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1.5.0-DEV-f014071421.log
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Julia Version 1.5.0-DEV.232
Commit f014071421 (2020-02-03 21:36 UTC)
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: Intel(R) Xeon(R) Silver 4114 CPU @ 2.20GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-9.0.1 (ORCJIT, skylake)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_NUM_THREADS = 2
Resolving package versions...
Installed IniFile ─────────────── v0.5.0
Installed JSONSchema ──────────── v0.2.0
Installed BinDeps ─────────────── v1.0.0
Installed HDF5 ────────────────── v0.12.5
Installed BufferedStreams ─────── v1.0.0
Installed CPLEX ───────────────── v0.6.3
Installed COBRA ───────────────── v0.3.0
Installed CMakeWrapper ────────── v0.2.3
Installed MathOptInterface ────── v0.9.10
Installed CodecZlib ───────────── v0.6.0
Installed CMake ───────────────── v1.1.2
Installed GLPKMathProgInterface ─ v0.4.4
Installed CodecBzip2 ──────────── v0.6.0
Installed Blosc ───────────────── v0.5.1
Installed TranscodingStreams ──── v0.9.5
Installed MAT ─────────────────── v0.7.0
Installed GLPK ────────────────── v0.12.1
Installed JSON ────────────────── v0.21.0
Installed MathProgBase ────────── v0.7.7
Installed Parsers ─────────────── v0.3.11
Installed OrderedCollections ──── v1.1.0
Installed BenchmarkTools ──────── v0.4.3
Installed MbedTLS ─────────────── v0.7.0
Installed MutableArithmetics ──── v0.2.2
Installed Parameters ──────────── v0.12.0
Installed HTTP ────────────────── v0.8.8
Installed BinaryProvider ──────── v0.5.8
Installed URIParser ───────────── v0.4.0
Installed Compat ──────────────── v2.2.0
Updating `~/.julia/environments/v1.5/Project.toml`
[58298e0b] + COBRA v0.3.0
Updating `~/.julia/environments/v1.5/Manifest.toml`
[6e4b80f9] + BenchmarkTools v0.4.3
[9e28174c] + BinDeps v1.0.0
[b99e7846] + BinaryProvider v0.5.8
[a74b3585] + Blosc v0.5.1
[e1450e63] + BufferedStreams v1.0.0
[631607c0] + CMake v1.1.2
[d5fb7624] + CMakeWrapper v0.2.3
[58298e0b] + COBRA v0.3.0
[a076750e] + CPLEX v0.6.3
[523fee87] + CodecBzip2 v0.6.0
[944b1d66] + CodecZlib v0.6.0
[34da2185] + Compat v2.2.0
[60bf3e95] + GLPK v0.12.1
[3c7084bd] + GLPKMathProgInterface v0.4.4
[f67ccb44] + HDF5 v0.12.5
[cd3eb016] + HTTP v0.8.8
[83e8ac13] + IniFile v0.5.0
[682c06a0] + JSON v0.21.0
[7d188eb4] + JSONSchema v0.2.0
[23992714] + MAT v0.7.0
[b8f27783] + MathOptInterface v0.9.10
[fdba3010] + MathProgBase v0.7.7
[739be429] + MbedTLS v0.7.0
[d8a4904e] + MutableArithmetics v0.2.2
[bac558e1] + OrderedCollections v1.1.0
[d96e819e] + Parameters v0.12.0
[69de0a69] + Parsers v0.3.11
[3bb67fe8] + TranscodingStreams v0.9.5
[30578b45] + URIParser v0.4.0
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8bb1440f] + DelimitedFiles
[8ba89e20] + Distributed
[b77e0a4c] + InteractiveUtils
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[44cfe95a] + Pkg
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Building CodecZlib ─→ `~/.julia/packages/CodecZlib/5t9zO/deps/build.log`
Building MbedTLS ───→ `~/.julia/packages/MbedTLS/a1JFn/deps/build.log`
Building CodecBzip2 → `~/.julia/packages/CodecBzip2/T5yr7/deps/build.log`
Building CPLEX ─────→ `~/.julia/packages/CPLEX/VVr3o/deps/build.log`
┌ Error: Error building `CPLEX`:
│ ERROR: LoadError: Unable to locate CPLEX installation. Note this must be downloaded separately. See the CPLEX.jl README for further instructions.
