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CHECK report for monocle on malbec2

This page was generated on 2020-10-17 11:55:12 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE monocle PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1119/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
monocle 2.16.0
Cole Trapnell
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/monocle
Branch: RELEASE_3_11
Last Commit: a4d0e47
Last Changed Date: 2020-04-27 14:40:37 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: monocle
Version: 2.16.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:monocle.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings monocle_2.16.0.tar.gz
StartedAt: 2020-10-17 03:22:13 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:24:13 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 120.1 seconds
RetCode: 0
Status:  OK 
CheckDir: monocle.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:monocle.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings monocle_2.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/monocle.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (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 ‘2.16.0’
* 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 ... OK
* 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘biocViews’
  All declared Imports should be used.
Missing or unexported object: ‘scater::newSCESet’
* 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 global function definition for ‘quantile’
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’
exportCDS: no visible binding for global variable ‘use_for_ordering’
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 binding for global
  variable ‘pseudocount’
plot_multiple_branches_pseudotime: no visible binding for global
  variable ‘Branch’
project2MST: no visible global function definition for ‘nei’
reverseEmbeddingCDS : <anonymous>: no visible global function
  definition for ‘quantile’
Undefined global functions or variables:
  Branch Size_Factor nei next_node pseudocount quantile
  use_for_ordering
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/monocle.Rcheck/00check.log’
for details.



Installation output

monocle.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL monocle
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘monocle’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c clustering.cpp -o clustering.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o monocle.so RcppExports.o clustering.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-monocle/00new/monocle/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (monocle)

Tests output

monocle.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> #test_check("monocle")
> 
> proc.time()
   user  system elapsed 
  0.375   0.044   0.398 

Example timings

monocle.Rcheck/monocle-Ex.timings

nameusersystemelapsed
cellPairwiseDistances-set0.0000.0000.001
cellPairwiseDistances000
clusterGenes000
detectGenes0.0000.0000.001
estimate_t000
exportCDS0.0010.0000.000
importCDS0.0000.0000.001
minSpanningTree-set000
minSpanningTree000
newCellDataSet000
newCellTypeHierarchy000
package-deprecated0.0010.0000.000
plot_cell_clusters000
plot_cell_trajectory000
plot_clusters000
plot_complex_cell_trajectory000
plot_genes_in_pseudotime000
plot_genes_jitter000
plot_genes_positive_cells000
plot_genes_violin000
plot_pc_variance_explained000
plot_rho_delta000
reducedDimA-set0.0000.0010.000
reducedDimA0.0000.0000.001
reducedDimK-set000
reducedDimK000
reducedDimS-set000
reducedDimS000
reducedDimW-set0.0000.0000.001
reducedDimW000
relative2abs000