CRAN Package Check Results for Maintainer ‘Lachlan Coin <l.coin at imb.uq.edu.au>’

Last updated on 2024-12-22 13:49:14 CET.

Package	NOTE
MultiPhen	13

Package MultiPhen

Current CRAN status:

Version: 2.0.3
Check: Rd files
Result: NOTE checkRd: (-1) mPhen.defineOptions.Rd:4: Escaped LaTeX specials: \$ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 2.0.3
Check: re-building of vignette outputs
Result: NOTE Error(s) in re-building vignettes: --- re-building ‘MultiPhen.Rnw’ using Sweave Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.2-1). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning in betasg/normg : Recycling array of length 1 in vector-array arithmetic is deprecated. Use c() or as.vector() instead. Warning in betasg/normg : Recycling array of length 1 in vector-array arithmetic is deprecated. Use c() or as.vector() instead. Warning in betasg/normg : Recycling array of length 1 in vector-array arithmetic is deprecated. Use c() or as.vector() instead. Warning in plot.window(...) : "na.color" is not a graphical parameter Warning in plot.window(...) : "dendrogram" is not a graphical parameter Warning in plot.window(...) : "density.info" is not a graphical parameter Warning in plot.window(...) : "trace" is not a graphical parameter Warning in plot.window(...) : "key" is not a graphical parameter Warning in plot.window(...) : "symbreaks" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "na.color" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "dendrogram" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "density.info" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "trace" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "symbreaks" is not a graphical parameter Warning in title(...) : "na.color" is not a graphical parameter Warning in title(...) : "dendrogram" is not a graphical parameter Warning in title(...) : "density.info" is not a graphical parameter Warning in title(...) : "trace" is not a graphical parameter Warning in title(...) : "key" is not a graphical parameter Warning in title(...) : "symbreaks" is not a graphical parameter Warning in plot.window(...) : "na.color" is not a graphical parameter Warning in plot.window(...) : "dendrogram" is not a graphical parameter Warning in plot.window(...) : "density.info" is not a graphical parameter Warning in plot.window(...) : "trace" is not a graphical parameter Warning in plot.window(...) : "key" is not a graphical parameter Warning in plot.window(...) : "symbreaks" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "na.color" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "dendrogram" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "density.info" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "trace" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "symbreaks" is not a graphical parameter Warning in title(...) : "na.color" is not a graphical parameter Warning in title(...) : "dendrogram" is not a graphical parameter Warning in title(...) : "density.info" is not a graphical parameter Warning in title(...) : "trace" is not a graphical parameter Warning in title(...) : "key" is not a graphical parameter Warning in title(...) : "symbreaks" is not a graphical parameter Warning in .heatm(outC$beta, effPhe, logfun1, opts, TRUE, filek) : unable to make heatmap resultsDir/resultsJoint.heatm.pdf all all beta Warning in max(abs(as.vector(res[, snpinds, , 1]))[pvs < 0.05], na.rm = T) : no non-missing arguments to max; returning -Inf Warning in plot.window(...) : "na.color" is not a graphical parameter Warning in plot.window(...) : "dendrogram" is not a graphical parameter Warning in plot.window(...) : "density.info" is not a graphical parameter Warning in plot.window(...) : "trace" is not a graphical parameter Warning in plot.window(...) : "key" is not a graphical parameter Warning in plot.window(...) : "symbreaks" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "na.color" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "dendrogram" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "density.info" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "trace" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "symbreaks" is not a graphical parameter Warning in title(...) : "na.color" is not a graphical parameter Warning in title(...) : "dendrogram" is not a graphical parameter Warning in title(...) : "density.info" is not a graphical parameter Warning in title(...) : "trace" is not a graphical parameter Warning in title(...) : "key" is not a graphical parameter Warning in title(...) : "symbreaks" is not a graphical parameter Warning in plot.window(...) : "na.color" is not a graphical parameter Warning in plot.window(...) : "dendrogram" is not a graphical parameter Warning in plot.window(...) : "density.info" is not a graphical parameter Warning in plot.window(...) : "trace" is not a graphical parameter Warning in plot.window(...) : "key" is not a graphical parameter Warning in plot.window(...) : "symbreaks" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "na.color" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "dendrogram" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "density.info" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "trace" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "symbreaks" is not a graphical parameter Warning in title(...) : "na.color" is not a graphical parameter Warning in title(...) : "dendrogram" is not a graphical parameter Warning in title(...) : "density.info" is not a graphical parameter Warning in