Last updated on 2020-06-15 08:53:17 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.5.4 | 7.08 | 68.94 | 76.02 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.5.4 | 5.89 | 52.12 | 58.01 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.5.4 | 98.03 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.5.4 | 87.89 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 0.5.4 | 35.00 | 130.00 | 165.00 | ERROR | |
| r-patched-linux-x86_64 | 0.5.4 | 7.27 | 66.92 | 74.19 | ERROR | |
| r-patched-solaris-x86 | 0.5.4 | 129.10 | ERROR | |||
| r-release-linux-x86_64 | 0.5.4 | 5.75 | 66.11 | 71.86 | ERROR | |
| r-release-osx-x86_64 | 0.5.4 | OK | ||||
| r-release-windows-ix86+x86_64 | 0.5.4 | 40.00 | 82.00 | 122.00 | ERROR | |
| r-oldrel-osx-x86_64 | 0.5.4 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 0.5.4 | 23.00 | 100.00 | 123.00 | ERROR |
Version: 0.5.4
Check: examples
Result: ERROR
Running examples in 'IncucyteDRC-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculateEC50
> ### Title: calculateEC50
> ### Aliases: calculateEC50
>
> ### ** Examples
>
> pm_file <- system.file(file='extdata/example.PlateMap', package='IncucyteDRC')
> test_pm <- importPlatemapXML(pm_file)
Importing platemap xml from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/IncucyteDRC/extdata/example.PlateMap
Plate map import successful!
> data_file <- system.file(file='extdata/example_data.txt', package='IncucyteDRC')
> test_data <- importIncucyteData(data_file, metric='pc')
Getting pc data for plate example_data.txt from:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/IncucyteDRC/extdata/example_data.txt
>
> test_list <- splitIncucyteDRCPlateData(test_pm, test_data, group_columns='growthcondition')
>
> print(test_list)
## This is an IncucyteDRCSetList S3 object containing 4 IncucyteDRCSet objects
## Access using standard list notation ie my_list[[1]]
## Try lapply(my_list, print) to see more information on each object>
> test_idrc_set <- fitGrowthCurvesGrouped(test_list[[2]])
> test_idrc_set <- fitGrowthCurvesIndividual(test_idrc_set)
> test_idrc_set <- calculateDRCData(test_idrc_set, cut_time=100)
Using cut time provided to function
> test_idrc_set <- fitDoseResponseCurve(test_idrc_set)
Error: Problem with `mutate()` input `idx`.
x could not find function "row_number"
i Input `idx` is `row_number()`.
i The error occured in group 1: sampleid = "PDD00017273", conc = 0.3703704.
Backtrace:
x
1. \-IncucyteDRC::fitDoseResponseCurve(test_idrc_set)
2. \-IncucyteDRC::exportDRCDataToDataFrame(idrc_set, include_control)
3. \-`%>%`(...)
4. +-base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
5. \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
6. \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
7. \-IncucyteDRC:::`_fseq`(`_lhs`)
8. \-magrittr::freduce(value, `_function_list`)
9. \-function_list[[i]](value)
10. +-dplyr::mutate(., idx = row_number())
11. \-dplyr:::mutate.data.frame(., idx = row_number())
12. \-dplyr:::mutate_cols(.data, ...)
<parent: error/simpleError>
Backtrace:
x
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.5.4
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'IncucyteZoomExport.Rmd' using rmarkdown
--- finished re-building 'IncucyteZoomExport.Rmd'
--- re-building 'Overview.Rmd' using rmarkdown
Warning: `group_indices_()` is deprecated as of dplyr 0.7.0.
Please use `group_indices()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: The `...` argument of `group_keys()` is deprecated as of dplyr 1.0.0.
Please `group_by()` first
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: `select_()` is deprecated as of dplyr 0.7.0.
Please use `select()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Importing platemap xml from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/IncucyteDRC/extdata/example2.PlateMap
Plate map import successful!
Getting pc data for plate example_data2.txt from:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/IncucyteDRC/extdata/example_data2.txt
Using cut time provided to function
Quitting from lines 94-99 (Overview.Rmd)
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
Problem with `mutate()` input `idx`.
x could not find function "row_number"
i Input `idx` is `row_number()`.
i The error occured in group 1: sampleid = "PDD00014673", conc = 0.01371742.
--- failed re-building 'Overview.Rmd'
SUMMARY: processing the following file failed:
'Overview.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.5.4
Check: examples
Result: ERROR
Running examples in ‘IncucyteDRC-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculateEC50
> ### Title: calculateEC50
> ### Aliases: calculateEC50
>
> ### ** Examples
>
> pm_file <- system.file(file='extdata/example.PlateMap', package='IncucyteDRC')
> test_pm <- importPlatemapXML(pm_file)
Importing platemap xml from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/IncucyteDRC/extdata/example.PlateMap
Plate map import successful!
