===============================
R CMD BUILD
===============================
* checking for file ‘HiCPotts/DESCRIPTION’ ... OK
* preparing ‘HiCPotts’:
* 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
WARNING: directory ‘HiCPotts/data-raw’ is empty
Omitted ‘LazyData’ from DESCRIPTION
* building ‘HiCPotts_0.99.2.tar.gz’
===============================
BiocCheckGitClone('HiCPotts')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3832/a4f1ec59c0c307ed6f8253b1b5ff1e59aefbd692/HiCPotts
→ BiocVersion: 3.22
→ Package: HiCPotts
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3832/a4f1ec59c0c307ed6f8253b1b5ff1e59aefbd692/HiCPotts.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3832/a4f1ec59c0c307ed6f8253b1b5ff1e59aefbd692/HiCPotts
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* 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/3832/a4f1ec59c0c307ed6f8253b1b5ff1e59aefbd692/HiCPotts.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 ‘HiCPotts/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCPotts’ version ‘0.99.2’
* 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 ‘HiCPotts’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
installed size is 5.9Mb
sub-directories of 1Mb or more:
extdata 2.8Mb
libs 2.9Mb
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] 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 ... [30s/30s] 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 line endings in C/C++/Fortran sources/headers ... 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 ... [20s/20s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [45s/45s]
[46s/46s] 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 ... [4s/4s] OK
* DONE
Status: 4 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3832/a4f1ec59c0c307ed6f8253b1b5ff1e59aefbd692/HiCPotts.Rcheck/00check.log’
for details.
===============================
BiocCheck('HiCPotts_0.99.2.tar.gz')
===============================
── Installing HiCPotts ─────────────────────────────────────────────────────────
✔ Package installed successfully
── HiCPotts session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp8mFl7e/file2f347c2d4cdec3/HiCPotts
→ BiocVersion: 3.22
→ Package: HiCPotts
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3832/a4f1ec59c0c307ed6f8253b1b5ff1e59aefbd692/HiCPotts.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /tmp/Rtmp8mFl7e/file2f347c2d4cdec3/HiCPotts
→ installDir: /tmp/Rtmp8mFl7e/file2f347c1de73799
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on HiCPotts ───────────────────────────────────────────────
* 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 4.4 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 (64%).
* 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:
• HiCPotts_vignette.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of HiCPotts...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/compute_probabilities.R (line 189, column 23)
• ...
• R/sources_of_biases_model.R (line 79, column 11)
* 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:
• get_data() (R/prepare_data.R): 282 lines
• ...
• process_data() (R/process_data.R): 73 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• get_data.Rd
• Neighbours_combined.Rd
• run_metropolis_MCMC_betas.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 94% of man
pages use at least one of these tags.
Found in files:
• compute_HMRFHiC_probabilities.Rd
• ...
• size_prior.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• get_data.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; 437 lines (17%) are > 80 characters long.
First few lines:
• R/compute_probabilities.R#L1 #' @title Compute HMRFHiC Probabilities ...
• ...
• vignettes/HiCPotts_vignette.Rmd#L324 For further details, consult the package
...
i NOTE: Consider multiples of 4 spaces for line indents; 529 lines (20%) are
not.
First few lines:
• R/compute_probabilities.R#L113 # Check for required columns in data ...
• ...
• vignettes/HiCPotts_vignette.Rmd#L310 mc_cores = 1 ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 10 NOTES
i See the HiCPotts.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.