Cole Trapnell
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/monocle |
| Branch: RELEASE_3_7 |
| Last Commit: f36f3b5 |
| Last Changed Date: 2018-04-30 10:35:33 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:26:13 -0400 (Wed, 17 Oct 2018).
| Package 934/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| monocle 2.8.0 Cole Trapnell
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: monocle |
| Version: 2.8.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:monocle.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings monocle_2.8.0.tar.gz |
| StartedAt: 2018-10-16 02:06:58 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 02:08:18 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 79.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: monocle.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:monocle.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings monocle_2.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/monocle.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * 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 ‘2.8.0’ * 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 objects: ‘VGAM::gaussianff’ ‘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’ 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’ importCDS: no visible global function definition for ‘gaussianff’ 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’ Undefined global functions or variables: Branch Size_Factor gaussianff nei next_node pseudocount use_for_ordering * 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-3.7-bioc/meat/monocle.Rcheck/00check.log’ for details.
monocle.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL monocle ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘monocle’ ... ** libs g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c clustering.cpp -o clustering.o g++ -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o monocle.so RcppExports.o clustering.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.7-bioc/R/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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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
0.168 0.016 0.177
monocle.Rcheck/monocle-Ex.timings
| name | user | system | elapsed | |
| cellPairwiseDistances-set | 0.000 | 0.004 | 0.001 | |
| cellPairwiseDistances | 0.000 | 0.000 | 0.001 | |
| clusterGenes | 0 | 0 | 0 | |
| detectGenes | 0 | 0 | 0 | |
| estimate_t | 0.000 | 0.000 | 0.001 | |
| exportCDS | 0.000 | 0.000 | 0.001 | |
| importCDS | 0.000 | 0.000 | 0.001 | |
| minSpanningTree-set | 0.000 | 0.000 | 0.001 | |
| minSpanningTree | 0 | 0 | 0 | |
| newCellDataSet | 0 | 0 | 0 | |
| newCellTypeHierarchy | 0.000 | 0.000 | 0.002 | |
| package-deprecated | 0.000 | 0.000 | 0.001 | |
| plot_cell_clusters | 0 | 0 | 0 | |
| plot_cell_trajectory | 0.000 | 0.000 | 0.001 | |
| plot_clusters | 0.000 | 0.000 | 0.001 | |
| plot_complex_cell_trajectory | 0.004 | 0.000 | 0.000 | |
| plot_genes_in_pseudotime | 0 | 0 | 0 | |
| plot_genes_jitter | 0.000 | 0.000 | 0.001 | |
| plot_genes_positive_cells | 0.004 | 0.000 | 0.000 | |
| plot_genes_violin | 0.000 | 0.000 | 0.001 | |
| plot_pc_variance_explained | 0 | 0 | 0 | |
| plot_rho_delta | 0 | 0 | 0 | |
| reducedDimA-set | 0.000 | 0.000 | 0.001 | |
| reducedDimA | 0.000 | 0.000 | 0.001 | |
| reducedDimK-set | 0.004 | 0.000 | 0.000 | |
| reducedDimK | 0 | 0 | 0 | |
| reducedDimS-set | 0 | 0 | 0 | |
| reducedDimS | 0.000 | 0.000 | 0.001 | |
| reducedDimW-set | 0.000 | 0.000 | 0.001 | |
| reducedDimW | 0 | 0 | 0 | |
| relative2abs | 0 | 0 | 0 | |
| selectNegentropyGenes | 0.000 | 0.000 | 0.001 | |