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This page was generated on 2024-07-16 11:41 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 2130/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tradeSeq 1.19.0  (landing page)
Hector Roux de Bezieux
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/tradeSeq
git_branch: devel
git_last_commit: e85d386
git_last_commit_date: 2024-04-30 11:19:07 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for tradeSeq on palomino6

To the developers/maintainers of the tradeSeq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tradeSeq.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.

raw results


Summary

Package: tradeSeq
Version: 1.19.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tradeSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings tradeSeq_1.19.0.tar.gz
StartedAt: 2024-07-16 05:06:42 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 05:28:53 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 1331.7 seconds
RetCode: 0
Status:   OK  
CheckDir: tradeSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tradeSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings tradeSeq_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/tradeSeq.Rcheck'
* using R version 4.4.1 (2024-06-14 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 'tradeSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'tradeSeq' version '1.19.0'
* package encoding: UTF-8
* 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 'tradeSeq' 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 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:
  'Biobase' 'igraph'
  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
.earlyDETest: no visible binding for global variable 'X1'
.earlyDETest: no visible binding for global variable 'X2'
.findKnots: no visible binding for global variable 't1'
.findKnots: no visible binding for global variable 'l1'
.plotGeneCount: no visible binding for global variable 'dim1'
.plotGeneCount: no visible binding for global variable 'dim2'
.plotSmoothers: no visible binding for global variable 'time'
.plotSmoothers: no visible binding for global variable 'gene_count'
.plotSmoothers: no visible binding for global variable 'lineage'
.plotSmoothers_conditions: no visible binding for global variable
  'time'
.plotSmoothers_conditions: no visible binding for global variable
  'gene_count'
.plotSmoothers_conditions: no visible binding for global variable
  'lineage'
.plotSmoothers_conditions: no visible binding for global variable
  'pCol'
.plotSmoothers_sce: no visible binding for global variable 'time'
.plotSmoothers_sce: no visible binding for global variable 'gene_count'
.plotSmoothers_sce: no visible binding for global variable 'lineage'
.plotSmoothers_sce: no visible binding for global variable 'pCol'
Undefined global functions or variables:
  X1 X2 dim1 dim2 gene_count l1 lineage pCol t1 time
Consider adding
  importFrom("stats", "time")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) fitGAM.Rd:151-154: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitGAM.Rd:155-156: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitGAM.Rd:157-158: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitGAM.Rd:159-160: Lost braces in \itemize; meant \describe ?
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
conditionTest           93.86   4.36   98.46
associationTest         84.17   4.36  110.60
plotSmoothers           60.64   6.24   65.00
plotGeneCount           60.39   3.91   63.66
fitGAM                  56.35   5.84   62.78
plot_evalutateK_results 26.08   2.54   29.53
evaluateK               26.19   1.35   28.01
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/tradeSeq.Rcheck/00check.log'
for details.


Installation output

tradeSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL tradeSeq
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'tradeSeq' ...
** using staged installation
** R
** data
** 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 (tradeSeq)

Tests output

tradeSeq.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
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)
> library(tradeSeq)
> library(SingleCellExperiment)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> library(slingshot)
Loading required package: princurve
Loading required package: TrajectoryUtils
> 
> test_check("tradeSeq")
2 parameter combinations, 2 use sequential method, 2 use subsampling method
Running Clustering on Parameter Combinations...
done.
2 parameter combinations, 2 use sequential method, 2 use subsampling method
Running Clustering on Parameter Combinations...
done.
2 parameter combinations, 2 use sequential method, 2 use subsampling method
Running Clustering on Parameter Combinations...
done.
2 parameter combinations, 2 use sequential method, 2 use subsampling method
Running Clustering on Parameter Combinations...
done.
2 parameter combinations, 2 use sequential method, 2 use subsampling method
Running Clustering on Parameter Combinations...
done.
2 parameter combinations, 2 use sequential method, 2 use subsampling method
Running Clustering on Parameter Combinations...
done.
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 208 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 208 ]
> 
> proc.time()
   user  system elapsed 
 589.39   12.32  606.79 

Example timings

tradeSeq.Rcheck/tradeSeq-Ex.timings

nameusersystemelapsed
associationTest 84.17 4.36110.60
clusterExpressionPatterns000
conditionTest93.86 4.3698.46
diffEndTest0.020.000.02
earlyDETest0.010.010.03
evaluateK26.19 1.3528.01
fitGAM56.35 5.8462.78
getSmootherPvalues0.040.000.03
getSmootherTestStats0.030.000.03
nknots0.000.010.02
patternTest0.030.000.03
plotGeneCount60.39 3.9163.66
plotSmoothers60.64 6.2465.00
plot_evalutateK_results26.08 2.5429.53
predictCells0.010.000.01
predictSmooth0.030.000.04
startVsEndTest0.040.000.03