CRAN Package Check Results for Package fastqcr

Last updated on 2023-02-05 07:57:21 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.2 7.77 57.05 64.82 ERROR
r-devel-linux-x86_64-debian-gcc 0.1.2 5.44 41.34 46.78 ERROR
r-devel-linux-x86_64-fedora-clang 0.1.2 82.39 ERROR
r-devel-linux-x86_64-fedora-gcc 0.1.2 73.46 ERROR
r-devel-windows-x86_64 0.1.2 22.00 84.00 106.00 ERROR
r-patched-linux-x86_64 0.1.2 7.40 54.58 61.98 ERROR
r-release-linux-x86_64 0.1.2 5.93 54.95 60.88 ERROR
r-release-macos-arm64 0.1.2 41.00 NOTE
r-release-macos-x86_64 0.1.2 71.00 NOTE
r-release-windows-x86_64 0.1.2 34.00 154.00 188.00 NOTE
r-oldrel-macos-arm64 0.1.2 46.00 NOTE
r-oldrel-macos-x86_64 0.1.2 53.00 NOTE
r-oldrel-windows-ix86+x86_64 0.1.2 16.00 78.00 94.00 ERROR

Check Details

Version: 0.1.2
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-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.1.2
Check: examples
Result: ERROR
    Running examples in ‘fastqcr-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: qc_aggregate
    > ### Title: Aggregate FastQC Reports for Multiple Samples
    > ### Aliases: qc_aggregate summary.qc_aggregate qc_stats
    >
    > ### ** Examples
    >
    > # Demo QC dir
    > qc.dir <- system.file("fastqc_results", package = "fastqcr")
    > qc.dir
    [1] "/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/fastqcr/fastqc_results"
    >
    > # List of files in the directory
    > list.files(qc.dir)
    [1] "S1_fastqc.zip" "S2_fastqc.zip" "S3_fastqc.zip" "S4_fastqc.zip"
    [5] "S5_fastqc.zip"
    >
    > # Aggregate the report
    > qc <- qc_aggregate(qc.dir, progressbar = FALSE)
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 82.7616329532754
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 84.29622447696052
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 77.85759595869786
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 80.10708743156657
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 81.85424272012848
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Warning: `select_()` was deprecated in dplyr 0.7.0.
    ℹ Please use `select()` instead.
    ℹ The deprecated feature was likely used in the fastqcr package.
     Please report the issue at <https://github.com/kassambara/fastqcr/issues>.
    > qc
    # A tibble: 60 × 7
     sample module status tot.seq seq.length pct.gc pct.dup
     * <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
     1 S1 Basic Statistics PASS 50299587 35-76 48 17.2
     2 S1 Per base sequence quality PASS 50299587 35-76 48 17.2
     3 S1 Per tile sequence quality PASS 50299587 35-76 48 17.2
     4 S1 Per sequence quality scores PASS 50299587 35-76 48 17.2
     5 S1 Per base sequence content FAIL 50299587 35-76 48 17.2
     6 S1 Per sequence GC content WARN 50299587 35-76 48 17.2
     7 S1 Per base N content PASS 50299587 35-76 48 17.2
     8 S1 Sequence Length Distribution WARN 50299587 35-76 48 17.2
     9 S1 Sequence Duplication Levels PASS 50299587 35-76 48 17.2
    10 S1 Overrepresented sequences PASS 50299587 35-76 48 17.2
    # … with 50 more rows
    >
    > # Generates a summary of qc_aggregate
    > summary(qc)
    Warning: `group_by_()` was deprecated in dplyr 0.7.0.
    ℹ Please use `group_by()` instead.
    ℹ See vignette('programming') for more help
    ℹ The deprecated feature was likely used in the fastqcr package.
     Please report the issue at <https://github.com/kassambara/fastqcr/issues>.
    Error in `left_join()`:
    ! `...` must be empty.
    ✖ Problematic argument:
    • fill = "---"
    Backtrace:
     ▆
     1. ├─base::summary(qc)
     2. └─fastqcr:::summary.qc_aggregate(qc)
     3. ├─dplyr::left_join(res, failed, by = "module", fill = "---")
     4. └─dplyr:::left_join.data.frame(res, failed, by = "module", fill = "---")
     5. └─rlang::check_dots_empty0(...)
     6. └─rlang::check_dots_empty(call = call)
     7. └─rlang:::action_dots(...)
     8. ├─base (local) try_dots(...)
     9. └─rlang (local) action(...)
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.1.2
Check: examples
Result: ERROR
    Running examples in ‘fastqcr-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: qc_aggregate
