From paulgeeleher at gmail.com  Mon Mar 24 15:58:52 2014
From: paulgeeleher at gmail.com (Paul Geeleher)
Date: Mon, 24 Mar 2014 09:58:52 -0500
Subject: [Rd] "ERROR: installing package indices failed" message when
 building my package?
In-Reply-To: <21296.17939.287540.684827@stat.math.ethz.ch>
References: <CAKt-OfzKGBBvPmrA1vhwh-oqXevj=QJrVLUc8J=93oDH+o33Hw@mail.gmail.com>
	<21296.3752.592995.240438@stat.math.ethz.ch>
	<CAKt-OfyKXVP2CGgBc6ivFYLig3OC39zr7wtF_0akPLGTJY3RqQ@mail.gmail.com>
	<21296.17939.287540.684827@stat.math.ethz.ch>
Message-ID: <CAKt-OfwjneoA7LyRX3g2N0FRx+euxcSqw=69ttTc+YWjo7Yo+Q@mail.gmail.com>

Hey Martin,

The output looks similar:


> options(error=recover)
> tools:::.build_packages("pRRophetic")
* checking for file 'pRRophetic/DESCRIPTION' ... OK
* preparing 'pRRophetic':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
      -----------------------------------
* installing *source* package 'pRRophetic' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by 'genefilter::Anova' when loading
'pRRophetic'
** help
*** installing help indices
** building package indices
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  line 1 did not have 38 elements
ERROR: installing package indices failed
* removing '/tmp/Rtmpe59RbM/Rinst54e22da5e85a/pRRophetic'
      -----------------------------------
ERROR: package installation failed



Thanks again,

Paul.


On Mon, Mar 24, 2014 at 9:49 AM, Martin Maechler
<maechler at stat.math.ethz.ch> wrote:
>>>>>> Paul Geeleher <paulgeeleher at gmail.com>
>>>>>>     on Mon, 24 Mar 2014 09:37:57 -0500 writes:
>
>     > Hey Martin,
>     > Thanks for your reply. I actually have documentation, but I pasted a
>     > version of the output that was created when I removed the .Rd files
>     > (as I suspected they may be causing the problem). Here's the output
>     > when the man files are all included (its more or less the same):
>
>
>     > $ R CMD build --verbose r_package_files/
>     > Warning: unknown option '--verbose'
>     > * checking for file 'r_package_files/DESCRIPTION' ... OK
>     > * preparing 'pRRophetic':
>     > * checking DESCRIPTION meta-information ... OK
>     > * installing the package to build vignettes
>     > -----------------------------------
>     > * installing *source* package 'pRRophetic' ...
>     > ** R
>     > ** data
>     > ** inst
>     > ** preparing package for lazy loading
>     > Warning: replacing previous import by 'genefilter::Anova' when loading
>     > 'pRRophetic'
>     > ** help
>     > *** installing help indices
>     > ** building package indices
>     > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
>     > line 1 did not have 38 elements
>
> I see. Now try
>
>     options(error=recover)
>     tools:::.build_packages("<your_source_package_path>/pRRophetic")
>
>
>     > ERROR: installing package indices failed
>     > * removing '/tmp/Rtmp6cwCZH/Rinst2f8f69e1ee/pRRophetic'
>



-- 
Dr. Paul Geeleher, PhD
Section of Hematology-Oncology
Department of Medicine
The University of Chicago
900 E. 57th St.,
KCBD, Room 7144
Chicago, IL 60637
--
www.bioinformaticstutorials.com



[Rd] "ERROR: installing package indices failed" message when building my package?
Paul Geeleher