Last updated on 2020-06-15 08:53:20 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1 | 13.88 | 121.11 | 134.99 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.1 | 11.82 | 93.92 | 105.74 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1 | 164.45 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1 | 157.39 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 1.1 | 40.00 | 128.00 | 168.00 | ERROR | |
| r-patched-linux-x86_64 | 1.1 | 12.43 | 117.49 | 129.92 | ERROR | |
| r-patched-solaris-x86 | 1.1 | 230.80 | ERROR | |||
| r-release-linux-x86_64 | 1.1 | 14.27 | 116.00 | 130.27 | ERROR | |
| r-release-osx-x86_64 | 1.1 | NOTE | ||||
| r-release-windows-ix86+x86_64 | 1.1 | 52.00 | 118.00 | 170.00 | ERROR | |
| r-oldrel-osx-x86_64 | 1.1 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 1.1 | 37.00 | 113.00 | 150.00 | ERROR |
Version: 1.1
Check: examples
Result: ERROR
Running examples in 'metamicrobiomeR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: taxa.compare
> ### Title: Compare taxa relative abundance
> ### Aliases: taxa.compare
> ### Keywords: abundance comparison taxa
>
> ### ** Examples
>
> #Load summary tables of bacterial taxa relative abundance from Bangladesh data
> data(taxtab6)
> tl<-colnames(taxtab6)[grep("k__bacteria.p__fusobacteria",colnames(taxtab6))]
> taxacom.ex<-taxa.compare(taxtab=taxtab6[,c("personid","x.sampleid","bf","age.sample",tl)],
+ propmed.rel="gamlss",comvar="bf",adjustvar="age.sample",
+ longitudinal="yes",p.adjust.method="fdr")
Error: Corrupt `grouped_df` using old (< 0.8.0) format.
i Strip off old grouping with `ungroup()`.
Backtrace:
x
1. +-metamicrobiomeR::taxa.compare(...)
2. | \-base::as.data.frame(taxtab)
3. +-taxtab6[, c("personid", "x.sampleid", "bf", "age.sample", tl)]
4. \-dplyr:::`[.grouped_df`(...)
5. \-dplyr:::group_intersect(x, out)
6. +-generics::intersect(group_vars(x), names(new))
7. +-dplyr::group_vars(x)
8. \-dplyr:::group_vars.data.frame(x)
9. +-generics::setdiff(names(group_data(x)), ".rows")
10. +-dplyr::group_data(x)
11. \-dplyr:::group_data.grouped_df(x)
12. \-dplyr::validate_grouped_df(.data)
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.1
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'my-vignette.Rmd' using rmarkdown
Loading required package: gamlss
Loading required package: splines
Loading required package: gamlss.data
Attaching package: 'gamlss.data'
The following object is masked from 'package:datasets':
sleep
Loading required package: gamlss.dist
Loading required package: MASS
Loading required package: nlme
Loading required package: parallel
********** GAMLSS Version 5.1-6 **********
For more on GAMLSS look at http://www.gamlss.org/
Type gamlssNews() to see new features/changes/bug fixes.
Warning: `funs()` is deprecated as of dplyr 0.8.0.
Please use a list of either functions or lambdas:
# Simple named list:
list(mean = mean, median = median)
# Auto named with `tibble::lst()`:
tibble::lst(mean, median)
# Using lambdas
list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 61-65 (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
Corrupt `grouped_df` using old (< 0.8.0) format.
i Strip off old grouping with `ungroup()`.
--- failed re-building 'my-vignette.Rmd'
SUMMARY: processing the following file failed:
'my-vignette.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.1
Check: examples
Result: ERROR
Running examples in ‘metamicrobiomeR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: taxa.compare
> ### Title: Compare taxa relative abundance
> ### Aliases: taxa.compare
> ### Keywords: abundance comparison taxa
>
> ### ** Examples
>
> #Load summary tables of bacterial taxa relative abundance from Bangladesh data
> data(taxtab6)
> tl<-colnames(taxtab6)[grep("k__bacteria.p__fusobacteria",colnames(taxtab6))]
> taxacom.ex<-taxa.compare(taxtab=taxtab6[,c("personid","x.sampleid","bf","age.sample",tl)],
+ propmed.rel="gamlss",comvar="bf",adjustvar="age.sample",
+ longitudinal="yes",p.adjust.method="fdr")
Error: Corrupt `grouped_df` using old (< 0.8.0) format.
