| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:12 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1088/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MAST 1.25.1 (landing page) Andrew McDavid
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: MAST |
| Version: 1.25.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MAST.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MAST_1.25.1.tar.gz |
| StartedAt: 2023-02-07 06:54:52 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 07:03:34 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 522.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: MAST.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MAST.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MAST_1.25.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MAST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MAST’ 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 ... 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 for sufficient/correct file permissions ... OK
* checking whether package ‘MAST’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.0Mb
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’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
[ FAIL 1 | WARN 26 | SKIP 5 | PASS 292 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (5)
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-lrtest.R:25'): LRT and zlm are equivalent ────────────────────
all(lrout$lrstat[smallDOF] >= lrout2[smallDOF, 3, 1]) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 26 | SKIP 5 | PASS 292 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘MAITAnalysis.Rmd’ using ‘UTF-8’... OK
‘MAST-Intro.Rmd’ using ‘UTF-8’... OK
‘MAST-interoperability.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘MAITAnalysis.Rmd’ using rmarkdown
Warning: code chunks must not depend on the uncached chunk "data"
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAITAnalysis_files/figure-html/heatmap-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAITAnalysis_files/figure-html/pca-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAITAnalysis_files/figure-html/unnamed-chunk-1-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAITAnalysis_files/figure-html/pcaFilter-1.png" but not available.
Killed
--- re-building ‘MAST-Intro.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAST-Intro_files/figure-html/splitbyncells-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAST-Intro_files/figure-html/burdenOfFiltering-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAST-Intro_files/figure-html/zlmExample-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAST-Intro_files/figure-html/tests-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAST-Intro_files/figure-html/advancedArmExample-1.png" but not available.
--- finished re-building ‘MAST-Intro.Rmd’
--- re-building ‘MAST-interoperability.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAST-interoperability_files/figure-html/scaterQC-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/vign_test/MAST/vignettes/MAST-interoperability_files/figure-html/unnamed-chunk-1-1.png" but not available.
Killed
SUMMARY: processing the following files failed:
‘MAITAnalysis.Rmd’ ‘MAST-interoperability.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/MAST.Rcheck/00check.log’
for details.
MAST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MAST ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 ** 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)
MAST.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
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.
> 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, 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 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
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 1 | WARN 26 | SKIP 5 | PASS 292 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (5)
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-lrtest.R:25'): LRT and zlm are equivalent ────────────────────
all(lrout$lrstat[smallDOF] >= lrout2[smallDOF, 3, 1]) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 26 | SKIP 5 | PASS 292 ]
Error: Test failures
Execution halted
MAST.Rcheck/MAST-Ex.timings
| name | user | system | elapsed | |
| Drop | 0.000 | 0.000 | 0.001 | |
| FromFlatDF | 0.936 | 0.035 | 0.953 | |
| FromMatrix | 0.337 | 0.056 | 0.393 | |
| Hypothesis | 0.006 | 0.004 | 0.020 | |
| LRT | 0.281 | 0.015 | 0.295 | |
| ZlmFit-class | 1.222 | 0.001 | 1.230 | |
| applyFlat | 0.002 | 0.000 | 0.001 | |
| bootVcov1 | 0.853 | 0.000 | 0.853 | |
| calcZ | 1.542 | 0.003 | 1.547 | |
| collectResiduals | 1.468 | 0.009 | 1.476 | |
| computeEtFromCt | 0.051 | 0.000 | 0.051 | |
| convertMASTClassicToSingleCellAssay | 0.461 | 0.000 | 0.461 | |
| defaultAssay | 0.057 | 0.000 | 0.058 | |
| defaultPrior | 0.001 | 0.000 | 0.001 | |
| expavg | 0 | 0 | 0 | |
| filterLowExpressedGenes | 0.333 | 0.000 | 0.333 | |
| freq | 0.037 | 0.004 | 0.041 | |
| getConcordance | 0.585 | 0.000 | 0.583 | |
| getwellKey | 0.030 | 0.000 | 0.031 | |
| gseaAfterBoot | 1.523 | 0.007 | 1.530 | |
| hushWarning | 0.001 | 0.000 | 0.001 | |
| impute | 2.428 | 0.017 | 2.462 | |
| invlogit | 0.001 | 0.000 | 0.000 | |
| logFC | 0.416 | 0.012 | 0.428 | |
| logmean | 0.001 | 0.000 | 0.001 | |
| lrTest | 0.978 | 0.016 | 0.993 | |
| mast_filter | 1.588 | 0.000 | 1.588 | |
| meld_list_left | 0.001 | 0.000 | 0.001 | |
| melt.SingleCellAssay | 0.558 | 0.004 | 0.561 | |
| new_with_repaired_slots | 0.007 | 0.000 | 0.008 | |
| plot.thresholdSCRNACountMatrix | 0.679 | 0.016 | 0.696 | |
| plotSCAConcordance | 1.035 | 0.012 | 1.044 | |
| predict.ZlmFit | 1.570 | 0.004 | 1.574 | |
| se.coef | 1.719 | 0.004 | 1.725 | |
| split-SingleCellAssay-character-method | 1.225 | 0.000 | 1.225 | |
| stat_ell | 1.584 | 0.008 | 1.592 | |
| subset-SingleCellAssay-method | 0.332 | 0.004 | 0.336 | |
| summary-GSEATests-method | 1.568 | 0.016 | 1.584 | |
| summary-ZlmFit-method | 0.690 | 0.004 | 0.694 | |
| thresholdSCRNACountMatrix | 0.611 | 0.020 | 0.631 | |
| waldTest | 1.032 | 0.008 | 1.040 | |
| zlm | 0.560 | 0.008 | 0.569 | |