===============================
BiocCheckGitClone('CBN2Path')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3887/f8657897eded26c2f4767f6f515bc59d99825600/CBN2Path
→ BiocVersion: 3.22
→ Package: CBN2Path
→ PackageVersion: 0.99.11
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3887/f8657897eded26c2f4767f6f515bc59d99825600/CBN2Path.BiocCheck
→ BiocCheckVersion: 1.45.20
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3887/f8657897eded26c2f4767f6f515bc59d99825600/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 NAMESPACE...
* 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 v1.45.20 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/f8657897eded26c2f4767f6f515bc59d99825600/CBN2Path.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CBN2Path/DESCRIPTION’ ... OK
* this is package ‘CBN2Path’ version ‘0.99.11’
* 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 ... NOTE
Found the following CITATION file in a non-standard place:
CITATION.cff
Most likely ‘inst/CITATION’ should be used instead.
* 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 ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [10s/10s] 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 ... [31s/31s] NOTE
generateGeomNodePoint: no visible binding for global variable ‘nodes’
generateGeomNodeText: no visible binding for global variable ‘nodes’
generateGgText: no visible binding for global variable ‘x’
generateGgText: no visible binding for global variable ‘y’
generateGgText: no visible binding for global variable ‘label’
generateMatrixGenotypes : f1 : <anonymous>: no visible global function
definition for ‘combn’
variableCapSize: no visible binding for global variable ‘edges’
variableCapSize: no visible binding for global variable ‘x’
variableCapSize: 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:
combn edges label name nodes x y
Consider adding
importFrom("utils", "combn")
to your NAMESPACE file.
* 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 $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
‘-Werror=format-security’
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... [450s/451s] ERROR
Running examples in ‘CBN2Path-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: visualizeCBNModel
> ### Title: Visualize CBN Model
> ### Aliases: visualizeCBNModel
>
> ### ** Examples
>
> poset <- readPoset(getExamples()[1])
> visualizeCBNModel(poset$sets)
Error in add_vertices(gr, nrow(nodes) - gorder(gr)) :
At vendor/cigraph/src/graph/type_indexededgelist.c:388 : Cannot add negative number of vertices. Invalid value
Calls: visualizeCBNModel ... as_tbl_graph.list -> as_graph_node_edge -> add_vertices
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
hcbn 270.690 0.638 271.344
hcbnSingle 67.559 0.033 67.596
pathProbQuartetBCBN 29.662 0.269 29.934
bcbn 13.505 1.105 14.622
jensenShannonDivergence 8.986 0.346 9.333
Predictability 8.122 0.331 8.453
pathProbQuartetRCBN 6.979 0.244 7.224
pathProbQuartetHCBN 5.417 0.213 5.631
pathProbQuartetCTCBN 5.118 0.166 5.285
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [92s/92s]
[92s/92s] 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: 1 ERROR, 6 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3887/f8657897eded26c2f4767f6f515bc59d99825600/CBN2Path.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('CBN2Path_0.99.11.tar.gz')
===============================
── Installing CBN2Path ─────────────────────────────────────────────────────────
✔ Package installed successfully
── CBN2Path session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpyrTdRO/file2f5e961bd6fea/CBN2Path
→ BiocVersion: 3.22
→ Package: CBN2Path
→ PackageVersion: 0.99.11
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3887/f8657897eded26c2f4767f6f515bc59d99825600/CBN2Path.BiocCheck
→ BiocCheckVersion: 1.45.20
→ sourceDir: /tmp/RtmpyrTdRO/file2f5e961bd6fea/CBN2Path
→ installDir: /tmp/RtmpyrTdRO/file2f5e964ee72b36
→ 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 4.1.0 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...
i Bioconductor dependencies found in Imports & Depends (12%).
* 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 NAMESPACE...
* 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/ctcbn.R (line 152, 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 42, column 25)
• ...
• visualize.R (line 427, column 28)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/bcbn.R (line 43, column 7)
• ...
• print() in R/Spock.R (line 127, column 7)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/ctcbn.R (line 33, column 19)
• ...
• R/visualize.R (line 164, column 14)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/bcbn.R (line 30, column 13)
• R/ctcbn.R (line 160, column 15)
• R/hcbn.R (line 131, column 13)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
• suppressMessages() in R/tcga.R (line 37, column 40)
• ...
• 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 8
functions greater than 50 lines.
The longest 5 functions are:
• visualizeProbabilities() (R/visualize.R): 140 lines
• ...
• pathProbSSWM() (R/PathwayAnalysis.R): 66 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; 150 lines (5%) are > 80 characters long.
First few lines:
• R/bcbn.R#L28 bcbn <- function(data = defaultData(), n ...
• ...
• vignettes/CBN2Path.Rmd#L511 [7] Hosseini, et al. Estimating the pred ...
i NOTE: Consider multiples of 4 spaces for line indents; 520 lines (18%) are
not.
First few lines:
• R/bcbn.R#L2 poset <- matrix(0,3,3) ...
• ...
• vignettes/CBN2Path.Rmd#L236 genotypeMatrix = gMat ...
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 v1.45.20 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 14 NOTES
i See the CBN2Path.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.