> data_file <- system.file(file='extdata/example_data.txt', package='IncucyteDRC')
> test_data <- importIncucyteData(data_file, metric='pc')
Getting pc data for plate example_data.txt from:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/IncucyteDRC/extdata/example_data.txt
>
> test_list <- splitIncucyteDRCPlateData(test_pm, test_data, group_columns='growthcondition')
>
> print(test_list)
## This is an IncucyteDRCSetList S3 object containing 4 IncucyteDRCSet objects
## Access using standard list notation ie my_list[[1]]
## Try lapply(my_list, print) to see more information on each object>
> test_idrc_set <- fitGrowthCurvesGrouped(test_list[[2]])
> test_idrc_set <- fitGrowthCurvesIndividual(test_idrc_set)
> test_idrc_set <- calculateDRCData(test_idrc_set, cut_time=100)
Using cut time provided to function
> test_idrc_set <- fitDoseResponseCurve(test_idrc_set)
Error: Problem with `mutate()` input `idx`.
✖ could not find function "row_number"
ℹ Input `idx` is `row_number()`.
ℹ The error occured in group 1: sampleid = "PDD00017273", conc = 0.3703704.
Backtrace:
█
1. └─IncucyteDRC::fitDoseResponseCurve(test_idrc_set)
2. └─IncucyteDRC::exportDRCDataToDataFrame(idrc_set, include_control)
3. └─`%>%`(...)
4. ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
5. └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
6. └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
7. └─IncucyteDRC:::`_fseq`(`_lhs`)
8. └─magrittr::freduce(value, `_function_list`)
9. └─function_list[[i]](value)
10. ├─dplyr::mutate(., idx = row_number())
11. └─dplyr:::mutate.data.frame(., idx = row_number())
12. └─dplyr:::mutate_cols(.data, ...)
<parent: error/simpleError>
Backtrace:
█
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.5.4
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘IncucyteZoomExport.Rmd’ using rmarkdown
--- finished re-building ‘IncucyteZoomExport.Rmd’
--- re-building ‘Overview.Rmd’ using rmarkdown
Warning: `group_indices_()` is deprecated as of dplyr 0.7.0.
Please use `group_indices()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: The `...` argument of `group_keys()` is deprecated as of dplyr 1.0.0.
Please `group_by()` first
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: `select_()` is deprecated as of dplyr 0.7.0.
Please use `select()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Importing platemap xml from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/IncucyteDRC/extdata/example2.PlateMap
Plate map import successful!
Getting pc data for plate example_data2.txt from:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/IncucyteDRC/extdata/example_data2.txt
Using cut time provided to function
Quitting from lines 94-99 (Overview.Rmd)
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
Problem with `mutate()` input `idx`.
✖ could not find function "row_number"
ℹ Input `idx` is `row_number()`.
ℹ The error occured in group 1: sampleid = "PDD00014673", conc = 0.01371742.
--- failed re-building ‘Overview.Rmd’
SUMMARY: processing the following file failed:
‘Overview.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.5.4
Check: examples
Result: ERROR
Running examples in ‘IncucyteDRC-Ex.R’ failed
The error most likely occurred in:
> ### Name: calculateEC50
> ### Title: calculateEC50
> ### Aliases: calculateEC50
>
> ### ** Examples
>
> pm_file <- system.file(file='extdata/example.PlateMap', package='IncucyteDRC')
> test_pm <- importPlatemapXML(pm_file)
Importing platemap xml from /data/gannet/ripley/R/packages/tests-clang/IncucyteDRC.Rcheck/IncucyteDRC/extdata/example.PlateMap
Plate map import successful!
> data_file <- system.file(file='extdata/example_data.txt', package='IncucyteDRC')
> test_data <- importIncucyteData(data_file, metric='pc')
Getting pc data for plate example_data.txt from:
/data/gannet/ripley/R/packages/tests-clang/IncucyteDRC.Rcheck/IncucyteDRC/extdata/example_data.txt
>
> test_list <- splitIncucyteDRCPlateData(test_pm, test_data, group_columns='growthcondition')
>
> print(test_list)
## This is an IncucyteDRCSetList S3 object containing 4 IncucyteDRCSet objects
## Access using standard list notation ie my_list[[1]]
## Try lapply(my_list, print) to see more information on each object>
> test_idrc_set <- fitGrowthCurvesGrouped(test_list[[2]])
> test_idrc_set <- fitGrowthCurvesIndividual(test_idrc_set)
> test_idrc_set <- calculateDRCData(test_idrc_set, cut_time=100)
Using cut time provided to function
> test_idrc_set <- fitDoseResponseCurve(test_idrc_set)
Error: Problem with `mutate()` input `idx`.
