Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1281/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
monocle 2.33.0 (landing page) Cole Trapnell
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the monocle package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/monocle.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: monocle |
Version: 2.33.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:monocle.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings monocle_2.33.0.tar.gz |
StartedAt: 2024-06-10 05:40:33 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 05:45:30 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 297.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: monocle.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:monocle.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings monocle_2.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/monocle.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'monocle/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'monocle' version '2.33.0' * 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 whether package 'monocle' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * 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 ... NOTE Problems with news in 'NEWS': Cannot process chunk/lines: Monocle 2.0.0 Series NEWS * checking code 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 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 LazyData ... 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/monocle/libs/x64/monocle.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking sizes of PDF files under '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 ... 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 'F:/biocbuild/bbs-3.20-bioc/meat/monocle.Rcheck/00check.log' for details.
monocle.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL monocle ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'monocle' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c clustering.cpp -o clustering.o g++ -std=gnu++17 -shared -s -static-libgcc -o monocle.dll tmp.def RcppExports.o clustering.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-monocle/00new/monocle/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (monocle)
monocle.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 0.46 2.32 2.59
monocle.Rcheck/monocle-Ex.timings
name | user | system | elapsed | |
cellPairwiseDistances-set | 0 | 0 | 0 | |
cellPairwiseDistances | 0 | 0 | 0 | |
clusterGenes | 0 | 0 | 0 | |
detectGenes | 0 | 0 | 0 | |
estimate_t | 0 | 0 | 0 | |
exportCDS | 0 | 0 | 0 | |
importCDS | 0 | 0 | 0 | |
minSpanningTree-set | 0 | 0 | 0 | |
minSpanningTree | 0 | 0 | 0 | |
newCellDataSet | 0 | 0 | 0 | |
newCellTypeHierarchy | 0 | 0 | 0 | |
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 | 0 | 0 | |
plot_genes_jitter | 0 | 0 | 0 | |
plot_genes_positive_cells | 0 | 0 | 0 | |
plot_genes_violin | 0 | 0 | 0 | |
plot_pc_variance_explained | 0 | 0 | 0 | |
plot_rho_delta | 0 | 0 | 0 | |
reducedDimA-set | 0 | 0 | 0 | |
reducedDimA | 0 | 0 | 0 | |
reducedDimK-set | 0 | 0 | 0 | |
reducedDimK | 0 | 0 | 0 | |
reducedDimS-set | 0 | 0 | 0 | |
reducedDimS | 0 | 0 | 0 | |
reducedDimW-set | 0 | 0 | 0 | |
reducedDimW | 0 | 0 | 0 | |
relative2abs | 0 | 0 | 0 | |