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<div class="moz-cite-prefix">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. <br>
<br>
best,<br>
Maksim<br>
<br>
On 09/12/2013 19:02, Maarten Kooyman wrote:<br>
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<blockquote cite="mid:52A5B13A.7070908@erasmusmc.nl" type="cite">
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<div class="moz-cite-prefix">Dear all,<br>
<br>
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 <a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="http://www.karssen.org/jenkins/">http://www.karssen.org/jenkins/</a>)<br>
<br>
Kind regards,<br>
<br>
<pre class="moz-signature" cols="72">Maarten Kooyman
Erasmus MC
Department of Epidemiology
</pre>
On 12/09/2013 12:42 PM, Yury Aulchenko wrote:<br>
</div>
<blockquote
cite="mid:16B1D7C9-4E21-4B1F-B9E0-E3FA36DC36FC@gmail.com"
type="cite">
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charset=ISO-8859-1">
Getting many comments from prof. Ripley
<div><br>
</div>
<div>he does not sound very happy</div>
<div><br>
</div>
<div>Yurii<br>
<div><br>
<div>Begin forwarded message:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px;"><span
style="font-family:'Helvetica'; color:rgba(0, 0, 0,
1.0);"><b>From: </b></span><span
style="font-family:'Helvetica';">Prof Brian Ripley
<<a moz-do-not-send="true"
href="mailto:ripley@stats.ox.ac.uk">ripley@stats.ox.ac.uk</a>><br>
</span></div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px;"><span
style="font-family:'Helvetica'; color:rgba(0, 0, 0,
1.0);"><b>Subject: </b></span><span
style="font-family:'Helvetica';"><b>Re: CRAN
submission GenABEL 1.8-0</b><br>
</span></div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px;"><span
style="font-family:'Helvetica'; color:rgba(0, 0, 0,
1.0);"><b>Date: </b></span><span
style="font-family:'Helvetica';">December 9, 2013 at
12:28:15 PM GMT+1<br>
</span></div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px;"><span
style="font-family:'Helvetica'; color:rgba(0, 0, 0,
1.0);"><b>To: </b></span><span
style="font-family:'Helvetica';">Yurii Aulchenko <<a
moz-do-not-send="true"
href="mailto:yurii@bionet.nsc.ru">yurii@bionet.nsc.ru</a>>,
CRAN <<a moz-do-not-send="true"
href="mailto:cran@r-project.org">cran@r-project.org</a>><br>
</span></div>
<br>
<div>On 09/12/2013 09:49, Yurii Aulchenko wrote:<br>
<blockquote type="cite">[This was generated from <a
moz-do-not-send="true"
href="http://CRAN.R-project.org/submit.html]">CRAN.R-project.org/submit.html]</a><br>
<br>
The following package was uploaded to CRAN:<br>
===========================================<br>
<br>
Package Information:<br>
Package: GenABEL<br>
Version: 1.8-0<br>
Title: genome-wide SNP association analysis<br>
Author(s): GenABEL project developers<br>
Maintainer: Yurii Aulchenko <<a
moz-do-not-send="true"
href="mailto:yurii@bionet.nsc.ru">yurii@bionet.nsc.ru</a>><br>
Depends: R (>= 2.15.0), methods, MASS, utils,
GenABEL.data<br>
Suggests: qvalue, genetics, haplo.stats, DatABEL
(>= 0.9-0), hglm,<br>
MetABEL, PredictABEL, VariABEL, bigRR<br>
Description: a package for genome-wide association
analysis between<br>
quantitative or binary traits and single-nucleotide<br>
polymorphisms (SNPs).<br>
License: GPL (>= 2)<br>
<br>
<br>
The maintainer confirms that he or she<br>
has read and agrees to the CRAN policies.<br>
<br>
Submitter's comment: In this version of GenABEL, the
data is moved to a<br>
specially created new packaged called GenABEL.data<br>
(which was uploaded on CRAN earlier today).<br>
Additioanlly, memory leak is fixed for a number of<br>
functions and unused variables are deleted.<br>
</blockquote>
<br>
That package did not comply with the CRAN policies. You
need to re-submit if it is accepted.<br>
<br>
We see<br>
<br>
* checking foreign function calls ... NOTE<br>
Foreign function call to a different package:<br>
.Call("iterator", ..., PACKAGE = "DatABEL")<br>
<br>
Why can an R wrapper not be exported from DatABEL?<br>
<br>
* checking sizes of PDF files under ‘inst/doc’ ...
WARNING<br>
‘gs+qpdf’ made some significant size reductions:<br>
compacted ‘GenABEL-tutorial.pdf’ from 4.2Mb to 2.2Mb<br>
consider running tools::compactPDF(gs_quality =
"ebook") on these files<br>
<br>
which is a lot. Please re-think your use of figures: at
least one (ca p188) is full of overlapping symbols.<br>
<br>
And this fails to install with clang/libcxx as reported
before:<br>
<br>
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<br>
convert_snp_illumina.cpp:70:14: warning: comparison
between NULL and non-pointer ('ifstream' (aka
'basic_ifstream<char>') and NULL)
[-Wnull-arithmetic]<br>
if (illfile == NULL) {<br>
~~~~~~~ ^ ~~~~<br>
convert_snp_illumina.cpp:70:14: error: invalid operands
to binary expression ('ifstream' (aka
'basic_ifstream<char>') and 'long')<br>
if (illfile == NULL) {<br>
~~~~~~~ ^ ~~~~<br>
convert_snp_illumina.cpp:270:14: warning: comparison
between NULL and non-pointer ('ofstream' (aka
'basic_ofstream<char>') and NULL)
[-Wnull-arithmetic]<br>
if (outfile == NULL) {<br>
~~~~~~~ ^ ~~~~<br>
convert_snp_illumina.cpp:270:14: error: invalid operands
to binary expression ('ofstream' (aka
'basic_ofstream<char>') and 'long')<br>
if (outfile == NULL) {<br>
~~~~~~~ ^ ~~~~<br>
2 warnings and 2 errors generated.<br>
<br>
You really do need to do this as per the C++ standard
(check outfile.bad()?)<br>
<br>
Please show more respect for our time: all of these
reports could have been avoided by following the CRAN
policies.<br>
<br>
<br>
-- <br>
Brian D. Ripley, <a
moz-do-not-send="true"
href="mailto:ripley@stats.ox.ac.uk">ripley@stats.ox.ac.uk</a><br>
Professor of Applied Statistics, <a
moz-do-not-send="true"
href="http://www.stats.ox.ac.uk/%7Eripley/">http://www.stats.ox.ac.uk/~ripley/</a><br>
University of Oxford, Tel: +44 1865 272861
(self)<br>
1 South Parks Road, +44 1865 272866
(PA)<br>
Oxford OX1 3TG, UK Fax: +44 1865 272595<br>
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