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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings monocle_2.5.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/monocle.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘monocle/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘monocle’ version ‘2.5.4’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘monocle’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘dplyr::union’ by ‘igraph::union’ when loading ‘monocle’
Warning: replacing previous import ‘dplyr::as_data_frame’ by ‘igraph::as_data_frame’ when loading ‘monocle’
Warning: replacing previous import ‘dplyr::groups’ by ‘igraph::groups’ when loading ‘monocle’
Warning: replacing previous import ‘dplyr::arrange’ by ‘plyr::arrange’ when loading ‘monocle’
See ‘/Users/biocbuild/bbs-3.6-bioc/meat/monocle.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 ... NOTE
assign_cell_lineage: no visible global function definition for ‘nei’
buildBranchCellDataSet: no visible global function definition for ‘nei’
clusterCells: no visible binding for global variable ‘rho’
clusterCells: no visible binding for global variable ‘delta’
count_leaf_descendents: no visible global function definition for ‘nei’
cth_classifier_cds: no visible global function definition for ‘nei’
cth_classifier_cell: no visible global function definition for ‘nei’
diff_test_helper: no visible binding for global variable ‘Size_Factor’
extract_good_ordering: no visible global function definition for ‘nei’
fit_model_helper: no visible binding for global variable ‘Size_Factor’
get_next_node_id: no visible binding for '<<-' assignment to
‘next_node’
get_next_node_id: no visible binding for global variable ‘next_node’
make_canonical: no visible global function definition for ‘nei’
measure_diameter_path: no visible global function definition for ‘nei’
orderCells: no visible binding for '<<-' assignment to ‘next_node’
plot_multiple_branches_pseudotime: no visible global function
definition for ‘exprs<-’
plot_multiple_branches_pseudotime: no visible global function
definition for ‘esApply’
plot_multiple_branches_pseudotime : <anonymous>: no visible global
function definition for ‘lowess’
plot_multiple_branches_pseudotime: no visible binding for global
variable ‘pseudocount’
plot_multiple_branches_pseudotime: no visible binding for global
variable ‘Branch’
project2MST: no visible global function definition for ‘nei’
Undefined global functions or variables:
Branch Size_Factor delta esApply exprs<- lowess nei next_node
pseudocount rho
Consider adding
importFrom("stats", "lowess")
to your NAMESPACE file.
* checking Rd files ... WARNING
checkRd: (5) detectGenes.Rd:0-27: Must have a \description
checkRd: (5) plot_cell_trajectory.Rd:0-60: Must have a \description
prepare_Rd: reducedDimK.Rd:16-18: Dropping empty section \description
checkRd: (5) reducedDimK.Rd:0-24: Must have a \description
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘addCellType’ ‘plot_genes_violin’
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 ... WARNING
Codoc mismatches from documentation object 'estimateDispersionsForCellDataSet':
estimateDispersionsForCellDataSet
Code: function(cds, modelFormulaStr, relative_expr,
min_cells_detected, removeOutliers, cores, verbose =
F)
Docs: function(cds, modelFormulaStr, relative_expr,
min_cells_detected, removeOutliers, cores)
Argument names in code not in docs:
verbose
Codoc mismatches from documentation object 'plot_genes_branched_heatmap':
plot_genes_branched_heatmap
Code: function(cds_subset, branch_point = 1, branch_states = NULL,
branch_labels = c("Cell fate 1", "Cell fate 2"),
cluster_rows = TRUE, hclust_method = "ward.D2",
num_clusters = 6, hmcols = NULL, branch_colors =
c("#979797", "#F05662", "#7990C8"), add_annotation_row
= NULL, add_annotation_col = NULL, show_rownames =
FALSE, use_gene_short_name = TRUE, scale_max = 3,
scale_min = -3, norm_method = c("log", "vstExprs"),
trend_formula = "˜sm.ns(Pseudotime, df=3) * Branch",
return_heatmap = FALSE, cores = 1, ...)
Docs: function(cds_subset, branch_point = 1, branch_states = NULL,
branch_labels = c("Cell fate 1", "Cell fate 2"),
cluster_rows = TRUE, hclust_method = "ward.D2",
num_clusters = 6, hmcols = NULL, branch_colors =
c("#979797", "#F05662", "#7990C8"), add_annotation_row
= NULL, add_annotation_col = NULL, show_rownames =
FALSE, use_gene_short_name = TRUE, scale_max = 3,
scale_min = -3, norm_method = c("vstExprs", "log"),
trend_formula = "˜sm.ns(Pseudotime, df=3) * Branch",
return_heatmap = FALSE, cores = 1, ...)