    > ### Title: Aggregate FastQC Reports for Multiple Samples
    > ### Aliases: qc_aggregate summary.qc_aggregate qc_stats
    >
    > ### ** Examples
    >
    > # Demo QC dir
    > qc.dir <- system.file("fastqc_results", package = "fastqcr")
    > qc.dir
    [1] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/fastqcr/fastqc_results"
    >
    > # List of files in the directory
    > list.files(qc.dir)
    [1] "S1_fastqc.zip" "S2_fastqc.zip" "S3_fastqc.zip" "S4_fastqc.zip"
    [5] "S5_fastqc.zip"
    >
    > # Aggregate the report
    > qc <- qc_aggregate(qc.dir, progressbar = FALSE)
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 82.7616329532754
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 84.29622447696052
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 77.85759595869786
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 80.10708743156657
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 81.85424272012848
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Warning: `select_()` was deprecated in dplyr 0.7.0.
    ℹ Please use `select()` instead.
    ℹ The deprecated feature was likely used in the fastqcr package.
     Please report the issue at <https://github.com/kassambara/fastqcr/issues>.
    > qc
    # A tibble: 60 × 7
     sample module status tot.seq seq.length pct.gc pct.dup
     * <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
     1 S1 Basic Statistics PASS 50299587 35-76 48 17.2
     2 S1 Per base sequence quality PASS 50299587 35-76 48 17.2
     3 S1 Per tile sequence quality PASS 50299587 35-76 48 17.2
     4 S1 Per sequence quality scores PASS 50299587 35-76 48 17.2
     5 S1 Per base sequence content FAIL 50299587 35-76 48 17.2
     6 S1 Per sequence GC content WARN 50299587 35-76 48 17.2
     7 S1 Per base N content PASS 50299587 35-76 48 17.2
     8 S1 Sequence Length Distribution WARN 50299587 35-76 48 17.2
     9 S1 Sequence Duplication Levels PASS 50299587 35-76 48 17.2
    10 S1 Overrepresented sequences PASS 50299587 35-76 48 17.2
    # … with 50 more rows
    >
    > # Generates a summary of qc_aggregate
    > summary(qc)
    Warning: `group_by_()` was deprecated in dplyr 0.7.0.
    ℹ Please use `group_by()` instead.
    ℹ See vignette('programming') for more help
    ℹ The deprecated feature was likely used in the fastqcr package.
     Please report the issue at <https://github.com/kassambara/fastqcr/issues>.
    Error in `left_join()`:
    ! `...` must be empty.
    ✖ Problematic argument:
    • fill = "---"
    Backtrace:
     ▆
     1. ├─base::summary(qc)
     2. └─fastqcr:::summary.qc_aggregate(qc)
     3. ├─dplyr::left_join(res, failed, by = "module", fill = "---")
     4. └─dplyr:::left_join.data.frame(res, failed, by = "module", fill = "---")
     5. └─rlang::check_dots_empty0(...)
     6. └─rlang::check_dots_empty(call = call)
     7. └─rlang:::action_dots(...)
     8. ├─base (local) try_dots(...)
     9. └─rlang (local) action(...)
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.1.2
Check: examples
Result: ERROR
    Running examples in ‘fastqcr-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: qc_aggregate
    > ### Title: Aggregate FastQC Reports for Multiple Samples
    > ### Aliases: qc_aggregate summary.qc_aggregate qc_stats
    >
    > ### ** Examples
    >
    > # Demo QC dir
    > qc.dir <- system.file("fastqc_results", package = "fastqcr")
    > qc.dir
    [1] "/data/gannet/ripley/R/packages/tests-clang/fastqcr.Rcheck/fastqcr/fastqc_results"
    >
    > # List of files in the directory
    > list.files(qc.dir)
    [1] "S1_fastqc.zip" "S2_fastqc.zip" "S3_fastqc.zip" "S4_fastqc.zip"
    [5] "S5_fastqc.zip"
    >
    > # Aggregate the report
    > qc <- qc_aggregate(qc.dir, progressbar = FALSE)
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 82.7616329532754
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 84.29622447696052
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 77.85759595869786
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 80.10708743156657
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 81.85424272012848