│ Stacktrace:
│ [1] error(::String) at ./error.jl:33
│ [2] try_local_installation() at /home/pkgeval/.julia/packages/CPLEX/VVr3o/deps/build.jl:64
│ [3] top-level scope at /home/pkgeval/.julia/packages/CPLEX/VVr3o/deps/build.jl:80
│ [4] include(::String) at ./client.jl:439
│ [5] top-level scope at none:5
│ in expression starting at /home/pkgeval/.julia/packages/CPLEX/VVr3o/deps/build.jl:77
└ @ Pkg.Operations /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:892
Building CMake ─────→ `~/.julia/packages/CMake/nSK2r/deps/build.log`
Building Blosc ─────→ `~/.julia/packages/Blosc/lzFr0/deps/build.log`
Building HDF5 ──────→ `~/.julia/packages/HDF5/Zh9on/deps/build.log`
Building GLPK ──────→ `~/.julia/packages/GLPK/HjJiX/deps/build.log`
Testing COBRA
Status `/tmp/jl_Kutj4h/Manifest.toml`
[6e4b80f9] BenchmarkTools v0.4.3
[9e28174c] BinDeps v1.0.0
[b99e7846] BinaryProvider v0.5.8
[a74b3585] Blosc v0.5.1
[e1450e63] BufferedStreams v1.0.0
[631607c0] CMake v1.1.2
[d5fb7624] CMakeWrapper v0.2.3
[58298e0b] COBRA v0.3.0
[a076750e] CPLEX v0.6.3
[523fee87] CodecBzip2 v0.6.0
[944b1d66] CodecZlib v0.6.0
[34da2185] Compat v2.2.0
[60bf3e95] GLPK v0.12.1
[3c7084bd] GLPKMathProgInterface v0.4.4
[f67ccb44] HDF5 v0.12.5
[cd3eb016] HTTP v0.8.8
[83e8ac13] IniFile v0.5.0
[682c06a0] JSON v0.21.0
[7d188eb4] JSONSchema v0.2.0
[23992714] MAT v0.7.0
[b8f27783] MathOptInterface v0.9.10
[fdba3010] MathProgBase v0.7.7
[739be429] MbedTLS v0.7.0
[d8a4904e] MutableArithmetics v0.2.2
[bac558e1] OrderedCollections v1.1.0
[d96e819e] Parameters v0.12.0
[69de0a69] Parsers v0.3.11
[3bb67fe8] TranscodingStreams v0.9.5
[30578b45] URIParser v0.4.0
[2a0f44e3] Base64
[ade2ca70] Dates
[8bb1440f] DelimitedFiles
[8ba89e20] Distributed
[b77e0a4c] InteractiveUtils
[76f85450] LibGit2
[8f399da3] Libdl
[37e2e46d] LinearAlgebra
[56ddb016] Logging
[d6f4376e] Markdown
[a63ad114] Mmap
[44cfe95a] Pkg
[de0858da] Printf
[3fa0cd96] REPL
[9a3f8284] Random
[ea8e919c] SHA
[9e88b42a] Serialization
[1a1011a3] SharedArrays
[6462fe0b] Sockets
[2f01184e] SparseArrays
[10745b16] Statistics
[8dfed614] Test
[cf7118a7] UUIDs
[4ec0a83e] Unicode
┌ Warning: Pkg.installed() is deprecated
└ @ Pkg /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/Pkg.jl:531
ERROR: LoadError: CPLEX not properly installed. Please run Pkg.build("CPLEX")
Stacktrace:
[1] error(::String) at ./error.jl:33
[2] top-level scope at /home/pkgeval/.julia/packages/CPLEX/VVr3o/src/CPLEX.jl:13
[3] include(::Module, ::String) at ./Base.jl:377
[4] top-level scope at none:2
[5] eval at ./boot.jl:331 [inlined]
[6] eval(::Expr) at ./client.jl:449
[7] top-level scope at ./none:3
in expression starting at /home/pkgeval/.julia/packages/CPLEX/VVr3o/src/CPLEX.jl:10
┌ Warning: Pkg.installed() is deprecated
└ @ Pkg /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/Pkg.jl:531
>> Checking the system's configuration ...
