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BiocCheckGitClone('mist')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3647/bce91c57c1d10fc46da993e2e784b6e4614bd82a/mist
BiocVersion: 3.21
Package: mist
PackageVersion: 0.99.7
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3647/bce91c57c1d10fc46da993e2e784b6e4614bd82a/mist.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3647/bce91c57c1d10fc46da993e2e784b6e4614bd82a/mist
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
BiocCheck v1.43.2 results
0 ERRORS | 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3647/bce91c57c1d10fc46da993e2e784b6e4614bd82a/mist.Rcheck
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file mist/DESCRIPTION ... OK
* this is package mist version 0.99.7
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package mist can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [9s/9s] OK
* checking use of S3 registration ... 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 ... [27s/27s] NOTE
plotGene: no visible global function definition for ggplot
plotGene: no visible global function definition for aes
plotGene: no visible global function definition for geom_point
plotGene: no visible global function definition for geom_line
plotGene: no visible global function definition for labs
plotGene: no visible global function definition for theme_classic
Undefined global functions or variables:
aes geom_line geom_point ggplot labs theme_classic
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Data with usage in Rd file 'sampleData_sce.Rd' but not in code:
sampleData_sce
Data with usage in Rd file 'small_sampleData_sce.Rd' but not in code:
small_sampleData_sce
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in vignettes ... OK
* checking examples ... [42s/345s] ERROR
Running examples in mist-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotGene
> ### Title: Plot Methylation Levels vs. Pseudotime for a Specific Gene
> ### Aliases: plotGene
>
> ### ** Examples
>
> library(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
Loading required package: generics
Attaching package: generics
The following objects are masked from package:base:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, 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
> data <- readRDS(system.file("extdata", "small_sampleData_sce.rds", package = "mist"))
> Dat_sce_new <- estiParamSingle(
+ Dat_sce = data,
+ Dat_name = "Methy_level_group1",
+ ptime_name = "pseudotime"
+ )
Pseudotime cleaning and normalization to [0, 1] completed.
Removal of genomic features with too many 0/1 values completed.
> plotGene(Dat_sce = Dat_sce_new,
+ Dat_name = "Methy_level_group1",
+ ptime_name = "pseudotime",
+ gene_name = "ENSMUSG00000000037")
Error in ggplot(plot_data, aes(x = .data$Pseudotime)) :
could not find function "ggplot"
Calls: plotGene
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dmTwoGroups 8.786 0.554 99.903
estiParamTwo 7.108 0.518 88.659
dmSingle 5.418 0.308 55.806
estiParamSingle 3.605 0.210 44.250
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running runTest.R [19s/110s]
[19s/110s] ERROR
Running the tests in tests/runTest.R failed.
Last 20 lines of output:
RUNIT TEST PROTOCOL -- Tue Jan 7 21:35:41 2025
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 1
1 Test Suite :
mist RUnit Tests - 1 test function, 0 errors, 1 failure
FAILURE in test_mist: Error in checkTrue(all(names(beta_sigma_list_group) == c("Group1", "Group2"))) :
Test not TRUE
Test files with failing tests
test_mist.R
test_mist
Error in BiocGenerics:::testPackage("mist") :
unit tests failed for package mist
Execution halted
* 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 ... [3s/3s] OK
* DONE
Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3647/bce91c57c1d10fc46da993e2e784b6e4614bd82a/mist.Rcheck/00check.log
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('mist_0.99.7.tar.gz')
===============================
Installing mist
Package installed successfully
mist session metadata
sourceDir: /tmp/Rtmp04yz3K/filef148a1068b8c3/mist
BiocVersion: 3.21
Package: mist
PackageVersion: 0.99.7
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3647/bce91c57c1d10fc46da993e2e784b6e4614bd82a/mist.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/Rtmp04yz3K/filef148a1068b8c3/mist
installDir: /tmp/Rtmp04yz3K/filef148a66122607
isTarBall: TRUE
platform: unix
Running BiocCheck on mist
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
i NOTE: Update R version dependency from 4.3.0 to 4.5.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (46%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of mist...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 5
functions greater than 50 lines.
The longest 5 functions are:
run_bayesian_estimation() (R/utilityFunctions.R): 130 lines
...
dmTwoGroups() (R/dmTwo.R): 51 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 113 lines (13%) are > 80 characters long.
First few lines:
R/dmSingle.R#L1 #' Differential methylation evaluation o ...
...
vignettes/mist_vignette.Rmd#L131 `mist` provides a comprehensive suite of ...
i NOTE: Consider multiples of 4 spaces for line indents; 176 lines (21%) are
not.
First few lines:
R/dmSingle.R#L37 # Check if Dat_sce is a SingleCellExpe ...
...
vignettes/mist_vignette.Rmd#L91 gene_name = "ENSMUSG00000000037 ...
i See https://contributions.bioconductor.org/r-code.html
i See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
BiocCheck v1.43.2 results
0 ERRORS | 0 WARNINGS | i 4 NOTES
i See the mist.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.