CRAN Package Check Results for Maintainer ‘Henrik Bengtsson <henrikb at braju.com>’

Last updated on 2019-11-12 20:49:31 CET.

Package ERROR NOTE OK
ACNE 12
aroma.affymetrix 7 5
aroma.apd 1 11
aroma.cn 2 10
aroma.core 12
calmate 12
dChipIO 12
doFuture 12
future 12
future.apply 1 11
future.BatchJobs 12
future.batchtools 12
future.callr 12
globals 12
listenv 12
matrixStats 7 5
profmem 12
PSCBS 12
R.cache 12
R.devices 1 11
R.filesets 12
R.huge 12
R.matlab 12
R.methodsS3 12
R.oo 12
R.rsp 2 10
R.utils 12
startup 12

Package ACNE

Current CRAN status: OK: 12

Package aroma.affymetrix

Current CRAN status: NOTE: 7, OK: 5

Version: 3.2.0
Check: installed package size
Result: NOTE
     installed size is 5.8Mb
     sub-directories of 1Mb or more:
     R 2.3Mb
     help 1.1Mb
     testScripts 1.3Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 3.2.0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘AffymetrixDataTestFiles’
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Package aroma.apd

Current CRAN status: NOTE: 1, OK: 11

Version: 0.6.0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘affxparser’
Flavor: r-release-osx-x86_64

Version: 0.6.0
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘affxparser’
Flavor: r-release-osx-x86_64

Package aroma.cn

Current CRAN status: NOTE: 2, OK: 10

Version: 1.6.1
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘GLAD’
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Package aroma.core

Current CRAN status: NOTE: 12

Version: 3.2.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64

Version: 3.2.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'GLAD', 'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Flavor: r-release-osx-x86_64

Version: 3.2.0
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘GLAD’
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 3.2.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'sfit' 'expectile' 'HaarSeg' 'mpcbs'
Flavor: r-oldrel-windows-ix86+x86_64

Version: 3.2.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘GLAD’ ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
Flavor: r-oldrel-osx-x86_64

Package calmate

Current CRAN status: OK: 12

Package dChipIO

Current CRAN status: OK: 12

Package doFuture

Current CRAN status: OK: 12

Package future

Current CRAN status: OK: 12

Package future.apply

Current CRAN status: ERROR: 1, OK: 11

Version: 1.3.0
Check: examples
Result: ERROR
    Running examples in 'future.apply-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: future_by
    > ### Title: Apply a Function to a Data Frame Split by Factors via Futures
    > ### Aliases: future_by
    >
    > ### ** Examples
    >
    > ## ---------------------------------------------------------
    > ## by()
    > ## ---------------------------------------------------------
    > library(datasets) ## warpbreaks
    > library(stats) ## lm()
    >
    > y0 <- by(warpbreaks, warpbreaks[,"tension"],
    + function(x) lm(breaks ~ wool, data = x))
    >
    > plan(multiprocess)
    Warning in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE, :
     port 11835 cannot be opened
    Error in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE, :
     Failed to launch and connect to R worker on local machine 'localhost' from local machine 'CRANWIN'.
     * The error produced by socketConnection() was: 'cannot open the connection'
     * In addition, socketConnection() produced 1 warning(s):
     - Warning #1: 'port 11835 cannot be opened' (which suggests that this port is either already occupied by another process or blocked by the firewall on your local machine)
     * The localhost socket connection that failed to connect to the R worker used port 11835 using a communication timeout of 120 seconds and a connection timeout of 120 seconds.
     * Worker launch call: "D:/RCompile/recent/R/bin/x64/Rscript" --default-packages=datasets,utils,grDevices,graphics,stats,methods -e "#label=future.apply-Ex.R:70608:CRANWIN:CRAN" -e "try(suppressWarnings(cat(Sys.getpid(),file=\"D:/temp/RtmpqA7FoB/future.parent=70608.113d07ee46bc4.pid\")), silent = TRUE)" -e "parallel:::.slaveRSOCK()" MASTER=localhost PORT=11835 OUT=/dev/null TIMEOUT=120 XDR=TRUE.
     * Worker (PID 86236) was successfully killed: TRUE
     * Troubleshooting suggestions:
     - Suggestion #1: Set 'verbose=TRUE' to see more details.
     - Suggestion #2: On Windows, output from worker when using 'outfile=NULL' is only visible when running R from a terminal (not a GUI).
    Calls: plan ... tryCatchList -> tryCatchOne -> <Anonymous> -> <Anonymous>
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Package future.BatchJobs

