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zdk123 / SpiecEasi

Sparse InversE Covariance estimation for Ecological Association and Statistical Inference
GNU General Public License v3.0
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Update SpiecEasi on bioconda #171

Open nick-youngblut opened 3 years ago

nick-youngblut commented 3 years ago

For anyone getting the error:

Error: 
3 jobs failed with: "Error in get(as.character(FUN), mode = "function", envir = envir) : 
  object 'sparseLowRankiCov' of mode 'function' was not found"
Traceback:

1. spiec.easi(df %>% as.matrix, method = "slr", r = 10, lambda.min.ratio = lambda.min.ratio, 
 .     nlambda = nlambda, sel.criterion = "bstars", pulsar.select = TRUE, 
 .     pulsar.params = pargs)
2. spiec.easi.default(df %>% as.matrix, method = "slr", r = 10, 
 .     lambda.min.ratio = lambda.min.ratio, nlambda = nlambda, sel.criterion = "bstars", 
 .     pulsar.select = TRUE, pulsar.params = pargs)
3. eval(call, environment())
4. eval(call, environment())
5. pulsar(data = X, fun = match.fun(estFun), fargs = args, rep.num = 100, 
 .     seed = 8080, ncores = 12, criterion = "stars", ub.stars = TRUE, 
 .     lb.stars = TRUE, thresh = 0.05)
6. .try_mclapply(isamp, estFun, fargs = fargs, mc.cores = ncores, 
 .     mc.preschedule = FALSE, pass.errors = !lb.stars)
7. stop(msg, call. = FALSE)

It's likely due to the fact that the latest bioconda version is 1.1.0, and it appears that sparseLowRankiCov was not added until v1.1.1

zdk123 commented 3 years ago

Yep and thanks. I'll push an update.