Errors in running code in vignettes:
when running code in 'sybil.Rnw'

> library(sybil)
Loading required package: Matrix
Loading required package: lattice

> library(help = "sybil")

> help(doubleGeneDel)

> help.search("flux variability analysis")

> mp <- system.file(package = "sybil", "extdata")

> mod <- readTSVmod(prefix = "Ec_core", fpath = mp, 
+     quoteChar = "\"")
reading model description, ... OK
reading metabolite list ... OK
parsing reaction list ... OK
GPR mapping ... OK
sub systems ... OK
prepare modelorg object ... OK
validating object ... OK

> data(Ec_core)

> ex <- findExchReact(Ec_core)

> upt <- uptReact(ex)

> ex[upt]
 #   pos.  reaction id           metabolite id          uptake     lb     ub
[1]  23    EX_co2(e)             co2[e]                 TRUE     -Inf    Inf
[2]  28    EX_glc(e)             glc_D[e]               TRUE      -10    Inf
[3]  31    EX_h(e)               h[e]                   TRUE     -Inf    Inf
[4]  32    EX_h2o(e)             h2o[e]                 TRUE     -Inf    Inf
[5]  35    EX_nh4(e)             nh4[e]                 TRUE     -Inf    Inf
[6]  36    EX_o2(e)              o2[e]                  TRUE     -Inf    Inf
[7]  37    EX_pi(e)              pi[e]                  TRUE     -Inf    Inf

number of exchange reactions: 7

> mod <- changeBounds(Ec_core, ex[c("EX_glc(e)", "EX_lac_D(e)")], 
+     lb = c(0, -10))

> findExchReact(mod)
  #   pos.  reaction id           metabolite id          uptake     lb     ub
 [1]  20    EX_ac(e)              ac[e]                  FALSE       0    Inf
 [2]  21    EX_acald(e)           acald[e]               FALSE       0    Inf
 [3]  22    EX_akg(e)             akg[e]                 FALSE       0    Inf
 [4]  23    EX_co2(e)             co2[e]                 TRUE     -Inf    Inf
 [5]  24    EX_etoh(e)            etoh[e]                FALSE       0    Inf
 [6]  25    EX_for(e)             for[e]                 FALSE       0    Inf
 [7]  26    EX_fru(e)             fru[e]                 FALSE       0    Inf
 [8]  27    EX_fum(e)             fum[e]                 FALSE       0    Inf
 [9]  28    EX_glc(e)             glc_D[e]               FALSE       0    Inf
[10]  29    EX_gln_L(e)           gln_L[e]               FALSE       0    Inf
[11]  30    EX_glu_L(e)           glu_L[e]               FALSE       0    Inf
[12]  31    EX_h(e)               h[e]                   TRUE     -Inf    Inf
[13]  32    EX_h2o(e)             h2o[e]                 TRUE     -Inf    Inf
[14]  33    EX_lac_D(e)           lac_D[e]               TRUE      -10    Inf
[15]  34    EX_mal_L(e)           mal_L[e]               FALSE       0    Inf
[16]  35    EX_nh4(e)             nh4[e]                 TRUE     -Inf    Inf
[17]  36    EX_o2(e)              o2[e]                  TRUE     -Inf    Inf
[18]  37    EX_pi(e)              pi[e]                  TRUE     -Inf    Inf
[19]  38    EX_pyr(e)             pyr[e]                 FALSE       0    Inf
[20]  39    EX_succ(e)            succ[e]                FALSE       0    Inf

number of exchange reactions: 20

> optL <- optimizeProb(Ec_core, algorithm = "fba", retOptSol = FALSE)
Loading required package: glpkAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'glpkAPI'

  When sourcing 'sybil.R':
Error: package 'glpkAPI' not found
Execution halted

  'sybil.Rnw' using 'UTF-8'... failed