Last updated on 2025-05-17 02:53:24 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.4.7.1 | 3.57 | 55.92 | 59.49 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.4.7.2 | 2.52 | 42.36 | 44.88 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.4.7.2 | 98.63 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.4.7.2 | 91.32 | ERROR | |||
| r-devel-windows-x86_64 | 1.4.7.1 | 5.00 | 126.00 | 131.00 | OK | |
| r-patched-linux-x86_64 | 1.4.7.1 | 4.56 | 54.21 | 58.77 | OK | |
| r-release-linux-x86_64 | 1.4.7.1 | 4.03 | 54.90 | 58.93 | OK | |
| r-release-macos-arm64 | 1.4.7.2 | 78.00 | OK | |||
| r-release-macos-x86_64 | 1.4.7.2 | 92.00 | OK | |||
| r-release-windows-x86_64 | 1.4.7.2 | 6.00 | 143.00 | 149.00 | OK | |
| r-oldrel-macos-arm64 | 1.4.7.2 | 73.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.4.7.2 | 124.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.4.7.1 | 5.00 | 130.00 | 135.00 | OK |
Version: 1.4.7.1
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Karline Soetaert <karline.soetaert@nioz.nl>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = "Karline",
family = "Soetaert",
role = c("aut", "cre"),
email = "karline.soetaert@nioz.nl"),
person(given = "Dick",
family = "van Oevelen",
role = "aut",
email = "dick.vanoevelen@nioz.nl"))
as necessary.
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.4.7.2
Check: examples
Result: ERROR
Running examples in ‘LIM-Ex.R’ failed
The error most likely occurred in:
> ### Name: LIMEcoli
> ### Title: The Escherichia Coli Core Metabolism: Reaction network model
> ### specificiation
> ### Aliases: LIMEcoli
> ### Keywords: datasets
>
> ### ** Examples
>
>
>
> # 1. parsimonious (simplest) solution
> pars <- Ldei(LIMEcoli)
>
> # 2. the ranges of each reaction
> xr <- Xranges(LIMEcoli, central = TRUE, full = TRUE)
Warning in lsei(E = E, F = F, G = G, H = H) :
LSEI error: inequalities contradictory
>
> # 3. the optimal solution - solved with linear programming
> LP <- Linp(LIMEcoli)
> Optimal <- t(LP$X)
>
> # show the results
> data.frame(pars = pars$X, Optimal, xr[ ,1:3])
pars X1 X2 min max
GLK1 0.9042441896 0.000000 5.66169049 0.0000000 10.000000
PGI1 4.2002550929 807.532745 5.63978625 -15.8333333 807.532745
PFKA 4.6188137322 781.590686 5.55399466 0.8333333 2229.130000
FBP 0.4239323312 0.000000 0.00000000 0.0000000 1604.130000
FBA 4.1948814010 781.590686 5.55399466 0.8333333 781.590686
TPIA 4.1875554626 781.590686 5.55399466 0.8333333 781.590686
GAPA 8.3801801799 1541.434199 11.03607040 5.0000000 1541.434199
PGK 8.3801801799 1541.434199 11.03607040 5.0000000 1541.434199
GPMA 8.3825988273 1492.089090 10.87288384 5.0000000 1492.089090
ENO 8.3825988273 1492.089090 10.87288384 5.0000000 1492.089090
PPSA 0.5164462964 0.000000 0.00000000 0.0000000 1604.130000
PYKA 3.1245351936 466.657964 10.50489266 0.0000000 2136.630000
ACEE -0.0027256954 1149.295284 0.19494771 0.0000000 1158.949190
ZWF -0.0088929275 0.000000 0.00000000 0.0000000 75.000000
PGL -0.0088929275 0.000000 0.00000000 0.0000000 75.000000