GLPKMathProgInterface is installed.
Package Gurobi is not installed. In order to use Gurobi, you must first run `Pkg.add("Gurobi")`
ERROR: LoadError: CPLEX not properly installed. Please run Pkg.build("CPLEX")
Stacktrace:
[1] error(::String) at ./error.jl:33
[2] top-level scope at /home/pkgeval/.julia/packages/CPLEX/VVr3o/src/CPLEX.jl:13
[3] include(::Module, ::String) at ./Base.jl:377
[4] top-level scope at none:2
[5] eval at ./boot.jl:331 [inlined]
[6] eval(::Expr) at ./client.jl:449
[7] top-level scope at ./none:3
in expression starting at /home/pkgeval/.julia/packages/CPLEX/VVr3o/src/CPLEX.jl:10
Package CPLEX is not installed. In order to use CPLEX, you must first run `Pkg.add("CPLEX")`
>> Done. 1 solvers are installed and ready to use.
[ Info: Parallel version - Connecting the 4 workers ...
4 local workers are connected. (+1) on host: 0a9a9107b3c0
Downloading the ecoli_core model ...Done.
┌ Warning: Pkg.installed() is deprecated
└ @ Pkg /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/Pkg.jl:531
┌ Warning: The MATLAB package is not present. The tests for PALM.jl will not be run.
└ @ Main ~/.julia/packages/COBRA/fOo2U/test/runtests.jl:97
> Testing GLPKMathProgInterface ... Done.
> Testing CPLEX ... Not supported.
> Testing Gurobi ... Not supported.
-- Running 13 tests using the GLPKMathProgInterface solver. --
Running s_all.jl ...
[ Info: The ecoli_core model already exists.
[ Info: The model named model loaded from /home/pkgeval/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
>> Size of stoichiometric matrix: (72, 95)
preFBA! [osenseStr = max]: FBAobj = 0.8739215069685174, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865289, norm(fbaSol) = 106.8373155300231.
Original FBA solved. Solution time: 2.967987060546875 s.
>> All 95 reactions of the model will be solved (100 %).
-- Minimization (iRound = 0). Block 1 [95/95].
-- Maximization (iRound = 1). Block 1 [95/95].
Saving minFlux (T:> Array{Float64,1}) ...Done.
Saving maxFlux (T:> Array{Float64,1}) ...Done.
Saving optSol (T:> Float64) ...Done.
Saving fbaSol (T:> Array{Float64,1}) ...Done.
Saving fvamin (T:> Array{Float64,2}) ...Done.
Saving fvamax (T:> Array{Float64,2}) ...Done.
Saving statussolmin (T:> Array{Float64,1}) ...Done.
Saving statussolmax (T:> Array{Float64,1}) ...Done.
Saving rxnsList (T:> UnitRange{Int64}) ...Done.
All available variables saved to testFile.mat.
-- Solution summary --
/home/pkgeval/.julia/packages/COBRA/fOo2U/test/s_all.jl
Original FBA obj.val 0.8739215069685174
Maximum of maxFlux: 1000.0
Minimum of maxFlux: -20.93588573353488
Maximum of minFlux: 35.98482480548924
Minimum of minFlux: -32.258260515219455
Norm of maxFlux: 1427.0738873421458
Norm of minFlux: 93.66619388260854
Solution time [s]: 10.525077104568481
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Running s_core.jl ...
[ Info: The ecoli_core model already exists.
[ Info: The model named model loaded from /home/pkgeval/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
>> Size of stoichiometric matrix: (72, 95)
preFBA! [osenseStr = max]: FBAobj = 0.8739215069685174, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865289, norm(fbaSol) = 106.8373155300231.
Original FBA solved. Solution time: 0.0014460086822509766 s.
>> All 95 reactions of the model will be solved (100 %).
-- Minimization (iRound = 0). Block 1 [95/95].
-- Maximization (iRound = 1). Block 1 [95/95].
Saving minFlux (T:> Array{Float64,1}) ...Done.
Saving maxFlux (T:> Array{Float64,1}) ...Done.
Saving optSol (T:> Float64) ...Done.
Saving fbaSol (T:> Array{Float64,1}) ...Done.
Saving fvamin (T:> Array{Float64,2}) ...Done.