✖ could not find function "row_number"
ℹ Input `idx` is `row_number()`.
ℹ The error occured in group 1: sampleid = "PDD00017273", conc = 0.3703704.
Backtrace:
█
1. └─IncucyteDRC::fitDoseResponseCurve(test_idrc_set)
2. └─IncucyteDRC::exportDRCDataToDataFrame(idrc_set, include_control)
3. └─`%>%`(...)
4. ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
5. └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
6. └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
7. └─IncucyteDRC:::`_fseq`(`_lhs`)
8. └─magrittr::freduce(value, `_function_list`)
9. └─function_list[[i]](value)
10. ├─dplyr::mutate(., idx = row_number())
11. └─dplyr:::mutate.data.frame(., idx = row_number())
12. └─dplyr:::mutate_cols(.data, ...)
<parent: error/simpleError>
Backtrace:
█
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.5.4
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘IncucyteZoomExport.Rmd’ using rmarkdown
--- finished re-building ‘IncucyteZoomExport.Rmd’
--- re-building ‘Overview.Rmd’ using rmarkdown
Warning: `group_indices_()` is deprecated as of dplyr 0.7.0.
Please use `group_indices()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: The `...` argument of `group_keys()` is deprecated as of dplyr 1.0.0.
Please `group_by()` first
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: `select_()` is deprecated as of dplyr 0.7.0.
Please use `select()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Importing platemap xml from /data/gannet/ripley/R/packages/tests-clang/IncucyteDRC.Rcheck/IncucyteDRC/extdata/example2.PlateMap
Plate map import successful!
Getting pc data for plate example_data2.txt from:
/data/gannet/ripley/R/packages/tests-clang/IncucyteDRC.Rcheck/IncucyteDRC/extdata/example_data2.txt
Using cut time provided to function
Quitting from lines 94-99 (Overview.Rmd)
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
Problem with `mutate()` input `idx`.
✖ could not find function "row_number"
ℹ Input `idx` is `row_number()`.
ℹ The error occured in group 1: sampleid = "PDD00014673", conc = 0.01371742.
--- failed re-building ‘Overview.Rmd’
SUMMARY: processing the following file failed:
‘Overview.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.5.4
Check: examples
Result: ERROR
Running examples in ‘IncucyteDRC-Ex.R’ failed
The error most likely occurred in:
> ### Name: calculateEC50
> ### Title: calculateEC50
> ### Aliases: calculateEC50
>
> ### ** Examples
>
> pm_file <- system.file(file='extdata/example.PlateMap', package='IncucyteDRC')
> test_pm <- importPlatemapXML(pm_file)
Importing platemap xml from /data/gannet/ripley/R/packages/tests-devel/IncucyteDRC.Rcheck/IncucyteDRC/extdata/example.PlateMap
Plate map import successful!
> data_file <- system.file(file='extdata/example_data.txt', package='IncucyteDRC')
> test_data <- importIncucyteData(data_file, metric='pc')
Getting pc data for plate example_data.txt from:
/data/gannet/ripley/R/packages/tests-devel/IncucyteDRC.Rcheck/IncucyteDRC/extdata/example_data.txt
>
> test_list <- splitIncucyteDRCPlateData(test_pm, test_data, group_columns='growthcondition')
>
> print(test_list)
## This is an IncucyteDRCSetList S3 object containing 4 IncucyteDRCSet objects
## Access using standard list notation ie my_list[[1]]
## Try lapply(my_list, print) to see more information on each object>
> test_idrc_set <- fitGrowthCurvesGrouped(test_list[[2]])
> test_idrc_set <- fitGrowthCurvesIndividual(test_idrc_set)
> test_idrc_set <- calculateDRCData(test_idrc_set, cut_time=100)
Using cut time provided to function
> test_idrc_set <- fitDoseResponseCurve(test_idrc_set)
Error: Problem with `mutate()` input `idx`.
✖ could not find function "row_number"
ℹ Input `idx` is `row_number()`.
ℹ The error occured in group 1: sampleid = "PDD00017273", conc = 0.3703704.
Backtrace:
█
1. └─IncucyteDRC::fitDoseResponseCurve(test_idrc_set)
2. └─IncucyteDRC::exportDRCDataToDataFrame(idrc_set, include_control)
3. └─`%>%`(...)
4. ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
5. └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
6. └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
7. └─IncucyteDRC:::`_fseq`(`_lhs`)
8. └─magrittr::freduce(value, `_function_list`)
9. └─function_list[[i]](value)
10. ├─dplyr::mutate(., idx = row_number())
11. └─dplyr:::mutate.data.frame(., idx = row_number())
12. └─dplyr:::mutate_cols(.data, ...)
