Running 'FirstObsCensored.R' [174s]
  Running 'abmmWarningTest.R' [177s]
  Running 'tests.R' [165s]
Running the tests in 'tests/FirstObsCensored.R' failed.
Complete output:
  > ## In 1.3.0 there was an error when the first observation 
  > ## was censored. It was a problem in the abmm function.
  > ## fixed March 25, 2016
  > library(bpcp)
  Loading required package: survival
  Loading required package: ggplot2
  > time<-c(1:3)
  > status<-c(0,1,1)
  > bout<-bpcp(time,status)
  > summary(bout)
    time interval survival lower 95% CL upper 95% CL
  1         [0,1)      1.0   0.29240177    1.0000000
  2         [1,2)      1.0   0.15811388    1.0000000
  3         [2,3)      0.5   0.01257912    0.9874209
  4       [3,Inf)      0.0   0.00000000    0.8418861
  > 
  > proc.time()
     user  system elapsed 
     1.78    0.23    2.00 
Running the tests in 'tests/abmmWarningTest.R' failed.
Complete output:
  > ## Thanks to Marcel Wolbers for finding this problem.
  > ## It used to produce a warning, but the answers were correct.
  > ## Now should not produce a warning
  > 
  > library(bpcp)
  Loading required package: survival
  Loading required package: ggplot2
  > library(survival)
  > 
  > 
  > 
  > sim.exp <- function(n,prob1,prob2,cens.rate){
  +   # prob1 and prob2 are the absolute risks for an event at time t=1
  +   rate1 <- -log(1-prob1); rate2 <- -log(1-prob2)
  +   n1 <- n%/%2+n%%2; n2 <- n%/%2
  +   ttev.uncens <- rexp(n,rate=rep(c(rate1,rate2),times=c(n1,n2)))
  +   ttcens <- rexp(n,rate=cens.rate)  
  +   data.frame(arm=rep(c(0,1),c(n1,n2)),ttev=pmin(ttev.uncens,ttcens),ev=ifelse(ttev.uncens <=ttcens,1,0))
  + }
  > 
  > set.seed(1)
  > d <- sim.exp(400,prob1=0.1,prob2=0.05,cens.rate=0.05)
  > summary(survfit(Surv(ttev,ev)~arm,data=d),time=1)
  Call: survfit(formula = Surv(ttev, ev) ~ arm, data = d)
  
                  arm=0 
          time       n.risk      n.event     survival      std.err lower 95% CI 
        1.0000     172.0000      13.0000       0.9319       0.0182       0.8968 
  upper 95% CI 
        0.9684 
  
                  arm=1 
          time       n.risk      n.event     survival      std.err lower 95% CI 
        1.0000     175.0000      12.0000       0.9375       0.0175       0.9039 
  upper 95% CI 
        0.9724 
  
  > bpcp2samp(d$ttev,d$ev,d$arm,testtime=1,parmtype="difference")
  
  	Two-Sample Melded BPCP Test
  
  data:  S(1;group=1)-S(1;group=0)
  S(1;group=0) = 0.9319, S(1;group=1) = 0.93755, p-value = 0.9912
  alternative hypothesis: true difference is not equal to 0
  95 percent confidence interval:
   -0.05010352  0.06173469
  sample estimates:
   difference 
  0.005645451 
  
  > 
  > proc.time()
     user  system elapsed 
     1.89    0.28    2.18 
Running the tests in 'tests/tests.R' failed.
Complete output:
  > 
  > ## The following gave an error for versions<1.2.7
  > ## there was a problem if all the censoring happended 
  > ## at times where there was also failures
  > library(bpcp)
  Loading required package: survival
  Loading required package: ggplot2
  > x<-c(1,1,2,3)
  > status<-c(0,1,1,1)
  > plot(c(0,5),c(0,1),type="n")
  > ## also the default color for the survival line in 
  > ## lines.kmciLR was white...gray(1), 
  > ## it should be black...gray(0) 
  > lines(bpcp(x,status),linetype="surv")
  > 
  > proc.time()
     user  system elapsed 
     1.85    0.20    2.00