Last updated on 2024-12-25 13:50:40 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.0 | 20.05 | 246.28 | 266.33 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.0 | 15.60 | 157.59 | 173.19 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.0 | 463.42 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.0 | 463.33 | OK | |||
| r-devel-windows-x86_64 | 1.0.0 | 24.00 | 87.00 | 111.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.0 | 21.55 | 243.93 | 265.48 | OK | |
| r-release-linux-x86_64 | 1.0.0 | 22.42 | 244.86 | 267.28 | OK | |
| r-release-macos-arm64 | 1.0.0 | 112.00 | OK | |||
| r-release-macos-x86_64 | 1.0.0 | 184.00 | OK | |||
| r-release-windows-x86_64 | 1.0.0 | 24.00 | 275.00 | 299.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.0 | 114.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.0.0 | 210.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.0.0 | 27.00 | 312.00 | 339.00 | OK |
Version: 1.0.0
Check: examples
Result: ERROR
Running examples in 'MarZIC-Ex.R' failed
The error most likely occurred in:
> ### Name: MarZIC
> ### Title: Marginal Mediation Model for Zero-Inflated Compositional
> ### Mediators
> ### Aliases: MarZIC
>
> ### ** Examples
>
> {
+ library(MarZIC)
+
+ ## A make up example with 2 taxon and 20 subjects.
+ set.seed(1)
+ nSub <- 20
+ nTaxa <- 2
+ ## generate covariate of interest X
+ X <- rbinom(nSub, 1, 0.5)
+ ## generate confounders
+ conf1<-rnorm(nSub)
+ conf2<-rbinom(nSub,1,0.5)
+ ## generate mean of each taxon. All taxon are having the same mean for simplicity.
+ mu <- exp(-5 + X + 0.1 * conf1 + 0.1 * conf2) /
+ (1 + exp(-5 + X + 0.1 * conf1 + 0.1 * conf2))
+ phi <- 10
+
+ ## generate true RA
+ M_taxon<-t(sapply(mu,function(x) dirmult::rdirichlet(n=1,rep(x*phi,nTaxa))))
+
+ P_zero <- exp(-3 + 0.3 * X + 0.1 * conf1 + 0.1 * conf2) /
+ (1 + exp(-3 + 0.3 * X + 0.1 * conf1 + 0.1 * conf2))
+
+ non_zero_ind <- t(sapply(P_zero,function(x) 1-rbinom(nTaxa,1,rep(x,nTaxa))))
+
+ True_RA<-t(apply(M_taxon*non_zero_ind,1,function(x) x/sum(x)))
+
+ ## generate outcome Y based on true RA
+ Y <- 1 + 100 * True_RA[,1] + 5 * (True_RA[,1] > 0) + X + conf1 + conf2 + rnorm(nSub)
+
+ ## library size was set to 10,000 for all subjects for simplicity.
+ libsize <- 10000
+
+ ## generate observed RA
+ observed_AA <- floor(M_taxon*libsize*non_zero_ind)
+
+ observed_RA <- t(apply(observed_AA,1,function(x) x/sum(x)))
+ colnames(observed_RA)<-paste0("rawCount",seq_len(nTaxa))
+ CovData <- cbind(Y = Y, X = X, libsize = libsize, conf1 = conf1, conf2 = conf2)
+
+
+ ## run the analysis
+ res <- MarZIC(
+ MicrobData = observed_RA,
+ CovData = CovData,
+ lib_name = "libsize",
+ y_name = "Y",
+ x_name = "X",
+ conf_name = c("conf1","conf2"),
+ taxa_of_interest = NULL,
+ num_cores = 1,
+ mediator_mix_range = 1
+ )
+ }
One or more reads are missing. Subjects with missing were removed from analysis
Error in unserialize(socklist[[n]]) : error reading from connection
Calls: MarZIC
Execution halted
Error in serialize(data, node$con) : error writing to connection
Calls: <Anonymous> ... postNode -> sendData -> sendData.SOCKnode -> serialize
Flavor: r-devel-windows-x86_64
Version: 1.0.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'MarZIC.Rmd' using rmarkdown
Quitting from lines 113-127 [unnamed-chunk-3] (MarZIC.Rmd)
Error: processing vignette 'MarZIC.Rmd' failed with diagnostics:
error reading from connection
--- failed re-building 'MarZIC.Rmd'
SUMMARY: processing the following file failed:
'MarZIC.Rmd'
Error: Vignette re-building failed.
Execution halted
Error in serialize(data, node$con) : error writing to connection
Calls: <Anonymous> ... postNode -> sendData -> sendData.SOCKnode -> serialize
Flavor: r-devel-windows-x86_64