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grunwaldlab / metacoder

Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data
http://grunwaldlab.github.io/metacoder_documentation
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Allow install without emboss #40

Closed zachary-foster closed 8 years ago

zachary-foster commented 8 years ago

Currently, building the vignettes requires primersearch, from the emboss tool kit to be installed. This should not be.

zkamvar commented 8 years ago

Is this the reason why I can't install metacoder on my machine when building vignettes?

> devtools::install_github(repo="grunwaldlab/metacoder", build_vignettes = TRUE, force = TRUE)
Downloading GitHub repo grunwaldlab/metacoder@master
from URL https://api.github.com/repos/grunwaldlab/metacoder/zipball/master
Installing metacoder
Skipping 1 package ahead of CRAN: ape
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore CMD build  \
  '/private/var/folders/qd/dpdhfsz12wb3c7wz0xdm6dbm0000gn/T/RtmplB0bT6/devtoolsa517b998d4f/grunwaldlab-metacoder-41b09af'  \
  --no-resave-data --no-manual 

* checking for file ‘/private/var/folders/qd/dpdhfsz12wb3c7wz0xdm6dbm0000gn/T/RtmplB0bT6/devtoolsa517b998d4f/grunwaldlab-metacoder-41b09af/DESCRIPTION’ ... OK
* preparing ‘metacoder’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Warning in extract_taxonomy(names(sequences), regex = "^(.*)\\|(.*)\\|(.*)\\|.*\\|(.*)$",  :
  Insufficient information supplied to infer taxon IDs. Assigning arbitrary IDs.
Warning in extract_taxonomy(names(sequences), regex = "^(.*)\\|(.*)\\|(.*)\\|.*\\|(.*)$",  :
  Insufficient information supplied to infer taxon IDs. Assigning arbitrary IDs.
Warning in extract_taxonomy(names(sequences), regex = "^(.*)\\|(.*)\\|(.*)\\|.*\\|(.*)$",  :
  Insufficient information supplied to infer taxon IDs. Assigning arbitrary IDs.
Warning in min(x, na.rm = na.rm) :
  no non-missing arguments to min; returning Inf
Warning in max(x, na.rm = na.rm) :
  no non-missing arguments to max; returning -Inf
Warning in min(x, na.rm = na.rm) :
  no non-missing arguments to min; returning Inf
Warning in max(x, na.rm = na.rm) :
  no non-missing arguments to max; returning -Inf
Warning in extract_taxonomy(names(sequences), regex = "^(.*\\..*?)\\|(.*)$",  :
  Insufficient information supplied to infer taxon IDs. Assigning arbitrary IDs.
sh: primersearch: command not found
Warning in file(con, "r") :
  cannot open file '/var/folders/qd/dpdhfsz12wb3c7wz0xdm6dbm0000gn/T//RtmpJ1YIQK/filea931a3551d2': No such file or directory
Quitting from lines 161-167 (workflow.Rmd) 
Warning in file.remove(output_path) :
  cannot remove file '/var/folders/qd/dpdhfsz12wb3c7wz0xdm6dbm0000gn/T//RtmpJ1YIQK/filea931a3551d2', reason 'No such file or directory'
Error: processing vignette 'workflow.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error: Command failed (1)
> devtools::session_info()
Session info ----------------------------------------------------------------------------
 setting  value                       
 version  R version 3.2.3 (2015-12-10)
 system   x86_64, darwin13.4.0        
 ui       RStudio (0.99.876)          
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       America/Los_Angeles         
 date     2016-03-11                  

Packages --------------------------------------------------------------------------------
 package   * version  date       source                            
 curl        0.9.6    2016-02-17 CRAN (R 3.2.3)                    
 devtools    1.10.0   2016-01-23 CRAN (R 3.2.3)                    
 digest      0.6.9    2016-01-08 CRAN (R 3.2.3)                    
 git2r       0.13.1   2015-12-10 CRAN (R 3.2.3)                    
 httr        1.1.0    2016-01-28 CRAN (R 3.2.3)                    
 knitr       1.12.3   2016-01-22 CRAN (R 3.2.3)                    
 memoise     1.0.0    2016-01-29 CRAN (R 3.2.3)                    
 R6          2.1.2    2016-01-26 CRAN (R 3.2.3)                    
 rsconnect   0.4.1.11 2016-02-11 Github (rstudio/rsconnect@2419667)
 withr       1.0.1    2016-02-04 CRAN (R 3.2.3)
zachary-foster commented 8 years ago

Yes, that appears to be the problem. Thanks for trying to install it though. Perhaps you could try again once this issue is closed?

zachary-foster commented 8 years ago

This should be fixed, since vignettes are no longer built when the package is installed and the primersearch examples are not run. However, there is still no test to see if EMBOSS is installed. See #78