merida1 Summary
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| Package: RCX |
| Version: 0.99.2 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data RCX |
| BuildTime: 0 minutes 23.45 seconds |
| CheckCommand: BiocCheckGitClone('RCX') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RCX_0.99.2.tar.gz && BiocCheck('RCX_0.99.2.tar.gz', `new-package`=TRUE) |
| CheckTime: 0 minutes 59.91 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh RCX_0.99.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 6.66 seconds |
| PackageFileSize: 4680.25 KiB |
| BuildID:: RCX_20211220160901 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: RCX. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. Build Package status: 0. |
merida1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘RCX/DESCRIPTION’ ... OK
* preparing ‘RCX’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘RCX_0.99.2.tar.gz’
merida1 CHECK output
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===============================
BiocCheckGitClone('RCX')
===============================
This is BiocCheckGitClone version 1.31.19. 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/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2399/22d7eb0971a5f7dfc0d829a5424b4dda01006624/RCX.Rcheck’
* using R Under development (unstable) (2021-11-01 r81125)
* using platform: x86_64-apple-darwin17.0 (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 ‘0.99.2’
* 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 ‘RCX’ can be installed ... [6s/6s] 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 ... [11s/11s] OK
* checking Rd files ... [1s/1s] 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 ... [11s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [3s/3s]
[3s/3s] 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
‘/Users/pkgbuild/packagebuilder/workers/jobs/2399/22d7eb0971a5f7dfc0d829a5424b4dda01006624/RCX.Rcheck/00check.log’
for details.
===============================
BiocCheck('RCX_0.99.2.tar.gz')
===============================
This is BiocCheck version 1.31.19. 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...
* 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 for pinned package versions...
* 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 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/Json-fromJson.R (line 91, column 15)
cat() in R/Json-fromJson.R (line 101, column 15)
cat() in R/Json-fromJson.R (line 109, column 15)
cat() in R/Json-fromJson.R (line 113, column 15)
cat() in R/Json-fromJson.R (line 179, column 23)
cat() in R/Json-fromJson.R (line 181, column 23)
cat() in R/Json-fromJson.R (line 184, column 25)
cat() in R/Json-fromJson.R (line 200, column 25)
cat() in R/Json-fromJson.R (line 202, column 25)
cat() in R/Json-fromJson.R (line 211, column 25)
cat() in R/Json-fromJson.R (line 268, column 15)
cat() in R/Json-fromJson.R (line 276, column 15)
cat() in R/Json-fromJson.R (line 284, column 15)
cat() in R/Json-fromJson.R (line 292, column 15)
cat() in R/Json-fromJson.R (line 302, column 15)
cat() in R/Json-fromJson.R (line 310, column 15)
cat() in R/Json-fromJson.R (line 317, column 15)
cat() in R/Json-fromJson.R (line 321, column 15)
cat() in R/Json-fromJson.R (line 329, column 15)
cat() in R/Json-fromJson.R (line 337, column 15)
cat() in R/Json-fromJson.R (line 342, column 15)
cat() in R/Json-fromJson.R (line 350, column 15)
cat() in R/Json-fromJson.R (line 359, column 15)
cat() in R/Json-fromJson.R (line 366, column 15)
cat() in R/Json-fromJson.R (line 374, column 15)
cat() in R/Json-fromJson.R (line 383, column 15)
cat() in R/Json-fromJson.R (line 390, column 15)
cat() in R/Json-fromJson.R (line 398, column 15)
cat() in R/Json-fromJson.R (line 407, column 15)
cat() in R/Json-fromJson.R (line 413, column 15)
cat() in R/Json-fromJson.R (line 421, column 15)
cat() in R/Json-fromJson.R (line 430, column 15)
cat() in R/Json-fromJson.R (line 432, column 15)
