# Pumas 2.5.0 bugs

**URL:** <https://discourse.pumas.ai/t/pumas-2-5-0-bugs/985>\
**Category:** Pumas issues\
**Created:** [February 14, 2024, 5:40am UTC](https://discourse.pumas.ai/t/pumas-2-5-0-bugs/985 "2024-02-14T05:40:04Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![donaldlee3](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.pumas.ai/donaldlee3/32/165_2.png) [@donaldlee3](https://discourse.pumas.ai/u/donaldlee3)\
**Post date:** [February 14, 2024, 5:40am UTC](https://discourse.pumas.ai/t/pumas-2-5-0-bugs/985/1 "2024-02-14T05:40:04Z")

</div>

I’ve noticed a few bugs I’d like to report.

1. Sometimes, inspect df’s will be unreadable by CSV.write due to the wres\_approx column.
2. Simulations generate cmt column that utilizes type String7, which cannot be read into read\_pumas.
3. If you utilize LogNormal residual error, inspect will not calculate weighted residuals.

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<div class="post-metadata">

**Author:** ![donaldlee3](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.pumas.ai/donaldlee3/32/165_2.png) [@donaldlee3](https://discourse.pumas.ai/u/donaldlee3)\
**Post date:** [February 14, 2024, 5:40am UTC](https://discourse.pumas.ai/t/pumas-2-5-0-bugs/985/2 "2024-02-14T05:40:46Z")

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Here is the error for reading the inspect df:

```auto
julia> test = CSV.read("./programs/results/estimation/separated/parallel_absorption/inspect_zo_Erlang_R_logit.csv", DataFrame, missingstring=[""])
┌ Warning: thread = 27 warning: only found 17 / 45 columns around data row: 379. Filling remaining columns with `missing`
└ @ CSV /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/CSV/OnldF/src/file.jl:577
┌ Warning: thread = 11 warning: only found 17 / 45 columns around data row: 234. Filling remaining columns with `missing`
└ @ CSV /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/CSV/OnldF/src/file.jl:577
┌ Warning: thread = 2 warning: only found 17 / 45 columns around data row: 698. Filling remaining columns with `missing`
└ @ CSV /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/CSV/OnldF/src/file.jl:577
┌ Warning: thread = 12 warning: only found 17 / 45 columns around data row: 176. Filling remaining columns with `missing`
└ @ CSV /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/CSV/OnldF/src/file.jl:577
┌ Warning: thread = 32 warning: only found 17 / 45 columns around data row: 466. Filling remaining columns with `missing`
└ @ CSV /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/CSV/OnldF/src/file.jl:577
┌ Warning: thread = 22 warning: only found 17 / 45 columns around data row: 843. Filling remaining columns with `missing`
└ @ CSV /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/CSV/OnldF/src/file.jl:577
ERROR: TaskFailedException

    nested task error: thread = 8 fatal error, encountered an invalidly quoted field while parsing around row = 174, col = 29: ""FOCE{Optim.NewtonTrustRegion{Float64}, Optim.Options{Float64, Nothing}}(Optim.NewtonTrustRegion{Float64}(1.0, 100.0, 1.4901161193847656e-8, 0.1, 0.25, 0.75, false), Optim.Options(x_abstol = 0.0, x_reltol = 0.0, f_abstol = 0.0, f_reltol = 0.0, g_abstol = 1.0e-5, g_reltol = 1.0e-8, outer_x_abstol = 0.0, outer_x_reltol = 0.0, outer_f_abstol = 0.0, outer_f_reltol = 0.0, outer_g_abstol = 1.0e-8, outer_g_reltol = 1.0e-8, f_calls_limit = 0, g_calls_limit = 0, h_calls_limit = 0, allow_f_increases = false, allow_outer_f_increases = true, successive_f_tol = 1, iterations = 1000, outer_iterations = 1000, store_trace = false, trace_simplex = false, show_trace = false, extended_trace = false, show_every = 1, time_limit = NaN, )
    ", error=INVALID: OK | QUOTED | EOF | INVALID_QUOTED_FIELD , check your `quotechar` arguments or manually fix the field in the file itself
    
    Stacktrace:
     [1] fatalerror(buf::Vector{UInt8}, pos::Int64, len::Int64, code::Int16, row::Int64, col::Int64)
       @ CSV /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/CSV/OnldF/src/file.jl:581
     [2] parsevalue!(#unused#::Type{String}, buf::Vector{UInt8}, pos::Int64, len::Int64, row::Int64, rowoffset::Int64, i::Int64, col::CSV.Column, ctx::CSV.Context)
       @ CSV /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/CSV/OnldF/src/file.jl:789
     [3] parserow
       @ /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/CSV/OnldF/src/file.jl:631 [inlined]
     [4] parsefilechunk!(ctx::CSV.Context, pos::Int64, len::Int64, rowsguess::Int64, rowoffset::Int64, columns::Vector{CSV.Column}, #unused#::Type{Tuple{}})
       @ CSV /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/CSV/OnldF/src/file.jl:550
     [5] multithreadparse(ctx::CSV.Context, pertaskcolumns::Vector{Vector{CSV.Column}}, rowchunkguess::Int64, i::Int64, rows::Vector{Int64}, wholecolumnslock::ReentrantLock)
       @ CSV /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/CSV/OnldF/src/file.jl:360
     [6] macro expansion
       @ /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/WorkerUtilities/ey0fP/src/WorkerUtilities.jl:384 [inlined]
     [7] (::CSV.var"#34#39"{CSV.Context, Vector{Vector{CSV.Column}}, Int64, Int64, Vector{Int64}, ReentrantLock})()
       @ CSV ./threadingconstructs.jl:410

...and 5 more exceptions.

Stacktrace:
 [1] sync_end(c::Channel{Any})
   @ Base ./task.jl:445
 [2] macro expansion
   @ ./task.jl:477 [inlined]
 [3] CSV.File(ctx::CSV.Context, chunking::Bool)
   @ CSV /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/CSV/OnldF/src/file.jl:240
 [4] File
   @ /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/CSV/OnldF/src/file.jl:227 [inlined]
 [5] #File#32
   @ /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/CSV/OnldF/src/file.jl:223 [inlined]
 [6] read(source::String, sink::Type; copycols::Bool, kwargs::Base.Pairs{Symbol, Vector{String}, Tuple{Symbol}, NamedTuple{(:missingstring,), Tuple{Vector{String}}}})
   @ CSV /build/_work/PumasSystemImages/PumasSystemImages/julia_depot/packages/CSV/OnldF/src/CSV.jl:117
 [7] top-level scope
   @ ~/data/code/padagis_mibe/post_FDA_meeting_Nov2023/m5/analysis/programs/model_fitting/pilot1_3_estimation_RT_separated_(parallel absorption_zo_Erlang)_(logit).jl:248