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Warning: `select_()` was deprecated in dplyr 0.7.0.
    ℹ Please use `select()` instead.
    ℹ The deprecated feature was likely used in the fastqcr package.
     Please report the issue at <https://github.com/kassambara/fastqcr/issues>.
    > qc
    # A tibble: 60 × 7
     sample module status tot.seq seq.length pct.gc pct.dup
     * <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
     1 S1 Basic Statistics PASS 50299587 35-76 48 17.2
     2 S1 Per base sequence quality PASS 50299587 35-76 48 17.2
     3 S1 Per tile sequence quality PASS 50299587 35-76 48 17.2
     4 S1 Per sequence quality scores PASS 50299587 35-76 48 17.2
     5 S1 Per base sequence content FAIL 50299587 35-76 48 17.2
     6 S1 Per sequence GC content WARN 50299587 35-76 48 17.2
     7 S1 Per base N content PASS 50299587 35-76 48 17.2
     8 S1 Sequence Length Distribution WARN 50299587 35-76 48 17.2
     9 S1 Sequence Duplication Levels PASS 50299587 35-76 48 17.2
    10 S1 Overrepresented sequences PASS 50299587 35-76 48 17.2
    # … with 50 more rows
    >
    > # Generates a summary of qc_aggregate
    > summary(qc)
    Warning: `group_by_()` was deprecated in dplyr 0.7.0.
    ℹ Please use `group_by()` instead.
    ℹ See vignette('programming') for more help
    ℹ The deprecated feature was likely used in the fastqcr package.
     Please report the issue at <https://github.com/kassambara/fastqcr/issues>.
    Error in `left_join()`:
    ! `...` must be empty.
    ✖ Problematic argument:
    • fill = "---"
    Backtrace:
     ▆
     1. ├─base::summary(qc)
     2. └─fastqcr:::summary.qc_aggregate(qc)
     3. ├─dplyr::left_join(res, failed, by = "module", fill = "---")
     4. └─dplyr:::left_join.data.frame(res, failed, by = "module", fill = "---")
     5. └─rlang::check_dots_empty0(...)
     6. └─rlang::check_dots_empty(call = call)
     7. └─rlang:::action_dots(...)
     8. ├─base (local) try_dots(...)
     9. └─rlang (local) action(...)
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.1.2
Check: examples
Result: ERROR
    Running examples in ‘fastqcr-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: qc_aggregate
    > ### Title: Aggregate FastQC Reports for Multiple Samples
    > ### Aliases: qc_aggregate summary.qc_aggregate qc_stats
    >
    > ### ** Examples
    >
    > # Demo QC dir
    > qc.dir <- system.file("fastqc_results", package = "fastqcr")
    > qc.dir
    [1] "/data/gannet/ripley/R/packages/tests-devel/fastqcr.Rcheck/fastqcr/fastqc_results"
    >
    > # List of files in the directory
    > list.files(qc.dir)
    [1] "S1_fastqc.zip" "S2_fastqc.zip" "S3_fastqc.zip" "S4_fastqc.zip"
    [5] "S5_fastqc.zip"
    >
    > # Aggregate the report
    > qc <- qc_aggregate(qc.dir, progressbar = FALSE)
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 82.7616329532754
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 84.29622447696052
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 77.85759595869786
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 80.10708743156657
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 81.85424272012848
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Warning: `select_()` was deprecated in dplyr 0.7.0.
    ℹ Please use `select()` instead.
    ℹ The deprecated feature was likely used in the fastqcr package.
     Please report the issue at <https://github.com/kassambara/fastqcr/issues>.
    > qc
    # A tibble: 60 × 7
     sample module status tot.seq seq.length pct.gc pct.dup
     * <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
     1 S1 Basic Statistics PASS 50299587 35-76 48 17.2
     2 S1 Per base sequence quality PASS 50299587 35-76 48 17.2
     3 S1 Per tile sequence quality PASS 50299587 35-76 48 17.2
     4 S1 Per sequence quality scores PASS 50299587 35-76 48 17.2
     5 S1 Per base sequence content FAIL 50299587 35-76 48 17.2
     6 S1 Per sequence GC content WARN 50299587 35-76 48 17.2
     7 S1 Per base N content PASS 50299587 35-76 48 17.2
     8 S1 Sequence Length Distribution WARN 50299587 35-76 48 17.2
     9 S1 Sequence Duplication Levels PASS 50299587 35-76 48 17.2