Current CRAN status: OK: 12

Package future.batchtools

Current CRAN status: OK: 12

Package future.callr

Current CRAN status: OK: 12

Package globals

Current CRAN status: OK: 12

Package listenv

Current CRAN status: OK: 12

Package matrixStats

Current CRAN status: NOTE: 7, OK: 5

Version: 0.55.0
Check: installed package size
Result: NOTE
     installed size is 11.3Mb
     sub-directories of 1Mb or more:
     libs 10.5Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Package profmem

Current CRAN status: OK: 12

Package PSCBS

Current CRAN status: OK: 12

Package R.cache

Current CRAN status: OK: 12

Package R.devices

Current CRAN status: ERROR: 1, OK: 11

Version: 2.16.1
Check: tests
Result: ERROR
     Running ‘DevEvalFileProduct.R’
     Running ‘DevEvalProduct.R’
     Running ‘capabilitiesX11.R’
     Running ‘capturePlot.R’
     Running ‘dataURI.R’
     Running ‘devAll.R’
     Running ‘devDump.R’
     Running ‘devEqualTypes.R’
     Running ‘devEval,error.R’
     Running ‘devEval.R’ [7s/23s]
     Running ‘devIsInteractive.R’
     Running ‘devIsOpen.R’
     Running ‘devList.R’
     Running ‘devListIndexOf.R’
     Running ‘devNew.R’
     Running ‘devOptions.R’
     Running ‘devSet.R’
     Running ‘devTypeName.R’
     Running ‘favicon.R’
     Running ‘toNNN.R’
     Running ‘withPar.R’
    Running the tests in ‘tests/devEval.R’ failed.
    Complete output:
     > message("*** devEval() ...")
     *** devEval() ...
     >
     > library("R.devices")
     R.devices v2.16.1 successfully loaded. See ?R.devices for help.
     > library("R.utils")
     Loading required package: R.oo
     Loading required package: R.methodsS3
     R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
     R.oo v1.23.0 successfully loaded. See ?R.oo for help.
    
     Attaching package: 'R.oo'
    
     The following object is masked from 'package:R.methodsS3':
    
     throw
    
     The following objects are masked from 'package:methods':
    
     getClasses, getMethods
    
     The following objects are masked from 'package:base':
    
     attach, detach, load, save
    
     R.utils v2.9.0 successfully loaded. See ?R.utils for help.
    
     Attaching package: 'R.utils'
    
     The following object is masked from 'package:utils':
    
     timestamp
    
     The following objects are masked from 'package:base':
    
     cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
     warnings
    
     > graphics.off()
     >
     > png <- grDevices::png
     > jpeg <- grDevices::jpeg
     > tiff <- grDevices::tiff
     >
     >
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     > # Various types of single and multiple device outputs
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     > message("*** devEval() - single and multiple device outputs ...")
     *** devEval() - single and multiple device outputs ...
     >
     > types <- list(
     + character(0L),
     + "png",
     + "jpg",
     + "nulldev",
     + c("png", "png", "jpeg"),
     + "png,nulldev,pdf"
     + )
     >
     > for (type in types) {
     + cat("Device types: ", paste(sQuote(type), collapse=", "), "\n", sep="")
     + devList0 <- devList()
     + res <- devEval(type, name="multi", aspectRatio=2/3, {
     + plot(1:10)
     + })
     + print(res)
     + stopifnot(length(res) == length(unlist(strsplit(type, split=","))))
     + stopifnot(all.equal(devList(), devList0))
     + }
     Device types:
     character(0)
     Device types: 'png'
     [1] "figures/multi.png"
     Device types: 'jpg'
     [1] "figures/multi.jpg"
     Device types: 'nulldev'
     [1] "/dev/null"
     Device types: 'png', 'png', 'jpeg'
     $png
     [1] "figures/multi.png"
    
     $png
     [1] "figures/multi.png"
    
     $jpeg
     [1] "figures/multi.jpg"
    
