Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2024-05-20 11:38:05 -0400 (Mon, 20 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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 1169/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MAST 1.30.0  (landing page)
Andrew McDavid
Snapshot Date: 2024-05-19 14:00:13 -0400 (Sun, 19 May 2024)
git_url: https://git.bioconductor.org/packages/MAST
git_branch: RELEASE_3_19
git_last_commit: da42c5a
git_last_commit_date: 2024-04-30 10:54:15 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for MAST on lconway


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.

raw results


Summary

Package: MAST
Version: 1.30.0
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_1.30.0.tar.gz
StartedAt: 2024-05-19 21:57:21 -0400 (Sun, 19 May 2024)
EndedAt: 2024-05-19 22:03:24 -0400 (Sun, 19 May 2024)
EllapsedTime: 363.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MAST.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/MAST.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MAST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MAST’ version ‘1.30.0’
* 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 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/MAST.Rcheck/00check.log’
for details.


Installation output

MAST.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MAST
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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)

Tests output

MAST.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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
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 
 61.881   2.227  83.689 

Example timings

MAST.Rcheck/MAST-Ex.timings

nameusersystemelapsed
Drop0.0000.0000.001
FromFlatDF0.8530.0610.924
FromMatrix0.3640.0400.410
Hypothesis0.0070.0010.009
LRT0.1820.0180.204
ZlmFit-class1.1360.0431.191
applyFlat0.0020.0010.002
bootVcov10.8440.0190.871
calcZ1.4430.0371.546
collectResiduals1.9690.0322.019
computeEtFromCt0.0480.0100.060
convertMASTClassicToSingleCellAssay0.4320.0110.447
defaultAssay0.0490.0030.053
defaultPrior000
expavg0.0000.0000.001
filterLowExpressedGenes0.3140.0080.327
freq0.0330.0040.038
getConcordance0.5770.0400.622
getwellKey0.0170.0080.026
gseaAfterBoot1.3950.0401.450
hushWarning0.0010.0000.001
impute2.3160.0622.438
invlogit0.0000.0000.001
logFC0.3990.0140.417
logmean0.0010.0000.001
lrTest0.9240.0571.025
mast_filter1.4610.0371.515
meld_list_left0.0010.0000.001
melt.SingleCellAssay0.5180.0140.536
new_with_repaired_slots0.0070.0000.007
plot.thresholdSCRNACountMatrix1.2130.0401.299
plotSCAConcordance0.9340.0250.970
predict.ZlmFit1.7200.0401.817
se.coef0.8540.0320.930
split-SingleCellAssay-character-method1.1670.0281.208
stat_ell1.2870.0191.317
subset-SingleCellAssay-method0.2600.0070.269
summary-GSEATests-method1.3620.0271.434
summary-ZlmFit-method0.6310.0170.655
thresholdSCRNACountMatrix0.4600.0200.484
waldTest0.8980.0310.973
zlm0.4580.0130.476