Luke Zappia
| Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/splatter |
| git_branch: RELEASE_3_18 |
| git_last_commit: 07e5c7d |
| git_last_commit_date: 2023-10-24 10:55:11 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:38:17 -0400 (Fri, 29 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
| 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 2029/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| splatter 1.26.0 (landing page) Luke Zappia
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the splatter package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/splatter.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: splatter |
| Version: 1.26.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:splatter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings splatter_1.26.0.tar.gz |
| StartedAt: 2024-03-28 09:22:31 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 09:39:01 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 990.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: splatter.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:splatter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings splatter_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/splatter.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘splatter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘splatter’ version ‘1.26.0’
* 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 ‘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 56.619 0.915 59.146
mockBulkeQTL 9.280 0.773 10.384
BASiCSSimulate 8.620 0.508 9.440
mockEmpiricalSet 7.972 0.576 8.641
kersplatEstimate 7.738 0.225 8.089
splatPopEstimate 7.383 0.191 7.921
splatEstimate 5.932 0.098 6.159
compareSCEs 5.872 0.096 6.108
summariseDiff 5.794 0.094 6.215
diffSCEs 5.312 0.050 5.623
zinbEstimate 4.829 0.160 5.316
* 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL splatter ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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 version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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
0.356 0.119 0.440
splatter.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
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
382.642 14.841 424.296
splatter.Rcheck/splatter-Ex.timings
| name | user | system | elapsed | |
| BASiCSEstimate | 0.001 | 0.001 | 0.001 | |
| BASiCSSimulate | 8.620 | 0.508 | 9.440 | |
| addGeneLengths | 0.748 | 0.036 | 0.788 | |
| compareSCEs | 5.872 | 0.096 | 6.108 | |
| diffSCEs | 5.312 | 0.050 | 5.623 | |
| getParam | 0.000 | 0.000 | 0.001 | |
| getParams | 0.001 | 0.001 | 0.001 | |
| kersplatEstimate | 7.738 | 0.225 | 8.089 | |
| kersplatSample | 2.591 | 0.137 | 2.795 | |
| kersplatSetup | 0.258 | 0.053 | 0.322 | |
| kersplatSimulate | 0.000 | 0.001 | 0.001 | |
| listSims | 0.053 | 0.007 | 0.059 | |
| lun2Estimate | 0 | 0 | 0 | |
| lun2Simulate | 0.669 | 0.046 | 0.721 | |
| lunEstimate | 0.894 | 0.010 | 0.909 | |
| lunSimulate | 0.612 | 0.027 | 0.641 | |
| makeCompPanel | 0.000 | 0.001 | 0.001 | |
| makeDiffPanel | 0.000 | 0.001 | 0.001 | |
| makeOverallPanel | 0.000 | 0.000 | 0.001 | |
| mfaEstimate | 0.182 | 0.021 | 0.214 | |
| mfaSimulate | 0.933 | 0.069 | 1.025 | |
| minimiseSCE | 2.387 | 0.060 | 2.465 | |
| mockBulkMatrix | 0.000 | 0.000 | 0.001 | |
| mockBulkeQTL | 9.280 | 0.773 | 10.384 | |
| mockEmpiricalSet | 7.972 | 0.576 | 8.641 | |
| mockGFF | 0.004 | 0.000 | 0.005 | |
| mockVCF | 0.238 | 0.001 | 0.239 | |
| newParams | 0.003 | 0.001 | 0.005 | |
| phenoEstimate | 1.052 | 0.019 | 1.082 | |
| phenoSimulate | 1.960 | 0.136 | 2.169 | |
| scDDEstimate | 56.619 | 0.915 | 59.146 | |
| scDDSimulate | 0.001 | 0.000 | 0.001 | |
| setParam | 0.020 | 0.002 | 0.024 | |
| setParams | 0.046 | 0.005 | 0.060 | |
| simpleEstimate | 0.779 | 0.018 | 0.816 | |
| simpleSimulate | 0.856 | 0.020 | 0.900 | |
| sparseDCEstimate | 2.005 | 0.139 | 2.611 | |
| sparseDCSimulate | 2.144 | 0.114 | 2.350 | |
| splatEstimate | 5.932 | 0.098 | 6.159 | |
| splatPopEstimate | 7.383 | 0.191 | 7.921 | |
| splatPopQuantNorm | 0.070 | 0.003 | 0.078 | |
| splatPopSimulate | 0.000 | 0.000 | 0.001 | |
| splatPopSimulateMeans | 0.000 | 0.000 | 0.001 | |
| splatPopSimulateSC | 0.001 | 0.000 | 0.000 | |
| splatSimulate | 2.760 | 0.061 | 2.941 | |
| summariseDiff | 5.794 | 0.094 | 6.215 | |
| zinbEstimate | 4.829 | 0.160 | 5.316 | |
| zinbSimulate | 0.381 | 0.004 | 0.414 | |