From maechler at stat.math.ethz.ch  Tue Mar 25 09:57:06 2014
From: maechler at stat.math.ethz.ch (Martin Maechler)
Date: Tue, 25 Mar 2014 09:57:06 +0100
Subject: [Rd] "ERROR: installing package indices failed" message when
 building my package?
In-Reply-To: <CAKt-OfwjneoA7LyRX3g2N0FRx+euxcSqw=69ttTc+YWjo7Yo+Q@mail.gmail.com>
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>
	<CAKt-OfwjneoA7LyRX3g2N0FRx+euxcSqw=69ttTc+YWjo7Yo+Q@mail.gmail.com>
Message-ID: <21297.17634.981924.366289@stat.math.ethz.ch>

>>>>> Paul Geeleher <paulgeeleher at gmail.com>
>>>>>     on Mon, 24 Mar 2014 09:58:52 -0500 writes:

    > Hey Martin,
    > The output looks similar:

Well, of course
but I assumed you would know how to continue after the error
which should have "jumped into the debugger" with the following

    >> options(error=recover)
       ----------------------
    >> tools:::.build_packages("pRRophetic")

and I assumed you know how to inspect things once inside there ...


    > * 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?
Martin Maechler