Last updated on 2019-10-13 10:47:06 CEST.
Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
---|---|---|---|---|---|---|
r-devel-linux-x86_64-debian-clang | 1.1.2 | 3.17 | 325.16 | 328.33 | WARN | |
r-devel-linux-x86_64-debian-gcc | 1.1.2 | 2.63 | 256.88 | 259.51 | WARN | |
r-devel-linux-x86_64-fedora-clang | 1.1.2 | 429.06 | WARN | |||
r-devel-linux-x86_64-fedora-gcc | 1.1.2 | 431.51 | WARN | |||
r-devel-windows-ix86+x86_64 | 1.1.2 | 8.00 | 525.00 | 533.00 | OK | |
r-patched-linux-x86_64 | 1.1.2 | 2.84 | 327.16 | 330.00 | OK | |
r-patched-solaris-x86 | 1.1.2 | 1003.40 | OK | |||
r-release-linux-x86_64 | 1.1.2 | 2.45 | 320.19 | 322.64 | OK | |
r-release-windows-ix86+x86_64 | 1.1.2 | 13.00 | 410.00 | 423.00 | OK | |
r-release-osx-x86_64 | 1.1.2 | WARN | ||||
r-oldrel-windows-ix86+x86_64 | 1.1.2 | 5.00 | 427.00 | 432.00 | OK | |
r-oldrel-osx-x86_64 | 1.1.2 | WARN |
Version: 1.1.2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'introduction.Rmd' using rmarkdown
ggtree v1.99.1 For help: https://yulab-smu.github.io/treedata-book/
If you use ggtree in published research, please cite the most appropriate paper(s):
<1b>[36m-<1b>[39m 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
<1b>[36m-<1b>[39m 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
Loading required package: ape
Attaching package: 'ape'
The following object is masked from 'package:ggtree':
rotate
Loading required package: maps
Warning in load_fasta(fasta.file.name) :
Characters not in acgtnACGTN- will be treated as missing (-)...
Warning in load_fasta(woodmouse) :
Characters not in acgtnACGTN- will be treated as missing (-)...
Read 1 item
Quitting from lines 126-127 (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
This function is defunct. Use treeio::tree_subset()
--- failed re-building 'introduction.Rmd'
SUMMARY: processing the following file failed:
'introduction.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.1.2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
ggtree v1.99.1 For help: https://yulab-smu.github.io/treedata-book/
If you use ggtree in published research, please cite the most appropriate paper(s):
<1b>[36m-<1b>[39m 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
<1b>[36m-<1b>[39m 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
Loading required package: ape
Attaching package: 'ape'
The following object is masked from 'package:ggtree':
rotate
Loading required package: maps
Warning in load_fasta(fasta.file.name) :
Characters not in acgtnACGTN- will be treated as missing (-)...
Warning in load_fasta(woodmouse) :
Characters not in acgtnACGTN- will be treated as missing (-)...
Read 1 item
Quitting from lines 126-127 (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
This function is defunct. Use treeio::tree_subset()
--- failed re-building ‘introduction.Rmd’
SUMMARY: processing the following file failed:
‘introduction.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.1.2
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘ggtree’
Flavor: r-release-osx-x86_64
Version: 1.1.2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 40-46 (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'ggtree'
--- failed re-building ‘introduction.Rmd’
SUMMARY: processing the following file failed:
‘introduction.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-osx-x86_64
Version: 1.1.2
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 40-46 (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
package or namespace load failed for 'ggtree':
object 'as_data_frame' is not exported by 'namespace:tidytree'
Execution halted
Flavor: r-oldrel-osx-x86_64