CRAN Package Check Results for Package rliger

Last updated on 2024-03-28 23:55:18 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0.0 156.26 534.18 690.44 ERROR
r-devel-linux-x86_64-debian-gcc 2.0.0 121.77 386.93 508.70 ERROR
r-devel-linux-x86_64-fedora-clang 2.0.0 1038.72 NOTE
r-devel-linux-x86_64-fedora-gcc 2.0.0 981.86 NOTE
r-devel-windows-x86_64 2.0.0 125.00 640.00 765.00 NOTE
r-patched-linux-x86_64 2.0.0 126.57 503.54 630.11 ERROR
r-release-linux-x86_64 2.0.0 112.23 513.33 625.56 ERROR
r-release-macos-arm64 2.0.0 194.00 ERROR
r-release-macos-x86_64 2.0.0 380.00 ERROR
r-release-windows-x86_64 2.0.0 126.00 671.00 797.00 NOTE
r-oldrel-macos-arm64 2.0.0 191.00 NOTE
r-oldrel-windows-x86_64 2.0.0 107.00 612.00 719.00 NOTE

Check Details

Version: 2.0.0
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'DoubletFinder', 'RcppPlanc' 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-windows-x86_64

Version: 2.0.0
Check: examples
Result: ERROR Running examples in ‘rliger-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: createH5LigerDataset > ### Title: Create on-disk ligerDataset Object > ### Aliases: createH5LigerDataset > > ### ** Examples > > h5Path <- system.file("extdata/ctrl.h5", package = "rliger") > ld <- createH5LigerDataset(h5Path) Error in H5File.open(filename, mode, file_create_pl, file_access_pl) : HDF5-API Errors: error #000: ../../../src/H5F.c in H5Fopen(): line 412: unable to open file class: HDF5 major: File accessibility minor: Unable to open file error #001: ../../../src/H5Fint.c in H5F_open(): line 1655: unable to open file: time = Tue Mar 26 08:55:16 2024 , name = '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rliger/extdata/ctrl.h5', tent_flags = 1 class: HDF5 major: File accessibility minor: Unable to open file error #002: ../../../src/H5FD.c in H5FD_open(): line 722: open failed class: HDF5 major: Virtual File Layer minor: Unable to initialize object error #003: ../../../src/H5FDsec2.c in H5FD__sec2_open(): line 351: unable to open file: name = '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rliger/extdata/ctrl.h5', errno = 30, error message = 'Read-only file system', flags = 1, o_flag class: HDF5 major: File accessibility Calls: createH5LigerDataset -> <Anonymous> -> initialize -> H5File.open Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.0.0
Check: examples
Result: ERROR Running examples in ‘rliger-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: createH5LigerDataset > ### Title: Create on-disk ligerDataset Object > ### Aliases: createH5LigerDataset > > ### ** Examples > > h5Path <- system.file("extdata/ctrl.h5", package = "rliger") > ld <- createH5LigerDataset(h5Path) Error in H5File.open(filename, mode, file_create_pl, file_access_pl) : HDF5-API Errors: error #000: ../../../src/H5F.c in H5Fopen(): line 412: unable to open file class: HDF5 major: File accessibility minor: Unable to open file error #001: ../../../src/H5Fint.c in H5F_open(): line 1655: unable to open file: time = Thu Mar 28 02:59:47 2024 , name = '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rliger/extdata/ctrl.h5', tent_flags = 1 class: HDF5 major: File accessibility minor: Unable to open file error #002: ../../../src/H5FD.c in H5FD_open(): line 722: open failed class: HDF5 major: Virtual File Layer minor: Unable to initialize object error #003: ../../../src/H5FDsec2.c in H5FD__sec2_open(): line 351: unable to open file: name = '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rliger/extdata/ctrl.h5', errno = 30, error message = 'Read-only file system', flags = 1, o_flags class: HDF5 major: File accessibility mi Calls: createH5LigerDataset -> <Anonymous> -> initialize -> H5File.open Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2.0.0
Check: Rd cross-references
Result: NOTE Undeclared package ‘viridisLite’ in Rd xrefs Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2.0.0
Check: examples
Result: ERROR Running examples in ‘rliger-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: createH5LigerDataset > ### Title: Create on-disk ligerDataset Object > ### Aliases: createH5LigerDataset > > ### ** Examples > > h5Path <- system.file("extdata/ctrl.h5", package = "rliger") > ld <- createH5LigerDataset(h5Path) Error in H5File.open(filename, mode, file_create_pl, file_access_pl) : HDF5-API Errors: error #000: ../../../src/H5F.c in H5Fopen(): line 412: unable to open file class: HDF5 major: File accessibility minor: Unable to open file error #001: ../../../src/H5Fint.c in H5F_open(): line 1655: unable to open file: time = Thu Mar 28 04:25:20 2024 , name = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rliger/extdata/ctrl.h5', tent_flags = 1 class: HDF5 major: File accessibility minor: Unable to open file error #002: ../../../src/H5FD.c in H5FD_open(): line 722: open failed class: HDF5 major: Virtual File Layer minor: Unable to initialize object error #003: ../../../src/H5FDsec2.c in H5FD__sec2_open(): line 351: unable to open file: name = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rliger/extdata/ctrl.h5', errno = 30, error message = 'Read-only file system', flags = 1, o_flag class: HDF5 major: File accessibility Calls: createH5LigerDataset -> <Anonymous> -> initialize -> H5File.open Execution halted Flavor: r-patched-linux-x86_64

