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

[Maarten Kooyman]

Dear all,

I think it is a smart move to add a clang/libcxx pipeline in Jenkins.
This prevents future rejection of CRAN submissions because something
does not build (Wich is pretty good and easy to test). It is inhuman to 
ask that every developer compiles their software with a bunch of
different compilers. But you can let a butler named Jenkins do this kind
of work.(a pic of our butler is visible at the left side of
http://www.karssen.org/jenkins/)

Kind regards,

Maarten Kooyman
Erasmus MC
Department of Epidemiology

On 12/09/2013 12:42 PM, Yury Aulchenko wrote:
> 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
>> <mailto: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
>> <mailto:yurii at bionet.nsc.ru>>, CRAN <cran at r-project.org
>> <mailto:cran at r-project.org>>
>>
>> On 09/12/2013 09:49, Yurii Aulchenko wrote:
>>> [This was generated from CRAN.R-project.org/submit.html]
>>> <http://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
>>> <mailto: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
>> <mailto:ripley at stats.ox.ac.uk>
>> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
>> <http://www.stats.ox.ac.uk/%7Eripley/>
>> 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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