Error of q2-ancom-bc installation

I am trying to install q2-ancom-bc and got an error. Could you help me? The error is at the bottom and thanks.

> (base) jinbingbai@son-bing-mbp ~ % conda activate qiime2-2023.7
> 
> (qiime2-2023.7) jinbingbai@son-bing-mbp ~ % R
> 
> R version 4.2.2 (2022-10-31) -- "Innocent and Trusting"
> 
> Copyright (C) 2022 The R Foundation for Statistical Computing
> 
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> 
> You are welcome to redistribute it under certain conditions.
> 
> Type 'license()' or 'licence()' for distribution details.
> 
> Natural language support but running in an English locale
> 
> R is a collaborative project with many contributors.
> 
> Type 'contributors()' for more information and
> 
> 'citation()' on how to cite R or R packages in publications.
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 
> 'help.start()' for an HTML browser interface to help.
> 
> Type 'q()' to quit R.
> 
> > if (!requireNamespace("BiocManager", quietly=TRUE))
> 
> install.packages("BiocManager")
> 
> BiocManager::install("ANCOMBC")
> 
> install.packages('tidyverse')
> 
> **Bioconductor version 3.16 (BiocManager 1.30.22), R 4.2.2 (2022-10-31)**
> 
> **Old packages: 'Cairo'**
> 
> Update all/some/none? [a/s/n]: a
> 
> **trying URL 'https://cloud.r-project.org/src/contrib/Cairo_1.6-1.tar.gz'**
> 
> **Content type 'application/x-gzip' length 99176 bytes (96 KB)**
> 
> **==================================================**
> 
> **downloaded 96 KB**
> 
> * installing *source* package ‘Cairo’ ...
> 
> ** package ‘Cairo’ successfully unpacked and MD5 sums checked
> 
> ** using staged installation
> 
> checking for x86_64-apple-darwin13.4.0-gcc... x86_64-apple-darwin13.4.0-clang
> 
> checking whether the C compiler works... yes
> 
> checking for C compiler default output file name... a.out
> 
> checking for suffix of executables...
> 
> checking whether we are cross compiling... no
> 
> checking for suffix of object files... o
> 
> checking whether the compiler supports GNU C... yes
> 
> checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes
> 
> checking for x86_64-apple-darwin13.4.0-clang option to enable C11 features... none needed
> 
> checking for sys/wait.h that is POSIX.1 compatible... yes
> 
> checking for stdio.h... yes
> 
> checking for stdlib.h... yes
> 
> checking for string.h... yes
> 
> checking for inttypes.h... yes
> 
> checking for stdint.h... yes
> 
> checking for strings.h... yes
> 
> checking for sys/stat.h... yes
> 
> checking for sys/types.h... yes
> 
> checking for unistd.h... yes
> 
> checking for string.h... (cached) yes
> 
> checking for sys/time.h... yes
> 
> checking for unistd.h... (cached) yes
> 
> checking for an ANSI C-conforming const... yes
> 
> checking for pkg-config... no
> 
> configure: CAIRO_LIBS is unset, attempting to guess it.
> 
> configure: CAIRO_CFLAGS=
> 
> checking if R was compiled with the RConn patch... no
> 
> checking for cairo.h... no
> 
> configure: error: Cannot find cairo.h! Please install cairo (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly.
> 
> ERROR: configuration failed for package ‘Cairo’
> 
> * removing ‘/Users/jinbingbai/opt/miniconda3/envs/qiime2-2023.7/lib/R/library/Cairo’
> 
> * restoring previous ‘/Users/jinbingbai/opt/miniconda3/envs/qiime2-2023.7/lib/R/library/Cairo’
> 
> **The downloaded source packages are in**
> 
> **‘/private/var/folders/20/g405t31x49b6f9p3nrlczrvh0000gq/T/Rtmp5gRbqU/downloaded_packages’**
> 
> **Updating HTML index of packages in '.Library'**
> 
> **Making 'packages.html' ... done**
> 
> **Warning messages:**
> 
> **1: package(s) not installed when version(s) same as or greater than current; use**
> 
> **`force = TRUE` to re-install: 'ANCOMBC'**
> 
> **2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,** **:**
> 
> **installation of package ‘Cairo’ had non-zero exit status**
> 
> --- Please select a CRAN mirror for use in this session ---
> 
> Secure CRAN mirrors
> 
> 1: 0-Cloud [https]
> 
> 2: Australia (Canberra) [https]
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> 3: Australia (Melbourne 1) [https]
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> 4: Australia (Melbourne 2) [https]
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> 5: Australia (Perth) [https]
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> 6: Austria [https]
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> 7: Belgium (Brussels) [https]
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> 8: Brazil (PR) [https]
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> 9: Brazil (RJ) [https]
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> 10: Brazil (SP 1) [https]
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> 11: Brazil (SP 2) [https]
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> 12: Bulgaria [https]
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> 13: Canada (MB) [https]
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> 14: Canada (ON) [https]
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> 15: Chile (Santiago) [https]
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> 16: China (Beijing 2) [https]
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> 17: China (Beijing 3) [https]
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> 18: China (Hefei) [https]
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> 19: China (Hong Kong) [https]
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> 20: China (Guangzhou) [https]
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> 21: China (Jinan) [https]
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> 22: China (Lanzhou) [https]
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> 23: China (Nanjing) [https]
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> 24: China (Shanghai 2) [https]
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> 25: China (Shenzhen) [https]
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> 26: Colombia (Cali) [https]
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> 27: Costa Rica [https]
