CRAN Package Check Results for Maintainer ‘Jason Vander Heiden <jason.vanderheiden at gmail.com>’

Last updated on 2021-06-25 11:53:04 CEST.

Package ERROR NOTE OK
airr 12 2
alakazam 1 13
scoper 1 13
shazam 12 2
tigger 1 13

Package airr

Current CRAN status: NOTE: 12, OK: 2

Version: 1.3.0
Check: LazyData
Result: NOTE
     'LazyData' is specified without a 'data' directory
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, r-devel-windows-x86_64, r-devel-windows-x86_64-gcc10-UCRT, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-ix86+x86_64

Package alakazam

Current CRAN status: ERROR: 1, OK: 13

Version: 1.1.0
Check: package dependencies
Result: ERROR
    Package required but not available: ‘GenomicAlignments’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-macos-arm64

Package scoper

Current CRAN status: ERROR: 1, OK: 13

Version: 1.1.0
Check: package dependencies
Result: ERROR
    Packages required but not available: 'alakazam', 'shazam'
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-macos-arm64

Package shazam

Current CRAN status: ERROR: 12, OK: 2

Version: 1.0.2
Check: examples
Result: ERROR
    Running examples in 'shazam-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: plotMutability
    > ### Title: Plot mutability probabilities
    > ### Aliases: plotMutability
    >
    > ### ** Examples
    >
    > # Plot one nucleotide in circular style
    > plotMutability(HH_S5F, "C")
    Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
    >
    > # Plot two nucleotides in barchart style
    > plotMutability(HH_S5F, c("G", "T"), style="bar")
    Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
    Error in `[[<-.data.frame`(`*tmp*`, i, value = c(`WRC/GYW` = "#e41a1c", :
     replacement has 3 rows, data has 5
    Calls: plotMutability ... lapply -> FUN -> modify_list -> [[<- -> [[<-.data.frame
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.0.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'Baseline-Vignette.Rmd' using rmarkdown
    Loading required package: ggplot2
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
    --- finished re-building 'Baseline-Vignette.Rmd'
    
    --- re-building 'DistToNearest-Vignette.Rmd' using rmarkdown
    Loading required package: ggplot2
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    --- finished re-building 'DistToNearest-Vignette.Rmd'
    
    --- re-building 'Mutation-Vignette.Rmd' using rmarkdown
    Loading required package: ggplot2
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    
    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
    
    --- finished re-building 'Mutation-Vignette.Rmd'
    
    --- re-building 'Shmulate-Vignette.Rmd' using rmarkdown
    Loading required package: ggplot2
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    --- finished re-building 'Shmulate-Vignette.Rmd'
    
    --- re-building 'Targeting-Vignette.Rmd' using rmarkdown
    Loading required package: ggplot2
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    Warning in createMutabilityMatrix(db, sub_mat, model = model, sequenceColumn = sequenceColumn, :
     Insufficient number of mutations to infer some 5-mers. Filled with 0.
    Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
    Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
    Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
    Quitting from lines 168-171 (Targeting-Vignette.Rmd)
    Error: processing vignette 'Targeting-Vignette.Rmd' failed with diagnostics:
    replacement has 3 rows, data has 5
    --- failed re-building 'Targeting-Vignette.Rmd'
    
    SUMMARY: processing the following file failed:
     'Targeting-Vignette.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.0.2
Check: examples
Result: ERROR
    Running examples in ‘shazam-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: plotMutability
    > ### Title: Plot mutability probabilities
    > ### Aliases: plotMutability
    >
    > ### ** Examples
    >
    > # Plot one nucleotide in circular style
    > plotMutability(HH_S5F, "C")
    Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
    >
    > # Plot two nucleotides in barchart style
    > plotMutability(HH_S5F, c("G", "T"), style="bar")
    Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
    Error in `[[<-.data.frame`(`*tmp*`, i, value = c(`WRC/GYW` = "#e41a1c", :
     replacement has 3 rows, data has 5
    Calls: plotMutability ... lapply -> FUN -> modify_list -> [[<- -> [[<-.data.frame
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-devel-windows-x86_64-gcc10-UCRT, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘Baseline-Vignette.Rmd’ using rmarkdown
    Loading required package: ggplot2
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
    --- finished re-building ‘Baseline-Vignette.Rmd’
    
