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

Last updated on 2024-11-09 02:49:15 CET.

Package FAIL ERROR NOTE OK
ACNE 3 10
aroma.affymetrix 9 4
aroma.apd 2 11
aroma.cn 2 11
aroma.core 11 2
calmate 1 12
dChipIO 13
doFuture 3 10
future 13
future.apply 13
future.batchtools 3 10
future.callr 13
future.mirai 13
future.tests 13
futureverse 13
globals 3 10
listenv 13
matrixStats 13
parallelly 13
port4me 13
profmem 1 12
progressr 1 12
PSCBS 3 10
R.cache 10 3
R.devices 1 12
R.filesets 13
R.huge 13
R.matlab 2 9 2
R.methodsS3 13
R.oo 13
R.rsp 13
R.utils 3 10
seguid 13
startup 13
TopDom 10 3

Package ACNE

Current CRAN status: NOTE: 3, OK: 10

Version: 0.9.1
Check: Rd cross-references
Result: NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: doACNE.Rd: AffymetrixCelSet, Verbose Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64

Package aroma.affymetrix

Current CRAN status: NOTE: 9, OK: 4

Version: 3.2.2
Check: Rd cross-references
Result: NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: SmoothMultiarrayModel.Rd: ChromosomalModel, CopyNumberSegmentationModel byPath.AffymetrixFileSet.Rd: GenericDataFile calculateBaseline.ChipEffectSet.Rd: getAverageFile doCRMAv1.Rd: Verbose doCRMAv2.Rd: Verbose doFIRMA.Rd: Verbose doGCRMA.Rd: Verbose doRMA.Rd: Verbose justRMA.Rd: Verbose Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64

Version: 3.2.2
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘AffymetrixDataTestFiles’ Flavors: r-release-macos-arm64, r-release-macos-x86_64

Version: 3.2.2
Check: installed package size
Result: NOTE installed size is 6.1Mb sub-directories of 1Mb or more: R 3.0Mb help 1.1Mb testScripts 1.1Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 3.2.2
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'affxparser', 'oligo', 'oligoClasses', 'pdInfoBuilder', 'AffymetrixDataTestFiles' Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 3.2.2
Check: Rd cross-references
Result: NOTE Packages unavailable to check Rd xrefs: ‘affxparser’, ‘oligo’, ‘oligoClasses’ Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package aroma.apd

Current CRAN status: NOTE: 2, OK: 11

Version: 0.7.0
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘affxparser’ Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 0.7.0
Check: Rd cross-references
Result: NOTE Package unavailable to check Rd xrefs: ‘affxparser’ Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package aroma.cn

Current CRAN status: NOTE: 2, OK: 11

Version: 1.7.1
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘GLAD’ Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package aroma.core

Current CRAN status: NOTE: 11, OK: 2

Version: 3.3.1
Check: Rd cross-references
Result: NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: writeDataFrame.AromaUnitSignalBinaryFile.Rd: TabularTextFile writeDataFrame.AromaUnitSignalBinarySet.Rd: TabularTextFileSet writeDataFrame.AromaUnitTabularBinaryFile.Rd: TabularTextFile Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64

Version: 3.3.1
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'sfit', 'expectile', 'HaarSeg', 'mpcbs' Flavors: r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 3.3.1
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'GLAD', 'sfit', 'expectile', 'HaarSeg', 'mpcbs' Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 3.3.1
Check: Rd cross-references
Result: NOTE Package unavailable to check Rd xrefs: ‘GLAD’ Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package calmate

Current CRAN status: ERROR: 1, OK: 12

Version: 0.13.0
Check: package dependencies
Result: ERROR Package required but not available: ‘aroma.core’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Flavor: r-oldrel-macos-arm64

Package dChipIO

Current CRAN status: OK: 13

Package doFuture

Current CRAN status: NOTE: 3, OK: 10

Version: 1.0.1
Check: Rd cross-references
Result: NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: doFuture.Rd: foreach, future grapes-dofuture-grapes.Rd: %dopar% Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64

Package future

Current CRAN status: OK: 13

Package future.apply

Current CRAN status: OK: 13

Package future.batchtools

Current CRAN status: NOTE: 3, OK: 10

Version: 0.12.1
Check: Rd cross-references
Result: NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: nbrOfWorkers.batchtools.Rd: plan Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64

Package future.callr

Current CRAN status: OK: 13

Package future.mirai

Current CRAN status: OK: 13

Package future.tests

Current CRAN status: OK: 13

Package futureverse

Current CRAN status: OK: 13

Package globals

Current CRAN status: NOTE: 3, OK: 10

Version: 0.16.3
Check: Rd cross-references
Result: NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: globalsOf.Rd: codetools Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64

Package listenv

Current CRAN status: OK: 13

Package matrixStats

Current CRAN status: OK: 13

Package parallelly

Current CRAN status: OK: 13

Package port4me

Current CRAN status: OK: 13

Package profmem

Current CRAN status: ERROR: 1, OK: 12

Version: 0.6.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘profmem.md.rsp’ using rsp R.utils v2.12.3 (2023-11-18 01:00:02 UTC) 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, isOpen, nullfile, parse, use, warnings Error: processing vignette 'profmem.md.rsp' failed with diagnostics: there is no package called ‘microbenchmark’ --- failed re-building ‘profmem.md.rsp’ SUMMARY: processing the following file failed: ‘profmem.md.rsp’ Error: Vignette re-building failed. Execution halted Flavor: r-release-macos-arm64