    10 S1 Overrepresented sequences PASS 50299587 35-76 48 17.2
    # … with 50 more rows
    >
    > # Generates a summary of qc_aggregate
    > summary(qc)
    Warning: `group_by_()` was deprecated in dplyr 0.7.0.
    ℹ Please use `group_by()` instead.
    ℹ See vignette('programming') for more help
    ℹ The deprecated feature was likely used in the fastqcr package.
     Please report the issue at <https://github.com/kassambara/fastqcr/issues>.
    Error in `left_join()`:
    ! `...` must be empty.
    ✖ Problematic argument:
    • fill = "---"
    Backtrace:
     ▆
     1. ├─base::summary(qc)
     2. └─fastqcr:::summary.qc_aggregate(qc)
     3. ├─dplyr::left_join(res, failed, by = "module", fill = "---")
     4. └─dplyr:::left_join.data.frame(res, failed, by = "module", fill = "---")
     5. └─rlang::check_dots_empty0(...)
     6. └─rlang::check_dots_empty(call = call)
     7. └─rlang:::action_dots(...)
     8. ├─base (local) try_dots(...)
     9. └─rlang (local) action(...)
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.1.2
Check: examples
Result: ERROR
    Running examples in 'fastqcr-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: qc_aggregate
    > ### Title: Aggregate FastQC Reports for Multiple Samples
    > ### Aliases: qc_aggregate summary.qc_aggregate qc_stats
    >
    > ### ** Examples
    >
    > # Demo QC dir
    > qc.dir <- system.file("fastqc_results", package = "fastqcr")
    > qc.dir
    [1] "D:/RCompile/CRANpkg/lib/4.3/fastqcr/fastqc_results"
    >
    > # List of files in the directory
    > list.files(qc.dir)
    [1] "S1_fastqc.zip" "S2_fastqc.zip" "S3_fastqc.zip" "S4_fastqc.zip"
    [5] "S5_fastqc.zip"
    >
    > # Aggregate the report
    > qc <- qc_aggregate(qc.dir, progressbar = FALSE)
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 82.7616329532754
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 84.29622447696052
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 77.85759595869786
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 80.10708743156657
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 81.85424272012848
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Warning: `select_()` was deprecated in dplyr 0.7.0.
    ℹ Please use `select()` instead.
    ℹ The deprecated feature was likely used in the fastqcr package.
     Please report the issue at <https://github.com/kassambara/fastqcr/issues>.
    > qc
    # A tibble: 60 × 7
     sample module status tot.seq seq.length pct.gc pct.dup
     * <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
     1 S1 Basic Statistics PASS 50299587 35-76 48 17.2
     2 S1 Per base sequence quality PASS 50299587 35-76 48 17.2
     3 S1 Per tile sequence quality PASS 50299587 35-76 48 17.2
     4 S1 Per sequence quality scores PASS 50299587 35-76 48 17.2
     5 S1 Per base sequence content FAIL 50299587 35-76 48 17.2
     6 S1 Per sequence GC content WARN 50299587 35-76 48 17.2
     7 S1 Per base N content PASS 50299587 35-76 48 17.2
     8 S1 Sequence Length Distribution WARN 50299587 35-76 48 17.2
     9 S1 Sequence Duplication Levels PASS 50299587 35-76 48 17.2
    10 S1 Overrepresented sequences PASS 50299587 35-76 48 17.2
    # … with 50 more rows
    >
    > # Generates a summary of qc_aggregate
    > summary(qc)
    Warning: `group_by_()` was deprecated in dplyr 0.7.0.
    ℹ Please use `group_by()` instead.
    ℹ See vignette('programming') for more help
    ℹ The deprecated feature was likely used in the fastqcr package.
     Please report the issue at <https://github.com/kassambara/fastqcr/issues>.
    Error in `left_join()`:
    ! `...` must be empty.
    ✖ Problematic argument:
    • fill = "---"
    Backtrace:
     ▆
     1. ├─base::summary(qc)
     2. └─fastqcr:::summary.qc_aggregate(qc)
     3. ├─dplyr::left_join(res, failed, by = "module", fill = "---")
     4. └─dplyr:::left_join.data.frame(res, failed, by = "module", fill = "---")
     5. └─rlang::check_dots_empty0(...)
     6. └─rlang::check_dots_empty(call = call)
     7. └─rlang:::action_dots(...)
     8. ├─base (local) try_dots(...)
     9. └─rlang (local) action(...)
    Execution halted
Flavor: r-devel-windows-x86_64

