* using log directory 'd:/Rcompile/CRANpkg/local/2.11/haplo.stats.Rcheck' * using R version 2.11.1 Patched (2010-07-29 r52657) * using session charset: ISO8859-1 * checking for file 'haplo.stats/DESCRIPTION' ... OK * this is package 'haplo.stats' version '1.4.4' * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'haplo.stats' can be installed ... OK * checking package directory ... OK * checking for portable file names ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking for unstated dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE glm.fit.nowarn: no visible binding for global variable 'n' haplo.glm: no visible binding for global variable 'eta' haplo.glm: no visible binding for global variable 'response' haplo.glm: no visible global function definition for 'as.family' * checking Rd files ... NOTE prepare_Rd: Ginv.Rd:107: Dropping empty section \keyword prepare_Rd: Ginv.Rd:76-78: Dropping empty section 'Side Effects' prepare_Rd: chisq.power.Rd:61: Dropping empty section \keyword prepare_Rd: chisq.power.Rd:49-51: Dropping empty section \details prepare_Rd: chisq.power.Rd:46-48: Dropping empty section 'Side Effects' prepare_Rd: chisq.power.Rd:52-54: Dropping empty section 'References' prepare_Rd: chisq.power.Rd:55-57: Dropping empty section \seealso prepare_Rd: chisq.power.Rd:58-60: Dropping empty section \examples prepare_Rd: f.power.Rd:61: Dropping empty section \keyword prepare_Rd: f.power.Rd:50-52: Dropping empty section \details prepare_Rd: f.power.Rd:47-49: Dropping empty section 'Side Effects' prepare_Rd: f.power.Rd:53-55: Dropping empty section 'References' prepare_Rd: f.power.Rd:56-57: Dropping empty section \seealso prepare_Rd: f.power.Rd:58-60: Dropping empty section \examples prepare_Rd: find.haplo.beta.qt.Rd:69: Dropping empty section \keyword prepare_Rd: find.haplo.beta.qt.Rd:57-59: Dropping empty section \details prepare_Rd: find.haplo.beta.qt.Rd:52-53: Dropping empty section \value prepare_Rd: find.haplo.beta.qt.Rd:54-56: Dropping empty section 'Side Effects' prepare_Rd: find.haplo.beta.qt.Rd:60-62: Dropping empty section 'References' prepare_Rd: find.haplo.beta.qt.Rd:63-65: Dropping empty section \seealso prepare_Rd: find.haplo.beta.qt.Rd:66-68: Dropping empty section \examples prepare_Rd: geno.count.pairs.Rd:97: Dropping empty section \keyword prepare_Rd: geno.count.pairs.Rd:63-65: Dropping empty section 'Side Effects' prepare_Rd: haplo.em.control.Rd:139: Dropping empty section \keyword prepare_Rd: haplo.em.control.Rd:116-118: Dropping empty section 'Side Effects' prepare_Rd: haplo.em.control.Rd:127-129: Dropping empty section 'References' prepare_Rd: haplo.em.fitter.Rd:96: Dropping empty section \keyword prepare_Rd: haplo.em.fitter.Rd:79-80: Dropping empty section \value prepare_Rd: haplo.em.fitter.Rd:81-83: Dropping empty section 'Side Effects' prepare_Rd: haplo.em.fitter.Rd:87-89: Dropping empty section 'References' prepare_Rd: haplo.em.fitter.Rd:90-92: Dropping empty section \seealso prepare_Rd: haplo.em.fitter.Rd:93-95: Dropping empty section \examples prepare_Rd: haplo.glm.Rd:395: Dropping empty section \keyword prepare_Rd: haplo.glm.control.Rd:114: Dropping empty section \keyword prepare_Rd: haplo.group.Rd:141: Dropping empty section \keyword prepare_Rd: haplo.group.Rd:109-111: Dropping empty section 'Side Effects' prepare_Rd: haplo.hash.Rd:62: Dropping empty section \keyword prepare_Rd: haplo.hash.Rd:44-46: Dropping empty section 'Side Effects' prepare_Rd: haplo.hash.Rd:53-55: Dropping empty section 'References' prepare_Rd: haplo.hash.Rd:59-61: Dropping