<parent: error/simpleError>
Backtrace:
█
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.5.4
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘IncucyteZoomExport.Rmd’ using rmarkdown
--- finished re-building ‘IncucyteZoomExport.Rmd’
--- re-building ‘Overview.Rmd’ using rmarkdown
Warning: `group_indices_()` is deprecated as of dplyr 0.7.0.
Please use `group_indices()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: The `...` argument of `group_keys()` is deprecated as of dplyr 1.0.0.
Please `group_by()` first
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: `select_()` is deprecated as of dplyr 0.7.0.
Please use `select()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Importing platemap xml from /data/gannet/ripley/R/packages/tests-devel/IncucyteDRC.Rcheck/IncucyteDRC/extdata/example2.PlateMap
Plate map import successful!
Getting pc data for plate example_data2.txt from:
/data/gannet/ripley/R/packages/tests-devel/IncucyteDRC.Rcheck/IncucyteDRC/extdata/example_data2.txt
Using cut time provided to function
Quitting from lines 94-99 (Overview.Rmd)
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
Problem with `mutate()` input `idx`.
✖ could not find function "row_number"
ℹ Input `idx` is `row_number()`.
ℹ The error occured in group 1: sampleid = "PDD00014673", conc = 0.01371742.
--- failed re-building ‘Overview.Rmd’
SUMMARY: processing the following file failed:
‘Overview.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.5.4
Check: examples
Result: ERROR
Running examples in 'IncucyteDRC-Ex.R' failed
The error most likely occurred in:
> ### Name: calculateEC50
> ### Title: calculateEC50
> ### Aliases: calculateEC50
>
> ### ** Examples
>
> pm_file <- system.file(file='extdata/example.PlateMap', package='IncucyteDRC')
> test_pm <- importPlatemapXML(pm_file)
Importing platemap xml from D:/temp/RtmpgtTs5A/RLIBS_1f7142378463d/IncucyteDRC/extdata/example.PlateMap
Plate map import successful!
> data_file <- system.file(file='extdata/example_data.txt', package='IncucyteDRC')
> test_data <- importIncucyteData(data_file, metric='pc')
Getting pc data for plate example_data.txt from:
D:/temp/RtmpgtTs5A/RLIBS_1f7142378463d/IncucyteDRC/extdata/example_data.txt
>
> test_list <- splitIncucyteDRCPlateData(test_pm, test_data, group_columns='growthcondition')
>
> print(test_list)
## This is an IncucyteDRCSetList S3 object containing 4 IncucyteDRCSet objects
## Access using standard list notation ie my_list[[1]]
## Try lapply(my_list, print) to see more information on each object>
> test_idrc_set <- fitGrowthCurvesGrouped(test_list[[2]])
> test_idrc_set <- fitGrowthCurvesIndividual(test_idrc_set)
> test_idrc_set <- calculateDRCData(test_idrc_set, cut_time=100)
Using cut time provided to function
> test_idrc_set <- fitDoseResponseCurve(test_idrc_set)
Error: Problem with `mutate()` input `idx`.
x could not find function "row_number"
i Input `idx` is `row_number()`.
i The error occured in group 1: sampleid = "PDD00017273", conc = 0.3703704.
Backtrace:
x
1. \-IncucyteDRC::fitDoseResponseCurve(test_idrc_set)
2. \-IncucyteDRC::exportDRCDataToDataFrame(idrc_set, include_control)
3. \-`%>%`(...)
4. +-base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
5. \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
6. \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
7. \-IncucyteDRC:::`_fseq`(`_lhs`)
8. \-magrittr::freduce(value, `_function_list`)
9. \-function_list[[i]](value)
10. +-dplyr::mutate(., idx = row_number())
11. \-dplyr:::mutate.data.frame(., idx = row_number())
12. \-dplyr:::mutate_cols(.data, ...)
<parent: error/simpleError>
Backtrace:
x
Execution halted
Flavor: r-devel-windows-ix86+x86_64
Version: 0.5.4
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building 'IncucyteZoomExport.Rmd' using rmarkdown
--- finished re-building 'IncucyteZoomExport.Rmd'
--- re-building 'Overview.Rmd' using rmarkdown
Warning: `group_indices_()` is deprecated as of dplyr 0.7.0.
Please use `group_indices()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: The `...` argument of `group_keys()` is deprecated as of dplyr 1.0.0.
Please `group_by()` first
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: `select_()` is deprecated as of dplyr 0.7.0.
Please use `select()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Importing platemap xml from D:/temp/RtmpgtTs5A/RLIBS_1f7142378463d/IncucyteDRC/extdata/example2.PlateMap
Plate map import successful!