ℹ Strip off old grouping with `ungroup()`.
Backtrace:
█
1. ├─metamicrobiomeR::taxa.compare(...)
2. │ └─base::as.data.frame(taxtab)
3. ├─taxtab6[, c("personid", "x.sampleid", "bf", "age.sample", tl)]
4. └─dplyr:::`[.grouped_df`(...)
5. └─dplyr:::group_intersect(x, out)
6. ├─generics::intersect(group_vars(x), names(new))
7. ├─dplyr::group_vars(x)
8. └─dplyr:::group_vars.data.frame(x)
9. ├─generics::setdiff(names(group_data(x)), ".rows")
10. ├─dplyr::group_data(x)
11. └─dplyr:::group_data.grouped_df(x)
12. └─dplyr::validate_grouped_df(.data)
Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.1
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Loading required package: gamlss
Loading required package: splines
Loading required package: gamlss.data
Attaching package: 'gamlss.data'
The following object is masked from 'package:datasets':
sleep
Loading required package: gamlss.dist
Loading required package: MASS
Loading required package: nlme
Loading required package: parallel
********** GAMLSS Version 5.1-6 **********
For more on GAMLSS look at http://www.gamlss.org/
Type gamlssNews() to see new features/changes/bug fixes.
Warning: `funs()` is deprecated as of dplyr 0.8.0.
Please use a list of either functions or lambdas:
# Simple named list:
list(mean = mean, median = median)
# Auto named with `tibble::lst()`:
tibble::lst(mean, median)
# Using lambdas
list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 61-65 (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
Corrupt `grouped_df` using old (< 0.8.0) format.
ℹ Strip off old grouping with `ungroup()`.
--- failed re-building ‘my-vignette.Rmd’
SUMMARY: processing the following file failed:
‘my-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.1
Check: package dependencies
Result: NOTE
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.1
Check: dependencies in R code
Result: NOTE
Namespaces in Imports field not imported from:
‘RCurl’ ‘foreign’ ‘gplots’ ‘httr’ ‘jsonlite’ ‘knitr’ ‘lmerTest’
‘magrittr’ ‘mgcv’ ‘repmis’ ‘reshape2’ ‘rmarkdown’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 1.1
Check: examples
Result: ERROR
Running examples in ‘metamicrobiomeR-Ex.R’ failed
The error most likely occurred in:
> ### Name: taxa.compare
> ### Title: Compare taxa relative abundance
> ### Aliases: taxa.compare
> ### Keywords: abundance comparison taxa
>
> ### ** Examples
>
> #Load summary tables of bacterial taxa relative abundance from Bangladesh data
> data(taxtab6)
> tl<-colnames(taxtab6)[grep("k__bacteria.p__fusobacteria",colnames(taxtab6))]
> taxacom.ex<-taxa.compare(taxtab=taxtab6[,c("personid","x.sampleid","bf","age.sample",tl)],
+ propmed.rel="gamlss",comvar="bf",adjustvar="age.sample",
+ longitudinal="yes",p.adjust.method="fdr")
Error: Corrupt `grouped_df` using old (< 0.8.0) format.
ℹ Strip off old grouping with `ungroup()`.
Backtrace:
█
1. ├─metamicrobiomeR::taxa.compare(...)
2. │ └─base::as.data.frame(taxtab)
3. ├─taxtab6[, c("personid", "x.sampleid", "bf", "age.sample", tl)]
4. └─dplyr:::`[.grouped_df`(...)
5. └─dplyr:::group_intersect(x, out)
6. ├─generics::intersect(group_vars(x), names(new))
7. ├─dplyr::group_vars(x)
8. └─dplyr:::group_vars.data.frame(x)
9. ├─generics::setdiff(names(group_data(x)), ".rows")
10. ├─dplyr::group_data(x)
11. └─dplyr:::group_data.grouped_df(x)
12. └─dplyr::validate_grouped_df(.data)
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86
Version: 1.1
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Loading required package: gamlss
Loading required package: splines
Loading required package: gamlss.data
Attaching package: 'gamlss.data'
The following object is masked from 'package:datasets':
sleep
Loading required package: gamlss.dist
Loading required package: MASS
Loading required package: nlme
Loading required package: parallel
********** GAMLSS Version 5.1-6 **********
For more on GAMLSS look at http://www.gamlss.org/
Type gamlssNews() to see new features/changes/bug fixes.