GND -0.0088929275 0.000000 0.00000000 0.0000000 75.000000
RPIA -0.0034056079 23.623833 0.07812511 0.0000000 28.202015
RPE -0.0054873196 -23.623833 -0.07812511 -23.6238328 50.000000
TKTA1 -0.0030358454 -5.850762 -0.01934874 -5.8507623 25.000000
TKTA2 -0.0024514742 -17.773070 -0.05877637 -17.7730705 25.000000
TALA -0.0030358454 -5.850762 -0.01934874 -5.8507623 25.000000
GLTA 1.4506095831 35.435749 0.11718767 0.0000000 40.847149
ACNA 1.4506095831 35.435749 0.11718767 0.0000000 40.847149
ICDA 0.0010797202 35.435749 0.11718767 0.0000000 40.847149
SUCA 0.0028166012 0.000000 0.00000000 0.0000000 30.000000
SUCC1 0.0028166012 0.000000 0.00000000 0.0000000 30.000000
SDHA1 1.4447322494 0.000000 0.00000000 0.0000000 100.000000
FRDA -0.0060662367 100.000000 0.00000000 0.0000000 100.000000
FUMA 1.4507984861 -100.000000 0.00000000 -100.0000000 8.333333
MDH -1.0408242721 -100.000000 0.00000000 -1168.3150000 16.666667
DLD1 4.2363876033 0.000000 9.59586683 0.0000000 10.000000
ADHE2 2.7032685548 1000.000000 0.07228398 0.0000000 1000.000000
PFLA 5.6003779535 10.000000 0.40413317 0.0000000 150.000000
PTA 0.5726846792 0.000000 0.00000000 0.0000000 1660.380000
ACKA 0.5726846792 0.000000 0.00000000 0.0000000 1660.380000
ACS 0.5723694545 0.000000 0.00000000 0.0000000 1604.130000
PCKA 1.0329233709 0.000000 0.00000000 0.0000000 1604.130000
PPC 3.5214678351 194.384939 0.31213537 0.0000000 1704.130000
MAEB 0.7099687275 0.000000 0.00000000 0.0000000 1068.315000
SFCA 3.2311838936 0.000000 0.00000000 0.0000000 1068.315000
ACEA 1.4495298629 0.000000 0.00000000 0.0000000 30.000000
ACEB 1.4495298629 0.000000 0.00000000 0.0000000 30.000000
PPA 0.5723694545 0.000000 0.00000000 0.0000000 1604.130000
GLPK -0.0073259384 0.000000 0.00000000 0.0000000 0.000000
GPSA1 -1.6503354161 0.000000 0.00000000 -140.0000000 0.000000
RBSK -0.0010749329 0.000000 0.00000000 0.0000000 0.000000
NUOA -0.0055374704 140.000000 0.00000000 0.0000000 140.000000
FDOH 0.0004589440 0.000000 0.00000000 0.0000000 140.000000
GLPD 1.6430094777 0.000000 0.00000000 0.0000000 140.000000
CYOA 3.0887294375 40.000000 0.00000000 0.0000000 40.000000
SDHA2 1.4507984861 -100.000000 0.00000000 -100.0000000 8.333333
PNT1A 1.0521927265 0.000000 0.00000000 0.0000000 3208.260000
PNT2A 1.9796898743 567.965512 1.87828831 0.0000000 3208.260000
ATPA -2.4469611368 -145.466329 -0.06247093 -460.0000000 1144.130000
GLCUP 0.9042441896 0.000000 5.66169049 0.0000000 10.000000
GLCPTS 3.2867933251 814.156250 0.00000000 0.0000000 814.156250
GLUP -0.0073259384 0.000000 0.00000000 0.0000000 0.000000
RIBUP -0.0010749329 0.000000 0.00000000 0.0000000 0.000000
ACUP -0.0003152247 0.000000 0.00000000 -75.0000000 0.000000
LACUP -4.2363876033 0.000000 -9.59586683 -10.0000000 0.000000
FORUP -5.5999190095 -10.000000 -0.40413317 -10.0000000 0.000000
ETHUP -2.7032685548 -1000.000000 -0.07228398 -1000.0000000 0.000000
SUCCUP -0.0015479780 -100.000000 0.00000000 -130.0000000 0.000000
PYRUP -0.0065887889 -27.796342 0.00000000 -150.0000000 0.000000
PIUP -0.0059086421 120.547782 0.39865711 0.0000000 120.547782