Mismatches in argument default values:
Name: 'norm_method' Code: c("log", "vstExprs") Docs: c("vstExprs", "log")
Codoc mismatches from documentation object 'plot_multiple_branches_heatmap':
plot_multiple_branches_heatmap
Code: function(cds, branches, branches_name = NULL, cluster_rows =
TRUE, hclust_method = "ward.D2", num_clusters = 6,
hmcols = NULL, add_annotation_row = NULL,
add_annotation_col = NULL, show_rownames = FALSE,
use_gene_short_name = TRUE, norm_method = c("log",
"vstExprs"), scale_max = 3, scale_min = -3,
trend_formula = "˜sm.ns(Pseudotime, df=3)",
return_heatmap = FALSE, cores = 1)
Docs: function(cds, branches, branches_name = NULL, cluster_rows =
TRUE, hclust_method = "ward.D2", num_clusters = 6,
hmcols = NULL, add_annotation_row = NULL,
add_annotation_col = NULL, show_rownames = FALSE,
use_gene_short_name = TRUE, norm_method =
c("vstExprs", "log"), scale_max = 3, scale_min = -3,
trend_formula = "˜sm.ns(Pseudotime, df=3)",
return_heatmap = FALSE, cores = 1)
Mismatches in argument default values:
Name: 'norm_method' Code: c("log", "vstExprs") Docs: c("vstExprs", "log")
Codoc mismatches from documentation object 'plot_pc_variance_explained':
plot_pc_variance_explained
Code: function(cds, max_components = 100, norm_method = c("log",
"vstExprs", "none"), residualModelFormulaStr = NULL,
pseudo_expr = NULL, return_all = F,
use_existing_pc_variance = FALSE, verbose = FALSE,
...)
Docs: function(cds, max_components = 100, norm_method = c("vstExprs",
"log", "none"), residualModelFormulaStr = NULL,
pseudo_expr = NULL, return_all = F,
use_existing_pc_variance = FALSE, verbose = FALSE,
...)
Mismatches in argument default values:
Name: 'norm_method' Code: c("log", "vstExprs", "none") Docs: c("vstExprs", "log", "none")
Codoc mismatches from documentation object 'plot_pseudotime_heatmap':
plot_pseudotime_heatmap
Code: function(cds_subset, cluster_rows = TRUE, hclust_method =
"ward.D2", num_clusters = 6, hmcols = NULL,
add_annotation_row = NULL, add_annotation_col = NULL,
show_rownames = FALSE, use_gene_short_name = TRUE,
norm_method = c("log", "vstExprs"), scale_max = 3,
scale_min = -3, trend_formula = "˜sm.ns(Pseudotime,
df=3)", return_heatmap = FALSE, cores = 1)
Docs: function(cds_subset, cluster_rows = TRUE, hclust_method =
"ward.D2", num_clusters = 6, hmcols = NULL,
add_annotation_row = NULL, add_annotation_col = NULL,
show_rownames = FALSE, use_gene_short_name = TRUE,
norm_method = c("vstExprs", "log"), scale_max = 3,
scale_min = -3, trend_formula = "˜sm.ns(Pseudotime,
df=3)", return_heatmap = FALSE, cores = 1)
Mismatches in argument default values:
Name: 'norm_method' Code: c("log", "vstExprs") Docs: c("vstExprs", "log")
Codoc mismatches from documentation object 'reduceDimension':
reduceDimension
Code: function(cds, max_components = 2, reduction_method =
c("DDRTree", "ICA", "tSNE", "SimplePPT", "L1-graph",
"SGL-tree"), norm_method = c("log", "vstExprs",
"none"), residualModelFormulaStr = NULL, pseudo_expr =
NULL, relative_expr = TRUE, auto_param_selection =
TRUE, verbose = FALSE, scaling = TRUE, ...)
Docs: function(cds, max_components = 2, reduction_method =
c("DDRTree", "ICA", "tSNE", "SimplePPT", "L1-graph",
"SGL-tree"), norm_method = c("vstExprs", "log",
"none"), residualModelFormulaStr = NULL, pseudo_expr =
NULL, relative_expr = TRUE, auto_param_selection =
TRUE, verbose = FALSE, scaling = TRUE, ...)
Mismatches in argument default values:
Name: 'norm_method' Code: c("log", "vstExprs", "none") Docs: c("vstExprs", "log", "none")
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'newCellTypeHierarchy'
‘cth’
Documented arguments not in \usage in documentation object 'plot_genes_branched_pseudotime':
‘multi_branch’
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 ... WARNING
Argument items with no description in Rd object 'plot_cell_trajectory':
‘show_state_number’ ‘state_number_size’
* 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 files in ‘vignettes’ ... NOTE
The following files look like leftovers/mistakes:
‘monocle-vignette-knitr.bbl’, ‘monocle-vignette-knitr.log’,
‘monocle-vignette-knitr.toc’
Please remove them from your package.
The following directory looks like a leftover from 'knitr':
‘figure’
Please remove from your package.
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 6 WARNINGs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/monocle.Rcheck/00check.log’
for details.
