Last updated on 2021-08-17 16:50:06 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.2 | 22.20 | 214.52 | 236.72 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.2 | 18.39 | 155.95 | 174.34 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.2 | 287.45 | WARN | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.2 | 254.46 | WARN | |||
| r-devel-windows-x86_64-gcc10-UCRT | 1.0.2 | OK | ||||
| r-patched-linux-x86_64 | 1.0.2 | 17.65 | 197.07 | 214.72 | OK | |
| r-patched-solaris-x86 | 1.0.2 | 374.60 | WARN | |||
| r-release-linux-x86_64 | 1.0.2 | 16.32 | 197.47 | 213.79 | OK | |
| r-release-macos-arm64 | 1.0.2 | ERROR | ||||
| r-release-macos-x86_64 | 1.0.2 | ERROR | ||||
| r-release-windows-ix86+x86_64 | 1.0.2 | 34.00 | 262.00 | 296.00 | OK | |
| r-oldrel-macos-x86_64 | 1.0.2 | ERROR | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0.2 | 48.00 | 197.00 | 245.00 | WARN |
Version: 1.0.2
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘ggtreeExtra’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86
Version: 1.0.2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘ggmsa.Rmd’ using rmarkdown
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Loading required package: dplyr
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: kableExtra
Attaching package: 'kableExtra'
The following object is masked from 'package:dplyr':
group_rows
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:dplyr':
combine, intersect, setdiff, union
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:dplyr':
first, rename
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following objects are masked from 'package:dplyr':
collapse, desc, slice
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'ape'
The following object is masked from 'package:Biostrings':
complement
ggtree v3.0.3 For help: https://yulab-smu.top/treedata-book/
If you use ggtree in published research, please cite the most appropriate paper(s):
1. Guangchuang Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics, 2020, 69:e96. doi:10.1002/cpbi.96
2. Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194
3. Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36. doi:10.1111/2041-210X.12628
Attaching package: 'ggtree'
The following object is masked from 'package:ape':
rotate
The following object is masked from 'package:Biostrings':
collapse
The following object is masked from 'package:IRanges':
collapse
The following object is masked from 'package:S4Vectors':
expand
Warning: Unknown or uninitialised column: `name`.
Warning: Unknown or uninitialised column: `name`.
Loading required package: gggenes
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Quitting from lines 210-224 (ggmsa.Rmd)
Error: processing vignette 'ggmsa.Rmd' failed with diagnostics:
there is no package called 'ggtreeExtra'
--- failed re-building ‘ggmsa.Rmd’
SUMMARY: processing the following file failed:
‘ggmsa.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘ggmsa.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Loading required package: dplyr
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: kableExtra
Attaching package: 'kableExtra'
The following object is masked from 'package:dplyr':
group_rows
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:dplyr':
combine, intersect, setdiff, union
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:dplyr':
first, rename
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following objects are masked from 'package:dplyr':
collapse, desc, slice
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'ape'
The following object is masked from 'package:Biostrings':
complement
ggtree v3.0.3 For help: https://yulab-smu.top/treedata-book/
If you use ggtree in published research, please cite the most appropriate paper(s):
1. Guangchuang Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics, 2020, 69:e96. doi:10.1002/cpbi.96
2. Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194
3. Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36. doi:10.1111/2041-210X.12628
Attaching package: 'ggtree'
The following object is masked from 'package:ape':
rotate
The following object is masked from 'package:Biostrings':
collapse
The following object is masked from 'package:IRanges':
collapse
The following object is masked from 'package:S4Vectors':
expand
Warning: Unknown or uninitialised column: `name`.
Warning: Unknown or uninitialised column: `name`.
Loading required package: gggenes
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Quitting from lines 210-224 (ggmsa.Rmd)
Error: processing vignette 'ggmsa.Rmd' failed with diagnostics:
there is no package called 'ggtreeExtra'
--- failed re-building ‘ggmsa.Rmd’
SUMMARY: processing the following file failed:
‘ggmsa.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-solaris-x86
Version: 1.0.2
Check: package dependencies
Result: ERROR
Package required but not available: ‘R4RNA’
Packages suggested but not available for checking: 'ggtreeExtra', 'ggtree'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-x86_64
Version: 1.0.2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building 'ggmsa.Rmd' using rmarkdown
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Loading required package: dplyr
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: kableExtra
Attaching package: 'kableExtra'
The following object is masked from 'package:dplyr':
group_rows
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:dplyr':
combine, intersect, setdiff, union
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:dplyr':
first, rename
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following objects are masked from 'package:dplyr':
collapse, desc, slice
The following object is masked from 'package:grDevices':
windows
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'ape'
The following object is masked from 'package:Biostrings':
complement
ggtree v2.4.2 For help: https://yulab-smu.top/treedata-book/
If you use ggtree in published research, please cite the most appropriate paper(s):
1. Guangchuang Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics, 2020, 69:e96. doi:10.1002/cpbi.96
2. Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194
3. Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36. doi:10.1111/2041-210X.12628
Attaching package: 'ggtree'
The following object is masked from 'package:ape':
rotate
The following object is masked from 'package:Biostrings':
collapse
The following object is masked from 'package:IRanges':
collapse
The following object is masked from 'package:S4Vectors':
expand
Quitting from lines 138-150 (ggmsa.Rmd)
Error: processing vignette 'ggmsa.Rmd' failed with diagnostics:
argument "caller_env" is missing, with no default
--- failed re-building 'ggmsa.Rmd'
SUMMARY: processing the following file failed:
'ggmsa.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64