Last updated on 2025-04-01 09:55:23 CEST.
| Package | ERROR | WARN | NOTE | OK |
|---|---|---|---|---|
| conos | 1 | 6 | 6 | |
| dendsort | 15 | |||
| edlibR | 15 | |||
| gapmap | 15 | |||
| ggrastr | 15 | |||
| leidenAlg | 4 | 7 | 2 | |
| N2R | 4 | 9 | ||
| pagoda2 | 4 | 9 | ||
| RMTstat | 15 | |||
| Rook | 15 | |||
| sccore | 4 | 9 | ||
| vrnmf | 15 |
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
Current CRAN status: OK: 15
Current CRAN status: OK: 15
Current CRAN status: OK: 15
Current CRAN status: OK: 15
Current CRAN status: WARN: 4, NOTE: 7, OK: 2
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/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
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
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
Current CRAN status: OK: 15
Current CRAN status: OK: 15
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
Current CRAN status: OK: 15