CRAN Package Check Results for Package pagoda2

Last updated on 2021-07-23 22:53:16 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.4 174.83 380.20 555.03 NOTE
r-devel-linux-x86_64-debian-gcc 1.0.4 118.68 283.02 401.70 NOTE
r-devel-windows-x86_64 1.0.4 164.00 322.00 486.00 NOTE
r-devel-windows-x86_64-gcc10-UCRT 1.0.4 NOTE
r-patched-linux-x86_64 1.0.4 141.66 353.66 495.32 NOTE
r-release-linux-x86_64 1.0.4 132.01 355.81 487.82 NOTE
r-release-macos-arm64 1.0.4 ERROR
r-release-macos-x86_64 1.0.4 WARN
r-release-windows-ix86+x86_64 1.0.4 395.00 416.00 811.00 WARN
r-oldrel-macos-x86_64 1.0.4 NOTE
r-oldrel-windows-ix86+x86_64 1.0.4 399.00 486.00 885.00 NOTE

Check Details

Version: 1.0.4
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'p2data'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64, r-devel-windows-x86_64-gcc10-UCRT, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0.4
Check: package dependencies
Result: ERROR
    Package required but not available: ‘N2R’
    
    Packages suggested but not available for checking:
     'BiocParallel', 'GO.db', 'org.Dr.eg.db', 'org.Hs.eg.db',
     'org.Mm.eg.db', 'p2data', 'pcaMethods', 'scde'
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-macos-arm64

Version: 1.0.4
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'GO.db', 'org.Dr.eg.db', 'org.Hs.eg.db', 'org.Mm.eg.db', 'p2data',
     'scde'
Flavor: r-release-macos-x86_64

Version: 1.0.4
Check: installed package size
Result: NOTE
     installed size is 8.5Mb
     sub-directories of 1Mb or more:
     doc 1.5Mb
     libs 5.2Mb
Flavors: r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0.4
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘pagoda2.walkthrough.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:igraph':
    
     as_data_frame, groups, union
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    Installing package into '/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/pagoda2.Rcheck'
    (as 'lib' is unspecified)
    trying URL 'https://kharchenkolab.github.io/drat/src/contrib/p2data_1.0.0.tar.gz'
    Content type 'application/gzip' length 6265057 bytes (6.0 MB)
    ==================================================
    downloaded 6.0 MB
    
    * installing *source* package ‘p2data’ ...
    ** using staged installation
    ** R
    ** data
    *** moving datasets to lazyload DB
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded from temporary location
    ** testing if installed package can be loaded from final location
    ** testing if installed package keeps a record of temporary installation path
    * DONE (p2data)
    
    The downloaded source packages are in
     '/Volumes/Temp/tmp/RtmpWIUKeC/downloaded_packages'
    3000 cells, 12546 genes; normalizing ...
    Using plain model
    Winsorizing ...
    log scale ...
    done.
    
    calculating variance fit ...
     using gam
    173 overdispersed genes ... 173
    persisting ...
    done.
    running PCA using 2000 OD genes .
    .
    .
    .
     done
    
    running tSNE using 1 cores:
    
    0% 10 20 30 40 50 60 70 80 90 100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    Quitting from lines 265-273 (pagoda2.walkthrough.Rmd)
    Error: processing vignette 'pagoda2.walkthrough.Rmd' failed with diagnostics:
    there is no package called 'org.Hs.eg.db'
    --- failed re-building ‘pagoda2.walkthrough.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘pagoda2.walkthrough.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-macos-x86_64

Version: 1.0.4
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'pagoda2.walkthrough.Rmd' using rmarkdown
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:igraph':
    
     as_data_frame, groups, union
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    Installing package into 'D:/temp/Rtmpm4IdR8/RLIBS_2fefc4be142a'
    (as 'lib' is unspecified)
    trying URL 'https://kharchenkolab.github.io/drat/src/contrib/p2data_1.0.0.tar.gz'
    Content type 'application/gzip' length 6265057 bytes (6.0 MB)
    ==================================================
    downloaded 6.0 MB
    
    * installing *source* package 'p2data' ...
    ** using staged installation
    ** R
    ** data
    *** moving datasets to lazyload DB
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded from temporary location
    *** arch - i386
    *** arch - x64
    ** testing if installed package can be loaded from final location
    *** arch - i386
    *** arch - x64
    ** testing if installed package keeps a record of temporary installation path
    * DONE (p2data)
    
    The downloaded source packages are in
     'D:\temp\Rtmp8afUYM\downloaded_packages'
    3000 cells, 12546 genes; normalizing ...
    Using plain model
    Winsorizing ...
    log scale ...
    done.
    
    calculating variance fit ...
     using gam
    173 overdispersed genes ... 173
    persisting ...
    done.
    running PCA using 2000 OD genes .
    .
    .
    .
     done
    
    running tSNE using 1 cores:
    
    0% 10 20 30 40 50 60 70 80 90 100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    Quitting from lines 284-285 (pagoda2.walkthrough.Rmd)
    Error: processing vignette 'pagoda2.walkthrough.Rmd' failed with diagnostics:
    argument is of length zero
    --- failed re-building 'pagoda2.walkthrough.Rmd'
    
    SUMMARY: processing the following file failed:
     'pagoda2.walkthrough.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 1.0.4
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'org.Dr.eg.db', 'p2data', 'scde'
Flavor: r-oldrel-macos-x86_64