cat() in R/Json-fromJson.R (line 440, column 15)
cat() in R/Json-fromJson.R (line 450, column 15)
cat() in R/Json-fromJson.R (line 457, column 15)
cat() in R/Json-fromJson.R (line 465, column 15)
cat() in R/Json-fromJson.R (line 473, column 15)
cat() in R/Json-fromJson.R (line 479, column 15)
cat() in R/Json-fromJson.R (line 487, column 15)
cat() in R/Json-fromJson.R (line 495, column 15)
cat() in R/Json-fromJson.R (line 497, column 15)
cat() in R/Json-fromJson.R (line 505, column 15)
cat() in R/Json-fromJson.R (line 512, column 15)
cat() in R/Json-fromJson.R (line 516, column 15)
cat() in R/Json-fromJson.R (line 524, column 15)
cat() in R/Json-fromJson.R (line 536, column 15)
cat() in R/Json-fromJson.R (line 542, column 15)
cat() in R/Json-fromJson.R (line 550, column 15)
cat() in R/Json-fromJson.R (line 578, column 15)
cat() in R/Json-fromJson.R (line 580, column 15)
cat() in R/Json-fromJson.R (line 593, column 15)
cat() in R/Json-fromJson.R (line 595, column 15)
cat() in R/Json-fromJson.R (line 601, column 15)
cat() in R/Json-toJson.R (line 62, column 17)
cat() in R/Json-toJson.R (line 73, column 17)
cat() in R/Json-toJson.R (line 82, column 5)
cat() in R/Json-toJson.R (line 83, column 27)
cat() in R/Json-toJson.R (line 176, column 15)
cat() in R/Json-toJson.R (line 184, column 15)
cat() in R/Json-toJson.R (line 200, column 15)
cat() in R/Json-toJson.R (line 208, column 15)
cat() in R/Json-toJson.R (line 218, column 15)
cat() in R/Json-toJson.R (line 226, column 15)
cat() in R/Json-toJson.R (line 237, column 15)
cat() in R/Json-toJson.R (line 245, column 15)
cat() in R/Json-toJson.R (line 262, column 15)
cat() in R/Json-toJson.R (line 270, column 15)
cat() in R/Json-toJson.R (line 287, column 15)
cat() in R/Json-toJson.R (line 295, column 15)
cat() in R/Json-toJson.R (line 311, column 15)
cat() in R/Json-toJson.R (line 319, column 15)
cat() in R/Json-toJson.R (line 324, column 15)
cat() in R/Json-toJson.R (line 332, column 15)
cat() in R/Json-toJson.R (line 345, column 15)
cat() in R/Json-toJson.R (line 353, column 15)
cat() in R/Json-toJson.R (line 369, column 15)
cat() in R/Json-toJson.R (line 377, column 15)
cat() in R/Json-toJson.R (line 389, column 15)
cat() in R/Json-toJson.R (line 398, column 15)
cat() in R/Json-toJson.R (line 409, column 15)
cat() in R/Json-toJson.R (line 417, column 15)
cat() in R/Json-toJson.R (line 435, column 15)
cat() in R/Json-toJson.R (line 443, column 15)
cat() in R/Json-toJson.R (line 454, column 15)
cat() in R/Json-toJson.R (line 462, column 15)
cat() in R/Json-toJson.R (line 497, column 15)
cat() in R/Json-toJson.R (line 505, column 15)
cat() in R/Json-toJson.R (line 513, column 15)
cat() in R/Json-toJson.R (line 521, column 15)
cat() in R/Json-toJson.R (line 529, column 15)
cat() in R/Json-toJson.R (line 536, column 15)
cat() in R/Json-toJson.R (line 545, column 15)
cat() in R/Print.R (line 26, column 5)
cat() in R/Print.R (line 41, column 5)
cat() in R/Print.R (line 49, column 5)
cat() in R/Print.R (line 57, column 5)
cat() in R/Print.R (line 65, column 5)
cat() in R/Print.R (line 73, column 5)
cat() in R/Print.R (line 81, column 5)
cat() in R/Print.R (line 89, column 5)
cat() in R/Print.R (line 97, column 5)
cat() in R/Print.R (line 105, column 5)
cat() in R/Print.R (line 113, column 5)
cat() in R/Print.R (line 127, column 13)
cat() in R/Print.R (line 137, column 9)
cat() in R/Print.R (line 159, column 5)
cat() in R/Print.R (line 161, column 9)
cat() in R/Print.R (line 163, column 9)
cat() in R/Print.R (line 170, column 5)
cat() in R/Print.R (line 178, column 5)
cat() in R/Print.R (line 186, column 5)
cat() in R/Print.R (line 194, column 5)
cat() in R/Print.R (line 210, column 20)
cat() in R/Print.R (line 211, column 9)
cat() in R/Print.R (line 218, column 24)
cat() in R/Print.R (line 219, column 13)
print() in R/Print.R (line 35, column 5)
print() in R/Print.R (line 43, column 5)
print() in R/Print.R (line 51, column 5)
print() in R/Print.R (line 59, column 5)
