CRAN Package Check Results for Package cgdsr

Last updated on 2019-05-24 04:46:28 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2.10 2.28 29.91 32.19 OK
r-devel-linux-x86_64-debian-gcc 1.2.10 1.82 25.04 26.86 OK
r-devel-linux-x86_64-fedora-clang 1.2.10 41.09 OK
r-devel-linux-x86_64-fedora-gcc 1.2.10 39.49 OK
r-devel-windows-ix86+x86_64 1.2.10 5.00 95.00 100.00 OK
r-patched-linux-x86_64 1.2.10 2.34 31.01 33.35 OK
r-patched-solaris-x86 1.2.10 52.70 OK
r-release-linux-x86_64 1.2.10 2.43 30.88 33.31 OK
r-release-windows-ix86+x86_64 1.2.10 8.00 97.00 105.00 OK
r-release-osx-x86_64 1.2.10 ERROR
r-oldrel-windows-ix86+x86_64 1.2.10 5.00 97.00 102.00 OK
r-oldrel-osx-x86_64 1.2.10 OK

Check Details

Version: 1.2.10
Check: tests
Result: ERROR
     Running ‘runTests.R’ [1s/3s]
    Running the tests in ‘tests/runTests.R’ failed.
    Last 13 lines of output:
     ── 4. Failure: getProfileData (@test_cgdsr.R#63) ──────────────────────────────
     rownames(...) not identical to make.names(c("TCGA-02-0001-01", "TCGA-02-0003-01")).
     Lengths differ: 0 is not 2
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 9 SKIPPED: 0 FAILED: 4
     1. Failure: getClinicalData (@test_cgdsr.R#44)
     2. Failure: getProfileData (@test_cgdsr.R#51)
     3. Failure: getProfileData (@test_cgdsr.R#59)
     4. Failure: getProfileData (@test_cgdsr.R#63)
    
     Error: testthat unit tests failed
     In addition: Warning message:
     Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead
     Execution halted
Flavor: r-release-osx-x86_64

Version: 1.2.10
Check: running R code from vignettes
Result: ERROR
    Errors in running code in vignettes:
    when running code in ‘cgdsr.Rnw’
     ...
    10 Relative linear copy-number values
    11 Methylation (HM27)
    12 Methylation (HM450)
    13 Mutations
    
    > getCaseLists(mycgds, "gbm_tcga")[, c(1:2)]
    
     When sourcing ‘cgdsr.R’:
    Error: undefined columns selected
    Execution halted
Flavor: r-release-osx-x86_64

Version: 1.2.10
Check: re-building of vignette outputs
Result: NOTE
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘cgdsr.Rnw’ using Sweave
    Please send questions to cbioportal@googlegroups.com
    
    Error: processing vignette 'cgdsr.Rnw' failed with diagnostics:
     chunk 5
    Error in `[.data.frame`(getCaseLists(mycgds, "gbm_tcga"), , c(1:2)) :
     undefined columns selected
    
    --- failed re-building ‘cgdsr.Rnw’
    
    SUMMARY: processing the following file failed:
     ‘cgdsr.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-osx-x86_64