Version: 0.1.2
Check: examples
Result: ERROR
    Running examples in ‘fastqcr-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: qc_aggregate
    > ### Title: Aggregate FastQC Reports for Multiple Samples
    > ### Aliases: qc_aggregate summary.qc_aggregate qc_stats
    >
    > ### ** Examples
    >
    > # Demo QC dir
    > qc.dir <- system.file("fastqc_results", package = "fastqcr")
    > qc.dir
    [1] "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/fastqcr/fastqc_results"
    >
    > # List of files in the directory
    > list.files(qc.dir)
    [1] "S1_fastqc.zip" "S2_fastqc.zip" "S3_fastqc.zip" "S4_fastqc.zip"
    [5] "S5_fastqc.zip"
    >
    > # Aggregate the report
    > qc <- qc_aggregate(qc.dir, progressbar = FALSE)
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 82.7616329532754
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 84.29622447696052
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 77.85759595869786
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 80.10708743156657
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 81.85424272012848
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Warning: `select_()` was deprecated in dplyr 0.7.0.
    ℹ Please use `select()` instead.
    ℹ The deprecated feature was likely used in the fastqcr package.
     Please report the issue at <https://github.com/kassambara/fastqcr/issues>.
    > qc
    # A tibble: 60 × 7
     sample module status tot.seq seq.length pct.gc pct.dup
     * <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
     1 S1 Basic Statistics PASS 50299587 35-76 48 17.2
     2 S1 Per base sequence quality PASS 50299587 35-76 48 17.2
     3 S1 Per tile sequence quality PASS 50299587 35-76 48 17.2
     4 S1 Per sequence quality scores PASS 50299587 35-76 48 17.2
     5 S1 Per base sequence content FAIL 50299587 35-76 48 17.2
     6 S1 Per sequence GC content WARN 50299587 35-76 48 17.2
     7 S1 Per base N content PASS 50299587 35-76 48 17.2
     8 S1 Sequence Length Distribution WARN 50299587 35-76 48 17.2
     9 S1 Sequence Duplication Levels PASS 50299587 35-76 48 17.2
    10 S1 Overrepresented sequences PASS 50299587 35-76 48 17.2
    # … with 50 more rows
    >
    > # Generates a summary of qc_aggregate
    > summary(qc)
    Warning: `group_by_()` was deprecated in dplyr 0.7.0.
    ℹ Please use `group_by()` instead.
    ℹ See vignette('programming') for more help
    ℹ The deprecated feature was likely used in the fastqcr package.
     Please report the issue at <https://github.com/kassambara/fastqcr/issues>.
    Error in `left_join()`:
    ! `...` must be empty.
    ✖ Problematic argument:
    • fill = "---"
    Backtrace:
     ▆
     1. ├─base::summary(qc)
     2. └─fastqcr:::summary.qc_aggregate(qc)
     3. ├─dplyr::left_join(res, failed, by = "module", fill = "---")
     4. └─dplyr:::left_join.data.frame(res, failed, by = "module", fill = "---")
     5. └─rlang::check_dots_empty0(...)
     6. └─rlang::check_dots_empty(call = call)
     7. └─rlang:::action_dots(...)
     8. ├─base (local) try_dots(...)
     9. └─rlang (local) action(...)
    Execution halted
Flavor: r-patched-linux-x86_64

