revdep/problems.md

In HenrikBengtsson/aroma.light: Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types

apmsWAPP

• Version: 1.0
• Source code: https://github.com/cran/apmsWAPP
• Date/Publication: 2014-04-22 14:39:54
• Number of recursive dependencies: 51

Run revdep_details(,"apmsWAPP") for more info

In both

• checking R code for possible problems ... NOTE ... TSPM: no visible global function definition for ‘p.adjust’ norm.inttable: no visible global function definition for ‘median’ norm.inttable : <anonymous>: no visible global function definition for ‘quantile’ saint_permF: no visible global function definition for ‘read.table’ saint_permF: no visible global function definition for ‘write.table’ saint_permF: no visible global function definition for ‘write.csv2’ tspm_apms: no visible global function definition for ‘read.table’ varFilter : <anonymous>: no visible global function definition for ‘median’ varFilter: no visible global function definition for ‘median’ varFilter: no visible global function definition for ‘quantile’ Undefined global functions or variables: deviance glm hatvalues median p.adjust pchisq pf poisson qchisq qf quantile read.table residuals write.csv2 write.table Consider adding importFrom("stats", "deviance", "glm", "hatvalues", "median", "p.adjust", "pchisq", "pf", "poisson", "qchisq", "qf", "quantile", "residuals") importFrom("utils", "read.table", "write.csv2", "write.table") to your NAMESPACE file.

aroma.affymetrix

• Version: 3.2.0
• Source code: https://github.com/cran/aroma.affymetrix
• URL: https://www.aroma-project.org/, https://github.com/HenrikBengtsson/aroma.affymetrix
• BugReports: https://github.com/HenrikBengtsson/aroma.affymetrix/issues
• Date/Publication: 2019-06-23 06:00:14 UTC
• Number of recursive dependencies: 80

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

In both

• checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: R 2.3Mb help 1.1Mb testScripts 1.3Mb

• checking dependencies in R code ... NOTE Error in setGeneric("getX", function(object, type) standardGeneric("getX")) : could not find function "setGeneric"

aroma.core

• Version: 3.2.0
• Source code: https://github.com/cran/aroma.core
• URL: https://github.com/HenrikBengtsson/aroma.core, https://www.aroma-project.org/
• BugReports: https://github.com/HenrikBengtsson/aroma.core/issues
• Date/Publication: 2019-06-17 18:20:03 UTC
• Number of recursive dependencies: 46

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'

EDASeq

• Version: 2.20.0
• Source code: https://github.com/cran/EDASeq
• URL: https://github.com/drisso/EDASeq
• BugReports: https://github.com/drisso/EDASeq/issues
• Date/Publication: 2019-10-29
• Number of recursive dependencies: 121

Run revdep_details(,"EDASeq") for more info

In both

• checking whether the namespace can be loaded with stated dependencies ... WARNING ``` Error in setGeneric("Makesense", function(expr, lib, ...) standardGeneric("Makesense")) : could not find function "setGeneric" Error: unable to load R code in package ‘geneplotter’ Execution halted

  A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start.

  Probably some imports need to be declared in the NAMESPACE file. ```

• checking examples ... WARNING ``` Found the following significant warnings:

  Warning: 'GenomicRangesList' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. ```

• checking R code for possible problems ... NOTE Error in setGeneric("Makesense", function(expr, lib, ...) standardGeneric("Makesense")) : could not find function "setGeneric" Error: unable to load R code in package ‘geneplotter’ Execution halted

scone

• Version: 1.10.0
• Source code: https://github.com/cran/scone
• BugReports: https://github.com/YosefLab/scone/issues
• Date/Publication: 2019-10-29
• Number of recursive dependencies: 218

Run revdep_details(,"scone") for more info

In both

• checking whether the namespace can be loaded with stated dependencies ... WARNING ``` Error in setGeneric("Makesense", function(expr, lib, ...) standardGeneric("Makesense")) : could not find function "setGeneric" Error: unable to load R code in package ‘geneplotter’ Execution halted

  A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start.