Version: 2.0.0
Check: examples
Result: ERROR Running examples in ‘rliger-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: createH5LigerDataset > ### Title: Create on-disk ligerDataset Object > ### Aliases: createH5LigerDataset > > ### ** Examples > > h5Path <- system.file("extdata/ctrl.h5", package = "rliger") > ld <- createH5LigerDataset(h5Path) Error in H5File.open(filename, mode, file_create_pl, file_access_pl) : HDF5-API Errors: error #000: ../../../src/H5F.c in H5Fopen(): line 412: unable to open file class: HDF5 major: File accessibility minor: Unable to open file error #001: ../../../src/H5Fint.c in H5F_open(): line 1655: unable to open file: time = Sun Mar 24 15:48:34 2024 , name = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/rliger/extdata/ctrl.h5', tent_flags = 1 class: HDF5 major: File accessibility minor: Unable to open file error #002: ../../../src/H5FD.c in H5FD_open(): line 722: open failed class: HDF5 major: Virtual File Layer minor: Unable to initialize object error #003: ../../../src/H5FDsec2.c in H5FD__sec2_open(): line 351: unable to open file: name = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/rliger/extdata/ctrl.h5', errno = 30, error message = 'Read-only file system', flags = 1, o_flag class: HDF5 major: File accessibility Calls: createH5LigerDataset -> <Anonymous> -> initialize -> H5File.open Execution halted Flavor: r-release-linux-x86_64

Version: 2.0.0
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'DoubletFinder', 'EnhancedVolcano', 'RcppPlanc', 'reactome.db' Flavors: r-release-macos-arm64, r-release-macos-x86_64

Version: 2.0.0
Check: installed package size
Result: NOTE installed size is 8.2Mb sub-directories of 1Mb or more: libs 5.3Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64

Version: 2.0.0
Check: Rd cross-references
Result: NOTE Package unavailable to check Rd xrefs: ‘EnhancedVolcano’ Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64

Version: 2.0.0
Check: tests
Result: ERROR Running ‘testthat.R’ [23s/30s] Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 1. ├─testthat::expect_warning(...) at test_downstream.R:245:9 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. ├─testthat::expect_is(...) at test_downstream.R:246:13 7. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 8. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 9. └─rliger::runGSEA(pbmcPlot, genesets = "Immune System") 10. └─cli::cli_abort("Package {.pkg reactome.db} is needed for this function to work.\n Please install it by command:\n {.code BiocManager::install('reactome.db')}") 11. └─rlang::abort(...) [ FAIL 1 | WARN 0 | SKIP 16 | PASS 1039 ] Error: Test failures Execution halted Flavor: r-release-macos-arm64

Version: 2.0.0
Check: tests
Result: ERROR Running ‘testthat.R’ [37s/61s] Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 1. ├─testthat::expect_warning(...) at test_downstream.R:245:9 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. ├─testthat::expect_is(...) at test_downstream.R:246:13 7. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 8. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 9. └─rliger::runGSEA(pbmcPlot, genesets = "Immune System") 10. └─cli::cli_abort("Package {.pkg reactome.db} is needed for this function to work.\n Please install it by command:\n {.code BiocManager::install('reactome.db')}") 11. └─rlang::abort(...) [ FAIL 1 | WARN 0 | SKIP 16 | PASS 1039 ] Error: Test failures Execution halted Flavor: r-release-macos-x86_64

Version: 2.0.0
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'DoubletFinder', 'EnhancedVolcano', 'RcppPlanc' Flavor: r-oldrel-macos-arm64