Andrew McDavid
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/MAST |
| Branch: RELEASE_3_10 |
| Last Commit: cd3b54a |
| Last Changed Date: 2019-10-29 13:10:09 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:27:25 -0400 (Wed, 15 Apr 2020).
| Package 961/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MAST 1.12.0 Andrew McDavid
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: MAST |
| Version: 1.12.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MAST.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings MAST_1.12.0.tar.gz |
| StartedAt: 2020-04-15 04:28:51 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:35:36 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 405.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MAST.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MAST.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings MAST_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/MAST.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.12.0'
* 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 ... 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 5.4Mb
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
* 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
* 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 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 data for ASCII and uncompressed saves ... 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/MAST.Rcheck/00check.log'
for details.
MAST.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/MAST_1.12.0.tar.gz && rm -rf MAST.buildbin-libdir && mkdir MAST.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MAST.buildbin-libdir MAST_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL MAST_1.12.0.zip && rm MAST_1.12.0.tar.gz MAST_1.12.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
77 5932k 77 4608k 0 0 15.3M 0 --:--:-- --:--:-- --:--:-- 15.5M
100 5932k 100 5932k 0 0 18.9M 0 --:--:-- --:--:-- --:--:-- 19.1M
install for i386
* 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
MAST-package html
SceToSingleCellAssay html
ZlmFit-class html
applyFlat html
bootVcov1 html
cData html
finding level-2 HTML links ... done
calcZ html
colData-set-SingleCellAssay-DataFrame-method
html
collectResiduals html
computeEtFromCt html
convertMASTClassicToSingleCellAssay html
defaultAssay html
defaultPrior html
dof html
ebayes html
expavg html
fData-methods html
featureData-methods 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
melt.SingleCellAssay html
model.matrix-set html
model.matrix html
myBiplot html
pbootVcov1 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
install for x64
* installing *source* package 'MAST' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MAST' as MAST_1.12.0.zip
* DONE (MAST)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'MAST' successfully unpacked and MD5 sums checked
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MAST.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.
> library(testthat)
> test_check("MAST")
Loading required package: MAST
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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, 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, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
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 in (function (x, y, weights = rep(1, nobs), start = NULL, etastart = NULL, :
NAs in V(mu)
== testthat results ===========================================================
[ OK: 279 | SKIPPED: 5 | WARNINGS: 10 | FAILED: 0 ]
>
> proc.time()
user system elapsed
44.09 1.59 58.28
|
MAST.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: GenomicRanges
Loading required package: stats4
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, 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, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
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 in (function (x, y, weights = rep(1, nobs), start = NULL, etastart = NULL, :
NAs in V(mu)
== testthat results ===========================================================
[ OK: 279 | SKIPPED: 5 | WARNINGS: 10 | FAILED: 0 ]
>
> proc.time()
user system elapsed
40.39 0.90 60.59
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MAST.Rcheck/examples_i386/MAST-Ex.timings
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MAST.Rcheck/examples_x64/MAST-Ex.timings
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