print() in R/Print.R (line 67, column 5)
print() in R/Print.R (line 75, column 5)
print() in R/Print.R (line 83, column 5)
print() in R/Print.R (line 91, column 5)
print() in R/Print.R (line 99, column 5)
print() in R/Print.R (line 107, column 5)
print() in R/Print.R (line 115, column 5)
print() in R/Print.R (line 139, column 113)
print() in R/Print.R (line 140, column 119)
print() in R/Print.R (line 141, column 107)
print() in R/Print.R (line 162, column 9)
print() in R/Print.R (line 172, column 5)
print() in R/Print.R (line 180, column 5)
print() in R/Print.R (line 188, column 5)
print() in R/Print.R (line 196, column 5)
print() in R/Print.R (line 212, column 9)
print() in R/Print.R (line 220, column 13)
cat() in R/RCX-Cytoscape-VisualProperties.R (line 623, column
17)
cat() in R/RCX-Cytoscape-VisualProperties.R (line 624, column
17)
cat() in R/RCX-Cytoscape-VisualProperties.R (line 625, column
17)
print() in R/RCX-Cytoscape-VisualProperties.R (line 626, column
17)
cat() in R/Utils-general.R (line 221, column 5)
cat() in R/Utils-general.R (line 223, column 9)
cat() in R/Utils-general.R (line 225, column 9)
cat() in R/Utils-general.R (line 227, column 19)
cat() in R/Validate.R (line 35, column 17)
cat() in R/Validate.R (line 44, column 17)
cat() in R/Validate.R (line 73, column 17)
cat() in R/Validate.R (line 162, column 17)
cat() in R/Validate.R (line 178, column 17)
cat() in R/Validate.R (line 194, column 17)
cat() in R/Validate.R (line 238, column 17)
cat() in R/Validate.R (line 281, column 17)
cat() in R/Validate.R (line 326, column 17)
cat() in R/Validate.R (line 339, column 25)
cat() in R/Validate.R (line 353, column 17)
cat() in R/Validate.R (line 376, column 25)
cat() in R/Validate.R (line 381, column 25)
cat() in R/Validate.R (line 386, column 25)
cat() in R/Validate.R (line 483, column 17)
cat() in R/Validate.R (line 497, column 17)
cat() in R/Validate.R (line 510, column 17)
cat() in R/Validate.R (line 541, column 17)
cat() in R/Validate.R (line 585, column 17)
cat() in R/Validate.R (line 624, column 17)
cat() in R/Validate.R (line 663, column 17)
cat() in R/Validate.R (line 774, column 21)
cat() in R/Validate.R (line 783, column 17)
cat() in R/Visualize.R (line 194, column 15)
cat() in R/Visualize.R (line 228, column 15)
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
= in R/AspectDependencies.R (line 36, column 8)
= in R/AspectDependencies.R (line 43, column 16)
= in R/AspectDependencies.R (line 50, column 20)
= in R/AspectDependencies.R (line 57, column 20)
= in R/AspectDependencies.R (line 64, column 23)
= in R/AspectDependencies.R (line 71, column 28)
= in R/AspectDependencies.R (line 104, column 12)
= in R/AspectDependencies.R (line 111, column 20)
= in R/AspectDependencies.R (line 118, column 24)
= in R/AspectDependencies.R (line 125, column 24)
= in R/AspectDependencies.R (line 132, column 27)
= in R/AspectDependencies.R (line 139, column 32)
= in R/AspectDependencies.R (line 169, column 10)
= in R/AspectDependencies.R (line 176, column 18)
= in R/AspectDependencies.R (line 183, column 22)
= in R/AspectDependencies.R (line 191, column 31)
= in R/AspectDependencies.R (line 192, column 10)
= in R/AspectDependencies.R (line 193, column 59)
= in R/AspectDependencies.R (line 200, column 31)
= in R/AspectDependencies.R (line 201, column 10)
= in R/AspectDependencies.R (line 202, column 59)
= in R/AspectDependencies.R (line 209, column 32)
= in R/AspectDependencies.R (line 210, column 10)
= in R/AspectDependencies.R (line 211, column 43)
= in R/AspectDependencies.R (line 218, column 25)
= in R/AspectDependencies.R (line 219, column 10)
= in R/AspectDependencies.R (line 220, column 45)
= in R/AspectDependencies.R (line 221, column 61)
= in R/AspectDependencies.R (line 222, column 61)
= in R/AspectDependencies.R (line 230, column 35)
= in R/AspectDependencies.R (line 231, column 10)
= in R/AspectDependencies.R (line 233, column 56)
