Hector Roux de Bezieux
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/tradeSeq |
| git_branch: master |
| git_last_commit: b8403da |
| git_last_commit_date: 2021-10-26 12:56:03 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:53 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the tradeSeq package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1986/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| tradeSeq 1.9.0 (landing page) Hector Roux de Bezieux
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: tradeSeq |
| Version: 1.9.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tradeSeq.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings tradeSeq_1.9.0.tar.gz |
| StartedAt: 2022-03-17 20:30:37 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:48:28 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 1070.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: tradeSeq.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tradeSeq.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings tradeSeq_1.9.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/tradeSeq.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'tradeSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'tradeSeq' version '1.9.0'
* 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 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:
'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 ... 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 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 100.91 4.06 111.80
associationTest 54.99 2.36 72.16
plotGeneCount 49.97 2.52 52.54
plotSmoothers 50.86 1.50 52.39
fitGAM 49.25 1.84 51.22
evaluateK 18.79 0.17 18.95
plot_evalutateK_results 17.22 0.17 17.39
* 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: 2 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/tradeSeq.Rcheck/00check.log'
for details.
tradeSeq.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL tradeSeq
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-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
converting help for package 'tradeSeq'
finding HTML links ... done
associationTest html
celltype html
clusterExpressionPatterns html
conditionTest html
countMatrix html
crv html
diffEndTest html
earlyDETest html
evaluateK html
fitGAM html
gamList html
getSmootherPvalues html
getSmootherTestStats html
nknots html
patternTest html
plotGeneCount html
finding level-2 HTML links ... done
plotSmoothers html
plot_evalutateK_results html
predictCells html
predictSmooth html
sds html
startVsEndTest html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'simplifyEnrichment' is missing or broken
done
tradeSeq.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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)
> 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, 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, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
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 0 | SKIP 0 | PASS 208 ]
>
> proc.time()
user system elapsed
523.04 1.82 524.81
tradeSeq.Rcheck/tradeSeq-Ex.timings
| name | user | system | elapsed | |
| associationTest | 54.99 | 2.36 | 72.16 | |
| clusterExpressionPatterns | 0 | 0 | 0 | |
| conditionTest | 100.91 | 4.06 | 111.80 | |
| diffEndTest | 0.01 | 0.00 | 0.02 | |
| earlyDETest | 0.03 | 0.00 | 0.03 | |
| evaluateK | 18.79 | 0.17 | 18.95 | |
| fitGAM | 49.25 | 1.84 | 51.22 | |
| getSmootherPvalues | 0.04 | 0.00 | 0.05 | |
| getSmootherTestStats | 0.05 | 0.00 | 0.04 | |
| nknots | 0.02 | 0.00 | 0.02 | |
| patternTest | 0.04 | 0.00 | 0.05 | |
| plotGeneCount | 49.97 | 2.52 | 52.54 | |
| plotSmoothers | 50.86 | 1.50 | 52.39 | |
| plot_evalutateK_results | 17.22 | 0.17 | 17.39 | |
| predictCells | 0.00 | 0.02 | 0.02 | |
| predictSmooth | 0.03 | 0.00 | 0.03 | |
| startVsEndTest | 0.03 | 0.00 | 0.03 | |