SurprisalAnalysis

Information Theoretic Analysis of Gene Expression Data

v3.0.0 · Jan 7, 2026 · MIT + file LICENSE

Description

Implements Surprisal analysis for gene expression data such as RNA-seq or microarray experiments. Surprisal analysis is an information-theoretic method that decomposes gene expression data into a baseline state and constraint-associated deviations, capturing coordinated gene expression patterns under different biological conditions. References: Kravchenko-Balasha N. et al. (2014) <doi:10.1371/journal.pone.0108549>. Zadran S. et al. (2014) <doi:10.1073/pnas.1414714111>. Su Y. et al. (2019) <doi:10.1371/journal.pcbi.1007034>. Bogaert K. A. et al. (2018) <doi:10.1371/journal.pone.0195142>.

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CRAN Check Status

5 ERROR

2 NOTE

7 OK

Show all 14 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	ERROR	278.8s
r-devel-linux-x86_64-debian-gcc	ERROR	210.8s
r-devel-linux-x86_64-fedora-clang	OK	450.1s
r-devel-linux-x86_64-fedora-gcc	OK	464.3s
r-devel-macos-arm64	OK	69s
r-devel-windows-x86_64	OK	327s
r-oldrel-macos-arm64	ERROR	11s
r-oldrel-macos-x86_64	NOTE	324s
r-oldrel-windows-x86_64	NOTE	394s
r-patched-linux-x86_64	OK	261.9s
r-release-linux-x86_64	ERROR	317.2s
r-release-macos-arm64	OK	74s
r-release-macos-x86_64	ERROR	182s
r-release-windows-x86_64	OK	304s

Check details (8 non-OK)

ERROR r-devel-linux-x86_64-debian-clang

re-building of vignette outputs

Error(s) in re-building vignettes:
  ...
--- re-building ‘NormalizationsZeroHandlingComparisons.Rmd’ using rmarkdown
--- finished re-building ‘NormalizationsZeroHandlingComparisons.Rmd’

--- re-building ‘RunTimeRecording.Rmd’ using rmarkdown
--- finished re-building ‘RunTimeRecording.Rmd’

--- re-building ‘SurprisalAnalysisGuideline.Rmd’ using rmarkdown
pandoc: /usr/share/javascript/mathjax/MathJax.js: withBinaryFile: does not exist (No such file or directory)
HasCallStack backtrace:
  collectBacktraces, called at libraries/ghc-internal/src/GHC/Internal/Exception.hs:169:13 in ghc-internal:GHC.Internal.Exception
  toExceptionWithBacktrace, called at libraries/ghc-internal/src/GHC/Internal/IO.hs:260:11 in ghc-internal:GHC.Internal.IO
  throwIO, called at libraries/ghc-internal/src/GHC/Internal/IO/Exception.hs:315:19 in ghc-internal:GHC.Internal.IO.Exception
  ioException, called at libraries/ghc-internal/src/GHC/Internal/IO/Exception.hs:319:20 in ghc-internal:GHC.Internal.IO.Exception


Error: processing vignette 'SurprisalAnalysisGuideline.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
--- failed re-building ‘SurprisalAnalysisGuideline.Rmd’

SUMMARY: processing the following file failed:
  ‘SurprisalAnalysisGuideline.Rmd’

Error: Vignette re-building failed.
Execution halted

ERROR r-devel-linux-x86_64-debian-gcc

re-building of vignette outputs

Error(s) in re-building vignettes:
  ...
--- re-building ‘NormalizationsZeroHandlingComparisons.Rmd’ using rmarkdown
--- finished re-building ‘NormalizationsZeroHandlingComparisons.Rmd’

--- re-building ‘RunTimeRecording.Rmd’ using rmarkdown
--- finished re-building ‘RunTimeRecording.Rmd’

--- re-building ‘SurprisalAnalysisGuideline.Rmd’ using rmarkdown
pandoc: /usr/share/javascript/mathjax/MathJax.js: withBinaryFile: does not exist (No such file or directory)
HasCallStack backtrace:
  collectBacktraces, called at libraries/ghc-internal/src/GHC/Internal/Exception.hs:169:13 in ghc-internal:GHC.Internal.Exception
  toExceptionWithBacktrace, called at libraries/ghc-internal/src/GHC/Internal/IO.hs:260:11 in ghc-internal:GHC.Internal.IO
  throwIO, called at libraries/ghc-internal/src/GHC/Internal/IO/Exception.hs:315:19 in ghc-internal:GHC.Internal.IO.Exception
  ioException, called at libraries/ghc-internal/src/GHC/Internal/IO/Exception.hs:319:20 in ghc-internal:GHC.Internal.IO.Exception


Error: processing vignette 'SurprisalAnalysisGuideline.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
--- failed re-building ‘SurprisalAnalysisGuideline.Rmd’

SUMMARY: processing the following file failed:
  ‘SurprisalAnalysisGuideline.Rmd’

Error: Vignette re-building failed.
Execution halted

NOTE r-oldrel-macos-arm64

package dependencies

Package suggested but not available for checking: ‘org.Mm.eg.db’

ERROR r-oldrel-macos-arm64

whether package can be installed

Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/SurprisalAnalysis.Rcheck/00install.out’ for details.

