===============================
R CMD BUILD
===============================
* checking for file ‘mist/DESCRIPTION’ ... OK
* preparing ‘mist’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘mist_0.99.1.tar.gz’
===============================
BiocCheckGitClone('mist')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3647/mist_20241127153325/mist
→ BiocVersion: 3.21
→ Package: mist
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3647/mist_20241127153325/mist.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3647/mist_20241127153325/mist
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
✖ ERROR: System files found that should not be Git tracked.
• mist.Rproj
* 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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3647/mist_20241127153325/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 ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘mist’
See ‘/home/pkgbuild/packagebuilder/workers/jobs/3647/mist_20241127153325/mist.Rcheck/00install.out’ for details.
* 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 ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [11s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [11s/11s] 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 ... [32s/32s] OK
* 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [252s/155s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dmTwoGroups 74.871 2.216 45.129
estiParamTwo 55.230 1.923 45.303
dmSingle 40.312 1.245 25.524
estiParamSingle 18.546 0.834 22.682
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTest.R’ [10s/10s]
[10s/10s] ERROR
Running the tests in ‘tests/runTest.R’ failed.
Complete output:
> BiocGenerics:::testPackage("mist")
Error in library("RUnit", quietly = TRUE) :
there is no package called 'RUnit'
Calls: <Anonymous> -> library
In addition: Warning message:
replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading '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: 1 ERROR, 1 WARNING
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3647/mist_20241127153325/mist.Rcheck/00check.log’
for details.
===============================
BiocCheck('mist_0.99.1.tar.gz')
===============================
── Installing mist ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── mist session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpLKqj4U/file3fb67c2c97f49d/mist
→ BiocVersion: 3.21
→ Package: mist
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3647/mist_20241127153325/mist.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /tmp/RtmpLKqj4U/file3fb67c2c97f49d/mist
→ installDir: /tmp/RtmpLKqj4U/file3fb67c5888d363
→ 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...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (43%).
* 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 3
functions greater than 50 lines.
The longest 5 functions are:
• run_bayesian_estimation() (R/utilityFunctions.R): 130 lines
• estiParamTwo() (R/estiParamTwo.R): 97 lines
• estiParamSingle() (R/estiParamSingle.R): 60 lines
* Checking man page documentation...
Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘mist’
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• plotGene.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 20% of man
pages use at least one of these tags.
Found in files:
• plotGene.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• plotGene.Rd
* 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; 101 lines (13%) are > 80 characters long.
First few lines:
• R/dmSingle.R#L1 #' Differential methylation evaluation o ...
• ...
• vignettes/mist_vignette.Rmd#L128 `mist` provides a comprehensive suite of ...
i NOTE: Consider multiples of 4 spaces for line indents; 139 lines (17%) are
not.
First few lines:
• R/estiParamSingle.R#L31 ######## 1. Input Validation ...
• ...
• vignettes/mist_vignette.Rmd#L87 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...
✖ ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.43.2 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 0 WARNINGS | i 8 NOTES
i See the mist.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.