| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:52 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 splatter package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1925/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| splatter 1.23.0 (landing page) Luke Zappia
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: splatter |
| Version: 1.23.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:splatter.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings splatter_1.23.0.tar.gz |
| StartedAt: 2022-12-29 03:51:10 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 03:58:39 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 448.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: splatter.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:splatter.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings splatter_1.23.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/splatter.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'splatter/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'splatter' version '1.23.0'
* 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 'splatter' 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 ... 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 ... 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
scDDEstimate 21.21 0.31 21.55
kersplatEstimate 6.94 0.05 7.00
splatPopEstimate 6.20 0.08 6.28
splatEstimate 6.11 0.04 6.16
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'spelling.R'
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: OK
splatter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL splatter ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'splatter' ... ** using staged installation ** R ** inst ** 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 (splatter)
splatter.Rcheck/tests/spelling.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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.
> if(requireNamespace('spelling', quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+ skip_on_cran = TRUE)
NULL
>
> proc.time()
user system elapsed
0.12 0.06 0.17
splatter.Rcheck/tests/testthat.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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.
> # setting R_TESTS to empty string because of
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
>
> library(testthat)
> library(splatter)
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, 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
>
> test_check("splatter")
-----------------------------------------------------
MCMC sampler has been started: 20000 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
-----------------------------------------------------
All 20000 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
Minimum acceptance rate among mu[i]'s: 0.216267
Average acceptance rate among mu[i]'s: 0.447751
Maximum acceptance rate among mu[i]'s: 0.581867
Minimum acceptance rate among delta[i]'s: 0.373467
Average acceptance rate among delta[i]'s: 0.446514
Maximum acceptance rate among delta[i]'s: 0.498
Acceptance rate for phi (joint): 0.455867
Minimum acceptance rate among nu[j]'s: 0.3964
Average acceptance rate among nu[j]'s: 0.450696
Maximum acceptance rate among nu[j]'s: 0.506933
Minimum acceptance rate among theta[k]'s: 0.431867
Average acceptance rate among theta[k]'s: 0.431867
Maximum acceptance rate among theta[k]'s: 0.431867
-----------------------------------------------------
-----------------------------------------------------
MCMC sampler has been started: 20000 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
-----------------------------------------------------
All 20000 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
Minimum acceptance rate among mu[i]'s: 0.167067
Average acceptance rate among mu[i]'s: 0.436682
Maximum acceptance rate among mu[i]'s: 0.578267
Minimum acceptance rate among delta[i]'s: 0.395933
Average acceptance rate among delta[i]'s: 0.454213
Maximum acceptance rate among delta[i]'s: 0.515067
Minimum acceptance rate among nu[jk]'s: 0.370533
Average acceptance rate among nu[jk]'s: 0.451502
Maximum acceptance rate among nu[jk]'s: 0.492467
Minimum acceptance rate among theta[k]'s: 0.4586
Average acceptance rate among theta[k]'s: 0.464833
Maximum acceptance rate among theta[k]'s: 0.471067
-----------------------------------------------------
[ FAIL 0 | WARN 14 | SKIP 0 | PASS 184 ]
[ FAIL 0 | WARN 14 | SKIP 0 | PASS 184 ]
>
> proc.time()
user system elapsed
219.53 5.62 225.31
splatter.Rcheck/splatter-Ex.timings
| name | user | system | elapsed | |
| BASiCSEstimate | 0 | 0 | 0 | |
| BASiCSSimulate | 3.61 | 0.17 | 3.79 | |
| addGeneLengths | 0.47 | 0.00 | 0.47 | |
| compareSCEs | 2.02 | 0.06 | 2.08 | |
| diffSCEs | 1.93 | 0.03 | 1.97 | |
| getParam | 0 | 0 | 0 | |
| getParams | 0 | 0 | 0 | |
| kersplatEstimate | 6.94 | 0.05 | 7.00 | |
| kersplatSample | 1.97 | 0.01 | 1.98 | |
| kersplatSetup | 0.17 | 0.02 | 0.19 | |
| kersplatSimulate | 0 | 0 | 0 | |
| listSims | 0.01 | 0.00 | 0.01 | |
| lun2Estimate | 0 | 0 | 0 | |
| lun2Simulate | 0.36 | 0.00 | 0.36 | |
| lunEstimate | 0.41 | 0.02 | 0.42 | |
| lunSimulate | 0.33 | 0.00 | 0.33 | |
| makeCompPanel | 0 | 0 | 0 | |
| makeDiffPanel | 0 | 0 | 0 | |
| makeOverallPanel | 0 | 0 | 0 | |
| mfaEstimate | 0.06 | 0.02 | 0.09 | |
| mfaSimulate | 0.48 | 0.06 | 0.55 | |
| minimiseSCE | 1.22 | 0.00 | 1.22 | |
| mockBulkMatrix | 0 | 0 | 0 | |
| mockBulkeQTL | 3.75 | 0.48 | 4.22 | |
| mockEmpiricalSet | 2.14 | 0.19 | 2.32 | |
| mockGFF | 0 | 0 | 0 | |
| mockVCF | 0.08 | 0.00 | 0.08 | |
| newParams | 0 | 0 | 0 | |
| phenoEstimate | 0.44 | 0.05 | 0.48 | |
| phenoSimulate | 1.73 | 0.06 | 1.80 | |
| scDDEstimate | 21.21 | 0.31 | 21.55 | |
| scDDSimulate | 0 | 0 | 0 | |
| setParam | 0 | 0 | 0 | |
| setParams | 0.01 | 0.00 | 0.02 | |
| simpleEstimate | 0.41 | 0.00 | 0.41 | |
| simpleSimulate | 0.45 | 0.02 | 0.47 | |
| sparseDCEstimate | 0.63 | 0.03 | 0.67 | |
| sparseDCSimulate | 1.45 | 0.02 | 1.47 | |
| splatEstimate | 6.11 | 0.04 | 6.16 | |
| splatPopEstimate | 6.20 | 0.08 | 6.28 | |
| splatPopQuantNorm | 0.02 | 0.00 | 0.01 | |
| splatPopSimulate | 0 | 0 | 0 | |
| splatPopSimulateMeans | 0 | 0 | 0 | |
| splatPopSimulateSC | 0 | 0 | 0 | |
| splatSimulate | 0.70 | 0.02 | 0.72 | |
| summariseDiff | 2.17 | 0.03 | 2.20 | |
| zinbEstimate | 1.75 | 0.06 | 1.83 | |
| zinbSimulate | 0.13 | 0.00 | 0.13 | |