Package progressr

Current CRAN status: ERROR: 1, OK: 12

Additional issues

M1mac

Version: 0.15.0
Check: examples
Result: ERROR Running examples in ‘progressr-Ex.R’ failed The error most likely occurred in: > ### Name: handler_ntfy > ### Title: Progression Handler: Progress Reported via the Ntfy.sh Messaging > ### Service > ### Aliases: handler_ntfy > ### Keywords: internal > > ### ** Examples > > pkg <- "ntfy" > if (requireNamespace(pkg, quietly = TRUE)) { + ## We need to specify a ntfy.sh topic that progress messages + ## should be sent to. See help("ntfy_topic", package = "ntfy") + ## for details + Sys.setenv("NTFY_TOPIC", "R-my-secret-topic") + + handlers("ntfy") + with_progress({ y <- slow_sum(1:10) }) + print(y) + } Error in Sys.setenv("NTFY_TOPIC", "R-my-secret-topic") : all arguments must be named Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Package PSCBS

Current CRAN status: NOTE: 3, OK: 10

Version: 0.67.0
Check: Rd cross-references
Result: NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: as.CBS.DNAcopy.Rd: DNAcopy as.DNAcopy.CBS.Rd: DNAcopy Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64

Package R.cache

Current CRAN status: NOTE: 10, OK: 3

Version: 0.16.0
Check: Rd files
Result: NOTE checkRd: (-1) R.cache-package.Rd:28-30: Lost braces in \itemize; meant \describe ? checkRd: (-1) R.cache-package.Rd:31-34: Lost braces in \itemize; meant \describe ? 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-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

Package R.devices

Current CRAN status: NOTE: 1, OK: 12

Version: 2.17.2
Check: package vignettes
Result: NOTE Package has ‘vignettes’ subdirectory but apparently no vignettes. Perhaps the ‘VignetteBuilder’ information is missing from the DESCRIPTION file? Flavor: r-release-macos-x86_64

Package R.filesets

Current CRAN status: OK: 13

Package R.huge

Current CRAN status: OK: 13

Package R.matlab

Current CRAN status: FAIL: 2, NOTE: 9, OK: 2

Version: 3.7.0
Check: Rd files
Result: NOTE checkRd: (-1) setOption.Matlab.Rd:37-39: Lost braces in \itemize; meant \describe ? checkRd: (-1) setOption.Matlab.Rd:40-41: Lost braces in \itemize; meant \describe ? 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-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

Version: 3.7.0
Check: tests
Result: FAIL Check process probably crashed or hung up for 20 minutes ... killed Most likely this happened in the example checks (?), if not, ignore the following last lines of example output: + }) ERROR: Detected objects with duplicated names (A). Only the last occurance of each duplicated object will be available in MATLAB if completed: writeMat.default(filename, A = A, B = B, A = C) > > > ## Not run: > ##D # When writing to a stream connection the receiver needs to know on > ##D # beforehand how many bytes are available. This can be done by using > ##D # the 'onWrite' argument. > ##D onWrite <- function(x) > ##D writeBin(x$length, con = x$con, size = 4, endian = "little") > ##D writeMat(con, A = A, B = B, onWrite = onWrite) > ## End(Not run) > > > > ### * <FOOTER> > ### > cleanEx() > options(digits = 7L) > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") Time elapsed: 49.46 503.66 556.61 NA NA > grDevices::dev.off() null device 1 > ### > ### Local variables: *** > ### mode: outline-minor *** > ### outline-regexp: "\\(> \\)?### [*]+" *** > ### End: *** > quit('no') ======== End of example output (where/before crash/hang up occured ?) ======== Flavor: r-devel-windows-x86_64

Version: 3.7.0
Check: tests
Result: FAIL Check process probably crashed or hung up for 20 minutes ... killed Most likely this happened in the example checks (?), if not, ignore the following last lines of example output: + }) ERROR: Detected objects with duplicated names (A). Only the last occurance of each duplicated object will be available in MATLAB if completed: writeMat.default(filename, A = A, B = B, A = C) > > > ## Not run: > ##D # When writing to a stream connection the receiver needs to know on > ##D # beforehand how many bytes are available. This can be done by using > ##D # the 'onWrite' argument. > ##D onWrite <- function(x) > ##D writeBin(x$length, con = x$con, size = 4, endian = "little") > ##D writeMat(con, A = A, B = B, onWrite = onWrite) > ## End(Not run) > > > > ### * <FOOTER> > ### > cleanEx() > options(digits = 7L) > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") Time elapsed: 71.14 248.5 323.99 NA NA > grDevices::dev.off() null device 1 > ### > ### Local variables: *** > ### mode: outline-minor *** > ### outline-regexp: "\\(> \\)?### [*]+" *** > ### End: *** > quit('no') ======== End of example output (where/before crash/hang up occured ?) ======== Flavor: r-oldrel-windows-x86_64

Package R.methodsS3

Current CRAN status: OK: 13

Package R.oo

Current CRAN status: OK: 13

Package R.rsp

Current CRAN status: OK: 13

Package R.utils

Current CRAN status: NOTE: 3, OK: 10

Version: 2.12.3
Check: Rd cross-references
Result: NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: TimeoutException.Rd: Exception Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64

Package seguid

Current CRAN status: OK: 13

Package startup

Current CRAN status: OK: 13

Package TopDom

Current CRAN status: NOTE: 10, OK: 3

Version: 0.10.1
Check: Rd files
Result: NOTE checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup? 21 | Recommended range is in {5, ..., 20}.} | ^ 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-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64