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> 33: France (Lyon 1) [https]
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> 34: France (Lyon 2) [https]
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> 35: France (Marseille) [https]
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> 36: France (Paris 1) [https]
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> 37: Germany (Erlangen) [https]
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> 38: Germany (Leipzig) [https]
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> 40: Germany (Münster) [https]
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> 41: Germany (Regensburg) [https]
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> 42: Greece [https]
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> 43: Iceland [https]
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> 44: India (Bengaluru) [https]
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> 45: India (Bhubaneswar) [https]
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> 46: Indonesia (Banda Aceh) [https]
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> 47: Iran (Mashhad) [https]
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> 48: Italy (Milano) [https]
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> 49: Italy (Padua) [https]
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> 50: Japan (Tokyo) [https]
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> 51: Japan (Yonezawa) [https]
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> 52: Korea (Gyeongsan-si) [https]
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> 53: Mexico (Mexico City) [https]
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> 54: Mexico (Texcoco) [https]
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> 55: Morocco [https]
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> 56: Netherlands (Dronten) [https]
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> 57: New Zealand [https]
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> 58: Norway [https]
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> 59: South Africa (Johannesburg) [https]
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> 60: Spain (A Coruña) [https]
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> 61: Spain (Madrid) [https]
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> 62: Sweden (Umeå) [https]
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> 63: Switzerland (Zurich 1) [https]
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> 64: Taiwan (Taipei) [https]
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> 65: Turkey (Denizli) [https]
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> 66: Turkey (Istanbul) [https]
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> 67: UK (Bristol) [https]
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> 68: UK (London 1) [https]
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> 69: USA (IA) [https]
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> 70: USA (MI) [https]
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> 71: USA (MO) [https]
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> 72: USA (OH) [https]
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> 73: USA (OR) [https]
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> 74: USA (TN) [https]
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> 75: United Arab Emirates [https]
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> 76: Uruguay [https]
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> 77: (other mirrors)
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> Selection: 71
> 
> **trying URL 'https://cran.wustl.edu/src/contrib/tidyverse_2.0.0.tar.gz'**
> 
> **Content type 'application/x-gzip' length 704618 bytes (688 KB)**
> 
> **==================================================**
> 
> **downloaded 688 KB**
> 
> * installing *source* package ‘tidyverse’ ...
> 
> ** package ‘tidyverse’ successfully unpacked and MD5 sums checked
> 
> ** using staged installation
> 
> ** R
> 
> ** inst
> 
> ** byte-compile and prepare package for lazy loading
> 
> ** help
> 
> *** installing help indices
> 
> *** copying figures
> 
> ** building package indices
> 
> ** installing vignettes
> 
> ** testing if installed package can be loaded from temporary location
> 
> Warning: package ‘ggplot2’ was built under R version 4.2.3
> 
> Warning: package ‘tibble’ was built under R version 4.2.3
> 
> Warning: package ‘tidyr’ was built under R version 4.2.3
> 
> Warning: package ‘readr’ was built under R version 4.2.3
> 
> Warning: package ‘purrr’ was built under R version 4.2.3
> 
> Warning: package ‘stringr’ was built under R version 4.2.3
> 
> Warning: package ‘forcats’ was built under R version 4.2.3
> 
> ** testing if installed package can be loaded from final location
> 
> Warning: package ‘ggplot2’ was built under R version 4.2.3
> 
> Warning: package ‘tibble’ was built under R version 4.2.3
> 
> Warning: package ‘tidyr’ was built under R version 4.2.3
> 
> Warning: package ‘readr’ was built under R version 4.2.3
> 
> Warning: package ‘purrr’ was built under R version 4.2.3
> 
> Warning: package ‘stringr’ was built under R version 4.2.3
> 
> Warning: package ‘forcats’ was built under R version 4.2.3
> 
> ** testing if installed package keeps a record of temporary installation path
> 
> * DONE (tidyverse)
> 
> **The downloaded source packages are in**
> 
> **‘/private/var/folders/20/g405t31x49b6f9p3nrlczrvh0000gq/T/Rtmp5gRbqU/downloaded_packages’**
> 
> **Updating HTML index of packages in '.Library'**
> 
> **Making 'packages.html' ... done**
> 
> *> pip install git+https://github.com/mortonjt/q2-ancombc.git*
*> *
*> qiime dev refresh-cache*
*> *
*> **Error: unexpected symbol in "pip install"***
> ```

Thanks

Hello @Bing,

It looks like you tried to use the pip command inside of the R shell. It's supposed to be run on the command line instead.

1 Like

Hello @Bing,

By the way, there is now an ancombc action inside of qiime composition, if that suits your needs.

1 Like

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