= in R/AspectDependencies.R (line 241, column 30)
= in R/AspectDependencies.R (line 242, column 10)
= in R/AspectDependencies.R (line 243, column 45)
= in R/AspectDependencies.R (line 244, column 45)
= in R/AspectDependencies.R (line 280, column 12)
= in R/AspectDependencies.R (line 281, column 8)
= in R/AspectDependencies.R (line 285, column 10)
= in R/AspectDependencies.R (line 288, column 9)
= in R/AspectDependencies.R (line 291, column 11)
= in R/AspectDependencies.R (line 294, column 13)
= in R/AspectDependencies.R (line 303, column 55)
= in R/AspectDependencies.R (line 304, column 25)
= in R/AspectDependencies.R (line 338, column 7)
= in R/AspectDependencies.R (line 344, column 15)
= in R/AspectDependencies.R (line 345, column 10)
= in R/AspectDependencies.R (line 354, column 11)
= in R/AspectDependencies.R (line 355, column 7)
= in R/AspectDependencies.R (line 356, column 10)
= in R/AspectDependencies.R (line 359, column 9)
= in R/AspectDependencies.R (line 360, column 58)
= in R/AspectDependencies.R (line 406, column 15)
= in R/AspectDependencies.R (line 412, column 23)
= in R/AspectDependencies.R (line 413, column 10)
= in R/AspectDependencies.R (line 425, column 19)
= in R/AspectDependencies.R (line 426, column 7)
= in R/AspectDependencies.R (line 427, column 10)
= in R/AspectDependencies.R (line 430, column 11)
= in R/AspectDependencies.R (line 431, column 60)
= in R/AspectDependencies.R (line 438, column 40)
= in R/AspectDependencies.R (line 444, column 30)
= in R/AspectDependencies.R (line 482, column 18)
= in R/AspectDependencies.R (line 483, column 10)
= in R/AspectDependencies.R (line 484, column 5)
= in R/AspectDependencies.R (line 486, column 12)
= in R/AspectDependencies.R (line 493, column 18)
= in R/AspectDependencies.R (line 494, column 10)
= in R/AspectDependencies.R (line 495, column 5)
= in R/AspectDependencies.R (line 497, column 12)
= in R/AspectDependencies.R (line 532, column 15)
= in R/AspectDependencies.R (line 550, column 18)
= in R/AspectDependencies.R (line 558, column 21)
= in R/AspectDependencies.R (line 559, column 10)
= in R/AspectDependencies.R (line 560, column 10)
= in R/AspectDependencies.R (line 563, column 19)
= in R/graphNEL.R (line 63, column 12)
= in R/graphNEL.R (line 64, column 11)
= in R/graphNEL.R (line 68, column 13)
= in R/graphNEL.R (line 71, column 11)
= in R/graphNEL.R (line 73, column 40)
= in R/graphNEL.R (line 74, column 9)
= in R/graphNEL.R (line 91, column 14)
= in R/graphNEL.R (line 95, column 11)
= in R/graphNEL.R (line 98, column 8)
= in R/graphNEL.R (line 100, column 9)
= in R/Igraph.R (line 29, column 19)
= in R/Igraph.R (line 31, column 60)
= in R/Igraph.R (line 32, column 61)
= in R/Igraph.R (line 33, column 60)
= in R/Igraph.R (line 37, column 10)
= in R/Igraph.R (line 38, column 10)
= in R/Igraph.R (line 39, column 14)
= in R/Igraph.R (line 43, column 25)
= in R/Igraph.R (line 44, column 22)
= in R/Igraph.R (line 45, column 22)
= in R/Igraph.R (line 46, column 21)
= in R/Igraph.R (line 48, column 48)
= in R/Igraph.R (line 50, column 58)
= in R/Igraph.R (line 53, column 57)
= in R/Igraph.R (line 56, column 21)
= in R/Igraph.R (line 60, column 29)
= in R/Igraph.R (line 63, column 53)
= in R/Igraph.R (line 65, column 29)
= in R/Igraph.R (line 66, column 29)
= in R/Igraph.R (line 70, column 59)
= in R/Igraph.R (line 72, column 21)
= in R/Igraph.R (line 74, column 20)
= in R/Igraph.R (line 75, column 34)
= in R/Igraph.R (line 78, column 21)
= in R/Igraph.R (line 79, column 23)
= in R/Igraph.R (line 80, column 20)
= in R/Igraph.R (line 84, column 24)
= in R/Igraph.R (line 89, column 21)
= in R/Igraph.R (line 90, column 23)
= in R/Igraph.R (line 91, column 20)
= in R/Igraph.R (line 95, column 24)
= in R/Igraph.R (line 100, column 20)
= in R/Igraph.R (line 104, column 24)
= in R/Igraph.R (line 114, column 18)
= in R/Igraph.R (line 176, column 10)
= in R/Igraph.R (line 177, column 11)
= in R/Igraph.R (line 181, column 13)
= in R/Igraph.R (line 182, column 8)
