phyloseq part warning: is this normal?

[spholmes]

When I run

knit("PartIIphyloseq.rnw")

I get:

Warning messages: 1: In is.na(e1) | is.na(e2) : longer object length is not a multiple of shorter object length 2: In!=.default(Phylum, c("", "uncharacterized")) : longer object length is not a multiple of shorter object length

My sessionInfo():

R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.2 (El Capitan)

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] gridExtra_2.2.1 ggplot2_2.1.0 phyloseq_1.17.2 BiocStyle_2.0.2 [5] knitr_1.13.1

loaded via a namespace (and not attached): [1] Rcpp_0.12.6 formatR_1.4 plyr_1.8.4
[4] highr_0.6 XVector_0.12.0 iterators_1.0.8
[7] tools_3.3.1 zlibbioc_1.18.0 digest_0.6.9
[10] jsonlite_1.0 evaluate_0.9 nlme_3.1-128
[13] rhdf5_2.16.0 gtable_0.2.0 lattice_0.20-33
[16] mgcv_1.8-12 Matrix_1.2-6 foreach_1.4.3
[19] igraph_1.0.1 parallel_3.3.1 stringr_1.0.0
[22] cluster_2.0.4 Biostrings_2.40.2 S4Vectors_0.10.2
[25] IRanges_2.6.1 stats4_3.3.1 ade4_1.7-4
[28] multtest_2.28.0 grid_3.3.1 Biobase_2.32.0
[31] data.table_1.9.6 survival_2.39-5 reshape2_1.4.1
[34] magrittr_1.5 MASS_7.3-45 splines_3.3.1
[37] scales_0.4.0 codetools_0.2-14 BiocGenerics_0.18.0 [40] biomformat_1.0.2 permute_0.9-0 ape_3.5
[43] colorspace_1.2-6 labeling_0.3 stringi_1.1.1
[46] munsell_0.4.3 vegan_2.4-0 chron_2.3-47

[joey711]

nope that's a problem... have more details? I didn't get that error. I think I know which line that is...

[spholmes]

The figure 5 also doesn't come out at all and the abundances do not have color, so there are quite a few things that are not working, I can upload a pdf if you want to see.

[joey711]

Was traveling and didn't hear follow-up, so I assumed you solved the error. Is that correct? What was the problem?

[spholmes]

I am waiting for you, the color and errors need fixing

On Aug 15, 2016 09:45, "Paul J. McMurdie" notifications@github.com wrote:

Was traveling and didn't hear follow-up, so I assumed you solved the error. Is that correct? What was the problem?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/spholmes/F1000_workflow/issues/3#issuecomment-239856245, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcvX1U1z1bX6q-jrFSZGqLVZvgYDgYks5qgJe6gaJpZM4JgnUK .

[joey711]

I need more info. Do you have a line-number for the first suspicious message when you execute?

[spholmes]

OK, running this step by step in file, line 154:

ps0 <- subset_taxa(ps0, !is.na(Phylum) & Phylum != c("", "uncharacterized"))

Warning messages: 1: In is.na(e1) | is.na(e2) : longer object length is not a multiple of shorter object length 2: In !=.default(Phylum, c("", "uncharacterized")) : longer object length is not a multiple of shorter object length

also the colors are missing in the figure 1 (prevalence).

On Mon, Aug 15, 2016 at 10:59 AM, Paul J. McMurdie <notifications@github.com

wrote:

I need more info. Do you have a line-number for the first suspicious message when you execute?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/spholmes/F1000_workflow/issues/3#issuecomment-239877014, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcvVD9omG7vnq8SuibIYKOPlNE3eg6ks5qgKjogaJpZM4JgnUK .

Susan Holmes Professor, Statistics and BioX John Henry Samter Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

[joey711]

Ah yes, the ole identity comparison vs. in-set comparison

The line

ps0 <- subset_taxa(ps0, !is.na(Phylum) & Phylum != c("", "uncharacterized"))

Should be

ps0 <- subset_taxa(ps0, !is.na(Phylum) & !Phylum %in% c("", "uncharacterized"))

[spholmes]

and are you going to help with getting some colors in the prevalences or do i have to do EVERYTHING!!

On Mon, Aug 15, 2016 at 4:24 PM, Paul J. McMurdie notifications@github.com wrote:

Ah yes, the ole identity comparison vs. in-set comparison

The line

ps0 <- subset_taxa(ps0, !is.na(Phylum) & Phylum != c("", "uncharacterized"))

Should be

ps0 <- subset_taxa(ps0, !is.na(Phylum) & !Phylum %in% c("", "uncharacterized"))

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/spholmes/F1000_workflow/issues/3#issuecomment-239958705, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcvep8FxqN66x7CDRhwnKJVggz3F_oks5qgPUagaJpZM4JgnUK .

Susan Holmes Professor, Statistics and BioX John Henry Samter Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

[joey711]

... 'everything'? :-P

[spholmes]

everything :-P.... nobody is interested in updating this.....I have Ben's bioinformatics running and I am redoing some of the network and ordinate stuff, I don't want to keep scrambling to find out why your colors aren't coming up.... do they come up on your machine and your violins don't show up at all,

On Mon, Aug 15, 2016 at 5:22 PM, Paul J. McMurdie notifications@github.com wrote:

... 'everything'? :-P

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/spholmes/F1000_workflow/issues/3#issuecomment-239968522, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcvWNrK4-LCKQRNnpvEJN4Fc8VNweJks5qgQK8gaJpZM4JgnUK .

Susan Holmes Professor, Statistics and BioX John Henry Samter Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

[joey711]

I just did a complete reinstall of latex. Maybe I can actually check it in-place. My separate pre-check obviously worked completely fine. I'll let you know.

[spholmes]

Of course not a latex problem...it is R: the generation is done with: library(knitr) knit("PartIIphyloseq.rnw")

then in the tex main.tex I just left PartIIphyloseq.tex in.

%%%%%%%%%%%% %\input{PartIdada.tex} %%%%%%%%%%%%% \input{PartIIphyloseq.tex} %%%%%%%%%%%%% %\input{PartIIIanalysis.tex} %%%%%%%%%%%%%

On Mon, Aug 15, 2016 at 5:40 PM, Paul J. McMurdie notifications@github.com wrote:

I just did a complete reinstall of latex. Maybe I can actually check it in-place. My separate pre-check obviously worked completely fine. I'll let you know.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/spholmes/F1000_workflow/issues/3#issuecomment-239970992, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcvUSN0j9WUISEmhMPxGX0LQukdY53ks5qgQb0gaJpZM4JgnUK .

Susan Holmes Professor, Statistics and BioX John Henry Samter Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

[joey711]

thanks, I'll try that

[joey711]

https://github.com/spholmes/F1000_workflow/pull/4

[joey711]

(I had only bare-bones latex until recently. A lot of my problems building were derived from that. I reproduced the warning and the weirdness in the figures. Posted the solution in that PR above)