===============================
R CMD BUILD
===============================
* checking for file ‘crumblr/DESCRIPTION’ ... OK
* preparing ‘crumblr’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
Loading required namespace: crumblr
* saving partial Rd database
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
WARNING: directory ‘crumblr/docs’ is empty
* looking to see if a ‘data/datalist’ file should be added
* building ‘crumblr_0.99.14.tar.gz’
===============================
BiocCheckGitClone('crumblr')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3699/de95d1b26c5eef78218953a2c7248b1d37b4fa87/crumblr
→ BiocVersion: 3.21
→ Package: crumblr
→ PackageVersion: 0.99.14
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3699/de95d1b26c5eef78218953a2c7248b1d37b4fa87/crumblr.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3699/de95d1b26c5eef78218953a2c7248b1d37b4fa87/crumblr
→ 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...
* Checking that provided CITATION file is correctly formatted...
! WARNING: The 'doi' argument is missing or empty in the CITATION's
'bibentry()'. Only include a CITATION file if there is a preprint or
publication associated with this Bioconductor package.
── BiocCheck v1.43.2 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3699/de95d1b26c5eef78218953a2c7248b1d37b4fa87/crumblr.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 ‘crumblr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘crumblr’ version ‘0.99.14’
* 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 ‘crumblr’ 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] 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 ... [25s/25s] OK
* checking Rd files ... [8s/8s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [99s/99s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
diffTree 27.941 0.420 28.363
treeTest 13.914 0.003 13.917
plotForest-methods 13.451 0.092 13.543
plotTreeTest 13.506 0.006 13.525
plotTreeTestBeta 13.465 0.004 13.469
* 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: OK
===============================
BiocCheck('crumblr_0.99.14.tar.gz')
===============================
── Installing crumblr ──────────────────────────────────────────────────────────
✔ Package installed successfully
── crumblr session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpfS4QUc/file1423a46847e3a4/crumblr
→ BiocVersion: 3.21
→ Package: crumblr
→ PackageVersion: 0.99.14
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3699/de95d1b26c5eef78218953a2c7248b1d37b4fa87/crumblr.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /tmp/RtmpfS4QUc/file1423a46847e3a4/crumblr
→ installDir: /tmp/RtmpfS4QUc/file1423a43c75904d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on crumblr ────────────────────────────────────────────────
* 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 (25%).
* 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...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpfS4QUc/file1423a46847e3a4/crumblr/man/clr.Rd:48: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpfS4QUc/file1423a46847e3a4/crumblr/man/clrInv.Rd:52: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpfS4QUc/file1423a46847e3a4/crumblr/man/IFNCellCounts.Rd:33: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpfS4QUc/file1423a46847e3a4/crumblr/man/IFNCellCounts.Rd:37: unknown macro '\insertRef'
* Checking for library/require of crumblr...
* Checking coding practice...
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/crumblr.R (line 98, column 8)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
The longest 5 functions are:
• dmn.mle() (R/dmn.mle.R): 84 lines
* Checking man page documentation...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpfS4QUc/file1423a46847e3a4/crumblr/man/clr.Rd:48: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpfS4QUc/file1423a46847e3a4/crumblr/man/clrInv.Rd:52: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpfS4QUc/file1423a46847e3a4/crumblr/man/IFNCellCounts.Rd:33: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpfS4QUc/file1423a46847e3a4/crumblr/man/IFNCellCounts.Rd:37: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpfS4QUc/file1423a46847e3a4/crumblr/man/clr.Rd:48: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpfS4QUc/file1423a46847e3a4/crumblr/man/clrInv.Rd:52: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpfS4QUc/file1423a46847e3a4/crumblr/man/IFNCellCounts.Rd:33: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpfS4QUc/file1423a46847e3a4/crumblr/man/IFNCellCounts.Rd:37: unknown macro '\insertRef'
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• buildClusterTree.Rd
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpfS4QUc/file1423a46847e3a4/crumblr/man/clr.Rd:48: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpfS4QUc/file1423a46847e3a4/crumblr/man/clrInv.Rd:52: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpfS4QUc/file1423a46847e3a4/crumblr/man/IFNCellCounts.Rd:33: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmpfS4QUc/file1423a46847e3a4/crumblr/man/IFNCellCounts.Rd:37: unknown macro '\insertRef'
* Checking package NEWS...
* Checking unit tests...
i NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 102 lines (6%) are > 80 characters long.
First few lines:
• R/crumblr.R#L11 #' @details The CLR of a vector \code{x} ...
• ...
• vignettes/integration.Rmd#L119 Given the results here, we see that CD8 ...
i NOTE: Consider 4 spaces instead of tabs; 7 lines (0%) contain tabs.
First few lines:
• R/data.R#L11 #' \item \code{info} is metadata for ea ...
• ...
• vignettes/integration.Rmd#L33 ``` ...
i NOTE: Consider multiples of 4 spaces for line indents; 368 lines (20%) are
not.
First few lines:
• R/crumblr.R#L45 if (!is.data.frame(counts) & !is.matri ...
• ...
• vignettes/integration.Rmd#L94 ...
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 8 NOTES
i See the crumblr.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.