CRAN Package Check Results for Package BiocManager

Last updated on 2019-07-24 00:47:28 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.30.4 1.94 123.93 125.87 NOTE
r-devel-linux-x86_64-debian-gcc 1.30.4 1.68 94.15 95.83 NOTE
r-devel-linux-x86_64-fedora-clang 1.30.4 154.44 NOTE
r-devel-linux-x86_64-fedora-gcc 1.30.4 145.66 NOTE
r-devel-windows-ix86+x86_64 1.30.4 6.00 38.00 44.00 ERROR
r-patched-linux-x86_64 1.30.4 2.05 167.95 170.00 ERROR
r-patched-solaris-x86 1.30.4 67.50 ERROR
r-release-linux-x86_64 1.30.4 2.02 157.58 159.60 ERROR
r-release-windows-ix86+x86_64 1.30.4 4.00 51.00 55.00 ERROR
r-release-osx-x86_64 1.30.4 NOTE
r-oldrel-windows-ix86+x86_64 1.30.4 6.00 66.00 72.00 OK
r-oldrel-osx-x86_64 1.30.4 NOTE

Check Details

Version: 1.30.4
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'BiocVersion'
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

Version: 1.30.4
Check: examples
Result: ERROR
    Running examples in 'BiocManager-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: available
    > ### Title: Discover packages available for installation.
    > ### Aliases: available
    >
    > ### ** Examples
    >
    > avail <- BiocManager::available()
    Error: Bioconductor version '3.9' requires R version '3.6'; see
     https://bioconductor.org/install
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 1.30.4
Check: tests
Result: ERROR
     Running 'testthat.R' [5s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(BiocManager)
     >
     > test_check("BiocManager")
     -- 1. Error: .install_repos() works (@test_install.R#26) ----------------------
     Bioconductor version '3.9' requires R version '3.6'; see
     https://bioconductor.org/install
     1: repositories() at testthat/test_install.R:26
     2: .version_validate(version)
     3: .stop(txt)
     4: stop(.msg(...), call. = call.)
    
     -- 2. Error: .install_github() works (@test_install.R#31) ---------------------
     Bioconductor version '3.9' requires R version '3.6'; see
     https://bioconductor.org/install
     1: repositories() at testthat/test_install.R:31
     2: .version_validate(version)
     3: .stop(txt)
     4: stop(.msg(...), call. = call.)
    
     -- 3. Error: repositories() returns all repos (@test_repositories.R#5) --------
     Bioconductor version '3.9' requires R version '3.6'; see
     https://bioconductor.org/install
     1: expect_true(all(allOS %in% names(repositories()))) at testthat/test_repositories.R:5
     2: quasi_label(enquo(object), label, arg = "object")
     3: eval_bare(get_expr(quo), get_env(quo))
     4: allOS %in% names(repositories())
     5: repositories()
     6: .version_validate(version)
     7: .stop(txt)
     8: stop(.msg(...), call. = call.)
    
     -- 4. Error: repositories() does not return any NA repos (@test_repositories.R#9
     Bioconductor version '3.9' requires R version '3.6'; see
     https://bioconductor.org/install
     1: expect_true(!anyNA(repositories())) at testthat/test_repositories.R:9
     2: quasi_label(enquo(object), label, arg = "object")
     3: eval_bare(get_expr(quo), get_env(quo))
     4: repositories()
     5: .version_validate(version)
     6: .stop(txt)
     7: stop(.msg(...), call. = call.)
    
     -- 5. Error: repositories() returns expected order (@test_repositories.R#13) --
     Bioconductor version '3.9' requires R version '3.6'; see
     https://bioconductor.org/install
     1: expect_identical("BioCsoft", names(repositories())[[1]]) at testthat/test_repositories.R:13
     2: quasi_label(enquo(expected), expected.label, arg = "expected")
     3: eval_bare(get_expr(quo), get_env(quo))
     4: repositories()
     5: .version_validate(version)
     6: .stop(txt)
     7: stop(.msg(...), call. = call.)
    
     -- 6. Error: 'site_repository=' inserted correctly (@test_repositories.R#18) --
     Bioconductor version '3.9' requires R version '3.6'; see
     https://bioconductor.org/install
     1: repositories(site_repository) at testthat/test_repositories.R:18
     2: .version_validate(version)
     3: .stop(txt)
     4: stop(.msg(...), call. = call.)
    