     Device types: 'png,nulldev,pdf'
     $png
     [1] "figures/multi.png"
    
     $nulldev
     [1] "/dev/null"
    
     $pdf
     [1] "figures/multi.pdf"
    
     >
     > # Sanity checks
     > print(devList())
     named integer(0)
     > stopifnot(length(devList()) == 0L)
     >
     > message("*** devEval() - single and multiple device outputs ... DONE")
     *** devEval() - single and multiple device outputs ... DONE
     >
     >
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     > # With 'initially' and 'finally' expression
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     > message("*** devEval() - initially and finally ...")
     *** devEval() - initially and finally ...
     >
     > devList0 <- devList()
     > devEval(c("png", "jpg"), name="count", {
     + plot(1:10)
     + count <- count + 1L
     + }, initially = {
     + # Emulate an overhead
     + cat("Initiate...")
     + count <- 0L
     + Sys.sleep(1)
     + cat("done\n")
     + }, finally = {
     + cat("Number of image files created: ", count, "\n", sep="")
     + })
     Initiate...done
     Number of image files created: 2
     $png
     [1] "figures/count.png"
    
     $jpeg
     [1] "figures/count.jpg"
    
     > stopifnot(all.equal(devList(), devList0))
     >
     > # Sanity checks
     > print(devList())
     named integer(0)
     > stopifnot(length(devList()) == 0L)
     >
     > message("*** devEval() - initially and finally ... DONE")
     *** devEval() - initially and finally ... DONE
     >
     >
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     > # Try several devices until first successful device is found
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     > message("*** devEval() - first successful device ...")
     *** devEval() - first successful device ...
     >
     > types <- list(
     + "png|jpg|pdf", # PNG, JPG and then PDF
     + "dummy|png|jpg|pdf", # "Non-existing", PNG, JPG and then PDF
     + "quartz|x11|windows", # Any interactive device (depending on OS)
     + c("png|jpg", "x11|windows"), # PNG or JPG and then x11 or windows
     + "eps|postscript|pdf", # EPS, Postscript or PDF
     + "jpeg2|jpeg", # JPEG via bitmap() or via jpeg()
     + "png,jpg|x11|windows", # == c("png", "jpg|x11|windows")
     + "nulldev|jpeg" # NULL devices, otherwise jpeg
     + )
     >
     > if (!capabilitiesX11()) {
     + message("Skipping test for X11")
     + types <- lapply(types, FUN=function(x) gsub("x11|", "", x, fixed=TRUE))
     + }
     >
     > devList0 <- devList()
     >
     > for (type in types) {
     + printf("Any of %s\n", paste(sQuote(type), collapse=" + "))
     +
     + # Use try-catch in case not supported on some test systems
     + tryCatch({
     + res <- devEval(type, name="any", aspectRatio=2/3, scale=1.2, {
     + plot(100:1)
     + })
     + printf("Result: %s (%s)\n\n", sQuote(res), attr(res, "type"))
     +
     + if (length(devList()) > 0) devOff()
     + }, error = function(ex) {
     + printf("Failed: %s\n\n", sQuote(ex$message))
     + })
     + } # for (type ...)
     Any of 'png|jpg|pdf'
     Any of 'dummy|png|jpg|pdf'
     Any of 'quartz|x11|windows'
     Failed: 'Failed to open graphics device: quartz'
    
     Any of 'png|jpg' + 'x11|windows'
     Any of 'eps|postscript|pdf'
     Any of 'jpeg2|jpeg'
     Any of 'png,jpg|x11|windows'
    
