Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

0.11.1 Build Tests Fail when building app tarball #58

Closed
ACastanza opened this issue Aug 4, 2022 · 3 comments
Closed

0.11.1 Build Tests Fail when building app tarball #58

ACastanza opened this issue Aug 4, 2022 · 3 comments
Assignees
@KwatMDPhD

Comments

@ACastanza
Copy link
Collaborator

ACastanza commented Aug 4, 2022 •
edited
Loading 

#12 390.5 [ Info: PackageCompiler: Executing /GSEA.jl/test/runtests.jl => /tmp/jl_packagecompiler_04WKdI/jl_Qgyo2H
#12 416.7 Before filtering sets
#12 416.9 50 keys and 50 unique values
#12 416.9 {
#12 416.9    ...
#12 416.9 }
#12 416.9 Keeping sets: 33 <= size <= 36
#12 416.9 After
#12 416.9 2 keys and 2 unique values
#12 416.9 {
#12 416.9    ...
#12 416.9 }
#12 418.0 Before filtering sets
#12 418.0 50 keys and 50 unique values
#12 418.0 {
#12 418.0    ...
#12 418.0 }
#12 418.0 Removing set genes not found in gene-x-sample genes
#12 418.1 Keeping sets: 1 <= size <= 5656
#12 418.1 After
#12 418.1 2 keys and 2 unique values
#12 418.1 {
#12 418.1    ...
#12 418.1 }
#12 430.9 Before filtering sets
#12 430.9 50 keys and 50 unique values
#12 430.9 {
#12 430.9    ...
#12 430.9 }
#12 430.9 Keeping sets: 15 <= size <= 500
#12 430.9 After
#12 430.9 50 keys and 50 unique values
#12 430.9 {
#12 430.9    ...
#12 430.9 }
#12 435.3 Printing 50 x 10
#12 435.4 1:3 x 1:3
#12 436.8 3×3 DataFrame
#12 436.8  Row │ Set                    BRAF-MAPK  EMT
#12 436.8      │ String                 Float64    Float64
#12 436.8 ─────┼───────────────────────────────────────────────
#12 436.8    1 │ HALLMARK_ANGIOGENESIS  0.0689969   0.00258519
#12 436.8    2 │ HALLMARK_MYOGENESIS    0.0345786  -0.0293882
#12 436.8    3 │ HALLMARK_PEROXISOME    0.0759652  -0.0146123
#12 436.8 1:3 x 8:10
#12 436.8 3×3 DataFrame
#12 436.8  Row │ MYC-E2F    RAS-WNT-PI3K  TNF-NFKB-YAP
#12 436.8      │ Float64    Float64       Float64
#12 436.8 ─────┼───────────────────────────────────────
#12 436.8    1 │ -0.333331   -0.048732      0.014379
#12 436.8    2 │ -0.152555    0.00639009   -0.00517372
#12 436.8    3 │ -0.274279    0.152952     -0.106246
#12 436.8 48:50 x 1:3
#12 436.8 3×3 DataFrame
#12 436.8  Row │ Set                               BRAF-MAPK   EMT
#12 436.8      │ String                            Float64     Float64
#12 436.8 ─────┼────────────────────────────────────────────────────────────
#12 436.8    1 │ HALLMARK_GLYCOLYSIS                0.0472282  -0.000195916
#12 436.8    2 │ HALLMARK_HEDGEHOG_SIGNALING       -0.054991   -0.105903
#12 436.8    3 │ HALLMARK_IL6_JAK_STAT3_SIGNALING   0.0611482  -0.172375
#12 436.8 48:50 x 8:10
#12 436.8 3×3 DataFrame
#12 436.8  Row │ MYC-E2F     RAS-WNT-PI3K  TNF-NFKB-YAP
#12 436.8      │ Float64     Float64       Float64
#12 436.8 ─────┼────────────────────────────────────────
#12 436.8    1 │  0.0474211     0.0631814     -0.122306
#12 436.8    2 │ -0.196474     -0.0585218     -0.19448
#12 436.8    3 │ -0.259747      0.0618397     -0.498493
#12 437.1 Before filtering sets
#12 437.1 50 keys and 50 unique values
#12 437.1 {
#12 437.1    ...
#12 437.1 }
#12 437.1 Keeping sets: 15 <= size <= 500
#12 437.1 After
#12 437.1 50 keys and 50 unique values
#12 437.1 {
#12 437.1    ...
#12 437.1 }
#12 438.0 Permuting sets to compute significance
100.0%┣██████████████████████████████████████████┫ 100/100 [00:10<00:00, 10it/s]
#12 453.6 Made /tmp/GSEA.test/user_rank/plot/hallmark_pancreas_beta_cells.html.
#12 454.5 ERROR: LoadError: IOError: could not spawn `powershell.exe -NoProfile -NonInteractive -Command start '"../tmp/GSEA.test/user_rank/plot/hallmark_pancreas_beta_cells.html"'`: no such file or directory (ENOENT)