    --- re-building ‘DistToNearest-Vignette.Rmd’ using rmarkdown
    Loading required package: ggplot2
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    --- finished re-building ‘DistToNearest-Vignette.Rmd’
    
    --- re-building ‘Mutation-Vignette.Rmd’ using rmarkdown
    Loading required package: ggplot2
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    
    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
    
    --- finished re-building ‘Mutation-Vignette.Rmd’
    
    --- re-building ‘Shmulate-Vignette.Rmd’ using rmarkdown
    Loading required package: ggplot2
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    --- finished re-building ‘Shmulate-Vignette.Rmd’
    
    --- re-building ‘Targeting-Vignette.Rmd’ using rmarkdown
    Loading required package: ggplot2
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    Warning in createMutabilityMatrix(db, sub_mat, model = model, sequenceColumn = sequenceColumn, :
     Insufficient number of mutations to infer some 5-mers. Filled with 0.
    Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
    Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
    Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
    Quitting from lines 168-171 (Targeting-Vignette.Rmd)
    Error: processing vignette 'Targeting-Vignette.Rmd' failed with diagnostics:
    replacement has 3 rows, data has 5
    --- failed re-building ‘Targeting-Vignette.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘Targeting-Vignette.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'Baseline-Vignette.Rmd' using rmarkdown
    Loading required package: ggplot2
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
    Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
    pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
    --- finished re-building 'Baseline-Vignette.Rmd'
    
    --- re-building 'DistToNearest-Vignette.Rmd' using rmarkdown
    Loading required package: ggplot2
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
    --- finished re-building 'DistToNearest-Vignette.Rmd'
    
    --- re-building 'Mutation-Vignette.Rmd' using rmarkdown
    Loading required package: ggplot2
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    
    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
    
    pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
    --- finished re-building 'Mutation-Vignette.Rmd'
    
    --- re-building 'Shmulate-Vignette.Rmd' using rmarkdown
    Loading required package: ggplot2
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
    --- finished re-building 'Shmulate-Vignette.Rmd'
    
    --- re-building 'Targeting-Vignette.Rmd' using rmarkdown
    Loading required package: ggplot2
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    Warning in createMutabilityMatrix(db, sub_mat, model = model, sequenceColumn = sequenceColumn, :
     Insufficient number of mutations to infer some 5-mers. Filled with 0.
    Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
    Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
    pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
    pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
    Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
    Quitting from lines 168-171 (Targeting-Vignette.Rmd)
    Error: processing vignette 'Targeting-Vignette.Rmd' failed with diagnostics:
    replacement has 3 rows, data has 5
    --- failed re-building 'Targeting-Vignette.Rmd'
    
    SUMMARY: processing the following file failed:
     'Targeting-Vignette.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 1.0.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘Baseline-Vignette.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Loading required package: ggplot2
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
    --- finished re-building ‘Baseline-Vignette.Rmd’
    
    --- re-building ‘DistToNearest-Vignette.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Loading required package: ggplot2
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    --- finished re-building ‘DistToNearest-Vignette.Rmd’
    
    --- re-building ‘Mutation-Vignette.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Loading required package: ggplot2
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    
    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
    
    --- finished re-building ‘Mutation-Vignette.Rmd’
    
    --- re-building ‘Shmulate-Vignette.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Loading required package: ggplot2
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    --- finished re-building ‘Shmulate-Vignette.Rmd’
    
    --- re-building ‘Targeting-Vignette.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Loading required package: ggplot2
    As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
    A description of the standard is available at https://docs.airr-community.org.
    The legacy Change-O format is supported through arguments to each function
    that allow the input column names to be explicitly defined.
    Warning in createMutabilityMatrix(db, sub_mat, model = model, sequenceColumn = sequenceColumn, :
     Insufficient number of mutations to infer some 5-mers. Filled with 0.
    Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
    Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
    Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
    Quitting from lines 168-171 (Targeting-Vignette.Rmd)
    Error: processing vignette 'Targeting-Vignette.Rmd' failed with diagnostics:
    replacement has 3 rows, data has 5
    --- failed re-building ‘Targeting-Vignette.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘Targeting-Vignette.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 1.0.2
Check: package dependencies
Result: ERROR
    Package required but not available: ‘alakazam’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-macos-arm64

Package tigger

Current CRAN status: ERROR: 1, OK: 13

Version: 1.0.0
Check: package dependencies
Result: ERROR
    Packages required but not available: 'alakazam', 'shazam'
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-macos-arm64