CRAN Package Check Results for Package GPseq

Last updated on 2018-05-03 10:50:25 CEST.

Check Details

Version: 0.5
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/GPseq.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.5
Check: top-level files
Result: NOTE
    Non-standard files/directories found at top level:
     ‘doc’ ‘scr’
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-release-linux-x86_64

Version: 0.5
Check: R code for possible problems
Result: NOTE
    calc_chisq_statistic: no visible global function definition for ‘dpois’
    generalized_poisson_likelihood: no visible global function definition
     for ‘var’
    perform_permutation_de: no visible binding for global variable ‘rbinom’
    perform_permutation_de: no visible global function definition for ‘var’
    perform_permutation_ds: no visible binding for global variable ‘rbinom’
    perform_permutation_ds: no visible global function definition for ‘var’
    Undefined global functions or variables:
     dpois rbinom var
    Consider adding
     importFrom("stats", "dpois", "rbinom", "var")
    to your NAMESPACE file.
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-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.5
Check: Rd line widths
Result: NOTE
    Rd file 'estimate_differential_expression.Rd':
     \examples lines wider than 100 characters:
     cat("Mark = ",output$gp_comparison[[1,1,2]]$mark," Test Statistic with Generalized Poisson Model = ", output$gp_comparison[[1,1,2]]$Gpt ... [TRUNCATED]
    
    Rd file 'estimate_differential_splicing.Rd':
     \examples lines wider than 100 characters:
     cat("Mark = ",output$out_gp[[2,1,1,2]]$mark," Test Statistic with Generalized Poisson Model = ", output$out_gp[[2,1,1,2]]$Gptest,"\n");
    
    Rd file 'estimate_exon_gene_expression.Rd':
     \examples lines wider than 100 characters:
     cat("Mark = ",output$exon_out[[1,1]]$mark," Theta = ",output$exon_out[[1,1]]$theta," Lambda = ",output$exon_out[[1,1]]$lambda," y_bar = ... [TRUNCATED]
     cat("Mark = ",output$chisq_exon_out[[1,1]]$mark1," Degrees of Freedom = ",output$chisq_exon_out[[1,1]]$df1," Chi Square Statistic ",out ... [TRUNCATED]
     cat("Mark = ",output$chisq_exon_out[[1,1]]$mark2," Degrees of Freedom = ",output$chisq_exon_out[[1,1]]$df2," Chi Square Statistic ",out ... [TRUNCATED]
     cat("Mark = ",output$gene_out[[1,1]]$mark," Theta = ",output$gene_out[[1,1]]$theta," Lambda = ",output$gene_out[[1,1]]$lambda," y_bar = ... [TRUNCATED]
     cat("Mark = ",output$chisq_gene_out[[1,1]]$mark1," Degrees of Freedom = ",output$chisq_gene_out[[1,1]]$df1," Chi Square Statistic ",out ... [TRUNCATED]
     cat("Mark = ",output$chisq_gene_out[[1,1]]$mark2," Degrees of Freedom = ",output$chisq_gene_out[[1,1]]$df2," Chi Square Statistic ",out ... [TRUNCATED]
    
    Rd file 'generalized_poisson_likelihood.Rd':
     \examples lines wider than 100 characters:
     cat("theta = ",out$theta,"lambda = ",out$lambda,"lambda_poisson = ",out$y_bar,"Length = ",out$length,"\n");
    
    Rd file 'likelihood_ratio_generalized_poisson_exon_gene.Rd':
     \usage lines wider than 90 characters:
     likelihood_ratio_generalized_poisson_exon_gene(z, theta1, lambda1, x, theta2, lambda2, v, theta3, lambda3, y, theta4, lambda4)
     \examples lines wider than 100 characters:
     output = likelihood_ratio_generalized_poisson_exon_gene(z,outz$theta,outz$lambda,x,outx$theta,outx$lambda,v,outv$theta,outv$lambda,y, ... [TRUNCATED]
    
    Rd file 'likelihood_ratio_tissue_generalized_poisson.Rd':
     \examples lines wider than 100 characters:
     output = likelihood_ratio_tissue_generalized_poisson(x,outx$lambda,outx$theta,y,outy$lambda,outy$theta,w);
    
    These lines will be truncated in the PDF manual.
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-release-linux-x86_64

Version: 0.5
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GPseq.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.5
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/data/gannet/ripley/R/packages/tests-clang/GPseq.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.5
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/data/gannet/ripley/R/packages/tests-devel/GPseq.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.5
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See 'd:/Rcompile/CRANpkg/local/3.5/GPseq.Rcheck/00install.out' for details.
    Information on the location(s) of code generating the 'Note's can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to 'yes'.
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64

Version: 0.5
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/GPseq.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-patched-linux-x86_64

Version: 0.5
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/ripley/R/packages/tests32/GPseq.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-patched-solaris-x86

Version: 0.5
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/GPseq.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-release-linux-x86_64

Version: 0.5
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Note: break used in wrong context: no loop is visible
    See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/GPseq.Rcheck/00install.out’ for details.
    Information on the location(s) of code generating the ‘Note’s can be
    obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
    to ‘yes’.
Flavor: r-release-osx-x86_64