CRAN Package Check Results for Package SanzCircos

Last updated on 2020-05-01 09:55:20 CEST.

Check Details

Version: 0.1.0
Check: examples
Result: ERROR
    Running examples in 'SanzCircos-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: make_circos_links
    > ### Title: make_circos_links
    > ### Aliases: make_circos_links
    >
    > ### ** Examples
    >
    >
    > links_df <- data.frame(chrom = c(rep("chr1", 5), rep("chr2", 5)),
    + band = c(rep("band1", 3), rep("band2", 2), "band1", rep("band2", 4)),
    + link = c(1, 2, 3, 1, 2, 1, 1, 3, 4, 5),
    + start = c(1, 3, 5, 10, 35, 1, 5, 8, 13, 15),
    + end = c(3, 5, 10, 35, 39, 5, 8, 13, 15, 21))
    >
    > links <- make_circos_links(links_df, "chrom", "band", "link", "start", "end", status = TRUE)
    Warning: `as.tibble()` is deprecated as of tibble 2.0.0.
    Please use `as_tibble()` instead.
    The signature and semantics have changed, see `?as_tibble`.
    This warning is displayed once every 8 hours.
    Call `lifecycle::last_warnings()` to see where this warning was generated.
    Error: Assigned data `as.character(df[[chromosome_grouping]][i])` must be compatible with existing data.
    i Error occurred for column `V2`.
    x Lossy cast from `value` <character> to `x` <logical>.
    * Locations: 1.
    Backtrace:
     x
     1. \-SanzCircos::make_circos_links(...)
     2. +-dplyr::bind_rows(...)
     3. | +-dplyr:::flatten_bindable(dots_values(...))
     4. | \-rlang::dots_values(...)
     5. \-pbapply::pblapply(...)
     6. \-base::lapply(X, FUN, ...)
     7. \-SanzCircos:::FUN(X[[i]], ...)
     8. +-base::`[<-`(`*tmp*`, 1, 2, value = "chr1")
     9. \-tibble:::`[<-.tbl_df`(`*tmp*`, 1, 2, value = "chr1")
     10. \-tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
     11. \-tibble:::tbl_subassign_row(xj, i, value, value_arg)
     12. \-base::tryCatch(...)
     13. \-base:::tryCatchList(expr, classes, parentenv, handlers)
     14. \-base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
     15.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.1.0
Check: examples
Result: ERROR
    Running examples in ‘SanzCircos-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: make_circos_links
    > ### Title: make_circos_links
    > ### Aliases: make_circos_links
    >
    > ### ** Examples
    >
    >
    > links_df <- data.frame(chrom = c(rep("chr1", 5), rep("chr2", 5)),
    + band = c(rep("band1", 3), rep("band2", 2), "band1", rep("band2", 4)),
    + link = c(1, 2, 3, 1, 2, 1, 1, 3, 4, 5),
    + start = c(1, 3, 5, 10, 35, 1, 5, 8, 13, 15),
    + end = c(3, 5, 10, 35, 39, 5, 8, 13, 15, 21))
    >
    > links <- make_circos_links(links_df, "chrom", "band", "link", "start", "end", status = TRUE)
    Warning: `as.tibble()` is deprecated as of tibble 2.0.0.
    Please use `as_tibble()` instead.
    The signature and semantics have changed, see `?as_tibble`.
    This warning is displayed once every 8 hours.
    Call `lifecycle::last_warnings()` to see where this warning was generated.
    Error: Assigned data `as.character(df[[chromosome_grouping]][i])` must be compatible with existing data.
    ℹ Error occurred for column `V2`.
    ✖ Lossy cast from `value` <character> to `x` <logical>.
    * Locations: 1.
    Backtrace:
     █
     1. └─SanzCircos::make_circos_links(...)
     2. ├─dplyr::bind_rows(...)
     3. │ ├─dplyr:::flatten_bindable(dots_values(...))
     4. │ └─rlang::dots_values(...)
     5. └─pbapply::pblapply(...)
     6. └─base::lapply(X, FUN, ...)
     7. └─SanzCircos:::FUN(X[[i]], ...)
     8. ├─base::`[<-`(`*tmp*`, 1, 2, value = "chr1")
     9. └─tibble:::`[<-.tbl_df`(`*tmp*`, 1, 2, value = "chr1")
     10. └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
     11. └─tibble:::tbl_subassign_row(xj, i, value, value_arg)
     12. └─base::tryCatch(...)
     13. └─base:::tryCatchList(expr, classes, parentenv, handlers)
     14. └
    Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.1.0
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     ‘purrr’ ‘tidyr’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.1.0
Check: examples
Result: ERROR
    Running examples in ‘SanzCircos-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: make_circos_links
    > ### Title: make_circos_links
    > ### Aliases: make_circos_links
    >
    > ### ** Examples
    >
    >
    > links_df <- data.frame(chrom = c(rep("chr1", 5), rep("chr2", 5)),
    + band = c(rep("band1", 3), rep("band2", 2), "band1", rep("band2", 4)),
    + link = c(1, 2, 3, 1, 2, 1, 1, 3, 4, 5),
    + start = c(1, 3, 5, 10, 35, 1, 5, 8, 13, 15),
    + end = c(3, 5, 10, 35, 39, 5, 8, 13, 15, 21))
    >
    > links <- make_circos_links(links_df, "chrom", "band", "link", "start", "end", status = TRUE)
    Warning: `as.tibble()` is deprecated as of tibble 2.0.0.
    Please use `as_tibble()` instead.
    The signature and semantics have changed, see `?as_tibble`.
    This warning is displayed once every 8 hours.
    Call `lifecycle::last_warnings()` to see where this warning was generated.
    Error: Assigned data `as.character(df[[chromosome_grouping]][i])` must be compatible with existing data.
    ℹ Error occurred for column `V2`.
    ✖ Lossy cast from `value` <character> to `x` <logical>.
    * Locations: 1.
    Backtrace:
     █
     1. └─SanzCircos::make_circos_links(...)
     2. ├─dplyr::bind_rows(...)
     3. │ ├─dplyr:::flatten_bindable(dots_values(...))
     4. │ └─rlang::dots_values(...)
     5. └─pbapply::pblapply(...)
     6. └─base::lapply(X, FUN, ...)
     7. └─SanzCircos:::FUN(X[[i]], ...)
     8. ├─base::`[<-`(`*tmp*`, 1, 2, value = "chr1")
     9. └─tibble:::`[<-.tbl_df`(`*tmp*`, 1, 2, value = "chr1")
     10. └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
     11. └─tibble:::tbl_subassign_row(xj, i, value, value_arg)
     12. └─base::tryCatch(...)
     13. └─base:::tryCatchList(expr, classes, parentenv, handlers)
     14. └
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64

