CRAN Package Check Results for Package LIM

Last updated on 2025-05-17 17:49:24 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

Check Details

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