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

Mon Dec 9 14:09:59 CET 2013

Looks like this is how we should deal with it. If they use clang/libcxx 
for compiling GenABEL code then we have to do the same.

best,
Maksim

On 09/12/2013 19:02, Maarten Kooyman wrote:
> 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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>
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