NOTE r-oldrel-macos-x86_64

installed package size

installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.0Mb
    shiny     3.1Mb

NOTE r-oldrel-windows-x86_64

installed package size

installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.0Mb
    shiny     3.1Mb

ERROR r-release-linux-x86_64

re-building of vignette outputs

Error(s) in re-building vignettes:
  ...
--- re-building ‘NormalizationsZeroHandlingComparisons.Rmd’ using rmarkdown
--- finished re-building ‘NormalizationsZeroHandlingComparisons.Rmd’

--- re-building ‘RunTimeRecording.Rmd’ using rmarkdown
--- finished re-building ‘RunTimeRecording.Rmd’

--- re-building ‘SurprisalAnalysisGuideline.Rmd’ using rmarkdown
pandoc: /usr/share/javascript/mathjax/MathJax.js: withBinaryFile: does not exist (No such file or directory)
HasCallStack backtrace:
  collectBacktraces, called at libraries/ghc-internal/src/GHC/Internal/Exception.hs:169:13 in ghc-internal:GHC.Internal.Exception
  toExceptionWithBacktrace, called at libraries/ghc-internal/src/GHC/Internal/IO.hs:260:11 in ghc-internal:GHC.Internal.IO
  throwIO, called at libraries/ghc-internal/src/GHC/Internal/IO/Exception.hs:315:19 in ghc-internal:GHC.Internal.IO.Exception
  ioException, called at libraries/ghc-internal/src/GHC/Internal/IO/Exception.hs:319:20 in ghc-internal:GHC.Internal.IO.Exception


Error: processing vignette 'SurprisalAnalysisGuideline.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
--- failed re-building ‘SurprisalAnalysisGuideline.Rmd’

SUMMARY: processing the following file failed:
  ‘SurprisalAnalysisGuideline.Rmd’

Error: Vignette re-building failed.
Execution halted

ERROR r-release-macos-x86_64

examples

Running examples in ‘SurprisalAnalysis-Ex.R’ failed
The error most likely occurred in:

> ### Name: runSurprisalApp
> ### Title: Launch the SurprisalAnalysis Shiny App
> ### Aliases: runSurprisalApp
> 
> ### ** Examples
> 
> 
> runSurprisalApp(port = httpuv::randomPort(), run = FALSE)
Loading required package: shiny

Attaching package: ‘shinyjs’

The following object is masked from ‘package:shiny’:

    runExample

The following objects are masked from ‘package:methods’:

    removeClass, show


Attaching package: ‘DT’

The following objects are masked from ‘package:shiny’:

    dataTableOutput, renderDataTable

clusterProfiler v4.15.1 Learn more at https://yulab-smu.top/contribution-knowledge-mining/

Please cite:

S Xu, E Hu, Y Cai, Z Xie, X Luo, L Zhan, W Tang, Q Wang, B Liu, R Wang,
W Xie, T Wu, L Xie, G Yu. Using clusterProfiler to characterize
multiomics data. Nature Protocols. 2024, 19(11):3292-3320

Attaching package: ‘clusterProfiler’

The following object is masked from ‘pack
...[truncated]...
, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:clusterProfiler’:

    rename

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname


Attaching package: ‘IRanges’

The following object is masked from ‘package:clusterProfiler’:

    slice


Attaching package: ‘AnnotationDbi’

The following object is masked from ‘package:clusterProfiler’:

    select


Error: Package 'org.Mm.eg.db' is required for this Shiny app. Install via BiocManager::install('org.Mm.eg.db')
Execution halted

Check History

ERROR 9 OK · 2 NOTE · 0 WARNING · 3 ERROR · 0 FAILURE Mar 10, 2026

ERROR r-patched-linux-x86_64

package dependencies

Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

ERROR r-release-macos-x86_64

examples

Running examples in ‘SurprisalAnalysis-Ex.R’ failed
The error most likely occurred in:

> ### Name: runSurprisalApp
> ### Title: Launch the SurprisalAnalysis Shiny App
> ### Aliases: runSurprisalApp
> 
> ### ** Examples
> 
> 
> runSurprisalApp(port =
...[truncated]...
  slice


Attaching package: ‘AnnotationDbi’

The following object is masked from ‘package:clusterProfiler’:

    select


Error: Package 'org.Mm.eg.db' is required for this Shiny app. Install via BiocManager::install('org.Mm.eg.db')
Execution halted

ERROR r-oldrel-macos-arm64

package dependencies

Package suggested but not available for checking: ‘org.Mm.eg.db’

NOTE r-oldrel-macos-x86_64

installed package size

installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.0Mb
    shiny     3.1Mb

NOTE r-oldrel-windows-x86_64

installed package size

installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.0Mb
    shiny     3.1Mb

Dependency Network

Version History

new 3.0.0 Mar 10, 2026

updated 3.0.0 ← 0.2 diff Jan 7, 2026

new 0.2 Sep 9, 2025