title(...) : "trace" is not a graphical parameter Warning in title(...) : "key" is not a graphical parameter Warning in title(...) : "symbreaks" is not a graphical parameter Warning in .heatm(outC$beta, effPhe, logfun1, opts, TRUE, filek) : unable to make heatmap resultsDir/resultsBackwardSelection.heatm.pdf all all beta Warning in plot.window(...) : "na.color" is not a graphical parameter Warning in plot.window(...) : "dendrogram" is not a graphical parameter Warning in plot.window(...) : "density.info" is not a graphical parameter Warning in plot.window(...) : "trace" is not a graphical parameter Warning in plot.window(...) : "key" is not a graphical parameter Warning in plot.window(...) : "symbreaks" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "na.color" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "dendrogram" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "density.info" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "trace" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "symbreaks" is not a graphical parameter Warning in title(...) : "na.color" is not a graphical parameter Warning in title(...) : "dendrogram" is not a graphical parameter Warning in title(...) : "density.info" is not a graphical parameter Warning in title(...) : "trace" is not a graphical parameter Warning in title(...) : "key" is not a graphical parameter Warning in title(...) : "symbreaks" is not a graphical parameter Warning in plot.window(...) : "na.color" is not a graphical parameter Warning in plot.window(...) : "dendrogram" is not a graphical parameter Warning in plot.window(...) : "density.info" is not a graphical parameter Warning in plot.window(...) : "trace" is not a graphical parameter Warning in plot.window(...) : "key" is not a graphical parameter Warning in plot.window(...) : "symbreaks" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "na.color" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "dendrogram" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "density.info" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "trace" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "symbreaks" is not a graphical parameter Warning in title(...) : "na.color" is not a graphical parameter Warning in title(...) : "dendrogram" is not a graphical parameter Warning in title(...) : "density.info" is not a graphical parameter Warning in title(...) : "trace" is not a graphical parameter Warning in title(...) : "key" is not a graphical parameter Warning in title(...) : "symbreaks" is not a graphical parameter Warning in .manhattan(topl, logfun, beta1 = NULL, paste(opts$mPhen.title, : NAs introduced by coercion Warning in plot.window(...) : "na.color" is not a graphical parameter Warning in plot.window(...) : "dendrogram" is not a graphical parameter Warning in plot.window(...) : "density.info" is not a graphical parameter Warning in plot.window(...) : "trace" is not a graphical parameter Warning in plot.window(...) : "key" is not a graphical parameter Warning in plot.window(...) : "symbreaks" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "na.color" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "dendrogram" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "density.info" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "trace" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "symbreaks" is not a graphical parameter Warning in title(...) : "na.color" is not a graphical parameter Warning in title(...) : "dendrogram" is not a graphical parameter Warning in title(...) : "density.info" is not a graphical parameter Warning in title(...) : "trace" is not a graphical parameter Warning in title(...) : "key" is not a graphical parameter Warning in title(...) : "symbreaks" is not a graphical parameter Warning in plot.window(...) : "na.color" is not a graphical parameter Warning in plot.window(...) : "dendrogram" is not a graphical parameter Warning in plot.window(...) : "density.info" is not a graphical parameter Warning in plot.window(...) : "trace" is not a graphical parameter Warning in plot.window(...) : "key" is not a graphical parameter Warning in plot.window(...) : "symbreaks" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "na.color" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "dendrogram" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "density.info" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "trace" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "symbreaks" is not a graphical parameter Warning in title(...) : "na.color" is not a graphical parameter Warning in title(...) : "dendrogram" is not a graphical parameter Warning in title(...) : "density.info" is not a graphical parameter Warning in title(...) : "trace" is not a graphical parameter Warning in title(...) : "key" is not a graphical parameter Warning in title(...) : "symbreaks" is not a graphical parameter Warning in betag/(betag %*% betag) : Recycling array of length 1 in vector-array arithmetic is deprecated. Use c() or as.vector() instead. Error: processing vignette 'MultiPhen.Rnw' failed with diagnostics: Running 'texi2dvi' on 'MultiPhen.tex' failed. LaTeX errors: ! LaTeX Error: File `underscore.sty' not found. Type X to quit or <RETURN> to proceed, or enter new name. (Default extension: sty) ! Emergency stop. <read *> l.12 \usepackage {Sweave}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘MultiPhen.Rnw’ SUMMARY: processing the following file failed: ‘MultiPhen.Rnw’ Error: Vignette re-building failed. Execution halted Flavor: r-oldrel-macos-x86_64