| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-03-28 11:32:23 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4376 |
| 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 1156/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MAST 1.28.0 (landing page) Andrew McDavid
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | ERROR | OK | ||||||||
|
To the developers/maintainers of the MAST 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: MAST |
| Version: 1.28.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MAST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MAST_1.28.0.tar.gz |
| StartedAt: 2024-03-27 17:57:36 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 18:03:22 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 345.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: MAST.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MAST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MAST_1.28.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/MAST.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MAST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MAST’ version ‘1.28.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘MAST’ 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 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 ... WARNING
Missing or unexported object: ‘gdata::xls2csv’
* 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:
══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• empty test (5): 'test-GSEA-by-boot.R:99:1', 'test-SingleCellAssay.R:298:1',
'test-lmWrapper-glmer.R:8:1', 'test-sparsematrix.R:18:1',
'test-sparsematrix.R:26:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-lrtest.R:25:5'): LRT and zlm are equivalent ──────────────────
all(lrout$lrstat[smallDOF] >= lrout2[smallDOF, 3, 1]) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 49 | 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/MAST.Rcheck/00check.log’
for details.
MAST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MAST ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 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
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 49 | SKIP 5 | PASS 292 ]
══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• empty test (5): 'test-GSEA-by-boot.R:99:1', 'test-SingleCellAssay.R:298:1',
'test-lmWrapper-glmer.R:8:1', 'test-sparsematrix.R:18:1',
'test-sparsematrix.R:26:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-lrtest.R:25:5'): LRT and zlm are equivalent ──────────────────
all(lrout$lrstat[smallDOF] >= lrout2[smallDOF, 3, 1]) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 49 | SKIP 5 | PASS 292 ]
Error: Test failures
Execution halted
MAST.Rcheck/MAST-Ex.timings
| name | user | system | elapsed | |
| Drop | 0 | 0 | 0 | |
| FromFlatDF | 1.586 | 0.019 | 1.605 | |
| FromMatrix | 0.278 | 0.012 | 0.290 | |
| Hypothesis | 0.008 | 0.001 | 0.008 | |
| LRT | 0.177 | 0.012 | 0.187 | |
| ZlmFit-class | 1.713 | 0.050 | 1.762 | |
| applyFlat | 0.002 | 0.000 | 0.002 | |
| bootVcov1 | 0.633 | 0.019 | 0.652 | |
| calcZ | 1.141 | 0.049 | 1.190 | |
| collectResiduals | 1.095 | 0.051 | 1.146 | |
| computeEtFromCt | 0.055 | 0.008 | 0.064 | |
| convertMASTClassicToSingleCellAssay | 0.356 | 0.009 | 0.364 | |
| defaultAssay | 0.053 | 0.004 | 0.057 | |
| defaultPrior | 0.000 | 0.000 | 0.001 | |
| expavg | 0 | 0 | 0 | |
| filterLowExpressedGenes | 0.306 | 0.007 | 0.313 | |
| freq | 0.038 | 0.005 | 0.044 | |
| getConcordance | 0.491 | 0.015 | 0.523 | |
| getwellKey | 0.020 | 0.009 | 0.028 | |
| gseaAfterBoot | 1.068 | 0.044 | 1.115 | |
| hushWarning | 0.001 | 0.000 | 0.001 | |
| impute | 1.399 | 0.035 | 1.444 | |
| invlogit | 0.000 | 0.000 | 0.001 | |
| logFC | 0.329 | 0.012 | 0.342 | |
| logmean | 0.001 | 0.000 | 0.002 | |
| lrTest | 0.767 | 0.018 | 0.790 | |
| mast_filter | 1.241 | 0.020 | 1.278 | |
| meld_list_left | 0.001 | 0.000 | 0.001 | |
| melt.SingleCellAssay | 0.451 | 0.012 | 0.462 | |
| new_with_repaired_slots | 0.01 | 0.00 | 0.01 | |
| plot.thresholdSCRNACountMatrix | 0.608 | 0.033 | 0.644 | |
| plotSCAConcordance | 0.779 | 0.024 | 0.804 | |
| predict.ZlmFit | 1.279 | 0.025 | 1.308 | |
| se.coef | 0.745 | 0.023 | 0.769 | |
| split-SingleCellAssay-character-method | 0.987 | 0.015 | 1.001 | |
| stat_ell | 1.075 | 0.016 | 1.092 | |
| subset-SingleCellAssay-method | 0.275 | 0.007 | 0.283 | |
| summary-GSEATests-method | 1.252 | 0.024 | 1.293 | |
| summary-ZlmFit-method | 0.556 | 0.009 | 0.577 | |
| thresholdSCRNACountMatrix | 0.535 | 0.015 | 0.562 | |
| waldTest | 0.822 | 0.022 | 0.871 | |
| zlm | 0.438 | 0.011 | 0.452 | |