CRAN Package Check Results for Maintainer ‘Evan Biederstedt <evan.biederstedt at gmail.com>’

Last updated on 2025-04-12 22:52:35 CEST.

Package	ERROR	WARN	NOTE	OK
conos	1		6	6
dendsort				14
edlibR				14
gapmap				14
ggrastr				14
leidenAlg		5	7	1
N2R			4	9
pagoda2			4	9
RMTstat				14
Rook				14
sccore			4	9
vrnmf				15

Package conos

Current CRAN status: ERROR: 1, NOTE: 6, OK: 6

Version: 1.5.2
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'conosPanel', 'p2data' Flavors: r-release-linux-x86_64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-windows-x86_64

Version: 1.5.2
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'conosPanel', 'org.Mm.eg.db', 'p2data' Flavor: r-release-macos-arm64

Version: 1.5.2
Check: installed package size
Result: NOTE installed size is 11.2Mb sub-directories of 1Mb or more: libs 9.4Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 1.5.2
Check: examples
Result: ERROR Running examples in ‘conos-Ex.R’ failed The error most likely occurred in: > ### Name: Conos > ### Title: Conos R6 class > ### Aliases: Conos > > ### ** Examples > > > ## ------------------------------------------------ > ## Method `Conos$new` > ## ------------------------------------------------ > > con <- Conos$new(small_panel.preprocessed, n.cores=1) > > > ## ------------------------------------------------ > ## Method `Conos$buildGraph` > ## ------------------------------------------------ > > con <- Conos$new(small_panel.preprocessed, n.cores=1) > con$buildGraph(k=10, k.self=5, space='PCA', ncomps=10, n.odgenes=20, matching.method='mNN', + metric='angular', score.component.variance=TRUE, verbose=TRUE) found 0 out of 1 cached PCA space pairs ... running 1 additional PCA space pairs Error in irlba::irlba(x, nv = ncomps, nu = 0, center = cm, right_only = FALSE, : function 'as_cholmod_sparse' not provided by package 'Matrix' Calls: <Anonymous> ... FUN -> quickPlainPCA -> lapply -> FUN -> <Anonymous> Execution halted Flavor: r-oldrel-macos-arm64

Version: 1.5.2
Check: tests
Result: ERROR Running ‘testthat.R’ [3s/3s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(conos) Loading required package: Matrix Loading required package: igraph Attaching package: 'igraph' The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union > > testthat::test_check("conos") Attaching package: 'testthat' The following object is masked from 'package:igraph': compare [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_functions.R:15:1'): (code run outside of `test_that()`) ──────── Error in `irlba::irlba(x, nv = ncomps, nu = 0, center = cm, right_only = FALSE, reorth = TRUE)`: function 'as_cholmod_sparse' not provided by package 'Matrix' Backtrace: ▆ 1. ├─base::suppressWarnings(con$buildGraph(ncomps = 25)) at test_functions.R:15:1 2. │ └─base::withCallingHandlers(...) 3. └─con$buildGraph(ncomps = 25) 4. └─private$updatePairs(...) 5. └─sccore::plapply(...) 6. └─base::lapply(...) 7. └─conos (local) FUN(X[[i]], ...) 8. └─conos:::quickPlainPCA(...) 9. └─base::lapply(...) 10. └─conos (local) FUN(X[[i]], ...) 11. └─irlba::irlba(...) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ] Error: Test failures Execution halted Flavor: r-oldrel-macos-arm64

Version: 1.5.2
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'conosPanel', 'org.Mm.eg.db', 'p2data', 'rhdf5' Flavor: r-oldrel-macos-x86_64

