Cole Trapnell
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/monocle |
| Branch: RELEASE_3_6 |
| Last Commit: bf39ea3 |
| Last Changed Date: 2018-04-02 13:54:04 -0400 (Mon, 02 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:38:41 -0400 (Thu, 12 Apr 2018).
| Package 883/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| monocle 2.6.4 Cole Trapnell
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: monocle |
| Version: 2.6.4 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings monocle_2.6.4.tar.gz |
| StartedAt: 2018-04-12 06:38:16 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 06:40:20 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 123.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: monocle.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings monocle_2.6.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/monocle.Rcheck’ * using R version 3.4.4 (2018-03-15) * 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 ‘2.6.4’ * 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 ... 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. * 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’ 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 binding for global variable ‘pseudocount’ plot_multiple_branches_pseudotime: no visible binding for global variable ‘Branch’ plot_multiple_branches_pseudotime: no visible binding for global variable ‘mutate’ project2MST: no visible global function definition for ‘nei’ Undefined global functions or variables: Branch Size_Factor exprs<- mutate 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 ... OK * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.6-bioc/meat/monocle.Rcheck/00check.log’ for details.
monocle.Rcheck/00install.out
* installing *source* package ‘monocle’ ... ** libs clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/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 /Users/biocbuild/bbs-3.6-bioc/meat/monocle.Rcheck/monocle/libs ** R ** data *** moving datasets to lazyload DB ** inst ** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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
0.246 0.041 0.272
monocle.Rcheck/monocle-Ex.timings
| name | user | system | elapsed | |
| cellPairwiseDistances-set | 0 | 0 | 0 | |
| cellPairwiseDistances | 0.001 | 0.000 | 0.000 | |
| clusterGenes | 0.001 | 0.000 | 0.001 | |
| detectGenes | 0 | 0 | 0 | |
| estimate_t | 0.001 | 0.000 | 0.000 | |
| exportCDS | 0.001 | 0.000 | 0.001 | |
| importCDS | 0.001 | 0.000 | 0.001 | |
| minSpanningTree-set | 0.000 | 0.000 | 0.001 | |
| minSpanningTree | 0 | 0 | 0 | |
| newCellDataSet | 0.000 | 0.000 | 0.001 | |
| newCellTypeHierarchy | 0.001 | 0.001 | 0.002 | |
| package-deprecated | 0.000 | 0.000 | 0.001 | |
| plot_cell_clusters | 0.000 | 0.000 | 0.001 | |
| plot_cell_trajectory | 0.000 | 0.001 | 0.001 | |
| plot_clusters | 0.001 | 0.000 | 0.000 | |
| plot_complex_cell_trajectory | 0.001 | 0.000 | 0.001 | |
| plot_genes_in_pseudotime | 0.001 | 0.000 | 0.001 | |
| plot_genes_jitter | 0.001 | 0.000 | 0.001 | |
| plot_genes_positive_cells | 0.001 | 0.000 | 0.000 | |
| plot_genes_violin | 0.001 | 0.000 | 0.001 | |
| plot_pc_variance_explained | 0.001 | 0.000 | 0.001 | |
| plot_rho_delta | 0.001 | 0.000 | 0.001 | |
| reducedDimA-set | 0.000 | 0.000 | 0.001 | |
| reducedDimA | 0.000 | 0.001 | 0.000 | |
| reducedDimK-set | 0.001 | 0.000 | 0.001 | |
| reducedDimK | 0.001 | 0.000 | 0.000 | |
| reducedDimS-set | 0 | 0 | 0 | |
| reducedDimS | 0.001 | 0.000 | 0.000 | |
| reducedDimW-set | 0.001 | 0.000 | 0.000 | |
| reducedDimW | 0.001 | 0.000 | 0.001 | |
| relative2abs | 0.001 | 0.001 | 0.001 | |
| selectNegentropyGenes | 0 | 0 | 0 | |