package ‘biom’ is not available (for R version 3.3.3)

[Daniel Laubitz]

Hi,

I wanted to run differential_abundance.py and got an error "Cannot find R. Is it installed? Is it in your path?". I have installed R and all packages. Now I got another error:

burrito.util.ApplicationError: R library not installed:

stdout:

stderr:

Library biom not found.

To install, open R and run the command:

  install.packages("biom")

I tried to install 'biom' but I got : 

Warning message:

package ‘biom’ is not available (for R version 3.3.3) 

Should I install different R version? Is there any other way to fix it?

Thanks!

Daniel

 

[Colin Brislawn]

Hello Daniel,

Yeah, setting up all the R packages always seems to be tricky. Try installing the biom format package using bioconductor, as described here: 

https://bioconductor.org/packages/release/bioc/html/biomformat.html 

This should install correctly with your current R version, and then elegantly work with qiime.

Let me know if this method works for you,

Colin

[Daniel Laubitz]

Hi Colin, 

Thank you for your suggeston but I am still getting this error:

Traceback (most recent call last):

  File "/macqiime/anaconda/bin/differential_abundance.py", line 159, in <module>

    main()

  File "/macqiime/anaconda/bin/differential_abundance.py", line 150, in main

    DA_DESeq2(input_path, out_path, mapping_fp, mapping_category, subcategory_1, subcategory_2, DESeq2_diagnostic_plots)

  File "/macqiime/anaconda/lib/python2.7/site-packages/qiime/differential_abundance.py", line 118, in DA_DESeq2

    run_DESeq2(temp_fh.name, out_path, mapping_category, subcategory_1, subcategory_2, DESeq2_diagnostic_plots, outfile_diagnostic) 

  File "/macqiime/anaconda/lib/python2.7/site-packages/qiime/differential_abundance.py", line 159, in run_DESeq2

    app_result = rsl(command_args=command_args, script_name='DESeq2_nbinom.r')

  File "/macqiime/anaconda/lib/python2.7/site-packages/qiime/util.py", line 1963, in __call__

    (stdout, stderr))

burrito.util.ApplicationError: R library not installed:

stdout:

stderr:

Library biom not found.

To install, open R and run the command:

  install.packages("biom")

If you already have the biom package installed in a local directory,

please store the path to that directory in an environment variable

called "R_LIBRARY_PATH". This may be necessary if you are running

QIIME on a cluster, and the cluster instances of R don't know about

your local R libraries. If you don't know your R library paths, you

can list them by opening R and running with the command, ".libPaths()".

The current R instance knows about these paths:

[/Library/Frameworks/R.framework/Versions/3.3/Resources/library] 

Warning message:

In library(lib.name, character.only = TRUE, logical.return = TRUE,  :

  there is no package called ‘biom’

[Colin Brislawn]

Hello Daniel,

Looks like it's still having trouble finding the biom packages for R. When you ran the bioconductor install commands, did these give you errors? Could you post that output for me?

Thanks!

Colin

[Daniel Laubitz]

I do not think there was any error:

> source("https://bioconductor.org/biocLite.R")

Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help

> biocLite("biomformat")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06).

Installing package(s) ‘biomformat’

trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/macosx/mavericks/contrib/3.3/biomformat_1.2.0.tgz'

Content type 'application/x-gzip' length 202107 bytes (197 KB)

==================================================

downloaded 197 KB

The downloaded binary packages are in

/var/folders/sz/vv7cb6cn6sx_g92vvl4m3c080000gp/T//RtmpptWZGJ/downloaded_packages

[Colin Brislawn]

Thanks for telling me more.

Yeah, that looks the install worked fine. This should provide the biom library, preventing the  'Library biom not found' error.

I've cc'ed one of the qiime devs who may be able to help more. 

Let me know if you discover any other clues,
Colin

[Daniel Laubitz]

Thanks you Colin. I really hope for help, I have already run out of clues. 

~Daniel

[Andrew_M]

I just had the same issue when I tried to install Tax4Fun on a new system  It appears that "biom" has been removed from the CRAN servers except for archived versions (none of which are compatible with R 3.3).

The fix is to use the development version, available on GitHub: https://github.com/joey711/biom

Easy install: From within R (or Rstudio):

install.packages("devtools") # if not already installed
devtools::install_github("biom", "joey711")

Done.  

Good luck!

[Manil]

Hello Andrew,

Could you please help me with Tax4fun I had the same problem while i was trying to install it, I had this msg Error :

installing to library ‘/usr/local/lib/R/site-library’
ERROR: dependencies ‘qiimer’, ‘biom’ are not available for package ‘Tax4Fun’
* removing ‘/usr/local/lib/R/site-library/Tax4Fun’

Thank you,

Manil

[Paige]

Thanks Andrew, This worked for me with 3.4.0 too.