Getting pc data for plate example_data2.txt from:
D:/temp/RtmpgtTs5A/RLIBS_1f7142378463d/IncucyteDRC/extdata/example_data2.txt
Using cut time provided to function
Quitting from lines 94-99 (Overview.Rmd)
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
Problem with `mutate()` input `idx`.
x could not find function "row_number"
i Input `idx` is `row_number()`.
i The error occured in group 1: sampleid = "PDD00014673", conc = 0.01371742.
--- failed re-building 'Overview.Rmd'
SUMMARY: processing the following file failed:
'Overview.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-ix86+x86_64
Version: 0.5.4
Check: examples
Result: ERROR
Running examples in ‘IncucyteDRC-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculateEC50
> ### Title: calculateEC50
> ### Aliases: calculateEC50
>
> ### ** Examples
>
> pm_file <- system.file(file='extdata/example.PlateMap', package='IncucyteDRC')
> test_pm <- importPlatemapXML(pm_file)
Importing platemap xml from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/IncucyteDRC/extdata/example.PlateMap
Plate map import successful!
> data_file <- system.file(file='extdata/example_data.txt', package='IncucyteDRC')
> test_data <- importIncucyteData(data_file, metric='pc')
Getting pc data for plate example_data.txt from:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/IncucyteDRC/extdata/example_data.txt
>
> test_list <- splitIncucyteDRCPlateData(test_pm, test_data, group_columns='growthcondition')
>
> print(test_list)
## This is an IncucyteDRCSetList S3 object containing 4 IncucyteDRCSet objects
## Access using standard list notation ie my_list[[1]]
## Try lapply(my_list, print) to see more information on each object>
> test_idrc_set <- fitGrowthCurvesGrouped(test_list[[2]])
> test_idrc_set <- fitGrowthCurvesIndividual(test_idrc_set)
> test_idrc_set <- calculateDRCData(test_idrc_set, cut_time=100)
Using cut time provided to function
> test_idrc_set <- fitDoseResponseCurve(test_idrc_set)
Error: Problem with `mutate()` input `idx`.
✖ could not find function "row_number"
ℹ Input `idx` is `row_number()`.
ℹ The error occured in group 1: sampleid = "PDD00017273", conc = 0.3703704.
Backtrace:
█
1. └─IncucyteDRC::fitDoseResponseCurve(test_idrc_set)
2. └─IncucyteDRC::exportDRCDataToDataFrame(idrc_set, include_control)
3. └─`%>%`(...)
4. ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
5. └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
6. └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
7. └─IncucyteDRC:::`_fseq`(`_lhs`)
8. └─magrittr::freduce(value, `_function_list`)
9. └─function_list[[i]](value)
10. ├─dplyr::mutate(., idx = row_number())
11. └─dplyr:::mutate.data.frame(., idx = row_number())
12. └─dplyr:::mutate_cols(.data, ...)
<parent: error/simpleError>
Backtrace:
█
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.5.4
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘IncucyteZoomExport.Rmd’ using rmarkdown
--- finished re-building ‘IncucyteZoomExport.Rmd’
--- re-building ‘Overview.Rmd’ using rmarkdown
Warning: `group_indices_()` is deprecated as of dplyr 0.7.0.
Please use `group_indices()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: The `...` argument of `group_keys()` is deprecated as of dplyr 1.0.0.
Please `group_by()` first
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: `select_()` is deprecated as of dplyr 0.7.0.
Please use `select()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Importing platemap xml from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/IncucyteDRC/extdata/example2.PlateMap
Plate map import successful!
Getting pc data for plate example_data2.txt from:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/IncucyteDRC/extdata/example_data2.txt
Using cut time provided to function
Quitting from lines 94-99 (Overview.Rmd)
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
Problem with `mutate()` input `idx`.
✖ could not find function "row_number"
ℹ Input `idx` is `row_number()`.
ℹ The error occured in group 1: sampleid = "PDD00014673", conc = 0.01371742.
--- failed re-building ‘Overview.Rmd’
SUMMARY: processing the following file failed:
‘Overview.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.5.4
Check: examples
Result: ERROR
Running examples in ‘IncucyteDRC-Ex.R’ failed
The error most likely occurred in:
> ### Name: calculateEC50
> ### Title: calculateEC50
> ### Aliases: calculateEC50
>
> ### ** Examples
>
> pm_file <- system.file(file='extdata/example.PlateMap', package='IncucyteDRC')
> test_pm <- importPlatemapXML(pm_file)
Importing platemap xml from /home/ripley/R/Lib32/IncucyteDRC/extdata/example.PlateMap
Plate map import successful!
