===============================
BiocCheckGitClone('RCX')
===============================
This is BiocCheckGitClone version 1.31.5. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2399/081a40561ce03867b1bebd3f5e849886f0ec27d9/RCX.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCX’ version ‘0.99.1’
* 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 ‘RCX’ can be installed ... [3s/3s] OK
* checking installed package size ... NOTE
installed size is 6.3Mb
sub-directories of 1Mb or more:
doc 4.8Mb
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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] 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 R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [1s/1s]
[2s/2s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2399/081a40561ce03867b1bebd3f5e849886f0ec27d9/RCX.Rcheck/00check.log’
for details.
===============================
BiocCheck('RCX_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.31.5. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* 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...
* NOTE: Update R version dependency from 4.0 to 4.1.0.
* 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 blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of RCX...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
R/Igraph.R (line 385, column 36)
R/Igraph.R (line 469, column 36)
R/Igraph.R (line 523, column 35)
R/Igraph.R (line 555, column 32)
R/Json-fromJson.R (line 122, column 15)
R/Json-fromJson.R (line 158, column 35)
R/Json-fromJson.R (line 567, column 11)
R/Json-fromJson.R (line 568, column 11)
R/Json-toJson.R (line 188, column 12)
R/Json-toJson.R (line 423, column 22)
R/Json-toJson.R (line 445, column 12)
R/Json-toJson.R (line 463, column 12)
R/RCX-Cytoscape-Groups.R (line 167, column 56)
R/RCX-Cytoscape-Groups.R (line 168, column 72)
R/RCX-Cytoscape-Groups.R (line 169, column 72)
R/RCX-Cytoscape-VisualProperties.R (line 247, column 14)
R/Summary.R (line 175, column 11)
R/Summary.R (line 373, column 35)
R/Summary.R (line 374, column 12)
R/Summary.R (line 377, column 39)
R/Summary.R (line 378, column 12)
R/Summary.R (line 381, column 31)
R/Summary.R (line 382, column 12)
R/Utils-checks.R (line 58, column 12)
R/Utils-checks.R (line 183, column 25)
R/Utils-checks.R (line 185, column 12)
R/Utils-checks.R (line 186, column 20)
R/Utils-checks.R (line 204, column 17)
R/Utils-checks.R (line 276, column 16)
R/Utils-checks.R (line 288, column 16)
R/Utils-general.R (line 258, column 12)
R/Utils-general.R (line 269, column 12)
R/Utils-json.R (line 29, column 12)
R/Utils-json.R (line 73, column 14)
R/Utils-json.R (line 76, column 22)
R/Utils-json.R (line 85, column 14)
R/Utils-json.R (line 166, column 18)
R/Utils-json.R (line 243, column 5)
R/Utils-json.R (line 247, column 15)
R/Utils-json.R (line 308, column 12)
R/Utils-json.R (line 338, column 14)
R/Utils-validation.R (line 43, column 17)
R/Utils-validation.R (line 80, column 20)
R/Utils-validation.R (line 103, column 16)
R/Utils-validation.R (line 119, column 16)
R/Utils-validation.R (line 157, column 16)
R/Utils-validation.R (line 208, column 16)
R/Utils-validation.R (line 222, column 16)
R/Utils-validation.R (line 229, column 16)
R/Utils-validation.R (line 236, column 16)
R/Utils-validation.R (line 243, column 16)
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/Utils-error-handling.R (line 93, column 10)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths * NOTE: Recommended function length <= 50 lines.
There are 14 functions > 50 lines.
The longest 5 functions are:
validate.RCX() (R/Validate.R, line 705): 353 lines
fromIgraph() (R/Igraph.R, line 288): 315 lines
updateCyVisualProperty.CyVisualProperty()
(R/RCX-Cytoscape-VisualProperties.R, line 471): 104 lines
toIgraph() (R/Igraph.R, line 176): 99 lines
processCX() (R/Json-fromJson.R, line 120): 95 lines
* Checking man page documentation...
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
1% of man pages use one of these cases.
Found in the following files:
visualize.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...
* NOTE: Consider shorter lines; 2109 lines (12%) are > 80
characters long.
First 6 lines:
R/AspectDependencies.R:9 ##############################################...
R/AspectDependencies.R:11 #############################################...
R/AspectDependencies.R:14 #############################################...
R/AspectDependencies.R:18 #' This function checks, if an aspect has IDs...
R/AspectDependencies.R:21 #' Aspects with IDs will be considered in the...
R/AspectDependencies.R:24 #' Uses method dispatch, so the default retur...
* NOTE: Consider 4 spaces instead of tabs; 55 lines (0%) contain
tabs.
First 6 lines:
vignettes/Appendix_The_RCX_and_CX_Data_Model.Rmd:114 |RCX property ...
vignettes/Appendix_The_RCX_and_CX_Data_Model.Rmd:121 |properties |...
vignettes/Appendix_The_RCX_and_CX_Data_Model.Rmd:122 |- ...
vignettes/Appendix_The_RCX_and_CX_Data_Model.Rmd:137 ## <a id="nodes">n...
vignettes/Appendix_The_RCX_and_CX_Data_Model.Rmd:139 |RCX property |C...
vignettes/Creating_RCX_from_scratch.Rmd:199 0, # RCX
* NOTE: Consider multiples of 4 spaces for line indents, 2435
lines(13%) are not.
First 6 lines:
R/AspectDependencies.R:37 UseMethod("hasIds", aspect)
R/AspectDependencies.R:44 return(FALSE)
R/AspectDependencies.R:51 return(TRUE)
R/AspectDependencies.R:58 return(TRUE)
R/AspectDependencies.R:65 return(TRUE)
R/AspectDependencies.R:72 return(TRUE)
See http://bioconductor.org/developers/how-to/coding-style/
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...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 8
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output