Saving fvamax (T:> Array{Float64,2}) ...Done.
Saving statussolmin (T:> Array{Float64,1}) ...Done.
Saving statussolmax (T:> Array{Float64,1}) ...Done.
Saving rxnsList (T:> UnitRange{Int64}) ...Done.
All available variables saved to testFile.mat.
[ Info: The model named modelCoupled loaded from modelCoupled.mat is a coupled model.
[ Info: The model objective is set to be maximized.
[ Info: The model named modelCoupled loaded from modelCoupled.mat is a coupled model.
[ Info: The model objective is set to be maximized.
-- Solution summary --
/home/pkgeval/.julia/packages/COBRA/fOo2U/test/s_core.jl
Original FBA obj.val 0.8739215069685174
Maximum of maxFlux: 1000.0
Minimum of maxFlux: -20.93588573353488
Maximum of minFlux: 35.98482480548924
Minimum of minFlux: -32.258260515219455
Norm of maxFlux: 1427.0738873421458
Norm of minFlux: 93.66619388260854
Solution time [s]: 0.2059769630432129
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Running s_distinct.jl ...
[ Info: The ecoli_core model already exists.
[ Info: The model named model loaded from /home/pkgeval/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
>> Size of stoichiometric matrix: (72, 95)
preFBA! [osenseStr = max]: FBAobj = 0.8739215069685174, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865289, norm(fbaSol) = 106.8373155300231.
Original FBA solved. Solution time: 0.003464937210083008 s.
>> All 95 reactions of the model will be solved (100 %).
-- Minimization (iRound = 0). Block 1 [95/95].
-- Maximization (iRound = 1). Block 1 [95/95].
>> Size of stoichiometric matrix: (73, 95)
preFBA! [osenseStr = max]: FBAobj = 0.8739215069685877, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865289, norm(fbaSol) = 106.83731553002139.
Original FBA solved. Solution time: 0.001580953598022461 s.
>> Only 17 reactions of 95 will be solved (~ 17.894736842105264 %).
-- Minimization (iRound = 0). Block 1 [17/95].
-- Maximization (iRound = 1). Block 1 [17/95].
>> Size of stoichiometric matrix: (74, 95)
preFBA! [osenseStr = max]: FBAobj = 0.8739215069685877, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865289, norm(fbaSol) = 106.83731553002139.
Original FBA solved. Solution time: 0.0027480125427246094 s.
>> Only 17 reactions of 95 will be solved (~ 17.894736842105264 %).
-- Minimization (iRound = 0). Block 1 [17/95].
-- Maximization (iRound = 1). Block 1 [17/95].
Saving minFlux (T:> Array{Float64,1}) ...Done.
Saving maxFlux (T:> Array{Float64,1}) ...Done.
Saving optSol (T:> Float64) ...Done.
Saving fbaSol (T:> Array{Float64,1}) ...Done.
Saving fvamin (T:> Array{Float64,2}) ...Done.
Saving fvamax (T:> Array{Float64,2}) ...Done.
Saving statussolmin (T:> Array{Float64,1}) ...Done.
Saving statussolmax (T:> Array{Float64,1}) ...Done.
Saving rxnsList (T:> Array{Int64,1}) ...Done.
All available variables saved to testFile.mat.
-- Solution summary --
/home/pkgeval/.julia/packages/COBRA/fOo2U/test/s_distinct.jl
Original FBA obj.val 0.8739215069685877
Maximum of maxFlux: 26.528869396061772
Minimum of maxFlux: -9.04660613349818
Maximum of minFlux: 15.206494614374979
Minimum of minFlux: -10.0
Norm of maxFlux: 37.02464689379309
Norm of minFlux: 22.00443371346725
Solution time [s]: 0.19455289840698242
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Running s_fba.jl ...
[ Info: The ecoli_core model already exists.
[ Info: The model named model loaded from /home/pkgeval/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
┌ Warning: Assignment to `startTime` in soft scope is ambiguous because a global variable by the same name exists: `startTime` will be treated as a new local. Disambiguate by using `local startTime` to suppress this warning or `global startTime` to assign to the existing global variable.