> data_file <- system.file(file='extdata/example_data.txt', package='IncucyteDRC')
> test_data <- importIncucyteData(data_file, metric='pc')
Getting pc data for plate example_data.txt from:
/home/ripley/R/Lib32/IncucyteDRC/extdata/example_data.txt
>
> test_list <- splitIncucyteDRCPlateData(test_pm, test_data, group_columns='growthcondition')
>
> print(test_list)
## This is an IncucyteDRCSetList S3 object containing 4 IncucyteDRCSet objects
## Access using standard list notation ie my_list[[1]]
## Try lapply(my_list, print) to see more information on each object>
> test_idrc_set <- fitGrowthCurvesGrouped(test_list[[2]])
> test_idrc_set <- fitGrowthCurvesIndividual(test_idrc_set)
> test_idrc_set <- calculateDRCData(test_idrc_set, cut_time=100)
Using cut time provided to function
> test_idrc_set <- fitDoseResponseCurve(test_idrc_set)
Error: Problem with `mutate()` input `idx`.
✖ could not find function "row_number"
ℹ Input `idx` is `row_number()`.
ℹ The error occured in group 1: sampleid = "PDD00017273", conc = 0.3703704.
Backtrace:
█
1. └─IncucyteDRC::fitDoseResponseCurve(test_idrc_set)
2. └─IncucyteDRC::exportDRCDataToDataFrame(idrc_set, include_control)
3. └─`%>%`(...)
4. ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
5. └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
6. └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
7. └─IncucyteDRC:::`_fseq`(`_lhs`)
8. └─magrittr::freduce(value, `_function_list`)
9. └─function_list[[i]](value)
10. ├─dplyr::mutate(., idx = row_number())
11. └─dplyr:::mutate.data.frame(., idx = row_number())
12. └─dplyr:::mutate_cols(.data, ...)
<parent: error/simpleError>
Backtrace:
█
Execution halted
Flavor: r-patched-solaris-x86
Version: 0.5.4
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘IncucyteZoomExport.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘IncucyteZoomExport.Rmd’
--- re-building ‘Overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: `group_indices_()` is deprecated as of dplyr 0.7.0.
Please use `group_indices()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: The `...` argument of `group_keys()` is deprecated as of dplyr 1.0.0.
Please `group_by()` first
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: `select_()` is deprecated as of dplyr 0.7.0.
Please use `select()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Importing platemap xml from /home/ripley/R/Lib32/IncucyteDRC/extdata/example2.PlateMap
Plate map import successful!
Getting pc data for plate example_data2.txt from:
/home/ripley/R/Lib32/IncucyteDRC/extdata/example_data2.txt
Using cut time provided to function
Quitting from lines 94-99 (Overview.Rmd)
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
Problem with `mutate()` input `idx`.
✖ could not find function "row_number"
ℹ Input `idx` is `row_number()`.
ℹ The error occured in group 1: sampleid = "PDD00014673", conc = 0.01371742.
--- failed re-building ‘Overview.Rmd’
SUMMARY: processing the following file failed:
‘Overview.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-solaris-x86
Version: 0.5.4
Check: examples
Result: ERROR
Running examples in ‘IncucyteDRC-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculateEC50
> ### Title: calculateEC50
> ### Aliases: calculateEC50
>
> ### ** Examples
>
> pm_file <- system.file(file='extdata/example.PlateMap', package='IncucyteDRC')
> test_pm <- importPlatemapXML(pm_file)
Importing platemap xml from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/IncucyteDRC/extdata/example.PlateMap
Plate map import successful!
> data_file <- system.file(file='extdata/example_data.txt', package='IncucyteDRC')
> test_data <- importIncucyteData(data_file, metric='pc')
Getting pc data for plate example_data.txt from:
/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/IncucyteDRC/extdata/example_data.txt
>
> test_list <- splitIncucyteDRCPlateData(test_pm, test_data, group_columns='growthcondition')
>
> print(test_list)
## This is an IncucyteDRCSetList S3 object containing 4 IncucyteDRCSet objects
## Access using standard list notation ie my_list[[1]]
## Try lapply(my_list, print) to see more information on each object>
> test_idrc_set <- fitGrowthCurvesGrouped(test_list[[2]])
> test_idrc_set <- fitGrowthCurvesIndividual(test_idrc_set)
> test_idrc_set <- calculateDRCData(test_idrc_set, cut_time=100)
Using cut time provided to function
> test_idrc_set <- fitDoseResponseCurve(test_idrc_set)
Error: Problem with `mutate()` input `idx`.
✖ could not find function "row_number"
ℹ Input `idx` is `row_number()`.
ℹ The error occured in group 1: sampleid = "PDD00017273", conc = 0.3703704.
