===============================
R CMD BUILD
===============================
* checking for file ‘decemedip/DESCRIPTION’ ... OK
* preparing ‘decemedip’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘decemedip_0.99.4.tar.gz’
===============================
BiocCheckGitClone('decemedip')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3730/f6966533b099fb75dd065cb8fc7e5c33f9c2b303/decemedip
→ BiocVersion: 3.22
→ Package: decemedip
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3730/f6966533b099fb75dd065cb8fc7e5c33f9c2b303/decemedip.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3730/f6966533b099fb75dd065cb8fc7e5c33f9c2b303/decemedip
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/home/pkgbuild/packagebuilder/workers/jobs/3730/f6966533b099fb75dd065cb8fc7e5c33f9c2b303/decemedip/.gitignore'
* Checking individual file sizes...
* 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 v1.45.7 results ───────────────────────────────────────────────────
✖ 0 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/3730/f6966533b099fb75dd065cb8fc7e5c33f9c2b303/decemedip.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decemedip/DESCRIPTION’ ... OK
* this is package ‘decemedip’ version ‘0.99.4’
* 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 ‘decemedip’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... OK
* checking installed package size ... INFO
installed size is 85.4Mb
sub-directories of 1Mb or more:
libs 83.7Mb
* 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 ... [15s/14s] OK
* checking whether the package can be loaded with stated dependencies ... [14s/14s] OK
* checking whether the package can be unloaded cleanly ... [14s/14s] OK
* checking whether the namespace can be loaded with stated dependencies ... [14s/14s] OK
* checking whether the namespace can be unloaded cleanly ... [16s/15s] OK
* checking loading without being on the library search path ... [17s/17s] 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 ... [47s/45s] NOTE
decemedip: no visible global function definition for ‘cor’
decemedip: no visible global function definition for ‘data’
decemedip: no visible binding for global variable ‘hg19.ref.cts.se’
decemedip: no visible binding for global variable ‘hg19.ref.anc.se’
decemedip: no visible binding for global variable ‘hg38.ref.cts.se’
decemedip: no visible global function definition for ‘quantile’
getSummaryOnPi: no visible global function definition for ‘data’
getSummaryOnPi: no visible binding for global variable
‘hg19.ref.cts.se’
getSummaryOnPi: no visible binding for global variable ‘cell_type’
makeReferencePanel: no visible global function definition for ‘colData’
plotDiagnostics: no visible binding for global variable ‘density’
plotDiagnostics: no visible binding for global variable ‘x’
plotDiagnostics: no visible binding for global variable ‘y_pred_2.5’
plotDiagnostics: no visible binding for global variable ‘y_pred_97.5’
plotDiagnostics: no visible binding for global variable ‘y_pred’
plotDiagnostics: no visible global function definition for ‘quantile’
plotDiagnostics: no visible global function definition for ‘xlim’
Undefined global functions or variables:
cell_type colData cor data density hg19.ref.anc.se hg19.ref.cts.se
hg38.ref.cts.se quantile x xlim y_pred y_pred_2.5 y_pred_97.5
Consider adding
importFrom("stats", "cor", "density", "quantile")
importFrom("utils", "data")
to your NAMESPACE file.
Found the following calls to data() loading into the global environment:
File ‘decemedip/R/getSummaryOnPi.R’:
data(hg19.ref.cts.se)
See section ‘Good practice’ in ‘?data’.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'getSummaryOnPi.Rd':
\examples lines wider than 100 characters:
output <- decemedip(counts_cts = counts_cts, counts_anc = counts_anc, iter = 100, cores = 1, chains = 1)
Rd file 'plotDiagnostics.Rd':
\examples lines wider than 100 characters:
output <- decemedip(counts_cts = counts_cts, counts_anc = counts_anc, iter = 100, cores = 1, chains = 1)
These lines will be truncated in the PDF manual.
* 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 ... [7s/7s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
‘-Werror=format-security’
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... [32s/32s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [19s/19s]
[19s/19s] 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 ... [3s/3s] OK
* DONE
Status: 4 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3730/f6966533b099fb75dd065cb8fc7e5c33f9c2b303/decemedip.Rcheck/00check.log’
for details.
===============================
BiocCheck('decemedip_0.99.4.tar.gz')
===============================
── Installing decemedip ────────────────────────────────────────────────────────
✔ Package installed successfully
── decemedip session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpJo2oCA/filec29b554d23a83/decemedip
→ BiocVersion: 3.22
→ Package: decemedip
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3730/f6966533b099fb75dd065cb8fc7e5c33f9c2b303/decemedip.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /tmp/RtmpJo2oCA/filec29b554d23a83/decemedip
→ installDir: /tmp/RtmpJo2oCA/filec29b5522189a9
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on decemedip ──────────────────────────────────────────────
* 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...
* 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...
i NOTE: Consider adding these automatically suggested biocViews: Microarray,
TissueMicroarray, Bayesian
i Search 'biocViews' at https://contributions.bioconductor.org
* 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 (26%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• how-to-use-decemedip.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of decemedip...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/stanmodels.R (line 11, column 15)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• getRoiReadCount.R (line 80, column 54)
• getSummaryOnPi.R (line 55, column 19)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/decemedip.R (line 206, column 17)
• R/decemedip.R (line 213, column 15)
• R/decemedip.R (line 219, column 13)
* 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 4
functions greater than 50 lines.
The longest 5 functions are:
• decemedip() (R/decemedip.R): 157 lines
• ...
• makeReferencePanel() (R/makeReferencePanel.R): 55 lines
* Checking man page documentation...
No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘MEDIPS’
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
• decemedip.Rd
• getRoiReadCount.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 25% of man
pages use at least one of these tags.
Found in files:
• getRoiReadCount.Rd
• getSummaryOnPi.Rd
• plotDiagnostics.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• getSummaryOnPi.Rd
• plotDiagnostics.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; 164 lines (15%) are > 80 characters long.
First few lines:
• R/decemedip-package.R#L3 #' @description The R package decemedip ...
• ...
• vignettes/how-to-use-decemedip.Rmd#L232 The `decemedip` package provides a
robus ...
i NOTE: Consider multiples of 4 spaces for line indents; 220 lines (21%) are
not.
First few lines:
• R/decemedip.R#L84 "s_mu" = 3, ...
• ...
• vignettes/how-to-use-decemedip.Rmd#L226 ylim(0, 300) ...
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 v1.45.7 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 11 NOTES
i See the decemedip.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.