└ @ ~/.julia/packages/COBRA/fOo2U/test/s_fba.jl:61
┌ Warning: Assignment to `minFlux` in soft scope is ambiguous because a global variable by the same name exists: `minFlux` will be treated as a new local. Disambiguate by using `local minFlux` to suppress this warning or `global minFlux` to assign to the existing global variable.
└ @ ~/.julia/packages/COBRA/fOo2U/test/s_fba.jl:62
┌ Warning: Assignment to `maxFlux` in soft scope is ambiguous because a global variable by the same name exists: `maxFlux` will be treated as a new local. Disambiguate by using `local maxFlux` to suppress this warning or `global maxFlux` to assign to the existing global variable.
└ @ ~/.julia/packages/COBRA/fOo2U/test/s_fba.jl:62
┌ Warning: Assignment to `optSol` in soft scope is ambiguous because a global variable by the same name exists: `optSol` will be treated as a new local. Disambiguate by using `local optSol` to suppress this warning or `global optSol` to assign to the existing global variable.
└ @ ~/.julia/packages/COBRA/fOo2U/test/s_fba.jl:62
┌ Warning: Assignment to `fbaSol` in soft scope is ambiguous because a global variable by the same name exists: `fbaSol` will be treated as a new local. Disambiguate by using `local fbaSol` to suppress this warning or `global fbaSol` to assign to the existing global variable.
└ @ ~/.julia/packages/COBRA/fOo2U/test/s_fba.jl:62
┌ Warning: Assignment to `fvamin` in soft scope is ambiguous because a global variable by the same name exists: `fvamin` will be treated as a new local. Disambiguate by using `local fvamin` to suppress this warning or `global fvamin` to assign to the existing global variable.
└ @ ~/.julia/packages/COBRA/fOo2U/test/s_fba.jl:62
┌ Warning: Assignment to `fvamax` in soft scope is ambiguous because a global variable by the same name exists: `fvamax` will be treated as a new local. Disambiguate by using `local fvamax` to suppress this warning or `global fvamax` to assign to the existing global variable.
└ @ ~/.julia/packages/COBRA/fOo2U/test/s_fba.jl:62
┌ Warning: Assignment to `statussolmin` in soft scope is ambiguous because a global variable by the same name exists: `statussolmin` will be treated as a new local. Disambiguate by using `local statussolmin` to suppress this warning or `global statussolmin` to assign to the existing global variable.
└ @ ~/.julia/packages/COBRA/fOo2U/test/s_fba.jl:62
┌ Warning: Assignment to `statussolmax` in soft scope is ambiguous because a global variable by the same name exists: `statussolmax` will be treated as a new local. Disambiguate by using `local statussolmax` to suppress this warning or `global statussolmax` to assign to the existing global variable.
└ @ ~/.julia/packages/COBRA/fOo2U/test/s_fba.jl:62
┌ Warning: Assignment to `solTime` in soft scope is ambiguous because a global variable by the same name exists: `solTime` will be treated as a new local. Disambiguate by using `local solTime` to suppress this warning or `global solTime` to assign to the existing global variable.
└ @ ~/.julia/packages/COBRA/fOo2U/test/s_fba.jl:63
┌ Warning: The value of optPercentage is > 0%, but preFBA = false. Set preFBA = true in order to take optPercentage into account.
│
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/distributedFBA.jl:547
Original FBA. No additional constraints have been added.
>> Only 1 reaction of 95 will be solved (~ 1.0526315789473684 %).
-- Maximization (iRound = 1). Block 1 [1/95].
-- Solution summary --
/home/pkgeval/.julia/packages/COBRA/fOo2U/test/s_fba.jl
Maximum of maxFlux: 0.8739215069685174
Minimum of maxFlux: 0.0
Maximum of minFlux: 0.0
Minimum of minFlux: 0.0
Norm of maxFlux: 0.8739215069685174
Norm of minFlux: 0.0
Solution time [s]: 1.636693000793457
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
┌ Warning: The value of optPercentage is > 0%, but preFBA = false. Set preFBA = true in order to take optPercentage into account.
│
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/distributedFBA.jl:547
Original FBA. No additional constraints have been added.
>> Only 1 reaction of 95 will be solved (~ 1.0526315789473684 %).
-- Maximization (iRound = 1). Block 1 [1/95].
