CRAN Package Check Results for Package tcR

Last updated on 2020-04-25 01:53:20 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.2.4.1 29.93 124.12 154.05 OK
r-devel-linux-x86_64-debian-gcc 2.2.4.1 22.15 93.85 116.00 OK
r-devel-linux-x86_64-fedora-clang 2.2.4.1 185.46 NOTE
r-devel-linux-x86_64-fedora-gcc 2.2.4.1 181.97 OK
r-devel-windows-ix86+x86_64 2.2.4.1 81.00 192.00 273.00 NOTE
r-patched-linux-x86_64 2.2.4.1 25.61 115.77 141.38 OK
r-patched-osx-x86_64 2.2.4.1 WARN
r-patched-solaris-x86 2.2.4.1 224.40 NOTE
r-release-linux-x86_64 2.2.4.1 24.69 112.45 137.14 OK
r-release-windows-ix86+x86_64 2.2.4.1 75.00 166.00 241.00 NOTE
r-release-osx-x86_64 2.2.4.1 NOTE
r-oldrel-windows-ix86+x86_64 2.2.4.1 48.00 254.00 302.00 NOTE
r-oldrel-osx-x86_64 2.2.4.1 NOTE

Check Details

Version: 2.2.4.1
Check: installed package size
Result: NOTE
     installed size is 5.8Mb
     sub-directories of 1Mb or more:
     data 1.2Mb
     doc 2.9Mb
     libs 1.2Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-osx-x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 2.2.4.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘tcrvignette.Rmd’ using rmarkdown
    Loading required package: ggplot2
    Loading required package: dplyr
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    Loading required package: gridExtra
    
    Attaching package: 'gridExtra'
    
    The following object is masked from 'package:dplyr':
    
     combine
    
    Loading required package: reshape2
    Loading required package: igraph
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:dplyr':
    
     as_data_frame, groups, union
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    
    ==================================
    ==================================
    The tcR package is no longer supported and current issues will not be fixed. A new package is available that is designed to replace tcR called immunarch.
    We have solved most of the problems tcR package had and improved the overall pipeline, providing functions for painless repertoire file parsing and publication-ready plot making.
    
    The mission of immunarch is to make immune repertoire data analysis as easy and possible - even with R.
    Please feel free to check it here:
    https://immunarch.com/
    
    We will be happy to help you to integrate the new package into your pipelines. Please do not hesitate to contact us, should any question arise:
    Email: vdm.nazarov at gmail.com
    LinkedIn: https://linkedin.com/in/vdnaz
    
    Sincerely,
     immunarch dev team and Vadim I. Nazarov, lead developer
    
    P.S. To suppress this message, just wrap any call to tcR as follows:
    suppressPackageStartupMessages(library(tcR))
    ==================================
    ==================================
    
    Attaching package: 'tcR'
    
    The following object is masked from 'package:igraph':
    
     diversity
    
    Using People as id variables
    Using Gene as id variables
    Using Gene as id variables
    Using Gene as id variables
    Warning: Ignoring unknown aesthetics: fill
    Warning: Transformation introduced infinite values in continuous y-axis
    Warning: Transformation introduced infinite values in continuous y-axis
    Warning: Removed 20 rows containing missing values (geom_point).
    Warning: Removed 20 row(s) containing missing values (geom_path).
    Warning: Transformation introduced infinite values in continuous y-axis
    Warning: Transformation introduced infinite values in continuous y-axis
    Warning: Removed 20 rows containing missing values (geom_point).
    Warning: Removed 20 row(s) containing missing values (geom_path).
    Warning: Transformation introduced infinite values in continuous y-axis
    Warning: Transformation introduced infinite values in continuous y-axis
    Warning: Transformation introduced infinite values in continuous y-axis
    Warning: Transformation introduced infinite values in continuous y-axis
    Warning: Removed 20 rows containing missing values (geom_point).
    Warning: Removed 20 row(s) containing missing values (geom_path).
    Warning: Removed 20 rows containing missing values (geom_point).
    Warning: Removed 20 row(s) containing missing values (geom_path).
    Using People as id variables
    Warning: Ignoring unknown aesthetics: fill
    Using Gene as id variables
    Using Gene as id variables
    Using Gene as id variables
    Using Gene as id variables
    Using Symbol as id variables
    Warning: Removed 7 rows containing missing values (geom_point).
    Warning: Removed 7 rows containing missing values (geom_text).
    dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
     Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
     Expected in: /usr/lib/libSystem.B.dylib
    
    dyld: Symbol not found: ____chkstk_darwin
     Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
     Expected in: /usr/lib/libSystem.B.dylib
    
    Error: processing vignette 'tcrvignette.Rmd' failed with diagnostics:
    pandoc document conversion failed with error 6
    --- failed re-building ‘tcrvignette.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘tcrvignette.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-osx-x86_64