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 |
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