#12 455.6 Stacktrace:
#12 455.6   [1] _spawn_primitive(file::String, cmd::Cmd, stdio::Vector{Any})
#12 456.0     @ Base ./process.jl:100
#12 456.1   [2] #690
#12 456.1     @ ./process.jl:113 [inlined]
#12 456.1   [3] setup_stdios(f::Base.var"#690#691"{Cmd}, stdios::Vector{Any})
#12 456.1     @ Base ./process.jl:197
#12 456.1   [4] _spawn
#12 456.1     @ ./process.jl:112 [inlined]
#12 456.1   [5] run(::Cmd; wait::Bool)
#12 456.1     @ Base ./process.jl:449
#12 456.1   [6] #open#1
#12 456.1     @ ~/.julia/packages/DefaultApplication/7wyMn/src/DefaultApplication.jl:28 [inlined]
#12 456.1   [7] open(filename::String)
#12 456.1     @ DefaultApplication ~/.julia/packages/DefaultApplication/7wyMn/src/DefaultApplication.jl:19
#12 456.1   [8] make(di::String, sr_::Vector{String}, sc::String, ht::String)
#12 456.1     @ OnePiece.html ~/.julia/packages/OnePiece/WncNA/src/html/make.jl:34
#12 456.1   [9] plot(data::Vector{Dict{String, Any}}, layout::Dict{String, Any}; config::Dict{Any, Any}, ou::String)
#12 456.1     @ OnePiece.figure ~/.julia/packages/OnePiece/WncNA/src/figure/plot.jl:30
#12 456.1  [10] _plot_mountain(fe_::Vector{String}, sc_::Vector{Float64}, in_::Vector{Bool}, en_::Vector{Float64}, ::Tuple{Float64, Float64}; title_text::String, ou::String)
#12 456.1     @ OnePiece.feature_set_enrichment ~/.julia/packages/OnePiece/WncNA/src/feature_set_enrichment/_plot_mountain.jl:171
#12 456.1  [11] score_set(fe_::Vector{String}, sc_::Vector{Float64}, fe1_::Vector{Any}, in_::Vector{Bool}; ex::Float64, pl::Bool, ke_ar::Base.Pairs{Symbol, String, Tuple{Symbol, Symbol}, NamedTuple{(:title_text, :ou), Tuple{String, String}}})
#12 456.2     @ OnePiece.feature_set_enrichment ~/.julia/packages/OnePiece/WncNA/src/feature_set_enrichment/score_set.jl:103
#12 456.2  [12] score_set(fe_::Vector{String}, sc_::Vector{Float64}, fe1_::Vector{Any}; ex::Float64, pl::Bool, ke_ar::Base.Pairs{Symbol, String, Tuple{Symbol, Symbol}, NamedTuple{(:title_text, :ou), Tuple{String, String}}})
#12 456.2     @ OnePiece.feature_set_enrichment ~/.julia/packages/OnePiece/WncNA/src/feature_set_enrichment/score_set.jl:113
#12 456.2  [13] _plot_mountain(se_x_st_x_nu::DataFrames.DataFrame, n_ex::Int64, pl_::Vector{Any}, fe_::Vector{String}, sc_::Vector{Float64}, se_fe_::Dict{String, Any}, sy_ar::Dict{Symbol, Real}, ou::String)
#12 456.2     @ GSEA /GSEA.jl/src/_plot_mountain.jl:13
#12 456.2  [14] user_rank(fe_::Vector{String}, sc_::Vector{Float64}, se_fe_::Dict{String, Any}, al::String, sy_ar::Dict{Symbol, Real}, ra::Int64, n_pe::Int64, n_ex::Int64, pl_::Vector{Any}, ou::String)
#12 456.2     @ GSEA /GSEA.jl/src/user_rank.jl:35
#12 456.2  [15] user_rank(setting_json::String, gene_x_metric_x_score_tsv::String, set_genes_json::String, output_directory::String)
#12 456.2     @ GSEA /GSEA.jl/src/user_rank.jl:76
#12 456.2  [16] top-level scope
#12 456.2     @ /GSEA.jl/test/runtests.jl:48
#12 456.2 in expression starting at /GSEA.jl/test/runtests.jl:48
#12 456.5 ERROR: LoadError: failed process: Process(setenv(`/usr/local/julia/bin/julia --color=auto --startup-file=no --sysimage=/tmp/jl_HGOuwI/sys.ji --compile=all --trace-compile=/tmp/jl_packagecompiler_04WKdI/jl_Qgyo2H /GSEA.jl/test/runtests.jl`,["PATH=/usr/local/julia/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin", "JULIA_VERSION=1.7.2", "PWD=/GSEA.jl", "OPENBLAS_NUM_THREADS=8", "JULIA_PATH=/usr/local/julia", "OLDPWD=/", "HOME=/root", "JULIA_GPG=3673DF529D9049477F76B37566E3C7DC03D6E495", "OPENBLAS_MAIN_FREE=1", "JULIA_LOAD_PATH=/GSEA.jl:@stdlib"]), ProcessExited(1)) [1]
#12 457.3
#12 457.3 Stacktrace:
#12 457.3   [1] pipeline_error