Backtrace:
█
1. └─IncucyteDRC::fitDoseResponseCurve(test_idrc_set)
2. └─IncucyteDRC::exportDRCDataToDataFrame(idrc_set, include_control)
3. └─`%>%`(...)
4. ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
5. └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
6. └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
7. └─IncucyteDRC:::`_fseq`(`_lhs`)
8. └─magrittr::freduce(value, `_function_list`)
9. └─function_list[[i]](value)
10. ├─dplyr::mutate(., idx = row_number())
11. └─dplyr:::mutate.data.frame(., idx = row_number())
12. └─dplyr:::mutate_cols(.data, ...)
<parent: error/simpleError>
Backtrace:
█
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.5.4
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘IncucyteZoomExport.Rmd’ using rmarkdown
--- finished re-building ‘IncucyteZoomExport.Rmd’
--- re-building ‘Overview.Rmd’ using rmarkdown
Warning: `group_indices_()` is deprecated as of dplyr 0.7.0.
Please use `group_indices()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: The `...` argument of `group_keys()` is deprecated as of dplyr 1.0.0.
Please `group_by()` first
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: `select_()` is deprecated as of dplyr 0.7.0.
Please use `select()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Importing platemap xml from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/IncucyteDRC/extdata/example2.PlateMap
Plate map import successful!
Getting pc data for plate example_data2.txt from:
/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/IncucyteDRC/extdata/example_data2.txt
Using cut time provided to function
Quitting from lines 94-99 (Overview.Rmd)
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
Problem with `mutate()` input `idx`.
✖ could not find function "row_number"
ℹ Input `idx` is `row_number()`.
ℹ The error occured in group 1: sampleid = "PDD00014673", conc = 0.01371742.
--- failed re-building ‘Overview.Rmd’
SUMMARY: processing the following file failed:
‘Overview.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.5.4
Check: examples
Result: ERROR
Running examples in 'IncucyteDRC-Ex.R' failed
The error most likely occurred in:
> ### Name: calculateEC50
> ### Title: calculateEC50
> ### Aliases: calculateEC50
>
> ### ** Examples
>
> pm_file <- system.file(file='extdata/example.PlateMap', package='IncucyteDRC')
> test_pm <- importPlatemapXML(pm_file)
Importing platemap xml from D:/temp/RtmpWqiD0n/RLIBS_bc687f763a8d/IncucyteDRC/extdata/example.PlateMap
Plate map import successful!
> data_file <- system.file(file='extdata/example_data.txt', package='IncucyteDRC')
> test_data <- importIncucyteData(data_file, metric='pc')
Getting pc data for plate example_data.txt from:
D:/temp/RtmpWqiD0n/RLIBS_bc687f763a8d/IncucyteDRC/extdata/example_data.txt
>
> test_list <- splitIncucyteDRCPlateData(test_pm, test_data, group_columns='growthcondition')
>
> print(test_list)
## This is an IncucyteDRCSetList S3 object containing 4 IncucyteDRCSet objects
## Access using standard list notation ie my_list[[1]]
## Try lapply(my_list, print) to see more information on each object>
> test_idrc_set <- fitGrowthCurvesGrouped(test_list[[2]])
> test_idrc_set <- fitGrowthCurvesIndividual(test_idrc_set)
> test_idrc_set <- calculateDRCData(test_idrc_set, cut_time=100)
Using cut time provided to function
> test_idrc_set <- fitDoseResponseCurve(test_idrc_set)
Error: Problem with `mutate()` input `idx`.
x could not find function "row_number"
i Input `idx` is `row_number()`.
i The error occured in group 1: sampleid = "PDD00017273", conc = 0.3703704.
Backtrace:
x
1. \-IncucyteDRC::fitDoseResponseCurve(test_idrc_set)
2. \-IncucyteDRC::exportDRCDataToDataFrame(idrc_set, include_control)
3. \-`%>%`(...)
4. +-base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
5. \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
6. \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
7. \-IncucyteDRC:::`_fseq`(`_lhs`)
8. \-magrittr::freduce(value, `_function_list`)
9. \-function_list[[i]](value)
10. +-dplyr::mutate(., idx = row_number())
11. \-dplyr:::mutate.data.frame(., idx = row_number())
12. \-dplyr:::mutate_cols(.data, ...)
<parent: error/simpleError>
Backtrace:
x
Execution halted
Flavor: r-release-windows-ix86+x86_64
Version: 0.5.4
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building 'IncucyteZoomExport.Rmd' using rmarkdown
--- finished re-building 'IncucyteZoomExport.Rmd'
--- re-building 'Overview.Rmd' using rmarkdown
Warning: `group_indices_()` is deprecated as of dplyr 0.7.0.
Please use `group_indices()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: The `...` argument of `group_keys()` is deprecated as of dplyr 1.0.0.
