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

Last updated on 2024-03-29 04:55:05 CET.

Package ERROR NOTE OK
ACNE 12
aroma.affymetrix 7 5
aroma.apd 2 10
aroma.cn 2 10
aroma.core 12
calmate 1 11
dChipIO 12
doFuture 1 11
future 12
future.apply 12
future.batchtools 12
future.callr 12
future.tests 12
globals 12
listenv 12
matrixStats 12
parallelly 12
port4me 12
profmem 12
progressr 12
PSCBS 12
R.cache 6 6
R.devices 12
R.filesets 12
R.huge 12
R.matlab 6 6
R.methodsS3 12
R.oo 12
R.rsp 12
R.utils 12
seguid 12
startup 12
TopDom 6 6

Package ACNE

Current CRAN status: OK: 12

Package aroma.affymetrix

Current CRAN status: NOTE: 7, OK: 5

Version: 3.2.2
Check: installed package size
Result: NOTE installed size is 5.9Mb sub-directories of 1Mb or more: R 2.3Mb help 1.2Mb testScripts 1.3Mb Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, 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-release-macos-arm64, r-release-macos-x86_64

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

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

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

Package aroma.apd

Current CRAN status: NOTE: 2, OK: 10

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

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

Package aroma.cn

Current CRAN status: NOTE: 2, OK: 10

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

Package aroma.core

Current CRAN status: NOTE: 12

Version: 3.3.1
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-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, 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-release-macos-arm64, r-release-macos-x86_64