= in R/Igraph.R (line 184, column 11)
= in R/Igraph.R (line 186, column 15)
= in R/Igraph.R (line 187, column 15)
= in R/Igraph.R (line 189, column 11)
= in R/Igraph.R (line 191, column 11)
= in R/Igraph.R (line 192, column 20)
= in R/Igraph.R (line 193, column 16)
= in R/Igraph.R (line 195, column 8)
= in R/Igraph.R (line 198, column 8)
= in R/Igraph.R (line 201, column 20)
= in R/Igraph.R (line 202, column 12)
= in R/Igraph.R (line 206, column 20)
= in R/Igraph.R (line 207, column 12)
= in R/Igraph.R (line 211, column 20)
= in R/Igraph.R (line 212, column 12)
= in R/Igraph.R (line 216, column 21)
= in R/Igraph.R (line 218, column 20)
= in R/Igraph.R (line 220, column 20)
= in R/Igraph.R (line 226, column 20)
= in R/Igraph.R (line 235, column 20)
= in R/Igraph.R (line 238, column 29)
= in R/Igraph.R (line 241, column 18)
= in R/Igraph.R (line 245, column 23)
= in R/Igraph.R (line 246, column 23)
= in R/Igraph.R (line 247, column 23)
= in R/Igraph.R (line 249, column 25)
= in R/Igraph.R (line 251, column 29)
= in R/Igraph.R (line 253, column 29)
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= in R/Validate.R (line 660, column 30)
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= in R/Validate.R (line 1042, column 22)
= in R/Visualize.R (line 83, column 11)
= in R/Visualize.R (line 90, column 15)
= in R/Visualize.R (line 91, column 6)
= in R/Visualize.R (line 99, column 14)
= in R/Visualize.R (line 186, column 11)
= in R/Visualize.R (line 193, column 15)
= in R/Visualize.R (line 195, column 6)
= in R/Visualize.R (line 196, column 7)
= in R/Visualize.R (line 203, column 14)
= in R/Visualize.R (line 204, column 36)
= in R/Visualize.R (line 205, column 12)
= in R/Visualize.R (line 208, column 12)
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* 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
processCX() (R/Json-fromJson.R, line 120): 100 lines
toIgraph() (R/Igraph.R, line 176): 99 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, 2480
lines(14%) 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/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir RCX_0.99.2.tar.gz'
>>>>>>>
* installing *source* package ‘RCX’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RCX)
nebbiolo1 Summary
[top]
| Package: RCX |
| Version: 0.99.2 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RCX |
| BuildTime: 0 minutes 13.19 seconds |
| CheckCommand: BiocCheckGitClone('RCX') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings RCX_0.99.2.tar.gz && BiocCheck('RCX_0.99.2.tar.gz', `new-package`=TRUE) |
| CheckTime: 0 minutes 35.26 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 4680.34 KiB |
| BuildID:: RCX_20211220160901 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: RCX. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘RCX/DESCRIPTION’ ... OK
* preparing ‘RCX’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘RCX_0.99.2.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('RCX')
===============================
This is BiocCheckGitClone version 1.31.19. 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/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2399/22d7eb0971a5f7dfc0d829a5424b4dda01006624/RCX.Rcheck’
* using R Under development (unstable) (2021-11-10 r81171)
* 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 ‘0.99.2’
* 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 ‘RCX’ can be installed ... [3s/3s] OK
* 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 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 ... [7s/7s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [2s/2s]
[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: OK
===============================
BiocCheck('RCX_0.99.2.tar.gz')
===============================
This is BiocCheck version 1.31.19. 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...
* 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 for pinned package versions...
