Hector Roux de Bezieux
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/tradeSeq |
| Branch: RELEASE_3_10 |
| Last Commit: eb046aa |
| Last Changed Date: 2020-04-03 04:11:27 -0400 (Fri, 03 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:16:33 -0400 (Wed, 15 Apr 2020).
| Package 1743/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| tradeSeq 1.0.1 Hector Roux de Bezieux
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: tradeSeq |
| Version: 1.0.1 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:tradeSeq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings tradeSeq_1.0.1.tar.gz |
| StartedAt: 2020-04-15 07:04:57 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 07:11:48 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 411.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: tradeSeq.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:tradeSeq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings tradeSeq_1.0.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/tradeSeq.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘1.0.1’
* 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 or elapsed time > 5s
user system elapsed
fitGAM 51.588 0.076 51.783
plotGeneCount 38.272 0.120 38.511
evaluateK 21.244 0.056 21.324
clusterExpressionPatterns 8.544 0.096 8.656
* 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
‘/home/biocbuild/bbs-3.10-bioc/meat/tradeSeq.Rcheck/00check.log’
for details.
tradeSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL tradeSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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 version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
33.572 0.584 34.285
tradeSeq.Rcheck/tradeSeq-Ex.timings
| name | user | system | elapsed | |
| associationTest | 0.044 | 0.004 | 0.047 | |
| clusterExpressionPatterns | 8.544 | 0.096 | 8.656 | |
| diffEndTest | 0.028 | 0.000 | 0.030 | |
| earlyDETest | 0.052 | 0.004 | 0.057 | |
| evaluateK | 21.244 | 0.056 | 21.324 | |
| fitGAM | 51.588 | 0.076 | 51.783 | |
| getSmootherPvalues | 0.036 | 0.000 | 0.035 | |
| getSmootherTestStats | 0.032 | 0.000 | 0.031 | |
| patternTest | 0.048 | 0.000 | 0.046 | |
| plotGeneCount | 38.272 | 0.120 | 38.511 | |
| plotSmoothers | 0.268 | 0.000 | 0.266 | |
| startVsEndTest | 0.036 | 0.004 | 0.041 | |