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

Package calmate

Current CRAN status: ERROR: 1, OK: 11

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-release-macos-arm64

Package dChipIO

Current CRAN status: OK: 12

Package doFuture

Current CRAN status: ERROR: 1, OK: 11

Version: 1.0.1
Check: tests
Result: ERROR Running 'foreach_dofuture,cluster-missing-doFuture-pkg.R' [2s] Running 'foreach_dofuture,errors.R' [9s] Running 'foreach_dofuture,globals.R' [7s] Running 'foreach_dofuture,nested_colon.R' [1s] Running 'foreach_dofuture,nested_dofuture.R' [14s] Running 'foreach_dofuture,rng.R' [4s] Running 'foreach_dofuture.R' [3s] Running 'foreach_dopar,cluster-missing-doFuture-pkg.R' [2s] Running 'foreach_dopar,doRNG,dopar.R' [3s] Running 'foreach_dopar,doRNG,dorng.R' [5s] Running 'foreach_dopar,errors.R' [7s] Running 'foreach_dopar,globals.R' [7s] Running 'foreach_dopar,nested_colon.R' [1s] Running 'foreach_dopar,nested_dopar.R' [15s] Running 'foreach_dopar,options-for-export.R' [3s] Running 'foreach_dopar.R' [3s] Running 'makeChunks.R' [3s] Running 'options,nested.R' [3s] Running 'registerDoFuture.R' [2s] Running 'times.R' [2s] Running 'utils.R' [1s] Running 'withDoRNG.R' [4s] Running the tests in 'tests/foreach_dofuture,nested_colon.R' failed. Complete output: > source("incl/start.R") Loading required package: foreach Loading required package: future R version 4.4.0 alpha (2024-03-26 r86209 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows Server 2022 x64 (build 20348) Matrix products: default locale: [1] LC_COLLATE=C LC_CTYPE=German_Germany.utf8 [3] LC_MONETARY=C LC_NUMERIC=C [5] LC_TIME=C time zone: Europe/Berlin tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] doFuture_1.0.1 future_1.33.2 foreach_1.5.2 loaded via a namespace (and not attached): [1] compiler_4.4.0 parallelly_1.37.1 tools_4.4.0 [4] parallel_4.4.0 future.apply_1.11.1 listenv_0.9.1 [7] codetools_0.2-19 iterators_1.0.14 digest_0.6.35 [10] globals_0.16.3 > > strategies <- future:::supportedStrategies() > strategies <- setdiff(strategies, "multiprocess") > > message("*** doFuture - nested w/ %:% ...") *** doFuture - nested w/ %:% ... > > for (strategy1 in strategies) { + for (strategy2 in strategies) { + message(sprintf("- plan(list('%s', '%s')) ...", strategy1, strategy2)) + plan(list(a = strategy1, b = strategy2)) + nested <- plan("list") + + as <- 1:2 + bs <- 3:1 + + x <- foreach(a = as) %:% foreach(b = bs) %dofuture% { + list(a = a, b = b, plan_b = future::plan("list"), plan = future::plan("next")) + } + + stopifnot(length(x) == length(as)) + for (aa in seq_along(as)) { + x_aa <- x[[aa]] + stopifnot(length(x_aa) == length(bs)) + a <- as[aa] + for (bb in seq_along(bs)) { + x_aa_bb <- x_aa[[bb]] + b <- bs[bb] + stopifnot( + length(x_aa_bb) == 4L, + all(names(x_aa_bb) == c("a", "b", "plan_b", "plan")), + x_aa_bb$a == a, + x_aa_bb$b == b, + length(x_aa_bb$plan_b) == length(nested[-1]), + inherits(x_aa_bb$plan_b[[1]], strategy2), + inherits(x_aa_bb$plan, strategy2) + ) + } + } + + ## Cleanup in order make sure none of these variables exist as + ## proxies for missing globals of the name names + rm(list = c("as", "bs", "x", "nested")) + + ## WORKAROUND: Shut down *nested* parallel workers as an attempt to avoid + ## * checking for detritus in the temp directory ... NOTE + ## from 'R CMD check --as-cran' when running on MS Windows. This looks + ## like a bug in R, cf. https://bugs.r-project.org/show_bug.cgi?id=18133 + message("- shut down nested workers") + dummy <- foreach(ii = 1:nbrOfWorkers()) %dofuture% plan("sequential") + plan("sequential") + + message(sprintf("- plan(list('%s', '%s')) ... DONE", strategy1, strategy2)) + } + } - plan(list('sequential', 'sequential')) ... [11:06:26.534] doFuture2() ... Running the tests in 'tests/foreach_dopar,nested_colon.R' failed. Complete output: > source("incl/start.R") Loading required package: foreach Loading required package: future R version 4.4.0 alpha (2024-03-26 r86209 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows Server 2022 x64 (build 20348) Matrix products: default locale: [1] LC_COLLATE=C LC_CTYPE=German_Germany.utf8 [3] LC_MONETARY=C LC_NUMERIC=C [5] LC_TIME=C time zone: Europe/Berlin tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] doFuture_1.0.1 future_1.33.2 foreach_1.5.2 loaded via a namespace (and not attached): [1] compiler_4.4.0 parallelly_1.37.1 tools_4.4.0 [4] parallel_4.4.0 future.apply_1.11.1 listenv_0.9.1 [7] codetools_0.2-19 iterators_1.0.14 digest_0.6.35 [10] globals_0.16.3 > > strategies <- future:::supportedStrategies() > > message("*** doFuture - nested w/ %:% ...") *** doFuture - nested w/ %:% ... > > registerDoFuture() > > for (strategy1 in strategies) { + for (strategy2 in strategies) { + message(sprintf("- plan(list('%s', '%s')) ...", strategy1, strategy2)) + plan(list(a = strategy1, b = strategy2)) + nested <- plan("list") + + as <- 1:2 + bs <- 3:1 + + x <- foreach(a = as) %:% foreach(b = bs) %dopar% { + list(a = a, b = b, plan_b = future::plan("list"), plan = future::plan("next")) + } + + stopifnot(length(x) == length(as)) + for (aa in seq_along(as)) { + x_aa <- x[[aa]] + stopifnot(length(x_aa) == length(bs)) + a <- as[aa] + for (bb in seq_along(bs)) { + x_aa_bb <- x_aa[[bb]] + b <- bs[bb] + stopifnot( + length(x_aa_bb) == 4L, + all(names(x_aa_bb) == c("a", "b", "plan_b", "plan")), + x_aa_bb$a == a, + x_aa_bb$b == b, + length(x_aa_bb$plan_b) == length(nested[-1]), + inherits(x_aa_bb$plan_b[[1]], strategy2), + inherits(x_aa_bb$plan, strategy2) + ) + } + } + + ## Cleanup in order make sure none of these variables exist as + ## proxies for missing globals of the name names + rm(list = c("as", "bs", "x", "nested")) + + ## WORKAROUND: Shut down *nested* parallel workers as an attempt to avoid + ## * checking for detritus in the temp directory ... NOTE + ## from 'R CMD check --as-cran' when running on MS Windows. This looks + ## like a bug in R, cf. https://bugs.r-project.org/show_bug.cgi?id=18133 + message("- shut down nested workers") + dummy <- foreach(ii = 1:nbrOfWorkers()) %dopar% plan("sequential") + plan("sequential") + + message(sprintf("- plan(list('%s', '%s')) ... DONE", strategy1, strategy2)) + } + } - plan(list('sequential', 'sequential')) ... [11:07:10.713] doFuture() ... Flavor: r-devel-windows-x86_64

Package future

Current CRAN status: OK: 12

Package future.apply

Current CRAN status: OK: 12

Package future.batchtools

Current CRAN status: OK: 12

Package future.callr

Current CRAN status: OK: 12

Package future.tests

Current CRAN status: OK: 12

Package globals

Current CRAN status: OK: 12

Package listenv

Current CRAN status: OK: 12

Package matrixStats

Current CRAN status: OK: 12

Additional issues

rchk

Package parallelly

Current CRAN status: OK: 12

Package port4me

Current CRAN status: OK: 12

Package profmem

Current CRAN status: OK: 12

Package progressr

Current CRAN status: OK: 12

Package PSCBS

Current CRAN status: OK: 12

Package R.cache

Current CRAN status: NOTE: 6, OK: 6

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

Package R.devices

Current CRAN status: OK: 12

Package R.filesets

Current CRAN status: OK: 12

Package R.huge

Current CRAN status: OK: 12

Package R.matlab

Current CRAN status: NOTE: 6, OK: 6

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

Package R.methodsS3

Current CRAN status: OK: 12

Package R.oo

Current CRAN status: OK: 12

Package R.rsp

Current CRAN status: OK: 12

Package R.utils

Current CRAN status: OK: 12

Package seguid

Current CRAN status: OK: 12

Package startup

Current CRAN status: OK: 12

Package TopDom

Current CRAN status: NOTE: 6, OK: 6

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