Andrew McDavid
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/MAST |
| git_branch: devel |
| git_last_commit: 0c17e9a |
| git_last_commit_date: 2023-10-24 10:53:20 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:37:58 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 1153/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MAST 1.29.0 (landing page) Andrew McDavid
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the MAST package: - 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 Troubleshooting Build Report for more information. - 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: 1.29.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MAST.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings MAST_1.29.0.tar.gz |
| StartedAt: 2024-03-28 03:39:12 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 03:45:00 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 348.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MAST.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MAST.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings MAST_1.29.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/MAST.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MAST/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MAST' version '1.29.0'
* 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 ... 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 code 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 ... NOTE
checkRd: (-1) GSEATests-class.Rd:14: Lost braces; missing escapes or markup?
14 | \item{\code{tests}}{array: gene sets X {discrete,continuous} X {stat, variance, degrees of freedom, avg correlation} X {test, null}}
| ^
checkRd: (-1) GSEATests-class.Rd:14: Lost braces; missing escapes or markup?
14 | \item{\code{tests}}{array: gene sets X {discrete,continuous} X {stat, variance, degrees of freedom, avg correlation} X {test, null}}
| ^
checkRd: (-1) GSEATests-class.Rd:14: Lost braces; missing escapes or markup?
14 | \item{\code{tests}}{array: gene sets X {discrete,continuous} X {stat, variance, degrees of freedom, avg correlation} X {test, null}}
| ^
* 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 ... 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, 2 NOTEs
See
'F:/biocbuild/bbs-3.19-bioc/meat/MAST.Rcheck/00check.log'
for details.
MAST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL MAST ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-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
R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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, 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
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 49 | SKIP 5 | PASS 293 ]
══ 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'
[ FAIL 0 | WARN 49 | SKIP 5 | PASS 293 ]
>
> proc.time()
user system elapsed
68.60 2.56 88.29
MAST.Rcheck/MAST-Ex.timings
| name | user | system | elapsed | |
| Drop | 0 | 0 | 0 | |
| FromFlatDF | 0.67 | 0.03 | 0.71 | |
| FromMatrix | 0.30 | 0.04 | 0.35 | |
| Hypothesis | 0.01 | 0.00 | 0.01 | |
| LRT | 0.22 | 0.02 | 0.24 | |
| ZlmFit-class | 1.31 | 0.11 | 1.42 | |
| applyFlat | 0 | 0 | 0 | |
| bootVcov1 | 0.77 | 0.02 | 0.78 | |
| calcZ | 1.37 | 0.03 | 1.42 | |
| collectResiduals | 1.27 | 0.05 | 1.31 | |
| computeEtFromCt | 0.03 | 0.01 | 0.05 | |
| convertMASTClassicToSingleCellAssay | 0.34 | 0.02 | 0.35 | |
| defaultAssay | 0.03 | 0.02 | 0.05 | |
| defaultPrior | 0 | 0 | 0 | |
| expavg | 0 | 0 | 0 | |
| filterLowExpressedGenes | 0.27 | 0.03 | 0.30 | |
| freq | 0.05 | 0.00 | 0.05 | |
| getConcordance | 0.45 | 0.03 | 0.48 | |
| getwellKey | 0.03 | 0.00 | 0.03 | |
| gseaAfterBoot | 1.89 | 0.08 | 1.97 | |
| hushWarning | 0 | 0 | 0 | |
| impute | 1.33 | 0.03 | 1.36 | |
| invlogit | 0 | 0 | 0 | |
| logFC | 0.37 | 0.01 | 0.40 | |
| logmean | 0 | 0 | 0 | |
| lrTest | 0.84 | 0.02 | 0.85 | |
| mast_filter | 1.46 | 0.06 | 1.52 | |
| meld_list_left | 0 | 0 | 0 | |
| melt.SingleCellAssay | 0.54 | 0.03 | 0.56 | |
| new_with_repaired_slots | 0.02 | 0.00 | 0.02 | |
| plot.thresholdSCRNACountMatrix | 0.59 | 0.05 | 0.65 | |
| plotSCAConcordance | 1.13 | 0.02 | 1.15 | |
| predict.ZlmFit | 1.81 | 0.04 | 1.87 | |
| se.coef | 0.86 | 0.06 | 0.92 | |
| split-SingleCellAssay-character-method | 1.10 | 0.05 | 1.14 | |
| stat_ell | 1.40 | 0.03 | 1.44 | |
| subset-SingleCellAssay-method | 0.35 | 0.00 | 0.35 | |
| summary-GSEATests-method | 1.53 | 0.03 | 1.56 | |
| summary-ZlmFit-method | 0.59 | 0.05 | 0.64 | |
| thresholdSCRNACountMatrix | 1.41 | 0.03 | 1.44 | |
| waldTest | 1.05 | 0.06 | 1.11 | |
| zlm | 0.44 | 0.03 | 0.47 | |