CRAN Package Check Results for Package NanoStringNorm

Last updated on 2015-04-19 10:51:55.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1.19 1.06 37.33 38.39 OK
r-devel-linux-x86_64-debian-gcc 1.1.19 1.10 37.52 38.62 OK
r-devel-linux-x86_64-fedora-clang 1.1.19 74.41 OK
r-devel-linux-x86_64-fedora-gcc 1.1.19 72.25 OK
r-devel-osx-x86_64-clang 1.1.19 83.29 OK
r-devel-windows-ix86+x86_64 1.1.19 5.00 61.00 66.00 OK
r-patched-linux-x86_64 1.1.19 1.01 36.60 37.61 OK
r-patched-solaris-sparc 1.1.19 409.40 OK
r-patched-solaris-x86 1.1.19 96.00 OK
r-release-linux-x86_64 1.1.19 1.10 37.19 38.29 OK
r-release-osx-x86_64-mavericks 1.1.19 NOTE
r-release-osx-x86_64-snowleopard 1.1.19 ERROR
r-release-windows-ix86+x86_64 1.1.19 3.00 57.00 60.00 OK
r-oldrel-windows-ix86+x86_64 1.1.19 5.00 82.00 87.00 OK

Check Details

Version: 1.1.19
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: ‘vsn’ ‘lme4’
Flavor: r-release-osx-x86_64-mavericks

Version: 1.1.19
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘vsn’
Flavor: r-release-osx-x86_64-snowleopard

Version: 1.1.19
Check: examples
Result: ERROR
    Running examples in ‘NanoStringNorm-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: Plot.NanoStringNorm.gvis
    > ### Title: Plot.NanoStringNorm.gvis
    > ### Aliases: Plot.NanoStringNorm.gvis
    > ### Keywords: NanoString Normalization mRNA miRNA
    >
    > ### ** Examples
    >
    >
    > # load data
    > data(NanoString);
    >
    > # specify 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,
    + take.log = TRUE,
    + traits = trait.strain,
    + return.matrix.of.endogenous.probes = FALSE
    + );
    
    ##############################
    ### NanoStringNorm v1.1.19 ###
    ##############################
    
    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 sample/rna content 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 the sample summaries to your browser
    > if (requireNamespace("googleVis")) {
    + Plot.NanoStringNorm.gvis(
    + x = NanoString.mRNA.norm,
    + plot.type = c('gene.norm', 'sample'),
    + save.plot = FALSE
    + );
    +
    + # plot the gene summaries to a directory for distribution and later viewing
    + Plot.NanoStringNorm.gvis(
    + x = NanoString.mRNA.norm,
    + plot.type = c('gene.norm', 'sample'),
    + save.plot = TRUE,
    + path.to.mongoose = 'none',
    + output.directory = "NanoStringNorm_Interactive_Plot"
    + );
    + }
    Loading required namespace: googleVis
    Error in get("httpdPort", envir = environment(startDynamicHelp)) > 0 :
     comparison (6) is possible only for atomic and list types
    Calls: Plot.NanoStringNorm.gvis -> plot -> plot.gvis -> isServerRunning
    Execution halted
Flavor: r-release-osx-x86_64-snowleopard