===============================
BiocCheckGitClone('CBN2Path')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3887/634da84cadd01029031cb6f16901f75f2c2db42a/CBN2Path
→ BiocVersion: 3.22
→ Package: CBN2Path
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3887/634da84cadd01029031cb6f16901f75f2c2db42a/CBN2Path.BiocCheck
→ BiocCheckVersion: 1.45.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3887/634da84cadd01029031cb6f16901f75f2c2db42a/CBN2Path
→ 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 v1.45.12 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/3887/634da84cadd01029031cb6f16901f75f2c2db42a/CBN2Path.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 ‘CBN2Path/DESCRIPTION’ ... OK
* this is package ‘CBN2Path’ 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CBN2Path’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [7s/7s] NOTE
generate_geom_node_point: no visible binding for global variable
‘nodes’
generate_geom_node_text: no visible binding for global variable ‘nodes’
generate_gg_text: no visible binding for global variable ‘x’
generate_gg_text: no visible binding for global variable ‘y’
generate_gg_text: no visible binding for global variable ‘label’
variable_cap_size: no visible binding for global variable ‘edges’
variable_cap_size: no visible binding for global variable ‘x’
variable_cap_size: no visible binding for global variable ‘y’
visualizeCBNModel: no visible binding for global variable ‘name’
visualizeFitnessLandscape: no visible binding for global variable ‘x’
visualizeFitnessLandscape: no visible binding for global variable ‘y’
visualizeFitnessLandscape: no visible binding for global variable
‘name’
visualizeProbabilities: no visible binding for global variable ‘name’
Undefined global functions or variables:
edges label name nodes x y
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'visualizeProbabilities.Rd':
\examples lines wider than 100 characters:
visualizeProbabilities(c(0.05, 0.03, 0.12, 0.04, 0.02, 0, 0.05, 0.04, 0.05, 0.06, 0.04, 0.02, 0.03, 0.02, 0.05, 0.03, 0.01, 0.09, 0.06, ... [TRUNCATED]
visualizeProbabilities(c(0.05, 0.03, 0.12, 0.04, 0.02, 0, 0.05, 0.04, 0.05, 0.06, 0.04, 0.02, 0.03, 0.02, 0.05, 0.03, 0.01, 0.09, 0.06, ... [TRUNCATED]
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 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 ... OK
* 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 ... [467s/467s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
pathProbQuartetBCBN 390.986 0.486 391.507
visualizeProbabilities 16.727 0.004 16.732
hcbn 16.133 0.053 16.187
bcbn 13.632 1.106 14.739
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [22s/22s]
[23s/23s] 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: 5 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3887/634da84cadd01029031cb6f16901f75f2c2db42a/CBN2Path.Rcheck/00check.log’
for details.
===============================
BiocCheck('CBN2Path_0.99.4.tar.gz')
===============================
── Installing CBN2Path ─────────────────────────────────────────────────────────
✔ Package installed successfully
── CBN2Path session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpVWItKx/file4238962838420/CBN2Path
→ BiocVersion: 3.22
→ Package: CBN2Path
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3887/634da84cadd01029031cb6f16901f75f2c2db42a/CBN2Path.BiocCheck
→ BiocCheckVersion: 1.45.12
→ sourceDir: /tmp/RtmpVWItKx/file4238962838420/CBN2Path
→ installDir: /tmp/RtmpVWItKx/file4238964f9857a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CBN2Path ───────────────────────────────────────────────
* 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 3.5.0 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...
i NOTE: Consider adding these automatically suggested biocViews: Pathways
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...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
• CBN2Path.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of CBN2Path...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/utils.R (line 23, column 20)
• R/utils.R (line 54, column 18)
• R/visualize.R (line 52, column 20)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• bcbn.R (line 49, column 26)
• ...
• visualize.R (line 419, column 28)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/bcbn.R (line 50, column 7)
• ...
• print() in R/visualize.R (line 162, column 24)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/bcbn.R (line 44, column 4)
• ...
• R/PathwayAnalysis.R (line 587, column 6)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/bcbn.R (line 35, column 13)
• R/ctcbn.R (line 132, column 17)
• R/hcbn.R (line 116, column 17)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
• suppressWarnings() in R/utils.R (line 12, column 30)
• ...
• suppressWarnings() in R/utils.R (line 106, column 15)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 10
functions greater than 50 lines.
The longest 5 functions are:
• visualizeProbabilities() (R/visualize.R): 140 lines
• ...
• pathProbCBN() (R/PathwayAnalysis.R): 71 lines
* Checking man page documentation...
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 177 lines (6%) are > 80 characters long.
First few lines:
• R/bcbn.R#L32 bcbn <- function(data = default_data(), ...
• ...
• vignettes/CBN2Path.Rmd#L527 [7] Hosseini, et al. Estimating the pred ...
i NOTE: Consider multiples of 4 spaces for line indents; 442 lines (16%) are
not.
First few lines:
• R/bcbn.R#L2 ...
• ...
• vignettes/CBN2Path.Rmd#L251 loglik_h[i] <- results_h3[[i]]$summary ...
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 v1.45.12 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 14 NOTES
i See the CBN2Path.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.