Please `group_by()` first
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: `select_()` is deprecated as of dplyr 0.7.0.
Please use `select()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Importing platemap xml from D:/temp/RtmpWqiD0n/RLIBS_bc687f763a8d/IncucyteDRC/extdata/example2.PlateMap
Plate map import successful!
Getting pc data for plate example_data2.txt from:
D:/temp/RtmpWqiD0n/RLIBS_bc687f763a8d/IncucyteDRC/extdata/example_data2.txt
Using cut time provided to function
Quitting from lines 94-99 (Overview.Rmd)
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
Problem with `mutate()` input `idx`.
x could not find function "row_number"
i Input `idx` is `row_number()`.
i The error occured in group 1: sampleid = "PDD00014673", conc = 0.01371742.
--- failed re-building 'Overview.Rmd'
SUMMARY: processing the following file failed:
'Overview.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-windows-ix86+x86_64
Version: 0.5.4
Check: examples
Result: ERROR
Running examples in 'IncucyteDRC-Ex.R' failed
The error most likely occurred in:
> ### Name: calculateEC50
> ### Title: calculateEC50
> ### Aliases: calculateEC50
>
> ### ** Examples
>
> pm_file <- system.file(file='extdata/example.PlateMap', package='IncucyteDRC')
> test_pm <- importPlatemapXML(pm_file)
Importing platemap xml from D:/temp/RtmpuSf9Ki/RLIBS_13c281bdf7916/IncucyteDRC/extdata/example.PlateMap
Plate map import successful!
> data_file <- system.file(file='extdata/example_data.txt', package='IncucyteDRC')
> test_data <- importIncucyteData(data_file, metric='pc')
Getting pc data for plate example_data.txt from:
D:/temp/RtmpuSf9Ki/RLIBS_13c281bdf7916/IncucyteDRC/extdata/example_data.txt
>
> test_list <- splitIncucyteDRCPlateData(test_pm, test_data, group_columns='growthcondition')
>
> print(test_list)
## This is an IncucyteDRCSetList S3 object containing 4 IncucyteDRCSet objects
## Access using standard list notation ie my_list[[1]]
## Try lapply(my_list, print) to see more information on each object>
> test_idrc_set <- fitGrowthCurvesGrouped(test_list[[2]])
> test_idrc_set <- fitGrowthCurvesIndividual(test_idrc_set)
> test_idrc_set <- calculateDRCData(test_idrc_set, cut_time=100)
Using cut time provided to function
> test_idrc_set <- fitDoseResponseCurve(test_idrc_set)
Error: Problem with `mutate()` input `idx`.
x could not find function "row_number"
i Input `idx` is `row_number()`.
i The error occured in group 1: sampleid = "PDD00017273", conc = 0.3703704.
Backtrace:
x
1. \-IncucyteDRC::fitDoseResponseCurve(test_idrc_set)
2. \-IncucyteDRC::exportDRCDataToDataFrame(idrc_set, include_control)
3. \-`%>%`(...)
4. +-base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
5. \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
6. \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
7. \-IncucyteDRC:::`_fseq`(`_lhs`)
8. \-magrittr::freduce(value, `_function_list`)
9. \-function_list[[i]](value)
10. +-dplyr::mutate(., idx = row_number())
11. \-dplyr:::mutate.data.frame(., idx = row_number())
12. \-dplyr:::mutate_cols(.data, ...)
<parent: error/simpleError>
Backtrace:
x
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64
Version: 0.5.4
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building 'IncucyteZoomExport.Rmd' using rmarkdown
--- finished re-building 'IncucyteZoomExport.Rmd'
--- re-building 'Overview.Rmd' using rmarkdown
Warning: `group_indices_()` is deprecated as of dplyr 0.7.0.
Please use `group_indices()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: The `...` argument of `group_keys()` is deprecated as of dplyr 1.0.0.
Please `group_by()` first
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: `select_()` is deprecated as of dplyr 0.7.0.
Please use `select()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Importing platemap xml from D:/temp/RtmpuSf9Ki/RLIBS_13c281bdf7916/IncucyteDRC/extdata/example2.PlateMap
Plate map import successful!
Getting pc data for plate example_data2.txt from:
D:/temp/RtmpuSf9Ki/RLIBS_13c281bdf7916/IncucyteDRC/extdata/example_data2.txt
Using cut time provided to function
Quitting from lines 94-99 (Overview.Rmd)
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
Problem with `mutate()` input `idx`.
x could not find function "row_number"
i Input `idx` is `row_number()`.
i The error occured in group 1: sampleid = "PDD00014673", conc = 0.01371742.
--- failed re-building 'Overview.Rmd'
SUMMARY: processing the following file failed:
'Overview.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64