Package dendsort

Current CRAN status: OK: 14

Package edlibR

Current CRAN status: OK: 14

Package gapmap

Current CRAN status: OK: 14

Package ggrastr

Current CRAN status: OK: 14

Package leidenAlg

Current CRAN status: WARN: 5, NOTE: 7, OK: 1

Version: 1.1.4
Check: compiled code
Result: WARN File ‘leidenAlg/libs/leidenAlg.so’: Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++) Objects: ‘libleidenalg.a’, ‘librigraph.a’ Found ‘__vprintf_chk’, possibly from ‘vprintf’ (C) Object: ‘librigraph.a’ Found ‘abort’, possibly from ‘abort’ (C) Object: ‘librigraph.a’ Found ‘rand’, possibly from ‘rand’ (C) Object: ‘libleidenalg.a’ Found ‘stderr’, possibly from ‘stderr’ (C) Object: ‘librigraph.a’ Found ‘stdout’, possibly from ‘stdout’ (C) Object: ‘librigraph.a’ 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 nor [v]sprintf. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.1.4
Check: compiled code
Result: WARN File ‘leidenAlg/libs/leidenAlg.so’: Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++) Objects: ‘libleidenalg.a’, ‘librigraph.a’ Found ‘__printf_chk’, possibly from ‘printf’ (C) Object: ‘librigraph.a’ Found ‘abort’, possibly from ‘abort’ (C) Object: ‘librigraph.a’ Found ‘putchar’, possibly from ‘putchar’ (C) Object: ‘librigraph.a’ Found ‘rand’, possibly from ‘rand’ (C) Object: ‘libleidenalg.a’ Found ‘stderr’, possibly from ‘stderr’ (C) Object: ‘librigraph.a’ Found ‘stdout’, possibly from ‘stdout’ (C) Object: ‘librigraph.a’ 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 nor [v]sprintf. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64

Version: 1.1.4
Check: compiled code
Result: WARN File ‘leidenAlg/libs/leidenAlg.so’: Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++) Objects: ‘libleidenalg.a’, ‘librigraph.a’ Found ‘___stderrp’, possibly from ‘stderr’ (C) Object: ‘librigraph.a’ Found ‘_abort’, possibly from ‘abort’ (C) Object: ‘librigraph.a’ Found ‘_printf’, possibly from ‘printf’ (C) Object: ‘librigraph.a’ Found ‘_putchar’, possibly from ‘putchar’ (C) Object: ‘librigraph.a’ Found ‘_rand’, possibly from ‘rand’ (C) Object: ‘libleidenalg.a’ 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 nor [v]sprintf. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. Flavor: r-devel-macos-arm64

Version: 1.1.4
Check: compiled code
Result: WARN File 'leidenAlg/libs/x64/leidenAlg.dll': Found '_ZSt4cerr', possibly from 'std::cerr' (C++) Objects: 'libleidenalg.a', 'librigraph.a' Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Object: 'librigraph.a' Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Object: 'librigraph.a' Found 'putchar', possibly from 'putchar' (C) Object: 'librigraph.a' Found 'rand', possibly from 'rand' (C) Object: 'libleidenalg.a' 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 nor [v]sprintf. See 'Writing portable packages' in the 'Writing R Extensions' manual. Flavor: r-devel-windows-x86_64

Version: 1.1.4
Check: for GNU extensions in Makefiles
Result: NOTE GNU make is a SystemRequirements. Flavors: r-release-linux-x86_64, 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

Package N2R

Current CRAN status: NOTE: 4, OK: 9

Version: 1.0.3
Check: installed package size
Result: NOTE installed size is 5.7Mb sub-directories of 1Mb or more: libs 5.6Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package pagoda2

Current CRAN status: NOTE: 4, OK: 9

Version: 1.0.12
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'org.Dr.eg.db', 'org.Mm.eg.db' Flavor: r-release-macos-arm64

Version: 1.0.12
Check: installed package size
Result: NOTE installed size is 6.8Mb sub-directories of 1Mb or more: libs 5.0Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 1.0.12
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘scde’ Flavor: r-oldrel-macos-arm64

Version: 1.0.12
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'org.Dr.eg.db', 'org.Mm.eg.db', 'scde' Flavor: r-oldrel-macos-x86_64

Package RMTstat

Current CRAN status: OK: 14

Package Rook

Current CRAN status: OK: 14

Additional issues

rchk

Package sccore

Current CRAN status: NOTE: 4, OK: 9

Version: 1.0.5
Check: installed package size
Result: NOTE installed size is 5.6Mb sub-directories of 1Mb or more: libs 4.8Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package vrnmf

Current CRAN status: OK: 15