#12 457.3     @ ./process.jl:531 [inlined]
#12 457.3   [2] run(::Cmd; wait::Bool)
#12 457.5     @ Base ./process.jl:446
#12 457.6   [3] run
#12 457.6     @ ./process.jl:444 [inlined]
#12 457.6   [4] run_precompilation_script(project::String, sysimg::String, precompile_file::String, precompile_dir::String)
#12 457.6     @ PackageCompiler ~/.julia/packages/PackageCompiler/o0ZdL/src/PackageCompiler.jl:239
#12 457.6   [5] create_sysimg_object_file(object_file::String, packages::Vector{String}, packages_sysimg::Set{Base.PkgId}; project::String, base_sysimage::String, precompile_execution_file::Vector{String}, precompile_statements_file::Vector{String}, cpu_target::String, script::Nothing, sysimage_build_args::Cmd, extra_precompiles::String, incremental::Bool)
#12 457.6     @ PackageCompiler ~/.julia/packages/PackageCompiler/o0ZdL/src/PackageCompiler.jl:261
#12 457.6   [6] create_sysimage(packages::Vector{String}; sysimage_path::String, project::String, precompile_execution_file::Vector{String}, precompile_statements_file::Vector{String}, incremental::Bool, filter_stdlibs::Bool, cpu_target::String, script::Nothing, sysimage_build_args::Cmd, include_transitive_dependencies::Bool, base_sysimage::Nothing, julia_init_c_file::Nothing, version::Nothing, soname::Nothing, compat_level::String, extra_precompiles::String)
#12 457.6     @ PackageCompiler ~/.julia/packages/PackageCompiler/o0ZdL/src/PackageCompiler.jl:510
#12 457.6   [7] create_app(package_dir::String, app_dir::String; executables::Vector{Pair{String, String}}, precompile_execution_file::Vector{String}, precompile_statements_file::Vector{String}, incremental::Bool, filter_stdlibs::Bool, force::Bool, c_driver_program::String, cpu_target::String, include_lazy_artifacts::Bool, sysimage_build_args::Cmd, include_transitive_dependencies::Bool)
#12 457.6     @ PackageCompiler ~/.julia/packages/PackageCompiler/o0ZdL/src/PackageCompiler.jl:722
#12 457.6   [8] build_application(m::Module, options::Comonicon.Configs.Comonicon)
#12 457.6     @ Comonicon.Builder ~/.julia/packages/Comonicon/YiFWj/src/builder/app.jl:10
#12 457.6   [9] command_main(m::Module, options::Comonicon.Configs.Comonicon)
#12 457.6     @ Comonicon.Builder ~/.julia/packages/Comonicon/YiFWj/src/builder/cli.jl:74
#12 457.6  [10] #command_main#1
#12 457.6     @ ~/.julia/packages/Comonicon/YiFWj/src/builder/cli.jl:49 [inlined]
#12 457.6  [11] command_main
#12 457.6     @ ~/.julia/packages/Comonicon/YiFWj/src/builder/cli.jl:48 [inlined]
#12 457.6  [12] #comonicon_install#13
#12 457.6     @ ~/.julia/packages/Comonicon/YiFWj/src/frontend/cast.jl:483 [inlined]
#12 457.6  [13] comonicon_install()
#12 457.6     @ GSEA ~/.julia/packages/Comonicon/YiFWj/src/frontend/cast.jl:483
#12 457.6  [14] top-level scope
#12 457.6     @ /GSEA.jl/deps/build.jl:3
#12 457.6 in expression starting at /GSEA.jl/deps/build.jl:3
------
executor failed running [/bin/sh -c cd GSEA.jl && julia --project deps/build.jl app tarball]: exit code: 1
@KwatMDPhD
Copy link
Member 

#12 454.5 ERROR: LoadError: IOError: could not spawn `powershell.exe -NoProfile -NonInteractive -Command start '"../tmp/GSEA.test/user_rank/plot/hallmark_pancreas_beta_cells.html"'`: no such file or directory (ENOENT)

I wonder if this is due to auto browser opening.

@KwatMDPhD
Copy link
Member

Try 0.11.2, please. Hope it works.

@KwatMDPhD KwatMDPhD self-assigned this Aug 4, 2022
@ACastanza
Copy link
Collaborator Author

This error has been fixed however a new error has arisen at a later stage (see #59)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@KwatMDPhD KwatMDPhD

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@KwatMDPhD @ACastanza