revdep/problems.md

In HenrikBengtsson/R.methodsS3: S3 Methods Simplified

aroma.core

• Version: 3.3.0
• GitHub: https://github.com/HenrikBengtsson/aroma.core
• Source code: https://github.com/cran/aroma.core
• Date/Publication: 2022-11-15 18:30:13 UTC
• Number of recursive dependencies: 72

Run revdep_details(, "aroma.core") for more info

In both

• checking package dependencies ... NOTE Packages suggested but not available for checking: 'sfit', 'expectile', 'HaarSeg', 'mpcbs'

aroma.light

• Version: 3.30.0
• GitHub: https://github.com/HenrikBengtsson/aroma.light
• Source code: https://github.com/cran/aroma.light
• Date/Publication: 2023-04-25
• Number of recursive dependencies: 6

Run revdep_details(, "aroma.light") for more info

In both

• checking for hidden files and directories ... NOTE Found the following hidden files and directories: inst/rsp/.rspPlugins These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

• checking Rd files ... NOTE checkRd: (-1) averageQuantile.Rd:49: Escaped LaTeX specials: \& checkRd: (-1) normalizeQuantileRank.Rd:97: Escaped LaTeX specials: \& checkRd: (-1) normalizeQuantileRank.matrix.Rd:83: Escaped LaTeX specials: \&

bioCancer

• Version: 1.28.0
• GitHub: https://github.com/kmezhoud/bioCancer
• Source code: https://github.com/cran/bioCancer
• Date/Publication: 2023-04-25
• Number of recursive dependencies: 224

Run revdep_details(, "bioCancer") for more info

In both

• checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘AlgDesign’ ‘GO.db’ ‘R.methodsS3’ ‘import’ ‘methods’ ‘org.Bt.eg.db’ ‘shinythemes’ All declared Imports should be used.

• checking R code for possible problems ... NOTE getGenesClassification: no visible global function definition for ‘new’ Undefined global functions or variables: new Consider adding importFrom("methods", "new") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

• checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'getCancerStudies.CGDS': ‘getCancerStudies.CGDS’

  S3 methods shown with full name in documentation object 'getCaseLists.CGDS': ‘getCaseLists.CGDS’

  S3 methods shown with full name in documentation object 'getClinicalData.CGDS': ‘getClinicalData.CGDS’

  S3 methods shown with full name in documentation object 'getGeneticProfiles.CGDS': ... S3 methods shown with full name in documentation object 'setVerbose.CGDS': ‘setVerbose.CGDS’

  S3 methods shown with full name in documentation object 'test.CGDS': ‘test.CGDS’

  The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

canceR

• Version: 1.34.0
• GitHub: https://github.com/kmezhoud/canceR
• Source code: https://github.com/cran/canceR
• Date/Publication: 2023-04-25
• Number of recursive dependencies: 169

Run revdep_details(, "canceR") for more info

In both

• checking whether package ‘canceR’ can be installed ... WARNING Found the following significant warnings: Warning: loading Rplot failed Warning: no DISPLAY variable so Tk is not available See ‘/wynton/home/cbi/hb/repositories/R.methodsS3/revdep/checks/canceR/new/canceR.Rcheck/00install.out’ for details.

• checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘R.methodsS3’ All declared Imports should be used.

• checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'cbind.na': ‘cbind.na’

  S3 methods shown with full name in documentation object 'rbind.na': ‘rbind.na’

  The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

DEGraph

• Version: 1.52.0
• GitHub: NA
• Source code: https://github.com/cran/DEGraph
• Date/Publication: 2023-04-25
• Number of recursive dependencies: 66

Run revdep_details(, "DEGraph") for more info

In both

• 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 DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘graph’ ‘KEGGgraph’ ‘lattice’ ‘RBGL’ ‘rrcov’ ‘Rgraphviz’ ‘NCIgraph’ A package should be listed in only one of these fields.

• checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘R.utils’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported object imported by a ':::' call: ‘graph:::getIndices’ See the note in ?`:::` about the use of this operator.

• checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘randomWAMGraph.xml’

R.devices

• Version: 2.17.1
• GitHub: https://github.com/HenrikBengtsson/R.devices
• Source code: https://github.com/cran/R.devices
• Date/Publication: 2022-06-21 08:00:02 UTC
• Number of recursive dependencies: 8

Run revdep_details(, "R.devices") for more info

In both

• checking dependencies in R code ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘devAll’

• checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: ... --- re-building ‘R.devices-overview.tex.rsp’ using rsp R.devices v2.17.1 (2022-06-21 08:00:02 UTC) successfully loaded. See ?R.devices for help. Error: processing vignette 'R.devices-overview.tex.rsp' failed with diagnostics: Running 'texi2dvi' on 'R.devices-overview.tex' failed. LaTeX errors: ! Undefined control sequence. l.55 \pdfsuppressptexinfo =-1 ... See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... --- failed re-building ‘R.devices-overview.tex.rsp’

  SUMMARY: processing the following file failed: ‘R.devices-overview.tex.rsp’

  Error: Vignette re-building failed. Execution halted ```

R.rsp

• Version: 0.45.0
• GitHub: https://github.com/HenrikBengtsson/R.rsp
• Source code: https://github.com/cran/R.rsp
• Date/Publication: 2022-06-27 18:30:09 UTC
• Number of recursive dependencies: 19

Run revdep_details(, "R.rsp") for more info

In both

• checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘R_packages-Static_PDF_and_HTML_vignettes.pdf.asis’ using asis --- finished re-building ‘R_packages-Static_PDF_and_HTML_vignettes.pdf.asis’

  --- re-building ‘R_packages-LaTeX_vignettes.ltx’ using tex Error: processing vignette 'R_packages-LaTeX_vignettes.ltx' failed with diagnostics: Running 'texi2dvi' on 'R_packages-LaTeX_vignettes.ltx' failed. LaTeX errors: ! Undefined control sequence. l.21 \pdfsuppressptexinfo ... ... --- failed re-building ‘R_packages-Vignettes_prior_to_R300.tex.rsp’

  SUMMARY: processing the following files failed: ‘R_packages-LaTeX_vignettes.ltx’ ‘Dynamic_document_creation_using_RSP.tex.rsp’ ‘RSP_refcard.tex.rsp’ ‘R_packages-Vignettes_prior_to_R300.tex.rsp’

  Error: Vignette re-building failed. Execution halted ```

roxygen2

• Version: 7.2.3
• GitHub: https://github.com/r-lib/roxygen2
• Source code: https://github.com/cran/roxygen2
• Date/Publication: 2022-12-08 23:40:02 UTC
• Number of recursive dependencies: 67

Run revdep_details(, "roxygen2") for more info

In both

• checking C++ specification ... NOTE Specified C++11: please drop specification unless essential

rtf

• Version: 0.4-14.1
• GitHub: https://github.com/schaffman5/rtf
• Source code: https://github.com/cran/rtf
• Date/Publication: 2020-03-22 09:32:44 UTC
• Number of recursive dependencies: 33

Run revdep_details(, "rtf") for more info

In both

• checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’ ‘test_addTable.doc’

HenrikBengtsson/R.methodsS3 documentation built on Nov. 5, 2024, 8:51 a.m.