     *** caught segfault ***
     address f7fb6018, cause 'memory not mapped'
    
     Traceback:
     1: .External2(C_X11, d$display, d$width, d$height, d$pointsize, d$gamma, d$colortype, d$maxcubesize, d$bg, d$canvas, d$fonts, NA_integer_, d$xpos, d$ypos, d$title, type, antialias, d$family)
     2: (function (display = "", width, height, pointsize, gamma, bg, canvas, fonts, family, xpos, ypos, title, type, antialias, ...) { if (display != "XImage") { check <- Sys.getenv("_R_CHECK_SCREEN_DEVICE_", "") msg <- "screen devices should not be used in examples etc" if (identical(check, "stop")) stop(msg, domain = NA) else if (identical(check, "warn")) warning(msg, immediate. = TRUE, noBreaks. = TRUE, domain = NA) } if (display == "" && .Platform$GUI == "AQUA" && is.na(Sys.getenv("DISPLAY", NA))) Sys.setenv(DISPLAY = ":0") new <- list() if (!missing(display)) new$display <- display if (!missing(width)) new$width <- width if (!missing(height)) new$height <- height if (!missing(gamma)) new$gamma <- gamma if (!missing(pointsize)) new$pointsize <- pointsize if (!missing(bg)) new$bg <- bg if (!missing(canvas)) new$canvas <- canvas if (!missing(xpos)) new$xpos <- xpos if (!missing(ypos)) new$ypos <- ypos if (!missing(title)) new$title <- title if (!checkIntFormat(new$title)) stop("invalid 'title'") if (!missing(type)) { new$type <- match.arg(type, c("Xlib", "cairo", "nbcairo", "dbcairo")) if (!capabilities("cairo") && type != "Xlib") warning("cairo-based types are not supported on this build - using \"Xlib\"") } if (!missing(family)) new$family <- family if (!missing(fonts)) new$fonts <- fonts if (!missing(antialias) && type != "Xlib") new$antialias <- match.arg(antialias, aa.cairo) d <- check.options(new, name.opt = ".X11.Options", envir = .X11env) if (d$type == "Xlib" && !missing(family)) { fns <- X11Fonts() if (!family %in% names(fns)) stop("unknown family for X11(type = \"XLib\")") d$fonts[1] <- fns[[family]] } type <- if (capabilities("cairo")) switch(d$type, cairo = 1L, nbcairo = 2L, dbcairo = 3L, 0L) else 0L if (display == "XImage") type <- 0L antialias <- match(d$antialias, aa.cairo) if (grepl("darwin", R.version$os)) check_for_XQuartz() .External2(C_X11, d$display, d$width, d$height, d$pointsize, d$gamma, d$colortype, d$maxcubesize, d$bg, d$canvas, d$fonts, NA_integer_, d$xpos, d$ypos, d$title, type, antialias, d$family) invisible()})()
     3: do.call(typeT, args = args)
     4: devNew(type, which = fullname, ..., .allowUnknownArgs = .allowUnknownArgs)
     5: devEval(type = type, expr = expr, initially = NULL, finally = NULL, envir = envir, name = nameOrg, tags = tags, sep = sep, ..., ext = ext, filename = filename, path = path, field = field, onIncomplete = onIncomplete, force = force, .exprAsIs = TRUE, .allowUnknownArgs = TRUE)
     6: FUN(X[[i]], ...)
     7: lapply(types, FUN = function(type) { devEval(type = type, expr = expr, initially = NULL, finally = NULL, envir = envir, name = nameOrg, tags = tags, sep = sep, ..., ext = ext, filename = filename, path = path, field = field, onIncomplete = onIncomplete, force = force, .exprAsIs = TRUE, .allowUnknownArgs = TRUE)})
     8: devEval(type, name = "any", aspectRatio = 2/3, scale = 1.2, { plot(100:1)})
     9: doTryCatch(return(expr), name, parentenv, handler)
     10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11: tryCatchList(expr, classes, parentenv, handlers)
     12: tryCatch({ res <- devEval(type, name = "any", aspectRatio = 2/3, scale = 1.2, { plot(100:1) }) printf("Result: %s (%s)\n\n", sQuote(res), attr(res, "type")) if (length(devList()) > 0) devOff()}, error = function(ex) { printf("Failed: %s\n\n", sQuote(ex$message))})
     An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Package R.filesets

Current CRAN status: OK: 12

Package R.huge

Current CRAN status: OK: 12

Package R.matlab

Current CRAN status: OK: 12

Package R.methodsS3

Current CRAN status: OK: 12

Package R.oo

Current CRAN status: OK: 12

Package R.rsp

Current CRAN status: NOTE: 2, OK: 10

Version: 0.43.2
Check: dependencies in R code
Result: NOTE
    No protocol specified
    No protocol specified
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Package R.utils

Current CRAN status: OK: 12

Package startup

Current CRAN status: OK: 12