Andrew McDavid
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/MAST |
| git_branch: master |
| git_last_commit: 1843019 |
| git_last_commit_date: 2021-12-17 10:41:45 -0400 (Fri, 17 Dec 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:56 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 MAST package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MAST.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1059/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MAST 1.21.3 (landing page) Andrew McDavid
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: MAST |
| Version: 1.21.3 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MAST.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MAST_1.21.3.tar.gz |
| StartedAt: 2022-03-17 19:29:15 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:33:15 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 239.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MAST.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MAST.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MAST_1.21.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MAST.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MAST/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MAST' version '1.21.3'
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'MAST' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
data 3.7Mb
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
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: 2 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/MAST.Rcheck/00check.log'
for details.
MAST.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MAST
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'MAST' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MAST'
finding HTML links ... done
BayesGLMlike-class html
CovFromBoots html
Drop html
FromFlatDF html
FromMatrix html
GLMlike-class html
GSEATests-class html
Hypothesis html
LMERlike-class html
LMlike-class html
LRT html
MAST-defunct html
finding level-2 HTML links ... done
MAST-package html
SceToSingleCellAssay html
ZlmFit-class html
applyFlat html
bootVcov1 html
calcZ html
colData-set-SingleCellAssay-DataFrame-method
html
collectResiduals html
computeEtFromCt html
convertMASTClassicToSingleCellAssay html
defaultAssay html
defaultPrior html
dof html
ebayes html
expavg html
filterLowExpressedGenes html
fit html
freq html
getConcordance html
getwellKey html
gseaAfterBoot html
hushWarning html
impute html
influence.bayesglm html
invlogit html
logFC html
logmean html
lrTest-ZlmFit-character-method html
lrTest html
maits-dataset html
mast_filter html
meld_list_left html
melt.SingleCellAssay html
model.matrix-set html
model.matrix html
myBiplot html
plot.thresholdSCRNACountMatrix html
plotSCAConcordance html
plotlrt html
predict.ZlmFit html
predicted_sig-dataset html
primerAverage html
print.summaryZlmFit html
read.fluidigm html
removeResponse html
rstandard.bayesglm html
se.coef html
show html
split-SingleCellAssay-character-method
html
stat_ell html
subset-SingleCellAssay-method html
summarize html
summary-GSEATests-method html
summary-ZlmFit-method html
summary.thresholdSCRNACountMatrix html
thresholdSCRNACountMatrix html
vbeta-dataset html
vbetaFA-dataset html
waldTest-ZlmFit-matrix-method html
waldTest html
xform html
zlm html
** 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 (MAST)
Making 'packages.html' ... done
MAST.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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.
> library(testthat)
> test_check("MAST")
Loading required package: MAST
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, 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
Error : number of levels of each grouping factor must be < number of observations (problems: Subject.ID)
(0.0426,0.354] (0.354,0.757] (0.757,1.28] (1.28,1.96] (1.96,2.84]
2.258200 2.258200 2.258200 2.258200 2.258200
(2.84,3.99] (3.99,13.2]
2.258200 3.313588
(0.0602,0.436] (0.436,0.67] (0.67,0.944] (0.944,1.26] (1.26,1.63]
1.967142 1.967142 1.967142 2.003488 2.003488
(1.63,2.06] (2.06,2.56] (2.56,3.83]
2.600202 2.600202 2.600202
(0.03,1.56] (1.56,5.36] (5.36,14.8] (14.8,9.25e+03]
238.2279 238.2279 238.2279 4525.1912
Error : grouping factors must have > 1 sampled level
NULL
NULL
NULL
Error in (function (x, y, weights = rep.int(1, nobs), start = NULL, etastart = NULL, :
NAs in V(mu)
[ FAIL 0 | WARN 3 | SKIP 5 | PASS 293 ]
== Skipped tests ===============================================================
* empty test (5)
[ FAIL 0 | WARN 3 | SKIP 5 | PASS 293 ]
>
> proc.time()
user system elapsed
46.68 1.56 58.67
MAST.Rcheck/MAST-Ex.timings
| name | user | system | elapsed | |
| Drop | 0 | 0 | 0 | |
| FromFlatDF | 0.91 | 0.06 | 0.96 | |
| FromMatrix | 0.20 | 0.05 | 0.25 | |
| Hypothesis | 0 | 0 | 0 | |
| LRT | 0.10 | 0.03 | 0.14 | |
| ZlmFit-class | 1.08 | 0.00 | 1.08 | |
| applyFlat | 0 | 0 | 0 | |
| bootVcov1 | 0.44 | 0.02 | 0.45 | |
| calcZ | 0.79 | 0.03 | 0.82 | |
| collectResiduals | 0.75 | 0.00 | 0.75 | |
| computeEtFromCt | 0.05 | 0.00 | 0.05 | |
| convertMASTClassicToSingleCellAssay | 0.23 | 0.00 | 0.23 | |
| defaultAssay | 0.02 | 0.01 | 0.04 | |
| defaultPrior | 0 | 0 | 0 | |
| expavg | 0 | 0 | 0 | |
| filterLowExpressedGenes | 0.2 | 0.0 | 0.2 | |
| freq | 0.02 | 0.00 | 0.01 | |
| getConcordance | 0.34 | 0.00 | 0.35 | |
| getwellKey | 0.02 | 0.00 | 0.01 | |
| gseaAfterBoot | 0.84 | 0.02 | 0.86 | |
| hushWarning | 0 | 0 | 0 | |
| impute | 0.92 | 0.00 | 0.93 | |
| invlogit | 0 | 0 | 0 | |
| logFC | 0.24 | 0.00 | 0.23 | |
| logmean | 0 | 0 | 0 | |
| lrTest | 0.57 | 0.00 | 0.56 | |
| mast_filter | 1.26 | 0.03 | 1.29 | |
| meld_list_left | 0 | 0 | 0 | |
| melt.SingleCellAssay | 0.31 | 0.00 | 0.32 | |
| plot.thresholdSCRNACountMatrix | 0.38 | 0.05 | 0.43 | |
| plotSCAConcordance | 0.83 | 0.03 | 0.86 | |
| predict.ZlmFit | 0.84 | 0.00 | 0.85 | |
| se.coef | 0.84 | 0.00 | 0.86 | |
| split-SingleCellAssay-character-method | 1.10 | 0.04 | 1.14 | |
| stat_ell | 0.80 | 0.00 | 0.79 | |
| subset-SingleCellAssay-method | 0.17 | 0.00 | 0.18 | |
| summary-GSEATests-method | 0.89 | 0.02 | 0.91 | |
| summary-ZlmFit-method | 0.39 | 0.02 | 0.40 | |
| thresholdSCRNACountMatrix | 0.86 | 0.01 | 0.88 | |
| waldTest | 0.52 | 0.02 | 0.62 | |
| zlm | 0.28 | 0.00 | 0.29 | |