* 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 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/Json-fromJson.R (line 91, column 15)
cat() in R/Json-fromJson.R (line 101, column 15)
cat() in R/Json-fromJson.R (line 109, column 15)
cat() in R/Json-fromJson.R (line 113, column 15)
cat() in R/Json-fromJson.R (line 179, column 23)
cat() in R/Json-fromJson.R (line 181, column 23)
cat() in R/Json-fromJson.R (line 184, column 25)
cat() in R/Json-fromJson.R (line 200, column 25)
cat() in R/Json-fromJson.R (line 202, column 25)
cat() in R/Json-fromJson.R (line 211, column 25)
cat() in R/Json-fromJson.R (line 268, column 15)
cat() in R/Json-fromJson.R (line 276, column 15)
cat() in R/Json-fromJson.R (line 284, column 15)
cat() in R/Json-fromJson.R (line 292, column 15)
cat() in R/Json-fromJson.R (line 302, column 15)
cat() in R/Json-fromJson.R (line 310, column 15)
cat() in R/Json-fromJson.R (line 317, column 15)
cat() in R/Json-fromJson.R (line 321, column 15)
cat() in R/Json-fromJson.R (line 329, column 15)
cat() in R/Json-fromJson.R (line 337, column 15)
cat() in R/Json-fromJson.R (line 342, column 15)
cat() in R/Json-fromJson.R (line 350, column 15)
cat() in R/Json-fromJson.R (line 359, column 15)
cat() in R/Json-fromJson.R (line 366, column 15)
cat() in R/Json-fromJson.R (line 374, column 15)
cat() in R/Json-fromJson.R (line 383, column 15)
cat() in R/Json-fromJson.R (line 390, column 15)
cat() in R/Json-fromJson.R (line 398, column 15)
cat() in R/Json-fromJson.R (line 407, column 15)
cat() in R/Json-fromJson.R (line 413, column 15)
cat() in R/Json-fromJson.R (line 421, column 15)
cat() in R/Json-fromJson.R (line 430, column 15)
cat() in R/Json-fromJson.R (line 432, column 15)
cat() in R/Json-fromJson.R (line 440, column 15)
cat() in R/Json-fromJson.R (line 450, column 15)
cat() in R/Json-fromJson.R (line 457, column 15)
cat() in R/Json-fromJson.R (line 465, column 15)
cat() in R/Json-fromJson.R (line 473, column 15)
cat() in R/Json-fromJson.R (line 479, column 15)
cat() in R/Json-fromJson.R (line 487, column 15)
cat() in R/Json-fromJson.R (line 495, column 15)
cat() in R/Json-fromJson.R (line 497, column 15)
cat() in R/Json-fromJson.R (line 505, column 15)
cat() in R/Json-fromJson.R (line 512, column 15)
cat() in R/Json-fromJson.R (line 516, column 15)
cat() in R/Json-fromJson.R (line 524, column 15)
cat() in R/Json-fromJson.R (line 536, column 15)
cat() in R/Json-fromJson.R (line 542, column 15)
cat() in R/Json-fromJson.R (line 550, column 15)
cat() in R/Json-fromJson.R (line 578, column 15)
cat() in R/Json-fromJson.R (line 580, column 15)
cat() in R/Json-fromJson.R (line 593, column 15)
cat() in R/Json-fromJson.R (line 595, column 15)
cat() in R/Json-fromJson.R (line 601, column 15)
cat() in R/Json-toJson.R (line 62, column 17)
cat() in R/Json-toJson.R (line 73, column 17)
cat() in R/Json-toJson.R (line 82, column 5)
cat() in R/Json-toJson.R (line 83, column 27)
cat() in R/Json-toJson.R (line 176, column 15)
cat() in R/Json-toJson.R (line 184, column 15)
cat() in R/Json-toJson.R (line 200, column 15)
cat() in R/Json-toJson.R (line 208, column 15)
cat() in R/Json-toJson.R (line 218, column 15)
cat() in R/Json-toJson.R (line 226, column 15)
cat() in R/Json-toJson.R (line 237, column 15)
cat() in R/Json-toJson.R (line 245, column 15)
cat() in R/Json-toJson.R (line 262, column 15)
cat() in R/Json-toJson.R (line 270, column 15)
cat() in R/Json-toJson.R (line 287, column 15)
cat() in R/Json-toJson.R (line 295, column 15)
cat() in R/Json-toJson.R (line 311, column 15)
cat() in R/Json-toJson.R (line 319, column 15)
cat() in R/Json-toJson.R (line 324, column 15)
cat() in R/Json-toJson.R (line 332, column 15)
cat() in R/Json-toJson.R (line 345, column 15)
cat() in R/Json-toJson.R (line 353, column 15)
cat() in R/Json-toJson.R (line 369, column 15)
cat() in R/Json-toJson.R (line 377, column 15)
cat() in R/Json-toJson.R (line 389, column 15)
cat() in R/Json-toJson.R (line 398, column 15)
cat() in R/Json-toJson.R (line 409, column 15)
cat() in R/Json-toJson.R (line 417, column 15)
cat() in R/Json-toJson.R (line 435, column 15)
cat() in R/Json-toJson.R (line 443, column 15)
cat() in R/Json-toJson.R (line 454, column 15)
cat() in R/Json-toJson.R (line 462, column 15)
cat() in R/Json-toJson.R (line 497, column 15)
cat() in R/Json-toJson.R (line 505, column 15)
cat() in R/Json-toJson.R (line 513, column 15)
cat() in R/Json-toJson.R (line 521, column 15)
cat() in R/Json-toJson.R (line 529, column 15)
cat() in R/Json-toJson.R (line 536, column 15)
cat() in R/Json-toJson.R (line 545, column 15)
cat() in R/Print.R (line 26, column 5)
cat() in R/Print.R (line 41, column 5)
cat() in R/Print.R (line 49, column 5)
cat() in R/Print.R (line 57, column 5)
cat() in R/Print.R (line 65, column 5)
cat() in R/Print.R (line 73, column 5)
cat() in R/Print.R (line 81, column 5)
cat() in R/Print.R (line 89, column 5)
cat() in R/Print.R (line 97, column 5)
cat() in R/Print.R (line 105, column 5)
