Hector Roux de Bezieux
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/tradeSeq |
| Branch: master |
| Last Commit: 894a79b |
| Last Changed Date: 2019-10-29 13:43:48 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:56:03 -0500 (Thu, 16 Jan 2020).
| Package 1738/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| tradeSeq 1.1.0 Hector Roux de Bezieux
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | NA | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: tradeSeq |
| Version: 1.1.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:tradeSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings tradeSeq_1.1.0.tar.gz |
| StartedAt: 2020-01-16 09:34:33 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 09:47:04 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 750.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: tradeSeq.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:tradeSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings tradeSeq_1.1.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/tradeSeq.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tradeSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tradeSeq’ version ‘1.1.0’
* 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 ‘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
':::' call which should be '::': ‘mgcv:::s’
See the note in ?`:::` about the use of this operator.
* 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’
.fitGAM: no visible binding for global variable ‘t1’
.fitGAM: no visible binding for global variable ‘l1’
.fitGAM: no visible binding for global variable ‘X’
.fitGAM: no visible binding for global variable ‘dm’
.fitGAM: no visible binding for global variable ‘knotPoints’
.plotSmoothers: no visible binding for global variable ‘gene_count’
.plotSmoothers: no visible binding for global variable ‘lineage’
.plotSmoothers_sce: no visible binding for global variable ‘gene_count’
.plotSmoothers_sce: no visible binding for global variable ‘lineage’
plotGeneCount: no visible binding for global variable ‘dim1’
plotGeneCount: no visible binding for global variable ‘dim2’
fitGAM,matrix: no visible binding for global variable ‘X’
fitGAM,matrix: no visible binding for global variable ‘dm’
Undefined global functions or variables:
X X1 X2 dim1 dim2 dm gene_count knotPoints l1 lineage t1
* 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
fitGAM 85.170 14.696 109.409
plotGeneCount 62.766 10.159 74.818
evaluateK 41.982 1.961 45.817
clusterExpressionPatterns 15.809 0.272 16.082
* 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
‘/Users/biocbuild/bbs-3.11-bioc/meat/tradeSeq.Rcheck/00check.log’
for details.
tradeSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL tradeSeq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘tradeSeq’ ... ** using staged installation ** R ** data ** 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)
tradeSeq.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)
tradeSeq has been updated to accommodate singleCellExperiment objects as output, making it much more memory efficient. Please check the news file and the updated vignette for details.
> library(SingleCellExperiment)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
> library(slingshot)
Loading required package: princurve
> data("sds", package="tradeSeq")
>
> set.seed(3)
> n <- nrow(reducedDim(sds))
> G <- 100
> pseudotime <- slingPseudotime(sds, na=FALSE)
> cellWeights <- slingCurveWeights(sds)
> means <- matrix(rep(rlnorm(n=G, meanlog=4, sdlog=1), n),
+ nrow=G, ncol=n, byrow=FALSE)
> dispersions <- matrix(rep(runif(n=G, min=0.8, max=3), n),
+ nrow=G, ncol=n, byrow=FALSE)
> # add pseudotime effects for a few
> id <- sample(1:100, 20)
> means[id,] <- sweep(means[id,],2,FUN="*",STATS=(pseudotime[,1]/50))
> # simulate NB counts
> counts <- matrix(rnbinom(n=G*n, mu=means, size=1/dispersions), nrow=G, ncol=n)
>
>
> # fitGAM tests
> set.seed(3)
> sdsFit <- tradeSeq::fitGAM(counts, sds, nknots=3, verbose=FALSE, parallel=FALSE)
> set.seed(3)
> listFit <- tradeSeq::fitGAM(counts, pseudotime = pseudotime,
+ cellWeights = cellWeights, nknots = 3,
+ verbose = FALSE, parallel = FALSE)
>
> test_check("tradeSeq")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
66.366 2.832 69.262
tradeSeq.Rcheck/tradeSeq-Ex.timings
| name | user | system | elapsed | |
| associationTest | 0.137 | 0.010 | 0.145 | |
| clusterExpressionPatterns | 15.809 | 0.272 | 16.082 | |
| diffEndTest | 0.059 | 0.001 | 0.060 | |
| earlyDETest | 0.101 | 0.003 | 0.105 | |
| evaluateK | 41.982 | 1.961 | 45.817 | |
| fitGAM | 85.170 | 14.696 | 109.409 | |
| getSmootherPvalues | 0.059 | 0.001 | 0.060 | |
| getSmootherTestStats | 0.057 | 0.001 | 0.059 | |
| patternTest | 0.093 | 0.003 | 0.096 | |
| plotGeneCount | 62.766 | 10.159 | 74.818 | |
| plotSmoothers | 0.481 | 0.004 | 0.487 | |
| startVsEndTest | 0.063 | 0.002 | 0.065 | |