-- Solution summary --
/home/pkgeval/.julia/packages/COBRA/fOo2U/test/s_fba.jl
Maximum of maxFlux: 0.8739215069685174
Minimum of maxFlux: 0.0
Maximum of minFlux: 0.0
Minimum of minFlux: 0.0
Norm of maxFlux: 0.8739215069685174
Norm of minFlux: 0.0
Solution time [s]: 0.0036818981170654297
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
┌ Warning: The value of optPercentage is > 0%, but preFBA = false. Set preFBA = true in order to take optPercentage into account.
│
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/distributedFBA.jl:547
Original FBA. No additional constraints have been added.
>> Only 1 reaction of 95 will be solved (~ 1.0526315789473684 %).
-- Maximization (iRound = 1). Block 1 [1/95].
-- Solution summary --
/home/pkgeval/.julia/packages/COBRA/fOo2U/test/s_fba.jl
Maximum of maxFlux: 0.8739215069685174
Minimum of maxFlux: 0.0
Maximum of minFlux: 0.0
Minimum of minFlux: 0.0
Norm of maxFlux: 0.8739215069685174
Norm of minFlux: 0.0
Solution time [s]: 0.003744840621948242
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Original FBA. No additional constraints have been added.
>> Only 1 reaction of 95 will be solved (~ 1.0526315789473684 %).
-- Maximization (iRound = 1). Block 1 [1/95].
-- Solution summary --
/home/pkgeval/.julia/packages/COBRA/fOo2U/test/s_fba.jl
Maximum of maxFlux: 0.8739215069685174
Minimum of maxFlux: 0.0
Maximum of minFlux: 0.0
Minimum of minFlux: 0.0
Norm of maxFlux: 0.8739215069685174
Norm of minFlux: 0.0
Solution time [s]: 0.041458845138549805
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Original FBA. No additional constraints have been added.
>> Only 1 reaction of 95 will be solved (~ 1.0526315789473684 %).
Saving minFlux (T:> Array{Float64,1}) ...Done.
Saving maxFlux (T:> Array{Float64,1}) ...Done.
Saving optSol (T:> Float64) ...Done.
Saving fbaSol (T:> Array{Float64,1}) ...Done.
Saving fvamin (T:> Array{Float64,2}) ...Done.
Saving fvamax (T:> Array{Float64,2}) ...Done.
Saving statussolmin (T:> Array{Float64,1}) ...Done.
Saving statussolmax (T:> Array{Float64,1}) ...Done.
Saving rxnsList (T:> Int64) ...Done.
All available variables saved to testFile.mat.
-- Solution summary --
/home/pkgeval/.julia/packages/COBRA/fOo2U/test/s_fba.jl
Maximum of maxFlux: 0.0
Minimum of maxFlux: 0.0
Maximum of minFlux: 0.0
Minimum of minFlux: 0.0
Norm of maxFlux: 0.0
Norm of minFlux: 0.0
Solution time [s]: 0.004139900207519531
Number of workers: 1
Solver: GLPKMathProgInterface
Distribution strategy: 0
Saving individual files: false
Running s_tools.jl ...
[ Info: The model named model loaded from /home/pkgeval/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
┌ Warning: Some reaction names are not in the model; their indices in the `rxnsList` are reported in `rxnIDsNE`.
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/tools.jl:88
Running z_all.jl ...
[ Info: The ecoli_core model already exists.
>> The following tests throw warning messages for testing purposes. <<
[ Info: Sequential version - Depending on the model size, expect long execution times.
┌ Warning: Assignment to `workersPool` in soft scope is ambiguous because a global variable by the same name exists: `workersPool` will be treated as a new local. Disambiguate by using `local workersPool` to suppress this warning or `global workersPool` to assign to the existing global variable.
└ @ ~/.julia/packages/COBRA/fOo2U/test/z_all.jl:68
┌ Warning: Assignment to `nWorkers` in soft scope is ambiguous because a global variable by the same name exists: `nWorkers` will be treated as a new local. Disambiguate by using `local nWorkers` to suppress this warning or `global nWorkers` to assign to the existing global variable.
└ @ ~/.julia/packages/COBRA/fOo2U/test/z_all.jl:68
┌ Warning: Assignment to `workersPool` in soft scope is ambiguous because a global variable by the same name exists: `workersPool` will be treated as a new local. Disambiguate by using `local workersPool` to suppress this warning or `global workersPool` to assign to the existing global variable.
