CRAN Package Check Results for Package GeoTcgaData

Last updated on 2021-07-24 07:49:26 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.0 23.27 74.21 97.48 ERROR
r-devel-linux-x86_64-debian-gcc 1.0.0 19.97 82.76 102.73 OK
r-devel-linux-x86_64-fedora-clang 1.0.0 140.19 ERROR
r-devel-linux-x86_64-fedora-gcc 1.0.0 136.22 NOTE
r-devel-windows-x86_64 1.0.0 28.00 100.00 128.00 OK
r-devel-windows-x86_64-gcc10-UCRT 0.2.5 OK
r-patched-linux-x86_64 1.0.0 22.37 101.68 124.05 OK
r-patched-solaris-x86 1.0.0 198.20 ERROR
r-release-linux-x86_64 1.0.0 21.51 102.29 123.80 OK
r-release-macos-arm64 0.2.5 NOTE
r-release-macos-x86_64 1.0.0 ERROR
r-release-windows-ix86+x86_64 1.0.0 36.00 122.00 158.00 OK
r-oldrel-macos-x86_64 1.0.0 ERROR
r-oldrel-windows-ix86+x86_64 1.0.0 37.00 117.00 154.00 OK

Check Details

Version: 1.0.0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'clusterProfiler'
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.0
Check: examples
Result: ERROR
    Running examples in 'GeoTcgaData-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: id_conversion
    > ### Title: Convert ENSEMBL gene id to gene Symbol in TCGA
    > ### Aliases: id_conversion
    >
    > ### ** Examples
    >
    > result <- id_conversion(profile)
    Error in loadNamespace(x) : there is no package called 'clusterProfiler'
    Calls: id_conversion ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'GeoTcgaData.Rmd' using rmarkdown
    Quitting from lines 210-211 (GeoTcgaData.Rmd)
    Error: processing vignette 'GeoTcgaData.Rmd' failed with diagnostics:
    there is no package called 'clusterProfiler'
    --- failed re-building 'GeoTcgaData.Rmd'
    
    SUMMARY: processing the following file failed:
     'GeoTcgaData.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘ChAMP’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86

Version: 1.0.0
Check: examples
Result: ERROR
    Running examples in ‘GeoTcgaData-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: id_conversion
    > ### Title: Convert ENSEMBL gene id to gene Symbol in TCGA
    > ### Aliases: id_conversion
    >
    > ### ** Examples
    >
    > result <- id_conversion(profile)
    
    Loading required package: org.Hs.eg.db
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called ‘org.Hs.eg.db’
    Error in eval(parse(text = OrgDb)) : object 'org.Hs.eg.db' not found
    Calls: id_conversion ... <Anonymous> -> idType -> load_OrgDb -> eval -> eval
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-patched-solaris-x86

Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘GeoTcgaData.Rmd’ using rmarkdown
    Quitting from lines 210-211 (GeoTcgaData.Rmd)
    Error: processing vignette 'GeoTcgaData.Rmd' failed with diagnostics:
    object 'org.Hs.eg.db' not found
    --- failed re-building ‘GeoTcgaData.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘GeoTcgaData.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘GeoTcgaData.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Quitting from lines 210-211 (GeoTcgaData.Rmd)
    Error: processing vignette 'GeoTcgaData.Rmd' failed with diagnostics:
    object 'org.Hs.eg.db' not found
    --- failed re-building ‘GeoTcgaData.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘GeoTcgaData.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.2.5
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘DESeq2’
Flavor: r-release-macos-arm64

Version: 1.0.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'ChAMP', 'clusterProfiler'
Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 1.0.0
Check: examples
Result: ERROR
    Running examples in ‘GeoTcgaData-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: id_conversion
    > ### Title: Convert ENSEMBL gene id to gene Symbol in TCGA
    > ### Aliases: id_conversion
    >
    > ### ** Examples
    >
    > result <- id_conversion(profile)
    Error in loadNamespace(x) : there is no package called ‘clusterProfiler’
    Calls: id_conversion ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
    Execution halted
Flavor: r-release-macos-x86_64

Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘GeoTcgaData.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Quitting from lines 210-211 (GeoTcgaData.Rmd)
    Error: processing vignette 'GeoTcgaData.Rmd' failed with diagnostics:
    there is no package called 'clusterProfiler'
    --- failed re-building ‘GeoTcgaData.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘GeoTcgaData.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 1.0.0
Check: examples
Result: ERROR
    Running examples in ‘GeoTcgaData-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: id_conversion
    > ### Title: Convert ENSEMBL gene id to gene Symbol in TCGA
    > ### Aliases: id_conversion
    >
    > ### ** Examples
    >
    > result <- id_conversion(profile)
    Error in loadNamespace(name) :
     there is no package called ‘clusterProfiler’
    Calls: id_conversion ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
    Execution halted
Flavor: r-oldrel-macos-x86_64