CRAN Package Check Results for Package SIMMS

Last updated on 2020-03-29 15:51:04 CEST.

Check Details

Version: 1.2.0
Check: examples
Result: ERROR
    Running examples in 'SIMMS-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: SIMMS-package
    > ### Title: SIMMS - Subnetwork Integration for Multi-Modal Signatures
    > ### Aliases: SIMMS-package SIMMS
    > ### Keywords: package
    >
    > ### ** Examples
    >
    >
    > options("warn" = -1);
    >
    > # get data directory
    > data.directory <- get.program.defaults(networks.database = "test")[["test.data.dir"]];
    >
    > # initialise params
    > output.directory <- ".";
    > data.types <- c("mRNA");
    > feature.selection.datasets <- c("Breastdata1");
    > training.datasets <- c("Breastdata1");
    > validation.datasets <- c("Breastdata2");
    > feature.selection.p.thresholds <- c(0.5);
    > feature.selection.p.threshold <- 0.5;
    > learning.algorithms <- c("backward", "forward", "glm");
    > top.n.features <- 5;
    >
    > # compute network HRs for all the subnet features
    > derive.network.features(
    + data.directory = data.directory,
    + output.directory = output.directory,
    + data.types = data.types,
    + feature.selection.datasets = feature.selection.datasets,
    + feature.selection.p.thresholds = feature.selection.p.thresholds,
    + networks.database = "test"
    + );
    Error in order(x[, 1], decreasing = TRUE) :
     unimplemented type 'list' in 'orderVector1'
    Calls: derive.network.features -> as.matrix -> order
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64

Version: 1.2.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'Using-SIMMS.Rmd' using rmarkdown
    Loading required package: survival
    Loading required package: MASS
    Loading required package: glmnet
    Loading required package: Matrix
    Loaded glmnet 3.0-2
    
    Loading required package: doParallel
    Loading required package: foreach
    Loading required package: iterators
    Loading required package: parallel
    Quitting from lines 125-232 (Using-SIMMS.Rmd)
    Error: processing vignette 'Using-SIMMS.Rmd' failed with diagnostics:
    unimplemented type 'list' in 'orderVector1'
    
    --- failed re-building 'Using-SIMMS.Rmd'
    
    SUMMARY: processing the following file failed:
     'Using-SIMMS.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64

Version: 1.2.0
Check: for non-standard things in the check directory
Result: NOTE
    Found the following files/directories:
     'graphs' 'output'
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-patched-linux-x86_64, r-patched-solaris-x86

Version: 1.2.0
Check: examples
Result: ERROR
    Running examples in ‘SIMMS-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: SIMMS-package
    > ### Title: SIMMS - Subnetwork Integration for Multi-Modal Signatures
    > ### Aliases: SIMMS-package SIMMS
    > ### Keywords: package
    >
    > ### ** Examples
    >
    >
    > options("warn" = -1);
    >
    > # get data directory
    > data.directory <- get.program.defaults(networks.database = "test")[["test.data.dir"]];
    >
    > # initialise params
    > output.directory <- ".";
    > data.types <- c("mRNA");
    > feature.selection.datasets <- c("Breastdata1");
    > training.datasets <- c("Breastdata1");
    > validation.datasets <- c("Breastdata2");
    > feature.selection.p.thresholds <- c(0.5);
    > feature.selection.p.threshold <- 0.5;
    > learning.algorithms <- c("backward", "forward", "glm");
    > top.n.features <- 5;
    >
    > # compute network HRs for all the subnet features
    > derive.network.features(
    + data.directory = data.directory,
    + output.directory = output.directory,
    + data.types = data.types,
    + feature.selection.datasets = feature.selection.datasets,
    + feature.selection.p.thresholds = feature.selection.p.thresholds,
    + networks.database = "test"
    + );
    Error in order(x[, 1], decreasing = TRUE) :
     unimplemented type 'list' in 'orderVector1'
    Calls: derive.network.features -> as.matrix -> order
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-solaris-x86

Version: 1.2.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘Using-SIMMS.Rmd’ using rmarkdown
    Loading required package: survival
    Loading required package: MASS
    Loading required package: glmnet
    Loading required package: Matrix
    Loaded glmnet 3.0-2
    
    Loading required package: doParallel
    Loading required package: foreach
    Loading required package: iterators
    Loading required package: parallel
    Quitting from lines 125-232 (Using-SIMMS.Rmd)
    Error: processing vignette 'Using-SIMMS.Rmd' failed with diagnostics:
    unimplemented type 'list' in 'orderVector1'
    
    --- failed re-building ‘Using-SIMMS.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘Using-SIMMS.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64

Version: 1.2.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘Using-SIMMS.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Loading required package: survival
    Loading required package: MASS
    Loading required package: glmnet
    Loading required package: Matrix
    Loaded glmnet 3.0-2
    
    Loading required package: doParallel
    Loading required package: foreach
    Loading required package: iterators
    Loading required package: parallel
    Quitting from lines 125-232 (Using-SIMMS.Rmd)
    Error: processing vignette 'Using-SIMMS.Rmd' failed with diagnostics:
    unimplemented type 'list' in 'orderVector1'
    
    --- failed re-building ‘Using-SIMMS.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘Using-SIMMS.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86