• using R version 2.15.0 RC (2012-03-27 r58857)
• using platform: i386-apple-darwin9.8.0 (32-bit)
• using session charset: ASCII
• checking for file 'NanoStringNorm/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'NanoStringNorm' version '1.1.6'
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking whether package 'NanoStringNorm' can be installed ... OK
• checking installed package size ... OK
• checking package directory ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... 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 whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace 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 ... OK
• checking Rd files ... OK
• 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 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 sizes of PDF files under 'inst/doc' ... OK
• checking installed files from 'inst/doc' ... OK
• checking examples ... ERROR
  Running examples in 'NanoStringNorm-Ex.R' failed
  The error most likely occurred in:
  
  > ### Name: Plot.NanoStringNorm
  > ### Title: Plot.NanoStringNorm
  > ### Aliases: Plot.NanoStringNorm
  > ### Keywords: NanoString Normalization mRNA miRNA
  >
  > ### ** Examples
  >
  >
  > # load data
  > data(NanoString);
  >
  > # specifiy housekeeping genes in annotation
  > NanoString.mRNA[NanoString.mRNA$Name %in%
  + c('Eef1a1','Gapdh','Hprt1','Ppia','Sdha'),'Code.Class'] <- 'Housekeeping';
  >
  > # setup the traits
  > sample.names <- names(NanoString.mRNA)[-c(1:3)];
  > strain1 <- rep(1, times = (ncol(NanoString.mRNA)-3));
  > strain1[grepl('HW',sample.names)] <- 2;
  > strain2 <- rep(1, times = (ncol(NanoString.mRNA)-3));
  > strain2[grepl('WW',sample.names)] <- 2;
  > strain3 <- rep(1, times = (ncol(NanoString.mRNA)-3));
  > strain3[grepl('LE',sample.names)] <- 2;
  > trait.strain <- data.frame(
  + row.names = sample.names,
  + strain1 = strain1,
  + strain2 = strain2,
  + strain3 = strain3
  + );
  >
  > # normalize
  > NanoString.mRNA.norm <- NanoStringNorm(
  + x = NanoString.mRNA,
  + anno = NA,
  + CodeCount = 'geo.mean',
  + Background = 'mean.2sd',
  + SampleContent = 'housekeeping.geo.mean',
  + round.values = TRUE,
  + log = TRUE,
  + traits = trait.strain,
  + return.matrix.of.endogenous.probes = FALSE
  + );
  
  ##############################
  ### NanoStringNorm v1.1.6 ###
  ##############################
  
  There are 25 samples and 49 Endogenous genes
  
  Background: After correction 25 samples and 49
  Endogenous genes have less than 90% missing.
  
  SampleContent: The following samples have a normalization factor greater than
  3 standard deviations from the mean.
  
  rna.zscore
  LE4D51.a 3.13
  
  log: Setting values less than 1 to 1 in order to calculate the log in positive space.
  
  >
  > # plot all the plots as PDF report
  > pdf('NanoStringNorm_Example_Plots_All.pdf')
  > Plot.NanoStringNorm(
  + x = NanoString.mRNA.norm,
  + label.best.guess = TRUE,
  + plot.type = 'all'
  + );
  > dev.off()
  pdf
  2
  >
  > # publication quality tiff volcano plot
  > tiff('NanoStringNorm_Example_Plots_Volcano.tiff', units = 'in', height = 6,
  + width = 6, compression = 'lzw', res = 1200, pointsize = 10);
  Error in tiff("NanoStringNorm_Example_Plots_Volcano.tiff", units = "in", :
  argument "antialias" is missing, with no default
  Execution halted
• elapsed time (check, wall clock): 0:27