Luke Zappia
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/splatter |
| Branch: RELEASE_3_6 |
| Last Commit: 054eaf5 |
| Last Changed Date: 2018-03-26 19:55:26 -0400 (Mon, 26 Mar 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:29:17 -0400 (Thu, 12 Apr 2018).
| Package 1333/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| splatter 1.2.2 Luke Zappia
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: splatter |
| Version: 1.2.2 |
| Command: rm -rf splatter.buildbin-libdir splatter.Rcheck && mkdir splatter.buildbin-libdir splatter.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=splatter.buildbin-libdir splatter_1.2.2.tar.gz >splatter.Rcheck\00install.out 2>&1 && cp splatter.Rcheck\00install.out splatter-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=splatter.buildbin-libdir --install="check:splatter-install.out" --force-multiarch --no-vignettes --timings splatter_1.2.2.tar.gz |
| StartedAt: 2018-04-12 03:21:55 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 03:29:48 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 473.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: splatter.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf splatter.buildbin-libdir splatter.Rcheck && mkdir splatter.buildbin-libdir splatter.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=splatter.buildbin-libdir splatter_1.2.2.tar.gz >splatter.Rcheck\00install.out 2>&1 && cp splatter.Rcheck\00install.out splatter-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=splatter.buildbin-libdir --install="check:splatter-install.out" --force-multiarch --no-vignettes --timings splatter_1.2.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/splatter.Rcheck' * using R version 3.4.4 (2018-03-15) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'splatter/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'splatter' version '1.2.2' * 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 ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/addFeatureStats.Rd:33: missing file link 'rowData' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/addGeneLengths.Rd:29: missing file link 'rowData' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/lun2Estimate.Rd:32: missing file link 'BiocParallelParam' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/lun2Estimate.Rd:34: missing file link 'SerialParam' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/scDDEstimate.Rd:30: missing file link 'BiocParallelParam' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/scDDEstimate.Rd:32: missing file link 'SerialParam' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/scDDSimulate.Rd:20: missing file link 'BiocParallelParam' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/scDDSimulate.Rd:22: missing file link 'SerialParam' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/splatSimulate.Rd:65: missing file link 'colData' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/splatSimulate.Rd:66: missing file link 'rowData' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/splatSimulate.Rd:67: missing file link 'assays' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/zinbEstimate.Rd:44: missing file link 'BiocParallelParam' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/zinbEstimate.Rd:46: missing file link 'SerialParam' See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/splatter.Rcheck/00install.out' for details. * 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... 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: 1 WARNING See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/splatter.Rcheck/00check.log' for details.
splatter.Rcheck/00install.out
install for i386
* installing *source* package 'splatter' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'splatter'
finding HTML links ... done
BASiCSEstimate html
BASiCSParams html
BASiCSSimulate html
Lun2Params html
LunParams html
MFAParams html
Params html
PhenoParams html
SCDDParams html
SimpleParams html
SplatParams html
ZINBParams html
addFeatureStats html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/addFeatureStats.Rd:33: missing file link 'rowData'
addGeneLengths html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/addGeneLengths.Rd:29: missing file link 'rowData'
bridge html
compareSCEs html
diffSCEs html
expandParams html
getLNormFactors html
getParam html
getParams html
getPathOrder html
listSims html
logistic html
lun2Estimate html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/lun2Estimate.Rd:32: missing file link 'BiocParallelParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/lun2Estimate.Rd:34: missing file link 'SerialParam'
lun2Simulate html
lunEstimate html
lunSimulate html
makeCompPanel html
makeDiffPanel html
makeOverallPanel html
mfaEstimate html
mfaSimulate html
newParams html
phenoEstimate html
phenoSimulate html
rbindMatched html
scDDEstimate html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/scDDEstimate.Rd:30: missing file link 'BiocParallelParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/scDDEstimate.Rd:32: missing file link 'SerialParam'
scDDSimulate html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/scDDSimulate.Rd:20: missing file link 'BiocParallelParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/scDDSimulate.Rd:22: missing file link 'SerialParam'
setParam html
setParamUnchecked html
setParams html
setParamsUnchecked html
showPP html
simpleEstimate html
simpleSimulate html
splatEstBCV html
splatEstDropout html
splatEstLib html
splatEstMean html
splatEstOutlier html
splatEstimate html
splatSimBCVMeans html
splatSimBatchCellMeans html
splatSimBatchEffects html
splatSimCellMeans html
splatSimDE html
splatSimDropout html
splatSimGeneMeans html
splatSimLibSizes html
splatSimTrueCounts html
splatSimulate html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/splatSimulate.Rd:65: missing file link 'colData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/splatSimulate.Rd:66: missing file link 'rowData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/splatSimulate.Rd:67: missing file link 'assays'
splatter html
summariseDiff html
winsorize html
zinbEstimate html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/zinbEstimate.Rd:44: missing file link 'BiocParallelParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/zinbEstimate.Rd:46: missing file link 'SerialParam'
zinbSimulate html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'splatter' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'splatter' as splatter_1.2.2.zip
* DONE (splatter)
In R CMD INSTALL
In R CMD INSTALL
|
splatter.Rcheck/tests_i386/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: scater
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: ggplot2
Loading required package: 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
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
Attaching package: 'scater'
The following object is masked from 'package:S4Vectors':
rename
The following object is masked from 'package:stats':
filter
>
> test_check("splatter")
== testthat results ===========================================================
OK: 58 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
89.60 1.06 90.85
|
splatter.Rcheck/tests_x64/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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: scater
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: ggplot2
Loading required package: 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
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
Attaching package: 'scater'
The following object is masked from 'package:S4Vectors':
rename
The following object is masked from 'package:stats':
filter
>
> test_check("splatter")
== testthat results ===========================================================
OK: 58 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
76.50 0.78 77.37
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splatter.Rcheck/examples_i386/splatter-Ex.timings
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splatter.Rcheck/examples_x64/splatter-Ex.timings
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