===============================
BiocCheckGitClone('CBN2Path')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3887/4e373cfabea12abc52b6ee7e9e393148157cda55/CBN2Path
BiocVersion: 3.22
Package: CBN2Path
PackageVersion: 0.99.7
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3887/4e373cfabea12abc52b6ee7e9e393148157cda55/CBN2Path.BiocCheck
BiocCheckVersion: 1.45.20
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3887/4e373cfabea12abc52b6ee7e9e393148157cda55/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/3887/4e373cfabea12abc52b6ee7e9e393148157cda55/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 0.99.7
* 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 ... WARNING
Found the following files with non-ASCII characters:
R/ctcbn.R
R/hcbn.R
Portable packages must use only ASCII characters in their R code and
NAMESPACE directives, except perhaps in comments.
Use \uxxxx escapes for other characters.
Function tools::showNonASCIIfile can help in finding non-ASCII
characters in files.
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [2s/2s] 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 ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
BiocParallel TCGAbiolinks
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [8s/8s] NOTE
ctcbn: no visible global function definition for MulticoreParam
ctcbn: no visible global function definition for bplapply
ctcbn: no visible global function definition for bpoptions
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
getRawTCGAData: no visible global function definition for GDCquery
getRawTCGAData: no visible global function definition for GDCdownload
getRawTCGAData: no visible global function definition for GDCprepare
hcbn: no visible global function definition for MulticoreParam
hcbn: no visible global function definition for bplapply
hcbn: no visible global function definition for bpoptions
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:
GDCdownload GDCprepare GDCquery MulticoreParam bplapply bpoptions
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 $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
-Werror=format-security
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in vignettes ... OK
* checking examples ... [24s/24s] ERROR
Running examples in CBN2Path-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generateTCGAMatrix
> ### Title: Generate TCGA Genotype Matrix
> ### Aliases: generateTCGAMatrix
>
> ### ** Examples
>
> generateTCGAMatrix()
Error in GDCquery(project = project, data.category = "Simple Nucleotide Variation", :
could not find function "GDCquery"
Calls: generateTCGAMatrix ... suppressMessages -> withCallingHandlers -> getRawTCGAData
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bcbn 13.736 1.069 14.809
Predictability 5.788 0.219 6.008
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [89s/89s]
[89s/89s] ERROR
Running the tests in tests/testthat.R failed.
Last 20 lines of output:
[1,] 1 1
[2,] 1 1
[3,] 1 1
[4,] 1 1
[5,] 1 1
Multivariate psrf
1
[1] "##########################################"
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 9 ]
Failed tests
Failure ('test-ctcbn.R:6:3'): CT-CBN works
ctcbnSingle(bc, epsilon = 0.7)$summary[[14]] (`actual`) not equal to 11912.05034 (`expected`).
`actual`: 12562.5
`expected`: 11912.1
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 9 ]
Error: Test failures
Execution halted
* 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: 2 ERRORs, 1 WARNING, 7 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3887/4e373cfabea12abc52b6ee7e9e393148157cda55/CBN2Path.Rcheck/00check.log
for details.
===============================
BiocCheck('CBN2Path_0.99.7.tar.gz')
===============================
Installing CBN2Path
Package installed successfully
CBN2Path session metadata
sourceDir: /tmp/RtmpyOhEXB/filebdae02a1520e9/CBN2Path
BiocVersion: 3.22
Package: CBN2Path
PackageVersion: 0.99.7
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3887/4e373cfabea12abc52b6ee7e9e393148157cda55/CBN2Path.BiocCheck
BiocCheckVersion: 1.45.20
sourceDir: /tmp/RtmpyOhEXB/filebdae02a1520e9/CBN2Path
installDir: /tmp/RtmpyOhEXB/filebdae054cae07b
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 33, 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; 521 lines (19%) 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.