└ @ ~/.julia/packages/COBRA/fOo2U/test/z_all.jl:69
┌ Warning: Assignment to `nWorkers` in soft scope is ambiguous because a global variable by the same name exists: `nWorkers` will be treated as a new local. Disambiguate by using `local nWorkers` to suppress this warning or `global nWorkers` to assign to the existing global variable.
└ @ ~/.julia/packages/COBRA/fOo2U/test/z_all.jl:69
┌ Warning: Assignment to `workersPool` in soft scope is ambiguous because a global variable by the same name exists: `workersPool` will be treated as a new local. Disambiguate by using `local workersPool` to suppress this warning or `global workersPool` to assign to the existing global variable.
└ @ ~/.julia/packages/COBRA/fOo2U/test/z_all.jl:70
┌ Warning: Assignment to `nWorkers` in soft scope is ambiguous because a global variable by the same name exists: `nWorkers` will be treated as a new local. Disambiguate by using `local nWorkers` to suppress this warning or `global nWorkers` to assign to the existing global variable.
└ @ ~/.julia/packages/COBRA/fOo2U/test/z_all.jl:70
Loading SSH connection details from /home/pkgeval/.julia/packages/COBRA/fOo2U/src/../config/sshCfg.jl ...Done.
[ Info: Parallel version - Connecting the 56 workers ...
[ Info: Connecting SSH nodes ...
>> Connecting 8 workers on [email protected]
[ Info: Parallel version - Connecting the 4 workers ...
4 workers already connected. No further workers to connect.
[ Info: Parallel version - Connecting the 2 workers ...
2 workers already connected. No further workers to connect.
[ Info: The model named model loaded from /home/pkgeval/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
┌ Warning: The value of optPercentage is > 0%, but preFBA = false. Set preFBA = true in order to take optPercentage into account.
│
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/distributedFBA.jl:547
Original FBA. No additional constraints have been added.
┌ Warning: The `rxnsList` has more reactions than in the model. `rxnsList` shorted to the maximum number of reactions.
└ @ COBRA ~/.julia/packages/COBRA/fOo2U/src/distributedFBA.jl:637
>> Only 96 reactions of 95 will be solved (~ 101.05263157894737 %).
-- Minimization (iRound = 0). Block 1 [95/95].
-- Maximization (iRound = 1). Block 1 [95/95].
>> Size of stoichiometric matrix: (72, 95)
preFBA! [osenseStr = min]: FBAobj = 0.8739215069685174, optPercentage = 90.0, objValue = optPercentage * FBAobj = 0.7865298, norm(fbaSol) = 106.8373155300231.
┌ Warning: Assignment to `optSol` in soft scope is ambiguous because a global variable by the same name exists: `optSol` will be treated as a new local. Disambiguate by using `local optSol` to suppress this warning or `global optSol` to assign to the existing global variable.
└ @ ~/.julia/packages/COBRA/fOo2U/test/z_all.jl:88
┌ Warning: Assignment to `fbaSol` in soft scope is ambiguous because a global variable by the same name exists: `fbaSol` will be treated as a new local. Disambiguate by using `local fbaSol` to suppress this warning or `global fbaSol` to assign to the existing global variable.
└ @ ~/.julia/packages/COBRA/fOo2U/test/z_all.jl:88
>> Size of stoichiometric matrix: (73, 95)
No objective set (`c` is zero). objValue and fbaSol not defined. optPercentage = 90.0.
[ Info: The model named model loaded from /home/pkgeval/.julia/packages/COBRA/fOo2U/src/../test/ecoli_core_model.mat is a uncoupled model.
[ Info: The model objective is set to be maximized.
[ Info: All constraints assumed equality constaints.
-- Minimization (iRound = 0). Block 1 [1/2].
[ Info: The model named modelTest loaded from /home/pkgeval/.julia/packages/COBRA/fOo2U/src/../test/testData.mat is a uncoupled model.
-- Maximization (iRound = 1). Block 1 [1/2].
>> Note: Warnings above are thrown for testing purposes and can be safely ignored.
-- All tests passed. --
Testing COBRA tests passed