Cole Trapnell
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/monocle |
| Branch: RELEASE_3_8 |
| Last Commit: 2a006cf |
| Last Changed Date: 2019-01-04 13:40:16 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:57:40 -0400 (Tue, 16 Apr 2019).
| Package 989/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| monocle 2.10.1 Cole Trapnell
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: monocle |
| Version: 2.10.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:monocle.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings monocle_2.10.1.tar.gz |
| StartedAt: 2019-04-16 01:23:23 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:25:15 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 111.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: monocle.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:monocle.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings monocle_2.10.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/monocle.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.10.1’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.8-bioc/meat/monocle.Rcheck/00check.log’
for details.
monocle.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL monocle ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘monocle’ ... ** libs clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c clustering.cpp -o clustering.o clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o monocle.so RcppExports.o clustering.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/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 * DONE (monocle)
monocle.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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
0.247 0.060 0.280
monocle.Rcheck/monocle-Ex.timings
| name | user | system | elapsed | |
| cellPairwiseDistances-set | 0.001 | 0.001 | 0.000 | |
| cellPairwiseDistances | 0 | 0 | 0 | |
| clusterGenes | 0.001 | 0.000 | 0.001 | |
| detectGenes | 0.000 | 0.001 | 0.001 | |
| estimate_t | 0.000 | 0.000 | 0.001 | |
| exportCDS | 0.000 | 0.000 | 0.001 | |
| importCDS | 0.001 | 0.000 | 0.001 | |
| minSpanningTree-set | 0.000 | 0.001 | 0.001 | |
| minSpanningTree | 0.000 | 0.000 | 0.001 | |
| newCellDataSet | 0.000 | 0.000 | 0.001 | |
| newCellTypeHierarchy | 0.001 | 0.000 | 0.001 | |
| package-deprecated | 0 | 0 | 0 | |
| plot_cell_clusters | 0 | 0 | 0 | |
| plot_cell_trajectory | 0 | 0 | 0 | |
| plot_clusters | 0 | 0 | 0 | |
| plot_complex_cell_trajectory | 0 | 0 | 0 | |
| plot_genes_in_pseudotime | 0.000 | 0.001 | 0.000 | |
| plot_genes_jitter | 0.001 | 0.000 | 0.001 | |
| plot_genes_positive_cells | 0 | 0 | 0 | |
| plot_genes_violin | 0 | 0 | 0 | |
| plot_pc_variance_explained | 0.000 | 0.000 | 0.001 | |
| plot_rho_delta | 0 | 0 | 0 | |
| reducedDimA-set | 0.001 | 0.000 | 0.001 | |
| reducedDimA | 0 | 0 | 0 | |
| reducedDimK-set | 0 | 0 | 0 | |
| reducedDimK | 0 | 0 | 0 | |
| reducedDimS-set | 0.000 | 0.000 | 0.001 | |
| reducedDimS | 0 | 0 | 0 | |
| reducedDimW-set | 0.001 | 0.001 | 0.000 | |
| reducedDimW | 0 | 0 | 0 | |
| relative2abs | 0 | 0 | 0 | |