Luke Zappia
| Snapshot Date: 2024-05-18 09:00:01 -0400 (Sat, 18 May 2024) |
| git_url: https://git.bioconductor.org/packages/splatter |
| git_branch: devel |
| git_last_commit: 4018ddc |
| git_last_commit_date: 2024-05-06 07:40:26 -0400 (Mon, 06 May 2024) |
| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-20 11:32:21 -0400 (Mon, 20 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
| 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 1990/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| splatter 1.29.0 (landing page) Luke Zappia
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the splatter package: - 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: 1.29.0 |
| 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_1.29.0.tar.gz |
| StartedAt: 2024-05-20 03:56:51 -0400 (Mon, 20 May 2024) |
| EndedAt: 2024-05-20 04:05:39 -0400 (Mon, 20 May 2024) |
| EllapsedTime: 527.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: splatter.Rcheck |
| Warnings: 0 |
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### 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_1.29.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/splatter.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘splatter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘splatter’ version ‘1.29.0’
* 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 code 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 32.984 0.384 33.551
mockBulkeQTL 6.220 0.308 6.574
BASiCSSimulate 6.217 0.190 6.433
kersplatEstimate 5.017 0.126 5.158
* 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 ... 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/4.4-arm64/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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
0.221 0.063 0.268
splatter.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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, 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")
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 188 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 188 ]
>
> proc.time()
user system elapsed
220.812 12.041 234.347
splatter.Rcheck/splatter-Ex.timings
| name | user | system | elapsed | |
| BASiCSEstimate | 0 | 0 | 0 | |
| BASiCSSimulate | 6.217 | 0.190 | 6.433 | |
| addGeneLengths | 0.534 | 0.011 | 0.546 | |
| compareSCEs | 2.440 | 0.062 | 2.508 | |
| diffSCEs | 2.453 | 0.018 | 2.479 | |
| getParam | 0 | 0 | 0 | |
| getParams | 0.000 | 0.001 | 0.000 | |
| kersplatEstimate | 5.017 | 0.126 | 5.158 | |
| kersplatSample | 2.180 | 0.097 | 2.298 | |
| kersplatSetup | 0.167 | 0.019 | 0.187 | |
| kersplatSimulate | 0.000 | 0.000 | 0.001 | |
| listSims | 0.019 | 0.002 | 0.020 | |
| lun2Estimate | 0 | 0 | 0 | |
| lun2Simulate | 0.446 | 0.030 | 0.477 | |
| lunEstimate | 0.483 | 0.005 | 0.490 | |
| lunSimulate | 0.491 | 0.017 | 0.511 | |
| makeCompPanel | 0 | 0 | 0 | |
| makeDiffPanel | 0.001 | 0.000 | 0.000 | |
| makeOverallPanel | 0 | 0 | 0 | |
| mfaEstimate | 0.117 | 0.012 | 0.129 | |
| mfaSimulate | 0.508 | 0.047 | 0.555 | |
| minimiseSCE | 1.891 | 0.061 | 1.957 | |
| mockBulkMatrix | 0.001 | 0.001 | 0.000 | |
| mockBulkeQTL | 6.220 | 0.308 | 6.574 | |
| mockEmpiricalSet | 2.645 | 0.207 | 2.869 | |
| mockGFF | 0.002 | 0.002 | 0.005 | |
| mockVCF | 0.108 | 0.002 | 0.110 | |
| newParams | 0.001 | 0.000 | 0.002 | |
| phenoEstimate | 0.624 | 0.015 | 0.640 | |
| phenoSimulate | 0.859 | 0.042 | 0.904 | |
| scDDEstimate | 32.984 | 0.384 | 33.551 | |
| scDDSimulate | 0 | 0 | 0 | |
| setParam | 0.009 | 0.001 | 0.009 | |
| setParams | 0.024 | 0.002 | 0.025 | |
| simpleEstimate | 0.526 | 0.008 | 0.536 | |
| simpleSimulate | 0.662 | 0.009 | 0.673 | |
| sparseDCEstimate | 0.783 | 0.047 | 0.840 | |
| sparseDCSimulate | 0.647 | 0.089 | 0.743 | |
| splatEstimate | 3.209 | 0.137 | 3.358 | |
| splatPopEstimate | 3.119 | 0.095 | 3.223 | |
| splatPopQuantNorm | 0.029 | 0.001 | 0.030 | |
| splatPopSimulate | 0.000 | 0.000 | 0.001 | |
| splatPopSimulateMeans | 0 | 0 | 0 | |
| splatPopSimulateSC | 0.000 | 0.001 | 0.000 | |
| splatSimulate | 2.374 | 0.055 | 2.437 | |
| summariseDiff | 2.285 | 0.042 | 2.409 | |
| zinbEstimate | 2.061 | 0.086 | 2.158 | |
| zinbSimulate | 0.170 | 0.002 | 0.172 | |