     -- 7. Error: .version_validity('devel') works (@test_version.R#87) ------------
     non-character object(s)
     1: expect_true(startsWith(.version_validity("devel"), test)) at testthat/test_version.R:87
     2: quasi_label(enquo(object), label, arg = "object")
     3: eval_bare(get_expr(quo), get_env(quo))
     4: startsWith(.version_validity("devel"), test)
    
     -- 8. Failure: .version_validity() and BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS wor
     `value` not identical to TRUE.
     Types not compatible: character is not logical
    
     -- 9. Error: .version_validate() and BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS work
     Bioconductor version '3.9' requires R version '3.6'; see
     https://bioconductor.org/install
     1: withr::with_options(list(BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS = FALSE), {
     if ("BiocVersion" %in% rownames(installed.packages()))
     expect_identical(.version_validate("1.2"), package_version("1.2"))
     else expect_error(.version_validate("1.2"), .VERSION_MAP_UNABLE_TO_VALIDATE)
     }) at testthat/test_version.R:104
     2: force(code)
     3: expect_identical(.version_validate("1.2"), package_version("1.2")) at testthat/test_version.R:105
     4: quasi_label(enquo(object), label, arg = "object")
     5: eval_bare(get_expr(quo), get_env(quo))
     6: .version_validate("1.2")
     7: .stop(txt)
     8: stop(.msg(...), call. = call.)
    
     == testthat results ===========================================================
     OK: 67 SKIPPED: 2 WARNINGS: 1 FAILED: 9
     1. Error: .install_repos() works (@test_install.R#26)
     2. Error: .install_github() works (@test_install.R#31)
     3. Error: repositories() returns all repos (@test_repositories.R#5)
     4. Error: repositories() does not return any NA repos (@test_repositories.R#9)
     5. Error: repositories() returns expected order (@test_repositories.R#13)
     6. Error: 'site_repository=' inserted correctly (@test_repositories.R#18)
     7. Error: .version_validity('devel') works (@test_version.R#87)
     8. Failure: .version_validity() and BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS work (@test_version.R#92)
     9. Error: .version_validate() and BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS work (@test_version.R#104)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 1.30.4
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'BiocManager.Rmd' using rmarkdown
    Quitting from lines 67-68 (BiocManager.Rmd)
    Error: processing vignette 'BiocManager.Rmd' failed with diagnostics:
    Bioconductor version '3.9' requires R version '3.6'; see
     https://bioconductor.org/install
    --- failed re-building 'BiocManager.Rmd'
    
    SUMMARY: processing the following file failed:
     'BiocManager.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 1.30.4
Check: tests
Result: ERROR
     Running ‘testthat.R’ [48s/54s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(BiocManager)
     >
     > test_check("BiocManager")
     ── 1. Error: .version_validity('devel') works (@test_version.R#87) ────────────
     non-character object(s)
     1: expect_true(startsWith(.version_validity("devel"), test)) at testthat/test_version.R:87
     2: quasi_label(enquo(object), label, arg = "object")
     3: eval_bare(get_expr(quo), get_env(quo))
     4: startsWith(.version_validity("devel"), test)
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 78 SKIPPED: 2 WARNINGS: 1 FAILED: 1
     1. Error: .version_validity('devel') works (@test_version.R#87)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-patched-linux-x86_64

Version: 1.30.4
Check: tests
Result: ERROR
     Running ‘testthat.R’ [5s/66s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(BiocManager)
     >
     > test_check("BiocManager")
     ── 1. Error: .version_validity('devel') works (@test_version.R#87) ────────────
     non-character object(s)
     1: expect_true(startsWith(.version_validity("devel"), test)) at testthat/test_version.R:87
     2: quasi_label(enquo(object), label, arg = "object")
     3: eval_bare(get_expr(quo), get_env(quo))
     4: startsWith(.version_validity("devel"), test)
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 78 | SKIPPED: 2 | WARNINGS: 1 | FAILED: 1 ]
     1. Error: .version_validity('devel') works (@test_version.R#87)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-patched-solaris-x86

Version: 1.30.4
Check: tests
Result: ERROR
     Running ‘testthat.R’ [45s/51s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(BiocManager)
     >
     > test_check("BiocManager")
     ── 1. Error: .version_validity('devel') works (@test_version.R#87) ────────────
     non-character object(s)
     1: expect_true(startsWith(.version_validity("devel"), test)) at testthat/test_version.R:87
     2: quasi_label(enquo(object), label, arg = "object")
     3: eval_bare(get_expr(quo), get_env(quo))
     4: startsWith(.version_validity("devel"), test)
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 78 SKIPPED: 2 WARNINGS: 1 FAILED: 1
     1. Error: .version_validity('devel') works (@test_version.R#87)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-release-linux-x86_64

Version: 1.30.4
Check: tests
Result: ERROR
     Running 'testthat.R' [4s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(BiocManager)
     >
     > test_check("BiocManager")
     -- 1. Error: .version_validity('devel') works (@test_version.R#87) ------------
     non-character object(s)
     1: expect_true(startsWith(.version_validity("devel"), test)) at testthat/test_version.R:87
     2: quasi_label(enquo(object), label, arg = "object")
     3: eval_bare(get_expr(quo), get_env(quo))
     4: startsWith(.version_validity("devel"), test)
    
     == testthat results ===========================================================
     OK: 75 SKIPPED: 2 WARNINGS: 1 FAILED: 1
     1. Error: .version_validity('devel') works (@test_version.R#87)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 1.30.4
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'BiocStyle', 'BiocVersion'
Flavor: r-release-osx-x86_64

Version: 1.30.4
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘BiocStyle’ ‘BiocVersion’
Flavor: r-oldrel-osx-x86_64