  Probably some imports need to be declared in the NAMESPACE file. ```

• checking R code for possible problems ... NOTE Error in setGeneric("Makesense", function(expr, lib, ...) standardGeneric("Makesense")) : could not find function "setGeneric" Error: unable to load R code in package ‘geneplotter’ Execution halted

scran

• Version: 1.14.5
• Source code: https://github.com/cran/scran
• Date/Publication: 2019-11-19
• Number of recursive dependencies: 188

Run revdep_details(,"scran") for more info

In both

• checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 5478 | SKIPPED: 0 | WARNINGS: 843 | FAILED: 9 ]

  1. Error: findMarkers works correctly with subsetting and spikes (@test-markers.R#43)
  2. Error: pairwiseTTests works as expected with a design matrix (@test-pairwise-t.R#367)
  3. Error: pairwiseTTests with linear models works across multiple cores (@test-pairwise-t.R#388)
  4. Error: pairwiseTTests with linear models responds to non-standard level ordering (@test-pairwise-t.R#401)
  5. Error: pairwiseTTests with design matrices responds to restriction (@test-pairwise-t.R#428)
  6. Error: pairwiseTTests behaves as expected with subsetting (@test-pairwise-t.R#450)
  7. Error: pairwiseTTests behaves as expected with log-transformation (@test-pairwise-t.R#497)
  8. Error: pairwiseTTests behaves with standardization of the log-fold changes (@test-pairwise-t.R#526)
  9. Error: pairwiseTTests fails gracefully with silly inputs (@test-pairwise-t.R#553)

  Error: testthat unit tests failed Execution halted Error while shutting down parallel: unable to terminate some child processes ```

• checking examples ... WARNING ... Warning: 'normalizeSCE' is deprecated. Warning: 'centreSizeFactors' is deprecated. Warning: handling of spike-ins via 'isSpike()' is deprecated. Warning: 'overlapExprs' is deprecated. Warning: 'parallelPCA' is deprecated. Warning: 'technicalCV2' is deprecated. Warning: 'isSpike<-' is deprecated. Warning: 'spikeNames' is deprecated. Warning: 'isSpike' is deprecated. Warning: 'technicalCV2' is deprecated. Warning: 'testVar' is deprecated. Warning: 'testVar' is deprecated. Warning: 'testVar' is deprecated. Warning: handling of spike-ins via 'isSpike()' is deprecated. Warning: 'normalizeSCE' is deprecated. Warning: 'centreSizeFactors' is deprecated. Warning: 'trendVar' is deprecated. Warning: 'trendVar' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated.

• checking installed package size ... NOTE installed size is 25.2Mb sub-directories of 1Mb or more: doc 2.1Mb libs 22.0Mb

TIN

• Version: 1.18.0
• Source code: https://github.com/cran/TIN
• Date/Publication: 2019-10-29
• Number of recursive dependencies: 117

Run revdep_details(,"TIN") for more info

In both

• checking R code for possible problems ... NOTE ... scatterPlot: no visible global function definition for ‘pdf’ scatterPlot: no visible global function definition for ‘bmp’ scatterPlot: no visible global function definition for ‘plot’ scatterPlot: no visible global function definition for ‘ave’ scatterPlot: no visible global function definition for ‘axis’ scatterPlot: no visible global function definition for ‘text’ scatterPlot: no visible global function definition for ‘mtext’ scatterPlot: no visible global function definition for ‘points’ scatterPlot: no visible global function definition for ‘dev.off’ Undefined global functions or variables: ave axis bmp colorRampPalette data dev.off dist hclust hist jpeg median mtext par pdf plot png points postscript quantile read.table text Consider adding importFrom("grDevices", "bmp", "colorRampPalette", "dev.off", "jpeg", "pdf", "png", "postscript") importFrom("graphics", "axis", "hist", "mtext", "par", "plot", "points", "text") importFrom("stats", "ave", "dist", "hclust", "median", "quantile") importFrom("utils", "data", "read.table") to your NAMESPACE file.

HenrikBengtsson/aroma.light documentation built on July 3, 2023, 1:57 a.m.