R Development Page

ssize log file (check_x86_64_linux)

Tue May 26 12:46:39 2015: Checking package ssize (SVN revision 1196) ...
* using log directory ‘/mnt/building/build_2015-05-26-12-43/RF_PKG_CHECK/PKGS/ssize.Rcheck’
* using R version 3.2.0 Patched (2015-05-25 r68412)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘ssize/DESCRIPTION’ ... OK
* this is package ‘ssize’ version ‘1.1.1’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Gregory R. Warnes ’

Package duplicated from http://bioconductor.org/packages/3.1/bioc

Vignette sources in 'inst/doc' with no 'vignettes' directory:
  ‘ssize.Rnw’
A 'vignettes' directory is required as from R 3.1.0
Found the following (possibly) invalid URLs:
  URL: http://www.warnes.net/Research/PresentationFolder/SampleSize.pdf
    From: man/pow.Rd
    Status: 404
    Message: Not Found
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ssize’ can be installed ... [2s/2s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘gdata’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘ssize/R/First_lib.R’:
  .First.lib calls:
    library(stats)
    library(gdata)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

crit.fn: warning in pt(crit, df, lower = FALSE): partial argument match
  of 'lower' to 'lower.tail'
crit.fn: warning in pt(crit, df, ncp = ncp, lower = FALSE): partial
  argument match of 'lower' to 'lower.tail'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'power.t.test.FDR.Rd':
  ‘t.test.FDR’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘crit.fn’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Bad \usage lines found in documentation object 'power.t.test.FDR':
  power.t.test.FDR <- function (sd=1, n=NULL, delta=NULL,
                                FDR.level=0.05,
                                pi0,
                                power=NULL, 
                                type=c("two.sample", "one.sample", "paired"),
                                alternative=c("two.sided", "one.sided")) 

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following files contain a license that requires
distribution of original sources:
  ‘crop.sty’
Please ensure that you have complied with it.
The following files should probably not be installed:
  ‘alltt.sty’, ‘array.sty’, ‘biometrics.bst’, ‘biometrics2.sty’,
  ‘chngpage.sty’, ‘color.sty’, ‘crop.sty’, ‘float.sty’, ‘flushend.sty’,
  ‘graphicx.sty’, ‘hyperref.sty’, ‘landscap.sty’, ‘natbib.sty’,
  ‘rmgreek.sty’, ‘stfloats.sty’, ‘times.sty’, ‘url.sty’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘ssize.Rnw’
A ‘vignettes’ directory is required as from R 3.1.0
and these will not be indexed nor checked
* checking examples ... ERROR
Running examples in ‘ssize-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pow
> ### Title: Compute and plot power, reqired sample-size, or detectible
> ###   effect size for gene expression experiment
> ### Aliases: pow power.plot ssize ssize.plot delta delta.plot
> ### Keywords: htest design
> 
> ### ** Examples
> 
> library(gdata) # for nobs()
> 
> data(exp.sd)
> ## Don't show: 
> exp.sd <- exp.sd[1:1000]  # so calculations are more
>                           # speedy during tests
> ## End(Don't show)
> 
> # Histogram of the standard deviations
> 
> hist(exp.sd,n=20, col="cyan", border="blue", main="",
+      xlab="Standard Deviation (for data on the log scale)")
> dens <- density(exp.sd)
> lines(dens$x, dens$y*par("usr")[4]/max(dens$y),col="red",lwd=2)
> 
> title("Histogram of Standard Deviations")
> 
> # 1) What is the power if using 6 patients 3 measurements assuming
> #    Delta=1.0, Alpha=0.05 and Observed SDs?
> #
> n=6; fold.change=2.0; power=0.8; sig.level=0.05;
> #
> all.power <- pow(sd=exp.sd, n=n, delta=log2(fold.change),
+                  sig.level=sig.level)
....................................................................................................> 
> power.plot(all.power, lwd=2, col="blue")
> xmax <- par("usr")[2]-0.05; ymax <- par("usr")[4]-0.05
> legend(x=xmax, y=ymax,
+        legend= strsplit( paste("n=",n,",",
+                               "fold change=",fold.change,",",
+                               "alpha=", sig.level, ",",
+                               "# genes=", nobs(sd), sep=''), "," )[[1]],
+        xjust=1, yjust=1, cex=1.0)
Error: C stack usage  7969424 is too close to the limit
Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 WARNINGs, 6 NOTEs
See
  ‘/mnt/building/build_2015-05-26-12-43/RF_PKG_CHECK/PKGS/ssize.Rcheck/00check.log’
for details.

Run time: 33.29 seconds.