Version: 0.1.2
Check: examples
Result: ERROR
    Running examples in ‘fastqcr-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: qc_aggregate
    > ### Title: Aggregate FastQC Reports for Multiple Samples
    > ### Aliases: qc_aggregate summary.qc_aggregate qc_stats
    >
    > ### ** Examples
    >
    > # Demo QC dir
    > qc.dir <- system.file("fastqc_results", package = "fastqcr")
    > qc.dir
    [1] "/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/fastqcr/fastqc_results"
    >
    > # List of files in the directory
    > list.files(qc.dir)
    [1] "S1_fastqc.zip" "S2_fastqc.zip" "S3_fastqc.zip" "S4_fastqc.zip"
    [5] "S5_fastqc.zip"
    >
    > # Aggregate the report
    > qc <- qc_aggregate(qc.dir, progressbar = FALSE)
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 82.7616329532754
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 84.29622447696052
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 77.85759595869786
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 80.10708743156657
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (3): status, module, sample
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Measure, Value
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 81.85424272012848
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Warning: `select_()` was deprecated in dplyr 0.7.0.
    ℹ Please use `select()` instead.
    ℹ The deprecated feature was likely used in the fastqcr package.
     Please report the issue at <https://github.com/kassambara/fastqcr/issues>.
    > qc
    # A tibble: 60 × 7
     sample module status tot.seq seq.length pct.gc pct.dup
     * <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
     1 S1 Basic Statistics PASS 50299587 35-76 48 17.2
     2 S1 Per base sequence quality PASS 50299587 35-76 48 17.2
     3 S1 Per tile sequence quality PASS 50299587 35-76 48 17.2
     4 S1 Per sequence quality scores PASS 50299587 35-76 48 17.2
     5 S1 Per base sequence content FAIL 50299587 35-76 48 17.2
     6 S1 Per sequence GC content WARN 50299587 35-76 48 17.2
     7 S1 Per base N content PASS 50299587 35-76 48 17.2
     8 S1 Sequence Length Distribution WARN 50299587 35-76 48 17.2
     9 S1 Sequence Duplication Levels PASS 50299587 35-76 48 17.2
    10 S1 Overrepresented sequences PASS 50299587 35-76 48 17.2
    # … with 50 more rows
    >
    > # Generates a summary of qc_aggregate
    > summary(qc)
    Warning: `group_by_()` was deprecated in dplyr 0.7.0.
    ℹ Please use `group_by()` instead.
    ℹ See vignette('programming') for more help
    ℹ The deprecated feature was likely used in the fastqcr package.
     Please report the issue at <https://github.com/kassambara/fastqcr/issues>.
    Error in `left_join()`:
    ! `...` must be empty.
    ✖ Problematic argument:
    • fill = "---"
    Backtrace:
     ▆
     1. ├─base::summary(qc)
     2. └─fastqcr:::summary.qc_aggregate(qc)
     3. ├─dplyr::left_join(res, failed, by = "module", fill = "---")
     4. └─dplyr:::left_join.data.frame(res, failed, by = "module", fill = "---")
     5. └─rlang::check_dots_empty0(...)
     6. └─rlang::check_dots_empty(call = call)
     7. └─rlang:::action_dots(...)
     8. ├─base (local) try_dots(...)
     9. └─rlang (local) action(...)
    Execution halted
Flavor: r-release-linux-x86_64