cat() in R/Print.R (line 113, column 5)
cat() in R/Print.R (line 127, column 13)
cat() in R/Print.R (line 137, column 9)
cat() in R/Print.R (line 159, column 5)
cat() in R/Print.R (line 161, column 9)
cat() in R/Print.R (line 163, column 9)
cat() in R/Print.R (line 170, column 5)
cat() in R/Print.R (line 178, column 5)
cat() in R/Print.R (line 186, column 5)
cat() in R/Print.R (line 194, column 5)
cat() in R/Print.R (line 210, column 20)
cat() in R/Print.R (line 211, column 9)
cat() in R/Print.R (line 218, column 24)
cat() in R/Print.R (line 219, column 13)
print() in R/Print.R (line 35, column 5)
print() in R/Print.R (line 43, column 5)
print() in R/Print.R (line 51, column 5)
print() in R/Print.R (line 59, column 5)
print() in R/Print.R (line 67, column 5)
print() in R/Print.R (line 75, column 5)
print() in R/Print.R (line 83, column 5)
print() in R/Print.R (line 91, column 5)
print() in R/Print.R (line 99, column 5)
print() in R/Print.R (line 107, column 5)
print() in R/Print.R (line 115, column 5)
print() in R/Print.R (line 139, column 113)
print() in R/Print.R (line 140, column 119)
print() in R/Print.R (line 141, column 107)
print() in R/Print.R (line 162, column 9)
print() in R/Print.R (line 172, column 5)
print() in R/Print.R (line 180, column 5)
print() in R/Print.R (line 188, column 5)
print() in R/Print.R (line 196, column 5)
print() in R/Print.R (line 212, column 9)
print() in R/Print.R (line 220, column 13)
cat() in R/RCX-Cytoscape-VisualProperties.R (line 623, column
17)
cat() in R/RCX-Cytoscape-VisualProperties.R (line 624, column
17)
cat() in R/RCX-Cytoscape-VisualProperties.R (line 625, column
17)
print() in R/RCX-Cytoscape-VisualProperties.R (line 626, column
17)
cat() in R/Utils-general.R (line 221, column 5)
cat() in R/Utils-general.R (line 223, column 9)
cat() in R/Utils-general.R (line 225, column 9)
cat() in R/Utils-general.R (line 227, column 19)
cat() in R/Validate.R (line 35, column 17)
cat() in R/Validate.R (line 44, column 17)
cat() in R/Validate.R (line 73, column 17)
cat() in R/Validate.R (line 162, column 17)
cat() in R/Validate.R (line 178, column 17)
cat() in R/Validate.R (line 194, column 17)
cat() in R/Validate.R (line 238, column 17)
cat() in R/Validate.R (line 281, column 17)
cat() in R/Validate.R (line 326, column 17)
cat() in R/Validate.R (line 339, column 25)
cat() in R/Validate.R (line 353, column 17)
cat() in R/Validate.R (line 376, column 25)
cat() in R/Validate.R (line 381, column 25)
cat() in R/Validate.R (line 386, column 25)
cat() in R/Validate.R (line 483, column 17)
cat() in R/Validate.R (line 497, column 17)
cat() in R/Validate.R (line 510, column 17)
cat() in R/Validate.R (line 541, column 17)
cat() in R/Validate.R (line 585, column 17)
cat() in R/Validate.R (line 624, column 17)
cat() in R/Validate.R (line 663, column 17)
cat() in R/Validate.R (line 774, column 21)
cat() in R/Validate.R (line 783, column 17)
cat() in R/Visualize.R (line 194, column 15)
cat() in R/Visualize.R (line 228, column 15)
* NOTE: Avoid using '=' for assignment and use '<-' instead
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= in R/RCX-NodeEdgeNetworkAttributes.R (line 112, column 14)
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= in R/RCX-NodeEdgeNetworkAttributes.R (line 119, column 20)
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= in R/RCX-NodeEdgeNetworkAttributes.R (line 147, column 20)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 148, column 20)
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= in R/RCX-NodeEdgeNetworkAttributes.R (line 152, column 21)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 160, column 24)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 163, column 35)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 165, column 24)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 166, column 9)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 218, column 22)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 219, column 10)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 225, column 26)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 227, column 37)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 262, column 22)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 269, column 43)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 270, column 10)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 276, column 20)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 280, column 31)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 288, column 26)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 289, column 9)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 290, column 10)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 299, column 13)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 305, column 17)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 306, column 17)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 313, column 