Version: 0.1.0
Check: examples
Result: ERROR
    Running examples in 'SanzCircos-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: make_circos_links
    > ### Title: make_circos_links
    > ### Aliases: make_circos_links
    >
    > ### ** Examples
    >
    >
    > links_df <- data.frame(chrom = c(rep("chr1", 5), rep("chr2", 5)),
    + band = c(rep("band1", 3), rep("band2", 2), "band1", rep("band2", 4)),
    + link = c(1, 2, 3, 1, 2, 1, 1, 3, 4, 5),
    + start = c(1, 3, 5, 10, 35, 1, 5, 8, 13, 15),
    + end = c(3, 5, 10, 35, 39, 5, 8, 13, 15, 21))
    >
    > links <- make_circos_links(links_df, "chrom", "band", "link", "start", "end", status = TRUE)
    Warning: `as.tibble()` is deprecated as of tibble 2.0.0.
    Please use `as_tibble()` instead.
    The signature and semantics have changed, see `?as_tibble`.
    This warning is displayed once every 8 hours.
    Call `lifecycle::last_warnings()` to see where this warning was generated.
    Error: Assigned data `as.character(df[[chromosome_grouping]][i])` must be compatible with existing data.
    i Error occurred for column `V2`.
    x Lossy cast from `value` <character> to `x` <logical>.
    * Locations: 1.
    Backtrace:
     x
     1. \-SanzCircos::make_circos_links(...)
     2. +-dplyr::bind_rows(...)
     3. | +-dplyr:::flatten_bindable(dots_values(...))
     4. | \-rlang::dots_values(...)
     5. \-pbapply::pblapply(...)
     6. \-base::lapply(X, FUN, ...)
     7. \-SanzCircos:::FUN(X[[i]], ...)
     8. +-base::`[<-`(`*tmp*`, 1, 2, value = "chr1")
     9. \-tibble:::`[<-.tbl_df`(`*tmp*`, 1, 2, value = "chr1")
     10. \-tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
     11. \-tibble:::tbl_subassign_row(xj, i, value, value_arg)
     12. \-base::tryCatch(...)
     13. \-base:::tryCatchList(expr, classes, parentenv, handlers)
     14. \-base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
     15.
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64