaj141003 at gmail.com
Thu Jun 2 21:21:10 CEST 2011
I have run R CMD check trial1 and saw an error. This says that:
* checking pdf version of manual without hyperrefs or index ... ERROR
Re-running with no redirection of stdout/stderr.
Hmm... looks like a package
Error in texi2dvi("Rd2.tex", pdf = (out_ext == "pdf"), quiet = FALSE, :
pdflatex is not available
Error in running tools:: texi2dvi
Does this information hwlp you to suggest something? Please let me
know what else I can provide.
Thanks,
On Fri, Jun 3, 2011 at 12:00 AM, Nipesh Bajaj <bajaj141003 at gmail.com> 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:
> \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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