Version: 0.1.2
Check: examples
Result: ERROR
    Running examples in 'fastqcr-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: qc_aggregate
    > ### Title: Aggregate FastQC Reports for Multiple Samples
    > ### Aliases: qc_aggregate summary.qc_aggregate qc_stats
    >
    > ### ** Examples
    >
    > # Demo QC dir
    > qc.dir <- system.file("fastqc_results", package = "fastqcr")
    > qc.dir
    [1] "D:/temp/RtmpgHYSfR/RLIBS_165c6ee73ee4/fastqcr/fastqc_results"
    >
    > # List of files in the directory
    > list.files(qc.dir)
    [1] "S1_fastqc.zip" "S2_fastqc.zip" "S3_fastqc.zip" "S4_fastqc.zip"
    [5] "S5_fastqc.zip"
    >
    > # Aggregate the report
    > qc <- qc_aggregate(qc.dir, progressbar = FALSE)
    Rows: 12 Columns: 3
    -- Column specification --------------------------------------------------------
    Delimiter: "\t"
    chr (3): status, module, sample
    
    i Use `spec()` to retrieve the full column specification for this data.
    i Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    -- Column specification --------------------------------------------------------
    Delimiter: "\t"
    chr (2): Measure, Value
    
    i Use `spec()` to retrieve the full column specification for this data.
    i Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    -- Column specification --------------------------------------------------------
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    i Use `spec()` to retrieve the full column specification for this data.
    i Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    -- Column specification --------------------------------------------------------
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 82.7616329532754
    
    i Use `spec()` to retrieve the full column specification for this data.
    i Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    -- Column specification --------------------------------------------------------
    Delimiter: "\t"
    chr (3): status, module, sample
    
    i Use `spec()` to retrieve the full column specification for this data.
    i Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    -- Column specification --------------------------------------------------------
    Delimiter: "\t"
    chr (2): Measure, Value
    
    i Use `spec()` to retrieve the full column specification for this data.
    i Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    -- Column specification --------------------------------------------------------
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    i Use `spec()` to retrieve the full column specification for this data.
    i Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    -- Column specification --------------------------------------------------------
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 84.29622447696052
    
    i Use `spec()` to retrieve the full column specification for this data.
    i Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    -- Column specification --------------------------------------------------------
    Delimiter: "\t"
    chr (3): status, module, sample
    
    i Use `spec()` to retrieve the full column specification for this data.
    i Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    -- Column specification --------------------------------------------------------
    Delimiter: "\t"
    chr (2): Measure, Value
    
    i Use `spec()` to retrieve the full column specification for this data.
    i Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    -- Column specification --------------------------------------------------------
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    i Use `spec()` to retrieve the full column specification for this data.
    i Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    -- Column specification --------------------------------------------------------
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 77.85759595869786
    