```

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<div class="post-metadata">

**Author:** ![patrick](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.pumas.ai/patrick/32/206_2.png) [@patrick](https://discourse.pumas.ai/u/patrick)\
**Post date:** [February 16, 2024, 10:45am UTC](https://discourse.pumas.ai/t/pumas-2-5-0-bugs/985/3 "2024-02-16T10:45:32Z")

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Dear Donald,

Thank you for the feedback.

1. Yes, this is indeed a regression from v2.4.x . We now expose the inner optimization options through the `FOCE` and `LaplaceI` constructors. This had the unintended consequence that a very verbose print of the information in each type is written out as `wres_approx`. If the expression contains the separator used in the CSV file, it will fail to read later. We will include a fix for this in the next bug fix release of the v2.5.x series of Pumas. Until then, the only workaround is to overwrite the column with `"FOCE"` or `"LaplaceI"` or drop the column completely before storing the CSV.

2. Can you help me understand how this might happen? Do you mean if you create a data frame from a simulation? I will file an issue, but I may need a few more details for it to be actionable on our end. Thank you.

3. This is correct. We currently do not output wres for `LogNormal` dependent variables, only `Normal`. To get something close to it, you would need to specify the model in the log-domain and evaluate the residuals that way. There is already an open issue to include this feature.

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<div class="post-metadata">

**Author:** ![donaldlee3](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.pumas.ai/donaldlee3/32/165_2.png) [@donaldlee3](https://discourse.pumas.ai/u/donaldlee3)\
**Post date:** [February 16, 2024, 5:38pm UTC](https://discourse.pumas.ai/t/pumas-2-5-0-bugs/985/4 "2024-02-16T17:38:21Z")

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Thank you, Patrick.

Yes, when I create a dataframe from a simulation, the cmt column will be of type String7, instead of Int or Symbol as required for read\_pumas.