[GenABEL-dev] Fwd: CRAN submission GenABEL 1.8-0

[Yury Aulchenko]

Getting many comments from prof. Ripley

he does not sound very happy

Yurii

Begin forwarded message:

> From: Prof Brian Ripley <ripley at stats.ox.ac.uk>
> Subject: Re: CRAN submission GenABEL 1.8-0
> Date: December 9, 2013 at 12:28:15 PM GMT+1
> To: Yurii Aulchenko <yurii at bionet.nsc.ru>, CRAN <cran at r-project.org>
> 
> On 09/12/2013 09:49, Yurii Aulchenko wrote:
>> [This was generated from CRAN.R-project.org/submit.html]
>> 
>> The following package was uploaded to CRAN:
>> ===========================================
>> 
>> Package Information:
>> Package: GenABEL
>> Version: 1.8-0
>> Title: genome-wide SNP association analysis
>> Author(s): GenABEL project developers
>> Maintainer: Yurii Aulchenko <yurii at bionet.nsc.ru>
>> Depends: R (>= 2.15.0), methods, MASS, utils, GenABEL.data
>> Suggests: qvalue, genetics, haplo.stats, DatABEL (>= 0.9-0), hglm,
>>   MetABEL, PredictABEL, VariABEL, bigRR
>> Description: a package for genome-wide association analysis between
>>   quantitative or binary traits and single-nucleotide
>>   polymorphisms (SNPs).
>> License: GPL (>= 2)
>> 
>> 
>> The maintainer confirms that he or she
>> has read and agrees to the CRAN policies.
>> 
>> Submitter's comment: In this version of GenABEL, the data is moved to a
>>   specially created new packaged called GenABEL.data
>>   (which was uploaded on CRAN earlier today).
>>   Additioanlly, memory leak is fixed for a number of
>>   functions and unused variables are deleted.
> 
> That package did not comply with the CRAN policies.  You need to re-submit if it is accepted.
> 
> We see
> 
> * checking foreign function calls ... NOTE
> Foreign function call to a different package:
>  .Call("iterator", ..., PACKAGE = "DatABEL")
> 
> Why can an R wrapper not be exported from DatABEL?
> 
> * checking sizes of PDF files under ‘inst/doc’ ... WARNING
>  ‘gs+qpdf’ made some significant size reductions:
>     compacted ‘GenABEL-tutorial.pdf’ from 4.2Mb to 2.2Mb
>  consider running tools::compactPDF(gs_quality = "ebook") on these files
> 
> which is a lot.  Please re-think your use of figures: at least one (ca p188) is full of overlapping symbols.
> 
> And this fails to install with clang/libcxx as reported before:
> 
> clang++ -std=c++11 -stdlib=libc++ -fsanitize=undefined -fno-omit-frame-pointer -I/data/gannet/ripley/R/R-clang2/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2 -Wall -pedantic -mtune=native  -c convert_snp_illumina.cpp -o convert_snp_illumina.o
> convert_snp_illumina.cpp:70:14: warning: comparison between NULL and non-pointer ('ifstream' (aka 'basic_ifstream<char>') and NULL) [-Wnull-arithmetic]
>        if (illfile == NULL) {
>            ~~~~~~~ ^  ~~~~
> convert_snp_illumina.cpp:70:14: error: invalid operands to binary expression ('ifstream' (aka 'basic_ifstream<char>') and 'long')
>        if (illfile == NULL) {
>            ~~~~~~~ ^  ~~~~
> convert_snp_illumina.cpp:270:14: warning: comparison between NULL and non-pointer ('ofstream' (aka 'basic_ofstream<char>') and NULL) [-Wnull-arithmetic]
>        if (outfile == NULL) {
>            ~~~~~~~ ^  ~~~~
> convert_snp_illumina.cpp:270:14: error: invalid operands to binary expression ('ofstream' (aka 'basic_ofstream<char>') and 'long')
>        if (outfile == NULL) {
>            ~~~~~~~ ^  ~~~~
> 2 warnings and 2 errors generated.
> 
> You really do need to do this as per the C++ standard (check outfile.bad()?)
> 
> Please show more respect for our time: all of these reports could have been avoided by following the CRAN policies.
> 
> 
> -- 
> 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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