O2TX 1.5443647188 20.000000 0.00000000 0.0000000 20.000000
CO2TX -1.4453447994 -990.346093 0.00000000 -1000.0000000 0.000000
ATPM 5.8700000000 5.870000 5.87000000 5.8700000 5.870000
ADK 1.0888157509 0.000000 0.00000000 0.0000000 1604.130000
Growth -0.0016232533 33.117523 0.10952118 0.0000000 33.117523
central
GLK1 5.2217621
PGI1 216.5697207
PFKA 238.7778727
FBP 22.9161429
FBA 215.8617298
TPIA 215.8617298
GAPA 430.0614321
PGK 430.0614321
GPMA 422.7068367
ENO 422.7068367
PPSA 50.9755288
PYKA 162.1156839
ACEE 315.0391553
ZWF 4.7377785
PGL 4.7377785
GND 4.7377785
RPIA 5.1002515
RPE -0.3624730
TKTA1 0.7072381
TKTA2 -1.0697111
TALA 0.7072381
GLTA 8.0839604
ACNA 8.0839604
ICDA 6.3683952
SUCA 1.0869072
SUCC1 1.0869072
SDHA1 1.8617943
FRDA 43.4000979
FUMA -41.5383036
MDH -75.1064185
DLD1 6.0611808
ADHE2 293.8147256
PFLA 9.5011072
PTA 72.0346497
ACKA 72.0346497
ACS 69.5691667
PCKA 36.7907143
PPC 128.7671200
MAEB 27.6528586
SFCA 7.6308214
ACEA 1.7155652
ACEB 1.7155652
PPA 69.5691667
GLPK 0.0000000
GPSA1 -8.7841492
RBSK 0.0000000
NUOA 47.2738862
FDOH 5.5622880
GLPD 8.7841492
CYOA 20.0820198
SDHA2 -41.5383036
PNT1A 106.2471989
PNT2A 161.4679124
ATPA -66.0598334
GLCUP 5.2217621
GLCPTS 217.0729311
GLUP 0.0000000
RIBUP 0.0000000
ACUP -2.4654831
LACUP -6.0611808
FORUP -3.9388192
ETHUP -293.8147256
SUCCUP -44.3407761
PYRUP -18.9265277
PIUP 17.9669311
O2TX 10.0410099
CO2TX -276.1017986
ATPM 5.8700000
ADK 120.5446954
Growth 4.9359701
>
> # The central value of linear programming problem is a valid solution
> # the central point is a valid solution:
> X <- xr[ ,"central"]
> max(abs(LIMEcoli$A%*%X - LIMEcoli$B))
[1] 3.979039e-13
> min(LIMEcoli$G%*%X - LIMEcoli$H)
[1] 0
>
> # 4. Sample solution space - this takes a while - note that iter is not enough
> print(system.time(
+ xs <- Xsample(LIMEcoli, iter = 200, type = "mirror", test = TRUE) ))
Warning in lsei(A = A, B = B, E = E, F = F, G = G, H = H) :
LSEI error: inequalities contradictory
Error in xsample(A = A, B = B, E = E, F = F, G = G, H = H, ...) :
no particular solution found;incompatible constraints
Calls: print -> system.time -> Xsample -> xsample
Timing stopped at: 0.002 0 0.011
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.4.7.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘LIM.Rnw’ using Sweave
--- finished re-building ‘LIM.Rnw’
--- re-building ‘LIMecoli.Rnw’ using Sweave
Loading required package: limSolve
Loading required package: diagram
Loading required package: shape
Warning in lsei(E = E, F = F, G = G, H = H) :
LSEI error: inequalities contradictory
Warning in lsei(A = A, B = B, E = E, F = F, G = G, H = H) :
LSEI error: inequalities contradictory
Timing stopped at: 0.005 0 0.028
Error: processing vignette 'LIMecoli.Rnw' failed with diagnostics:
chunk 9
Error in xsample(A = A, B = B, E = E, F = F, G = G, H = H, ...) :
no particular solution found;incompatible constraints
--- failed re-building ‘LIMecoli.Rnw’
SUMMARY: processing the following file failed:
‘LIMecoli.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc