foreach: Provides Foreach Looping Construct

DepecheR

Version: 1.0.3
Source code: https://github.com/cran/DepecheR
Date/Publication: 2019-06-28
Number of recursive dependencies: 99

Run revdep_details(,"DepecheR") for more info

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: |=============================================================== | 90% | |======================================================================| 100% ── 1. Error: (unknown) (@test_sPLSDA.R#28) ──────────────────────────────────── 'newdata' must include all the variables of 'object$X' Backtrace:
1. DepecheR::dSplsda(...)
2. mixOmics:::predict.mixo_spls(...)
══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 23 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ] 1. Error: (unknown) (@test_sPLSDA.R#28)

Error: testthat unit tests failed Execution halted ```

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘BiocParallel’ All declared Imports should be used.
checking compiled code ... NOTE ``` File ‘DepecheR/libs/DepecheR.so’: Found ‘rand’, possibly from ‘rand’ (C) Object: ‘Clusterer.o’ Found ‘srand’, possibly from ‘srand’ (C) Objects: ‘Clusterer.o’, ‘InterfaceUtils.o’

Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```

MineICA

Version: 1.24.0
Source code: https://github.com/cran/MineICA
Date/Publication: 2019-05-02
Number of recursive dependencies: 185

Run revdep_details(,"MineICA") for more info

checking examples ... ERROR ``` ... > ### Aliases: clusterFastICARuns > > ### * Examples > > ## generate a data > set.seed(2004); > M <- matrix(rnorm(50006,sd=0.3),ncol=10) > M[1:100,1:3] <- M[1:100,1:3] + 2 > M[1:200,1:3] <- M[1:200,4:6] +1 > > ## Random initializations are used for each iteration of FastICA > ## Estimates are clustered using hierarchical clustering with average linkage > res <- clusterFastICARuns(X=M, nbComp=2, alg.type="deflation",
- nbIt=3, funClus="hclust", method="average") FastICA iteration 1 Warning: executing %dopar% sequentially: no parallel backend registered FastICA iteration 2 FastICA iteration 3 Error in solve.default(t(W) %*% W) : 'a' is 0-diml Calls: clusterFastICARuns -> solve -> solve.default Execution halted ```
checking running R code from vignettes ... ``` ‘MineICA.Rnw’... failed ERROR Errors in running code in vignettes: when running code in ‘MineICA.Rnw’ ... > resPath(params) [1] "mainz/"

resW <- writeProjByComp(icaSet = icaSetMainz, params = params, + mart = mart, level = "genes", selCutoffWrite = 2.5)

When sourcing ‘MineICA.R’: Error: task 1 failed - "The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this on the support site at http://support.bioconductor.org" Execution halted ```

checking package dependencies ... NOTE ``` Package which this enhances but not available for checking: ‘doMC’

Depends: includes the non-default packages: 'BiocGenerics', 'Biobase', 'plyr', 'ggplot2', 'scales', 'foreach', 'xtable', 'biomaRt', 'gtools', 'GOstats', 'cluster', 'marray', 'mclust', 'RColorBrewer', 'colorspace', 'igraph', 'Rgraphviz', 'graph', 'annotate', 'Hmisc', 'fastICA', 'JADE' Adding so many packages to the search path is excessive and importing selectively is preferable. ```
checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘biomaRt’ ‘GOstats’ ‘cluster’ ‘mclust’ ‘igraph’ A package should be listed in only one of these fields.
checking dependencies in R code ... NOTE 'library' or 'require' call to ‘GOstats’ which was already attached by Depends. Please remove these calls from your code. Namespace in Imports field not imported from: ‘lumiHumanAll.db’ All declared Imports should be used. Packages in Depends field not imported from: ‘GOstats’ ‘Hmisc’ ‘JADE’ ‘RColorBrewer’ ‘Rgraphviz’ ‘annotate’ ‘biomaRt’ ‘cluster’ ‘colorspace’ ‘fastICA’ ‘foreach’ ‘ggplot2’ ‘graph’ ‘gtools’ ‘igraph’ ‘marray’ ‘mclust’ ‘methods’ ‘plyr’ ‘scales’ ‘xtable’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. ':::' calls which should be '::': ‘Biobase:::annotation’ ‘Biobase:::validMsg’ ‘fpc:::pamk’ ‘lumi:::getChipInfo’ ‘mclust:::adjustedRandIndex’ See the note in ?`:::` about the use of this operator. Unexported object imported by a ':::' call: ‘Biobase:::isValidVersion’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE ... reorder scale_colour_gradientn scale_colour_manual scale_fill_manual scale_linetype_manual scale_shape_manual scale_x_continuous scale_x_discrete scale_y_continuous shapiro.test sigCategories terrain_hcl theme theme_bw title tkplot.fit.to.screen unit useMart validObject vcount viewport wilcox.test write.table xlab xtable Consider adding importFrom("grDevices", "cm.colors", "dev.off", "graphics.off", "heat.colors", "pdf") importFrom("graphics", "abline", "axis", "frame", "hist", "layout", "legend", "mtext", "par", "plot", "plot.new", "points", "title") importFrom("methods", "callNextMethod", "new", "validObject") importFrom("stats", "aggregate", "as.dendrogram", "as.dist", "as.hclust", "chisq.test", "cor", "cor.test", "cutree", "dist", "hclust", "kmeans", "kruskal.test", "lm", "median", "na.omit", "order.dendrogram", "p.adjust", "quantile", "reorder", "shapiro.test", "wilcox.test") importFrom("utils", "capture.output", "combn", "read.table", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').