empty section \examples prepare_Rd: haplo.score.Rd:292: Dropping empty section \keyword prepare_Rd: haplo.score.Rd:223-225: Dropping empty section 'Side Effects' prepare_Rd: haplo.score.merge.Rd:87: Dropping empty section \keyword prepare_Rd: haplo.score.slide.Rd:236: Dropping empty section \keyword prepare_Rd: haplo.score.slide.Rd:181-183: Dropping empty section 'Side Effects' prepare_Rd: hla.demo.Rd:51-53: Dropping empty section \details prepare_Rd: locator.haplo.Rd:74: Dropping empty section \keyword prepare_Rd: loci.Rd:124: Dropping empty section \keyword prepare_Rd: loci.Rd:94-96: Dropping empty section \details prepare_Rd: loci.Rd:91-93: Dropping empty section 'Side Effects' prepare_Rd: loci.Rd:97-99: Dropping empty section 'References' prepare_Rd: locus.Rd:86-88: Dropping empty section \details prepare_Rd: locus.Rd:83-85: Dropping empty section 'Side Effects' prepare_Rd: locus.Rd:89-91: Dropping empty section 'References' prepare_Rd: locus.Rd:92-94: Dropping empty section \seealso prepare_Rd: na.geno.keep.Rd:45: Dropping empty section \keyword prepare_Rd: na.geno.keep.Rd:33-35: Dropping empty section \details prepare_Rd: na.geno.keep.Rd:28-29: Dropping empty section \value prepare_Rd: na.geno.keep.Rd:30-32: Dropping empty section 'Side Effects' prepare_Rd: na.geno.keep.Rd:36-38: Dropping empty section 'References' prepare_Rd: na.geno.keep.Rd:39-41: Dropping empty section \seealso prepare_Rd: na.geno.keep.Rd:42-44: Dropping empty section \examples prepare_Rd: plot.haplo.score.Rd:87: Dropping empty section \keyword prepare_Rd: plot.haplo.score.Rd:54-56: Dropping empty section 'Side Effects' prepare_Rd: plot.haplo.score.slide.Rd:139: Dropping empty section \keyword prepare_Rd: plot.haplo.score.slide.Rd:96-98: Dropping empty section 'Side Effects' prepare_Rd: plot.seqhap.Rd:114: Dropping empty section \keyword prepare_Rd: plot.seqhap.Rd:84-86: Dropping empty section 'Side Effects' prepare_Rd: print.haplo.cc.Rd:77: Dropping empty section \keyword prepare_Rd: print.haplo.cc.Rd:66-68: Dropping empty section \details prepare_Rd: print.haplo.cc.Rd:63-65: Dropping empty section 'Side Effects' prepare_Rd: print.haplo.em.Rd:66: Dropping empty section \keyword prepare_Rd: print.haplo.em.Rd:54-56: Dropping empty section \details prepare_Rd: print.haplo.em.Rd:51-53: Dropping empty section 'Side Effects' prepare_Rd: print.haplo.em.Rd:57-59: Dropping empty section 'References' prepare_Rd: print.haplo.em.Rd:63-65: Dropping empty section \examples prepare_Rd: print.haplo.glm.Rd:70: Dropping empty section \keyword prepare_Rd: print.haplo.glm.Rd:58-60: Dropping empty section \details prepare_Rd: print.haplo.glm.Rd:55-57: Dropping empty section 'Side Effects' prepare_Rd: print.haplo.glm.Rd:61-63: Dropping empty section 'References' prepare_Rd: print.haplo.glm.Rd:67-69: Dropping empty section \examples prepare_Rd: print.haplo.group.Rd:77: Dropping empty section \keyword prepare_Rd: print.haplo.group.Rd:56-58: Dropping empty section 'Side Effects' prepare_Rd: print.haplo.group.Rd:74-76: Dropping empty section \examples prepare_Rd: print.haplo.scan.Rd:54: Dropping empty section \keyword prepare_Rd: print.haplo.scan.Rd:42-44: Dropping empty section \details prepare_Rd: print.haplo.scan.Rd:39-41: Dropping empty section 'Side Effects' prepare_Rd: print.haplo.scan.Rd:45-47: Dropping empty section 'References' prepare_Rd: print.haplo.scan.Rd:51-53: Dropping empty section \examples prepare_Rd: print.haplo.score.Rd:74: Dropping empty section \keyword prepare_Rd: print.haplo.score.Rd:59-61: Dropping empty section 