Back to Multiple platform build/check report for BioC 3.17:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2023-05-29 11:07:08 -0400 (Mon, 29 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.0 RC (2023-04-13 r84269) -- "Already Tomorrow" 4617
palomino3Windows Server 2022 Datacenterx644.3.0 RC (2023-04-13 r84269 ucrt) -- "Already Tomorrow" 4368
merida1macOS 12.6.4 Montereyx86_644.3.0 RC (2023-04-13 r84257) -- "Already Tomorrow" 4326
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

CHECK results for monocle on merida1


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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1275/2229HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
monocle 2.28.0  (landing page)
Cole Trapnell
Snapshot Date: 2023-05-28 14:00:13 -0400 (Sun, 28 May 2023)
git_url: https://git.bioconductor.org/packages/monocle
git_branch: RELEASE_3_17
git_last_commit: 03bcc6d
git_last_commit_date: 2023-04-25 10:32:15 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: monocle
Version: 2.28.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:monocle.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings monocle_2.28.0.tar.gz
StartedAt: 2023-05-29 04:19:09 -0400 (Mon, 29 May 2023)
EndedAt: 2023-05-29 04:23:20 -0400 (Mon, 29 May 2023)
EllapsedTime: 251.7 seconds
RetCode: 0
Status:   OK  
CheckDir: monocle.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:monocle.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings monocle_2.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/monocle.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84257)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘monocle/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘monocle’ version ‘2.28.0’
* 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
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 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 is not available
* 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 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
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/monocle.Rcheck/00check.log’
for details.



Installation output

monocle.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL monocle
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘monocle’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c clustering.cpp -o clustering.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/4.3-x86_64/Resources/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 4.3.0 RC (2023-04-13 r84257) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 
  0.725   0.148   0.965 

Example timings

monocle.Rcheck/monocle-Ex.timings

nameusersystemelapsed
cellPairwiseDistances-set0.0000.0010.001
cellPairwiseDistances0.0000.0010.001
clusterGenes0.0000.0010.000
detectGenes0.0000.0010.000
estimate_t0.0000.0010.000
exportCDS0.0000.0000.001
importCDS000
minSpanningTree-set0.0010.0000.000
minSpanningTree0.0000.0010.001
newCellDataSet0.0000.0010.001
newCellTypeHierarchy0.0010.0010.002
package-deprecated0.0000.0010.000
plot_cell_clusters000
plot_cell_trajectory0.0000.0000.001
plot_clusters0.0000.0000.001
plot_complex_cell_trajectory0.0000.0010.001
plot_genes_in_pseudotime0.0010.0000.001
plot_genes_jitter0.0010.0010.001
plot_genes_positive_cells0.0000.0010.005
plot_genes_violin000
plot_pc_variance_explained0.0000.0010.001
plot_rho_delta0.0010.0000.000
reducedDimA-set0.0000.0000.001
reducedDimA0.0000.0010.000
reducedDimK-set0.0000.0010.000
reducedDimK0.0010.0000.000
reducedDimS-set000
reducedDimS0.0000.0010.000
reducedDimW-set0.0000.0010.001
reducedDimW0.0000.0000.001
relative2abs0.0010.0010.001