Luke Zappia
| Snapshot Date: 2023-10-23 14:05:08 -0400 (Mon, 23 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/splatter |
| git_branch: devel |
| git_last_commit: 3ee127b |
| git_last_commit_date: 2023-10-11 09:55:31 -0400 (Wed, 11 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-10-24 11:41:34 -0400 (Tue, 24 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4724 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4459 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4473 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4461 |
| 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 2027/2264 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| splatter 1.25.1 (landing page) Luke Zappia
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.3.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: splatter |
| Version: 1.25.1 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:splatter.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings splatter_1.25.1.tar.gz |
| StartedAt: 2023-10-24 13:32:56 -0000 (Tue, 24 Oct 2023) |
| EndedAt: 2023-10-24 13:49:37 -0000 (Tue, 24 Oct 2023) |
| EllapsedTime: 1001.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: splatter.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:splatter.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings splatter_1.25.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/splatter.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘splatter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘splatter’ version ‘1.25.1’
* 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 ‘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 loading without being on the library search path ... 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 42.913 0.455 43.458
BASiCSSimulate 6.696 0.443 7.155
mockBulkeQTL 6.471 0.239 6.725
kersplatEstimate 5.123 0.088 5.221
* 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 ...
‘splatPop.Rmd’ using ‘UTF-8’... OK
‘splat_params.Rmd’ using ‘UTF-8’... OK
‘splatter.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
splatter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL splatter ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
> if(requireNamespace('spelling', quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+ skip_on_cran = TRUE)
NULL
>
> proc.time()
user system elapsed
0.203 0.029 0.218
splatter.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
> # 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 12 | SKIP 0 | PASS 184 ]
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 184 ]
>
> proc.time()
user system elapsed
350.230 4.529 355.370
splatter.Rcheck/splatter-Ex.timings
| name | user | system | elapsed | |
| BASiCSEstimate | 0.000 | 0.000 | 0.001 | |
| BASiCSSimulate | 6.696 | 0.443 | 7.155 | |
| addGeneLengths | 0.488 | 0.012 | 0.501 | |
| compareSCEs | 3.570 | 0.116 | 3.693 | |
| diffSCEs | 3.632 | 0.095 | 3.735 | |
| getParam | 0.001 | 0.000 | 0.001 | |
| getParams | 0 | 0 | 0 | |
| kersplatEstimate | 5.123 | 0.088 | 5.221 | |
| kersplatSample | 1.556 | 0.040 | 1.600 | |
| kersplatSetup | 1.128 | 0.112 | 1.242 | |
| kersplatSimulate | 0 | 0 | 0 | |
| listSims | 0.032 | 0.000 | 0.032 | |
| lun2Estimate | 0.001 | 0.000 | 0.000 | |
| lun2Simulate | 1.307 | 0.060 | 1.369 | |
| lunEstimate | 0.582 | 0.000 | 0.583 | |
| lunSimulate | 0.445 | 0.000 | 0.445 | |
| makeCompPanel | 0 | 0 | 0 | |
| makeDiffPanel | 0 | 0 | 0 | |
| makeOverallPanel | 0.000 | 0.000 | 0.001 | |
| mfaEstimate | 0.115 | 0.004 | 0.120 | |
| mfaSimulate | 0.701 | 0.016 | 0.718 | |
| minimiseSCE | 2.045 | 0.020 | 2.068 | |
| mockBulkMatrix | 0.001 | 0.000 | 0.000 | |
| mockBulkeQTL | 6.471 | 0.239 | 6.725 | |
| mockEmpiricalSet | 3.885 | 0.203 | 4.097 | |
| mockGFF | 0.003 | 0.000 | 0.003 | |
| mockVCF | 0.164 | 0.008 | 0.173 | |
| newParams | 0.002 | 0.000 | 0.002 | |
| phenoEstimate | 0.690 | 0.028 | 0.720 | |
| phenoSimulate | 2.741 | 0.167 | 2.915 | |
| scDDEstimate | 42.913 | 0.455 | 43.458 | |
| scDDSimulate | 0 | 0 | 0 | |
| setParam | 0.013 | 0.000 | 0.013 | |
| setParams | 0.036 | 0.000 | 0.036 | |
| simpleEstimate | 0.644 | 0.023 | 0.670 | |
| simpleSimulate | 0.643 | 0.000 | 0.645 | |
| sparseDCEstimate | 1.372 | 0.016 | 1.393 | |
| sparseDCSimulate | 0.751 | 0.004 | 0.757 | |
| splatEstimate | 4.030 | 0.008 | 4.046 | |
| splatPopEstimate | 3.958 | 0.020 | 3.986 | |
| splatPopQuantNorm | 0.039 | 0.000 | 0.040 | |
| splatPopSimulate | 0 | 0 | 0 | |
| splatPopSimulateMeans | 0 | 0 | 0 | |
| splatPopSimulateSC | 0.001 | 0.000 | 0.000 | |
| splatSimulate | 1.190 | 0.004 | 1.196 | |
| summariseDiff | 3.844 | 0.024 | 3.877 | |
| zinbEstimate | 4.286 | 0.120 | 4.416 | |
| zinbSimulate | 0.281 | 0.000 | 0.282 | |