Multiple platform build/check report for BioC 3.20 - CHECK results for slingshot on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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 slingshot on nebbiolo2

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

Version: 2.14.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:slingshot.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings slingshot_2.14.0.tar.gz

StartedAt: 2024-12-20 05:35:45 -0500 (Fri, 20 Dec 2024)

EndedAt: 2024-12-20 05:39:42 -0500 (Fri, 20 Dec 2024)

EllapsedTime: 237.2 seconds

RetCode: 0

Status: OK

CheckDir: slingshot.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:slingshot.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings slingshot_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/slingshot.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘slingshot/DESCRIPTION’ ... OK
* this is package ‘slingshot’ version ‘2.14.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘slingshot’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) SlingshotDataSet-class.Rd:76-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SlingshotDataSet-class.Rd:79-80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SlingshotDataSet-class.Rd:81-82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SlingshotDataSet-class.Rd:83-84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SlingshotDataSet-class.Rd:85-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SlingshotDataSet-class.Rd:88-89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SlingshotDataSet-class.Rd:93-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SlingshotDataSet-class.Rd:96-99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SlingshotDataSet-class.Rd:100-104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SlingshotDataSet-class.Rd:105-112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SlingshotDataSet-class.Rd:113-117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SlingshotDataSet-class.Rd:118-119: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SlingshotDataSet-class.Rd:119-121: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getCurves.Rd:99-100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getCurves.Rd:101-102: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) newSlingshotDataSet.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) newSlingshotDataSet.Rd:59-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) newSlingshotDataSet.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) newSlingshotDataSet.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) newSlingshotDataSet.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) newSlingshotDataSet.Rd:69-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) newSlingshotDataSet.Rd:72-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) newSlingshotDataSet.Rd:76-80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) newSlingshotDataSet.Rd:81-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) newSlingshotDataSet.Rd:89-93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) slingParams.Rd:25-27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) slingParams.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) slingParams.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) slingParams.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) slingParams.Rd:34-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) slingParams.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) slingParams.Rd:42-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) slingParams.Rd:45-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) slingParams.Rd:49-53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) slingParams.Rd:54-61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) slingParams.Rd:62-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) slingParams.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) slingParams.Rd:68-70: Lost braces in \itemize; \value handles \item{}{} directly
* 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
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/slingshot.Rcheck/00check.log’
for details.

Installation output

slingshot.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL slingshot
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘slingshot’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘slingshot’ with signature ‘data="ClusterExperiment"’: no definition for class “ClusterExperiment”
** 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 (slingshot)

Tests output

slingshot.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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(slingshot)
Loading required package: princurve
Loading required package: TrajectoryUtils
Loading required package: 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, saveRDS, 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
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

> 
> test_check("slingshot")
class: SlingshotDataSet 

 Samples Dimensions
     140          2

lineages: 2 
Lineage1: 1  2  3  5  
Lineage2: 1  2  3  4  

curves: 2 
Curve1: Length: 15.045	Samples: 100.61
Curve2: Length: 15.126	Samples: 103.49
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 262 ]
> 
> proc.time()
   user  system elapsed 
 37.209   1.480  38.628

Example timings

slingshot.Rcheck/slingshot-Ex.timings

name	user	system	elapsed
SlingshotDataSet	0.825	0.006	0.832
as.PseudotimeOrdering	0.902	0.022	0.924
as.SlingshotDataSet	0.270	0.001	0.271
embedCurves	0.306	0.001	0.307
getCurves	0.803	0.002	0.805
getLineages	0.057	0.002	0.059
newSlingshotDataSet	0.001	0.000	0.001
pairs-SlingshotDataSet	0.250	0.001	0.251
plot-SlingshotDataSet	0.259	0.016	0.275
plot3d-SlingshotDataSet	0	0	0
predict.SlingshotDataSet	0.269	0.000	0.269
slingBranchGraph	0.247	0.002	0.249
slingBranchID	0.245	0.003	0.249
slingClusterLabels	0.229	0.002	0.231
slingCurves	0.245	0.003	0.248
slingLineages	0.228	0.002	0.229
slingMST	0.230	0.001	0.231
slingParams	0.252	0.017	0.269
slingPseudotime	0.240	0.003	0.243
slingReducedDim	0.237	0.002	0.239
slingshot	0.264	0.000	0.265
slingshotExample	0.24	0.00	0.24