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BioC 3.6: CHECK report for monocle on tokay1

This page was generated on 2017-08-16 13:32:50 -0400 (Wed, 16 Aug 2017).

Package 854/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
monocle 2.5.4
Cole Trapnell
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/monocle
Last Changed Rev: 131851 / Revision: 131943
Last Changed Date: 2017-08-08 11:45:40 -0400 (Tue, 08 Aug 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: monocle
Version: 2.5.4
Command: rm -rf monocle.buildbin-libdir monocle.Rcheck && mkdir monocle.buildbin-libdir monocle.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=monocle.buildbin-libdir monocle_2.5.4.tar.gz >monocle.Rcheck\00install.out 2>&1 && cp monocle.Rcheck\00install.out monocle-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=monocle.buildbin-libdir --install="check:monocle-install.out" --force-multiarch --no-vignettes --timings monocle_2.5.4.tar.gz
StartedAt: 2017-08-16 00:58:49 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:01:15 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 146.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: monocle.Rcheck
Warnings: 6

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf monocle.buildbin-libdir monocle.Rcheck && mkdir monocle.buildbin-libdir monocle.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=monocle.buildbin-libdir monocle_2.5.4.tar.gz >monocle.Rcheck\00install.out 2>&1 && cp monocle.Rcheck\00install.out monocle-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=monocle.buildbin-libdir --install="check:monocle-install.out" --force-multiarch --no-vignettes --timings monocle_2.5.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/monocle.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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::groups' by 'igraph::groups' when loading 'monocle'
  Warning: replacing previous import 'dplyr::as_data_frame' by 'igraph::as_data_frame' when loading 'monocle'
  Warning: replacing previous import 'dplyr::arrange' by 'plyr::arrange' when loading 'monocle'
See 'C:/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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/monocle.Rcheck/00check.log'
for details.


monocle.Rcheck/00install.out:


install for i386

* installing *source* package 'monocle' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Warning: replacing previous import 'dplyr::union' by 'igraph::union' when loading 'monocle'
Warning: replacing previous import 'dplyr::groups' by 'igraph::groups' when loading 'monocle'
Warning: replacing previous import 'dplyr::as_data_frame' by 'igraph::as_data_frame' when loading 'monocle'
Warning: replacing previous import 'dplyr::arrange' by 'plyr::arrange' when loading 'monocle'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'dplyr::union' by 'igraph::union' when loading 'monocle'
Warning: replacing previous import 'dplyr::groups' by 'igraph::groups' when loading 'monocle'
Warning: replacing previous import 'dplyr::as_data_frame' by 'igraph::as_data_frame' when loading 'monocle'
Warning: replacing previous import 'dplyr::arrange' by 'plyr::arrange' when loading 'monocle'

install for x64

* installing *source* package 'monocle' ...
** testing if installed package can be loaded
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'
* MD5 sums
packaged installation of 'monocle' as monocle_2.5.4.zip
* DONE (monocle)

monocle.Rcheck/examples_i386/monocle-Ex.timings:

nameusersystemelapsed
cellPairwiseDistances-set000
cellPairwiseDistances000
clusterGenes000
detectGenes000
estimate_t000
minSpanningTree-set000
minSpanningTree000
newCellDataSet000
newCellTypeHierarchy000
package-deprecated000
plot_cell_clusters000
plot_cell_trajectory000
plot_clusters000
plot_complex_cell_trajectory000
plot_genes_in_pseudotime000
plot_genes_jitter0.010.000.01
plot_genes_positive_cells000
plot_pc_variance_explained000
plot_rho_delta000
reducedDimA-set000
reducedDimA000
reducedDimK-set000
reducedDimK000
reducedDimS-set000
reducedDimS000
reducedDimW-set000
reducedDimW000
relative2abs000
selectNegentropyGenes000

monocle.Rcheck/examples_x64/monocle-Ex.timings:

nameusersystemelapsed
cellPairwiseDistances-set000
cellPairwiseDistances000
clusterGenes000
detectGenes000
estimate_t000
minSpanningTree-set000
minSpanningTree000
newCellDataSet000
newCellTypeHierarchy000
package-deprecated000
plot_cell_clusters000
plot_cell_trajectory000
plot_clusters000
plot_complex_cell_trajectory000
plot_genes_in_pseudotime000
plot_genes_jitter000
plot_genes_positive_cells000
plot_pc_variance_explained000
plot_rho_delta000
reducedDimA-set000
reducedDimA000
reducedDimK-set000
reducedDimK000
reducedDimS-set000
reducedDimS000
reducedDimW-set000
reducedDimW000
relative2abs000
selectNegentropyGenes000