qiime2R installation issue

[Pablo_V]

@jbisanz

devtools::install_github("jbisanz/qiime2R")

Dear @jbisanz,

I have a problem with the installation of package. Namely, when I try to install it using "devtools::install_github("jbisanz/qiime2R" I get the following error:

WARNING: Rtools is required to build R packages, but is not currently installed.

Please download and install Rtools custom from RTools: Toolchains for building R and R packages from source on Windows.
Skipping install of 'qiime2R' from a github remote, the SHA1 (4c2abcd1) has not changed since last install.
Use force = TRUE to force installation

Then I try to install Rtools, as recommended by the previous output, and I get the following result:

install.packages("rtools")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/u0114295/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘rtools’ is not available (for R version 3.6.1)

so it seems I cannot install rtools because the last version of it was for R 3.5.

Is there a way around this issue?

Thanks a lot for your help!!!!

Cheers,
Pablo

[jbisanz (Jordan Bisanz)]

It would appear that rtools is not a r package but a separate piece of software that can be installed outside of R. This post may be helpful for using rtools3.5 with r 3.6.1: Errors in Rtool installations - install.packages("Rtool") - package ‘Rtool’ is not available - General - Posit Community

[mpodar]

hello Jordan,

is qiime2R compatible with R 4.0? I am getting the following on trying to install. Also fails to install in RStudio. Thanks, Mircea

[jbisanz (Jordan Bisanz)]

Hi Mircea,
Yes it is. I'm wondering if this could be related to a previous version of R's install of readr and/or Rcpp. Could you try reinstalling the tidyverse and see if that makes a difference?

[Sammi (Jiyoung Kim)]

I am also having a same problem where I cannot install Qiime2R and it says it is not compatible with R.4.0 which I just updated..any advice?

[jbisanz (Jordan Bisanz)]

Could you try reinstalling the tidyverse or Rcpp from CRAN and see if you still have issues?

[Sammi (Jiyoung Kim)]

I reinstalled after i updated my R ver to 4.0 and the msg was like

devtools::install("qiime2R-master")
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘cachem’
install.packages("cachem")

[jbisanz (Jordan Bisanz)]

Try installing straight from github, hopefully all of the dependencies will be handled. Please post any error message that happens when you do that.

devtools::install_gihub("jbisanz/qiime2R")

[Sammi (Jiyoung Kim)]

I got this error?

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘cachem’

[emilyhoedt (Emily H)]

Hi, I'm also having install issues.

Error: package or namespace load failed for 'qiime2R' in library.dynam(lib, package, package.lib):
DLL 'tidyr' not found: maybe not installed for this architecture?

I have R v4.0.3, Tidyverse, tidyr and Rcpp all installed and up to date so I do not understand why qiime2r won't install.

Any suggestions?

------>
Never mind I fixed it... it was a broken install of tidyr which couldn't be removed
I fixed it by changing the name of the broken folder in R/win-library/4.0 (because it refused to be deleted, even after being uninstalled). The reinstall of tidyr fixed the install problems

[linama (Lina Maria Martinez)]

Dear @jbisanz,

I am trying to install qiime2R but I am getting the following message:

if (!requireNamespace("devtools", quietly = TRUE)){install.packages("devtools")}devtools::install_github("jbisanz/qiime2R")

Skipping install of 'qiime2R' from a github remote, the SHA1 (2a3cee18) has not changed since last install.
Use force = TRUE to force installation

Could you help me, please?

Thank you so much

[jbisanz (Jordan Bisanz)]

This means it is already installed and up to date and won't reinstall because your version is not different from the one on github.

[linama (Lina Maria Martinez)]

Thank you, Jordan. I also got these error messages when I tried one of the commands from the tutorial (all files contain 176 samples).

metadata<-read_q2metadata("metadata.tsv")
uwunifrac<-read_qza("unweighted_unifrac_pcoa_results.qza")
shannon<-read_qza("shannon_vector.qza")$data %>% rownames_to_column("SampleID")

uwunifrac$data$Vectors %>%
select(SampleID, PC1, PC2) %>%
left_join(metadata) %>%
left_join(shannon) %>%
ggplot(aes(x=PC1, y=PC2, color=Sample_type, shape=Blocking_Primer, size=shannon)) +
geom_point(alpha=0.5) +
theme_q2r() +
scale_shape_manual(values=c(16,1), name="Blocking_Primer") +
scale_size_continuous(name="Shannon Diversity") +
scale_color_discrete(name="Sample_type")

Error: Aesthetics must be either length 1 or the same as the data (176): size
Run rlang::last_error() to see where the error occurred.

<error/rlang_error>
Aesthetics must be either length 1 or the same as the data (176): size
Backtrace:

1. ggplot2::ggsave("PCoA.pdf", height = 4, width = 5, device = "pdf")
2. ggplot2:::grid.draw.ggplot(plot)
3. ggplot2:::print.ggplot(x)
4. ggplot2:::ggplot_build.ggplot(x)
5. ggplot2:::by_layer(function(l, d) l$compute_aesthetics(d, plot))
6. ggplot2:::f(l = layers[[i]], d = data[[i]])
7. l$compute_aesthetics(d, plot)
8. ggplot2:::f(..., self = self)
9. ggplot2:::check_aesthetics(evaled, n)

Do you know what the mistake is? thank you

[16sIceland (Emmett Smith)]

Hey - I've just tried this command, but I am getting the following error:

devtools::install_gihub("jbisanz/qiime2R")
Error: 'install_gihub' is not an exported object from 'namespace:devtools'

Any ideas?

[thermokarst]

Hi @16sIceland - I'm not the developer of qiime2r, but it looks like you have a typo in your command, you're missing the "t" in "github".

[16sIceland (Emmett Smith)]

Gold star for careful reading - that is indeed the problem!