Kelly Street
| Snapshot Date: 2024-05-21 14:00:15 -0400 (Tue, 21 May 2024) |
| git_url: https://git.bioconductor.org/packages/slingshot |
| git_branch: RELEASE_3_19 |
| git_last_commit: 2e8da38 |
| git_last_commit_date: 2024-04-30 11:07:02 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-22 11:36:13 -0400 (Wed, 22 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 3444 |
| 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 2003/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| slingshot 2.12.0 (landing page) Kelly Street
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: slingshot |
| Version: 2.12.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:slingshot.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings slingshot_2.12.0.tar.gz |
| StartedAt: 2024-05-22 06:44:25 -0400 (Wed, 22 May 2024) |
| EndedAt: 2024-05-22 06:48:25 -0400 (Wed, 22 May 2024) |
| EllapsedTime: 240.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: slingshot.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:slingshot.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings slingshot_2.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/slingshot.Rcheck'
* using R version 4.4.0 (2024-04-24 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 'slingshot/DESCRIPTION' ... OK
* this is package 'slingshot' version '2.12.0'
* 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 '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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
'F:/biocbuild/bbs-3.19-bioc/meat/slingshot.Rcheck/00check.log'
for details.
slingshot.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL slingshot ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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)
slingshot.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24 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)
> 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, 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
>
> 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
42.87 2.35 45.71
slingshot.Rcheck/slingshot-Ex.timings
| name | user | system | elapsed | |
| SlingshotDataSet | 1.08 | 0.07 | 1.15 | |
| as.PseudotimeOrdering | 1.10 | 0.02 | 1.11 | |
| as.SlingshotDataSet | 0.22 | 0.01 | 0.24 | |
| embedCurves | 0.30 | 0.00 | 0.29 | |
| getCurves | 0.39 | 0.02 | 0.41 | |
| getLineages | 0.09 | 0.02 | 0.11 | |
| newSlingshotDataSet | 0 | 0 | 0 | |
| pairs-SlingshotDataSet | 0.46 | 0.03 | 0.48 | |
| plot-SlingshotDataSet | 0.25 | 0.00 | 0.25 | |
| plot3d-SlingshotDataSet | 0 | 0 | 0 | |
| predict.SlingshotDataSet | 0.26 | 0.01 | 0.28 | |
| slingBranchGraph | 0.27 | 0.02 | 0.28 | |
| slingBranchID | 0.79 | 0.00 | 0.80 | |
| slingClusterLabels | 0.21 | 0.01 | 0.22 | |
| slingCurves | 0.22 | 0.05 | 0.27 | |
| slingLineages | 0.26 | 0.02 | 0.28 | |
| slingMST | 0.25 | 0.03 | 0.28 | |
| slingParams | 0.37 | 0.01 | 0.39 | |
| slingPseudotime | 0.27 | 0.00 | 0.27 | |
| slingReducedDim | 0.23 | 0.02 | 0.25 | |
| slingshot | 0.35 | 0.00 | 0.34 | |
| slingshotExample | 0.25 | 0.01 | 0.27 | |