Warning: `funs()` is deprecated as of dplyr 0.8.0.
Please use a list of either functions or lambdas:
# Simple named list:
list(mean = mean, median = median)
# Auto named with `tibble::lst()`:
tibble::lst(mean, median)
# Using lambdas
list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 61-65 (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
Corrupt `grouped_df` using old (< 0.8.0) format.
ℹ Strip off old grouping with `ungroup()`.
--- failed re-building ‘my-vignette.Rmd’
SUMMARY: processing the following file failed:
‘my-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.1
Check: examples
Result: ERROR
Running examples in 'metamicrobiomeR-Ex.R' failed
The error most likely occurred in:
> ### Name: taxa.compare
> ### Title: Compare taxa relative abundance
> ### Aliases: taxa.compare
> ### Keywords: abundance comparison taxa
>
> ### ** Examples
>
> #Load summary tables of bacterial taxa relative abundance from Bangladesh data
> data(taxtab6)
> tl<-colnames(taxtab6)[grep("k__bacteria.p__fusobacteria",colnames(taxtab6))]
> taxacom.ex<-taxa.compare(taxtab=taxtab6[,c("personid","x.sampleid","bf","age.sample",tl)],
+ propmed.rel="gamlss",comvar="bf",adjustvar="age.sample",
+ longitudinal="yes",p.adjust.method="fdr")
Error: Corrupt `grouped_df` using old (< 0.8.0) format.
i Strip off old grouping with `ungroup()`.
Backtrace:
x
1. +-metamicrobiomeR::taxa.compare(...)
2. | \-base::as.data.frame(taxtab)
3. +-taxtab6[, c("personid", "x.sampleid", "bf", "age.sample", tl)]
4. \-dplyr:::`[.grouped_df`(...)
5. \-dplyr:::group_intersect(x, out)
6. +-generics::intersect(group_vars(x), names(new))
7. +-dplyr::group_vars(x)
8. \-dplyr:::group_vars.data.frame(x)
9. +-generics::setdiff(names(group_data(x)), ".rows")
10. +-dplyr::group_data(x)
11. \-dplyr:::group_data.grouped_df(x)
12. \-dplyr::validate_grouped_df(.data)
Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.1
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building 'my-vignette.Rmd' using rmarkdown
Loading required package: gamlss
Loading required package: splines
Loading required package: gamlss.data
Attaching package: 'gamlss.data'
The following object is masked from 'package:datasets':
sleep
Loading required package: gamlss.dist
Loading required package: MASS
Loading required package: nlme
Loading required package: parallel
********** GAMLSS Version 5.1-6 **********
For more on GAMLSS look at http://www.gamlss.org/
Type gamlssNews() to see new features/changes/bug fixes.
Warning: `funs()` is deprecated as of dplyr 0.8.0.
Please use a list of either functions or lambdas:
# Simple named list:
list(mean = mean, median = median)
# Auto named with `tibble::lst()`:
tibble::lst(mean, median)
# Using lambdas
list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 61-65 (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
Corrupt `grouped_df` using old (< 0.8.0) format.
i Strip off old grouping with `ungroup()`.
--- failed re-building 'my-vignette.Rmd'
SUMMARY: processing the following file failed:
'my-vignette.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.1
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘my-vignette.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.
Loading required package: gamlss
Loading required package: splines
Loading required package: gamlss.data
Attaching package: 'gamlss.data'
The following object is masked from 'package:datasets':
sleep
Loading required package: gamlss.dist
Loading required package: MASS
Loading required package: nlme
Loading required package: parallel
********** GAMLSS Version 5.1-6 **********
For more on GAMLSS look at http://www.gamlss.org/
Type gamlssNews() to see new features/changes/bug fixes.
Warning: `funs()` is deprecated as of dplyr 0.8.0.
Please use a list of either functions or lambdas:
# Simple named list:
list(mean = mean, median = median)
# Auto named with `tibble::lst()`:
tibble::lst(mean, median)
# Using lambdas
list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 61-65 (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
Corrupt `grouped_df` using old (< 0.8.0) format.
ℹ Strip off old grouping with `ungroup()`.
--- failed re-building ‘my-vignette.Rmd’
SUMMARY: processing the following file failed:
‘my-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-solaris-x86