Found more than one class "phylo" in cache
CedricMidoux opened this issue · 8 comments
CedricMidoux commented
Hello,
Like describe in #10 we have many incorrigible warnings in conflit with phyloseq.
We can't just ignore them, because they spam users during our package development.
library(phyloseq)
library(ggtree)
t <- read_tree(system.file("extdata", "esophagus.tree.gz", package="phyloseq"))
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’What can we do?
Thanks in advance
GuangchuangYu commented
pls try the github version.
CedricMidoux commented
Warnings still present :-(
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
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#> os Windows 11 x64 (build 22621)
#> system x86_64, mingw32
#> ui RTerm
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#> collate French_France.utf8
#> ctype French_France.utf8
#> tz Europe/Paris
#> date 2023-11-29
#> pandoc 3.1.1 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#>
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#> aplot 0.2.2 2023-10-06 [1] CRAN (R 4.3.2)
#> Biobase 2.62.0 2023-10-24 [1] Bioconductor
#> BiocGenerics 0.48.1 2023-11-01 [1] Bioconductor
#> biomformat 1.30.0 2023-10-24 [1] Bioconductor
#> Biostrings 2.70.1 2023-10-25 [1] Bioconductor
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#> digest 0.6.33 2023-07-07 [1] CRAN (R 4.3.2)
#> dplyr 1.1.4 2023-11-17 [1] CRAN (R 4.3.2)
#> evaluate 0.23 2023-11-01 [1] CRAN (R 4.3.2)
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#> fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.2)
#> foreach 1.5.2 2022-02-02 [1] CRAN (R 4.3.2)
#> fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.2)
#> generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.2)
#> GenomeInfoDb 1.38.1 2023-11-08 [1] Bioconductor
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#> ggplotify 0.1.2 2023-08-09 [1] CRAN (R 4.3.2)
#> ggtree * 3.11.0 2023-11-29 [1] Github (YuLab-SMU/ggtree@33a07af)
#> glue 1.6.2 2022-02-24 [1] CRAN (R 4.3.2)
#> gridGraphics 0.5-1 2020-12-13 [1] CRAN (R 4.3.2)
#> gtable 0.3.4 2023-08-21 [1] CRAN (R 4.3.2)
#> htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.3.2)
#> igraph 1.5.1 2023-08-10 [1] CRAN (R 4.3.2)
#> IRanges 2.36.0 2023-10-24 [1] Bioconductor
#> iterators 1.0.14 2022-02-05 [1] CRAN (R 4.3.2)
#> jsonlite 1.8.7 2023-06-29 [1] CRAN (R 4.3.2)
#> knitr 1.45 2023-10-30 [1] CRAN (R 4.3.2)
#> lattice 0.22-5 2023-10-24 [2] CRAN (R 4.3.2)
#> lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.3.2)
#> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.2)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.2)
#> MASS 7.3-60 2023-05-04 [2] CRAN (R 4.3.2)
#> Matrix 1.6-3 2023-11-14 [2] CRAN (R 4.3.2)
#> memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.2)
#> mgcv 1.9-0 2023-07-11 [2] CRAN (R 4.3.2)
#> multtest 2.58.0 2023-10-24 [1] Bioconductor
#> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.2)
#> nlme 3.1-164 2023-11-27 [2] CRAN (R 4.3.2)
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#> permute 0.9-7 2022-01-27 [1] CRAN (R 4.3.2)
#> phyloseq * 1.41.1 2023-11-29 [1] Github (joey711/phyloseq@c260561)
#> pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.2)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.2)
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#> tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.2)
#> tidytree 0.4.5.001 2023-11-29 [1] Github (YuLab-SMU/tidytree@4e78b72)
#> treeio 1.27.0.001 2023-11-29 [1] Github (YuLab-SMU/treeio@abd7552)
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#>
#> [1] C:/Users/cmidoux/.R/win-library/4.3
#> [2] C:/Users/cmidoux/AppData/Local/Programs/R/R-4.3.2/library
#>
#> D ── DLL MD5 mismatch, broken installation.
#>
#> ──────────────────────────────────────────────────────────────────────────────GuangchuangYu commented
just ignore it.
CedricMidoux commented
It's a bit difficult
Loading required package: shiny
Listening on http://127.0.0.1:6397
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by ‘tidytree’Thanks anyway for your package
john123lol commented
The problem is not solved at all after so many years, and ignoring it is not a wise choice. Can we make a serious attempt on this issue .
john123lol commented
the only way that I found to suppress it was to modify chunk in R markdown with the message setting off which kind of turn off all the other console message at the same time as well.
kwilson62 commented
just ignore it.
just fix it.
GuangchuangYu commented
see my explanation in #48 (comment).