24)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 317, column 24)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 318, column 9)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 364, column 25)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 365, column 10)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 370, column 31)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 375, column 29)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 379, column 35)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 381, column 36)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 382, column 38)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 384, column 32)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 385, column 36)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 390, column 46)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 394, column 40)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 427, column 25)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 434, column 49)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 435, column 26)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 436, column 10)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 442, column 43)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 443, column 40)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 444, column 18)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 447, column 23)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 450, column 14)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 452, column 14)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 458, column 21)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 459, column 29)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 462, column 27)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 466, column 40)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 468, column 34)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 476, column 29)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 477, column 9)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 478, column 10)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 488, column 17)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 489, column 17)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 495, column 60)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 500, column 27)
= in R/RCX-NodeEdgeNetworkAttributes.R (line 501, column 9)
= in R/RCX-NodesAndEdges.R (line 46, column 13)
= in R/RCX-NodesAndEdges.R (line 47, column 10)
= in R/RCX-NodesAndEdges.R (line 50, column 16)
= in R/RCX-NodesAndEdges.R (line 53, column 20)
= in R/RCX-NodesAndEdges.R (line 55, column 20)
= in R/RCX-NodesAndEdges.R (line 65, column 11)
= in R/RCX-NodesAndEdges.R (line 71, column 20)
= in R/RCX-NodesAndEdges.R (line 73, column 20)
= in R/RCX-NodesAndEdges.R (line 77, column 26)
= in R/RCX-NodesAndEdges.R (line 79, column 26)
= in R/RCX-NodesAndEdges.R (line 82, column 22)
= in R/RCX-NodesAndEdges.R (line 110, column 13)
= in R/RCX-NodesAndEdges.R (line 117, column 25)
= in R/RCX-NodesAndEdges.R (line 118, column 17)
= in R/RCX-NodesAndEdges.R (line 119, column 10)
= in R/RCX-NodesAndEdges.R (line 125, column 12)
= in R/RCX-NodesAndEdges.R (line 129, column 23)
= in R/RCX-NodesAndEdges.R (line 136, column 17)
= in R/RCX-NodesAndEdges.R (line 137, column 9)
= in R/RCX-NodesAndEdges.R (line 138, column 10)
= in R/RCX-NodesAndEdges.R (line 144, column 15)
= in R/RCX-NodesAndEdges.R (line 146, column 15)
= in R/RCX-NodesAndEdges.R (line 147, column 26)
= in R/RCX-NodesAndEdges.R (line 150, column 15)
= in R/RCX-NodesAndEdges.R (line 151, column 9)
= in R/RCX-NodesAndEdges.R (line 194, column 13)
= in R/RCX-NodesAndEdges.R (line 195, column 10)
= in R/RCX-NodesAndEdges.R (line 199, column 12)
= in R/RCX-NodesAndEdges.R (line 209, column 11)
= in R/RCX-NodesAndEdges.R (line 216, column 27)
= in R/RCX-NodesAndEdges.R (line 218, column 27)
= in R/RCX-NodesAndEdges.R (line 221, column 22)
= in R/RCX-NodesAndEdges.R (line 249, column 13)
= in R/RCX-NodesAndEdges.R (line 256, column 25)
= in R/RCX-NodesAndEdges.R (line 257, column 16)
= in R/RCX-NodesAndEdges.R (line 258, column 10)
= in R/RCX-NodesAndEdges.R (line 264, column 12)
= in R/RCX-NodesAndEdges.R (line 268, column 23)
= in R/RCX-NodesAndEdges.R (line 276, column 17)
= in R/RCX-NodesAndEdges.R (line 277, column 9)
= in R/RCX-NodesAndEdges.R (line 278, column 10)
= in R/RCX-NodesAndEdges.R (line 284, column 15)
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* 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
processCX() (R/Json-fromJson.R, line 120): 100 lines
toIgraph() (R/Igraph.R, line 176): 99 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, 2480
lines(14%) 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/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
nebbiolo1 BUILD BIN output
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