<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">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 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 href="mailto:yurii@bionet.nsc.ru">yurii@bionet.nsc.ru</a>>, CRAN <<a 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 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 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 href="mailto:ripley@stats.ox.ac.uk">ripley@stats.ox.ac.uk</a><br>Professor of Applied Statistics, <a href="http://www.stats.ox.ac.uk/~ripley/">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></div></blockquote></div><br></div></body></html>