'Side Effects' prepare_Rd: print.haplo.score.Rd:71-73: Dropping empty section \examples prepare_Rd: print.haplo.score.merge.Rd:110: Dropping empty section \keyword prepare_Rd: print.haplo.score.merge.Rd:89-91: Dropping empty section 'Side Effects' prepare_Rd: print.haplo.score.slide.Rd:51: Dropping empty section \keyword prepare_Rd: print.haplo.score.slide.Rd:39-41: Dropping empty section \details prepare_Rd: print.haplo.score.slide.Rd:34-35: Dropping empty section \value prepare_Rd: print.haplo.score.slide.Rd:36-38: Dropping empty section 'Side Effects' prepare_Rd: print.haplo.score.slide.Rd:42-44: Dropping empty section 'References' prepare_Rd: print.haplo.score.slide.Rd:45-47: Dropping empty section \seealso prepare_Rd: print.haplo.score.slide.Rd:48-50: Dropping empty section \examples prepare_Rd: print.seqhap.Rd:59: Dropping empty section \keyword prepare_Rd: print.seqhap.Rd:47-49: Dropping empty section \details prepare_Rd: print.seqhap.Rd:44-46: Dropping empty section 'Side Effects' prepare_Rd: print.seqhap.Rd:50-52: Dropping empty section 'References' prepare_Rd: print.seqhap.Rd:56-58: Dropping empty section \examples prepare_Rd: printBanner.Rd:81: Dropping empty section \keyword prepare_Rd: printBanner.Rd:59-60: Dropping empty section \value prepare_Rd: printBanner.Rd:61-63: Dropping empty section 'Side Effects' prepare_Rd: printBanner.Rd:67-69: Dropping empty section 'References' prepare_Rd: score.sim.control.Rd:110: Dropping empty section \keyword prepare_Rd: score.sim.control.Rd:84-86: Dropping empty section 'Side Effects' prepare_Rd: seqhap.Rd:207: Dropping empty section \keyword prepare_Rd: seqhap.Rd:182-184: Dropping empty section \details prepare_Rd: seqhap.Rd:179-181: Dropping empty section 'Side Effects' prepare_Rd: setupData.Rd:48: Dropping empty section \keyword prepare_Rd: setupData.Rd:32-34: Dropping empty section \details prepare_Rd: setupData.Rd:27-28: Dropping empty section \value prepare_Rd: setupData.Rd:29-31: Dropping empty section 'Side Effects' prepare_Rd: setupData.Rd:35-37: Dropping empty section 'References' prepare_Rd: setupData.Rd:38-40: Dropping empty section \seealso prepare_Rd: setupGeno.Rd:84: Dropping empty section \keyword prepare_Rd: setupGeno.Rd:54-56: Dropping empty section \details prepare_Rd: setupGeno.Rd:51-53: Dropping empty section 'Side Effects' prepare_Rd: setupGeno.Rd:57-59: Dropping empty section 'References' prepare_Rd: summary.haplo.em.Rd:66: Dropping empty section \keyword prepare_Rd: summary.haplo.em.Rd:54-56: Dropping empty section \details prepare_Rd: summary.haplo.em.Rd:49-50: Dropping empty section \value prepare_Rd: summary.haplo.em.Rd:51-53: Dropping empty section 'Side Effects' prepare_Rd: summary.haplo.em.Rd:57-59: Dropping empty section 'References' prepare_Rd: summary.haplo.em.Rd:63-65: Dropping empty section \examples prepare_Rd: summaryGeno.Rd:66: Dropping empty section \keyword prepare_Rd: summaryGeno.Rd:49-51: Dropping empty section 'Side Effects' prepare_Rd: summaryGeno.Rd:63-65: Dropping empty section \examples prepare_Rd: x.sexcheck.Rd:62: Dropping empty section \keyword prepare_Rd: x.sexcheck.Rd:44-46: Dropping empty section \details prepare_Rd: x.sexcheck.Rd:41-43: Dropping empty section 'Side Effects' prepare_Rd: x.sexcheck.Rd:47-49: Dropping empty section 'References' * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking data for non-ASCII characters ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for portable use of $BLAS_LIBS ... OK * checking examples ... OK * checking PDF version of manual ... OK