    i Use `spec()` to retrieve the full column specification for this data.
    i Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    -- Column specification --------------------------------------------------------
    Delimiter: "\t"
    chr (3): status, module, sample
    
    i Use `spec()` to retrieve the full column specification for this data.
    i Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    -- Column specification --------------------------------------------------------
    Delimiter: "\t"
    chr (2): Measure, Value
    
    i Use `spec()` to retrieve the full column specification for this data.
    i Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    -- Column specification --------------------------------------------------------
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    i Use `spec()` to retrieve the full column specification for this data.
    i Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    -- Column specification --------------------------------------------------------
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 80.10708743156657
    
    i Use `spec()` to retrieve the full column specification for this data.
    i Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 12 Columns: 3
    -- Column specification --------------------------------------------------------
    Delimiter: "\t"
    chr (3): status, module, sample
    
    i Use `spec()` to retrieve the full column specification for this data.
    i Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 7 Columns: 2
    -- Column specification --------------------------------------------------------
    Delimiter: "\t"
    chr (2): Measure, Value
    
    i Use `spec()` to retrieve the full column specification for this data.
    i Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 16 Columns: 3
    -- Column specification --------------------------------------------------------
    Delimiter: "\t"
    chr (1): Duplication Level
    dbl (2): Percentage of deduplicated, Percentage of total
    
    i Use `spec()` to retrieve the full column specification for this data.
    i Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 0 Columns: 2
    -- Column specification --------------------------------------------------------
    Delimiter: "\t"
    chr (2): Total Deduplicated Percentage, 81.85424272012848
    
    i Use `spec()` to retrieve the full column specification for this data.
    i Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Warning: `select_()` was deprecated in dplyr 0.7.0.
    i Please use `select()` instead.
    i The deprecated feature was likely used in the fastqcr package.
     Please report the issue at <https://github.com/kassambara/fastqcr/issues>.
    > qc
    # A tibble: 60 x 7
     sample module status tot.seq seq.length pct.gc pct.dup
     * <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
     1 S1 Basic Statistics PASS 50299587 35-76 48 17.2
     2 S1 Per base sequence quality PASS 50299587 35-76 48 17.2
     3 S1 Per tile sequence quality PASS 50299587 35-76 48 17.2
     4 S1 Per sequence quality scores PASS 50299587 35-76 48 17.2
     5 S1 Per base sequence content FAIL 50299587 35-76 48 17.2
     6 S1 Per sequence GC content WARN 50299587 35-76 48 17.2
     7 S1 Per base N content PASS 50299587 35-76 48 17.2
     8 S1 Sequence Length Distribution WARN 50299587 35-76 48 17.2
     9 S1 Sequence Duplication Levels PASS 50299587 35-76 48 17.2
    10 S1 Overrepresented sequences PASS 50299587 35-76 48 17.2
    # ... with 50 more rows
    >
    > # Generates a summary of qc_aggregate
    > summary(qc)
    Warning: `group_by_()` was deprecated in dplyr 0.7.0.
    i Please use `group_by()` instead.
    i See vignette('programming') for more help
    i The deprecated feature was likely used in the fastqcr package.
     Please report the issue at <https://github.com/kassambara/fastqcr/issues>.
    Error in `left_join()`:
    ! `...` must be empty.
    x Problematic argument:
    * fill = "---"
    Backtrace:
     x
     1. +-base::summary(qc)
     2. \-fastqcr:::summary.qc_aggregate(qc)
     3. +-dplyr::left_join(res, failed, by = "module", fill = "---")
     4. \-dplyr:::left_join.data.frame(res, failed, by = "module", fill = "---")
     5. \-rlang::check_dots_empty0(...)
     6. \-rlang::check_dots_empty(call = call)
     7. \-rlang:::action_dots(...)
     8. +-base (local) try_dots(...)
     9. \-rlang (local) action(...)
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64