BioServices.jl Efetch

The efetch function is giving me errors when I run the following command: where request_str is a array of pmids.

EUtils.efetch(db = "pubmed", tool = "BioJulia", retmode = "xml", rettype = "null", id = request_str)

Expected Behavior

The function should return formatted data records for a the list of pmids.

Current Behavior

This is the output that I get when I try to run efetch.

.jl:613 caused by [exception 5] error compiling #getconnection#11: error compiling #sslconnection#18: error compiling global_sslconfig: error compiling #SSLConfig#46: could not load library "C:\Users\Thor.julia\packages\MbedTLS\a1JFn\deps\usr\bin\libmbedtls.dll" The specified procedure could not be found.

Stacktrace: [1] #request#1(::Nothing, ::Type, ::Int64, ::Base.Iterators.Pairs{Symbol,Nothing,Tuple{Symbol},NamedTuple{(:iofunction,),Tuple{Nothing}}}, ::typeof(HTTP.request), ::Type{ConnectionPoolLayer{StreamLayer{Union{}}}}, ::HTTP.URIs.URI, ::HTTP.Messages.Request, ::String) at C:\Users\Thor.julia\packages\HTTP\6Smhf\src\ConnectionRequest.jl:41 [2] (::getfield(HTTP, Symbol("#kw##request")))(::NamedTuple{(:iofunction,),Tuple{Nothing}}, ::typeof(HTTP.request), ::Type{ConnectionPoolLayer{StreamLayer{Union{}}}}, ::HTTP.URIs.URI, ::HTTP.Messages.Request, ::String) at .\none:0 [3] #request#1(::Base.Iterators.Pairs{Symbol,Nothing,Tuple{Symbol},NamedTuple{(:iofunction,),Tuple{Nothing}}}, ::typeof(HTTP.request), ::Type{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}, ::HTTP.URIs.URI, ::Vararg{Any,N} where N) at C:\Users\Thor.julia\packages\HTTP\6Smhf\src\ExceptionRequest.jl:19 [4] (::getfield(HTTP, Symbol("#kw##request")))(::NamedTuple{(:iofunction,),Tuple{Nothing}}, ::typeof(HTTP.request), ::Type{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}, ::HTTP.URIs.URI, ::HTTP.Messages.Request, ::String) at .\none:0 [5] (::getfield(Base, Symbol("###50#51#53")){ExponentialBackOff,getfield(HTTP.RetryRequest, Symbol("##2#3")){Bool,HTTP.Messages.Request},typeof(HTTP.request)})(::Base.Iterators.Pairs{Symbol,Nothing,Tuple{Symbol},NamedTuple{(:iofunction,),Tuple{Nothing}}}, ::getfield(Base, Symbol("##50#52")){getfield(Base, Symbol("###50#51#53")){ExponentialBackOff,getfield(HTTP.RetryRequest, Symbol("##2#3")){Bool,HTTP.Messages.Request},typeof(HTTP.request)}}, ::Type, ::Vararg{Any,N} where N) at .\error.jl:249 [6] #request#1(::VersionNumber, ::String, ::Nothing, ::Nothing, ::Base.Iterators.Pairs{Symbol,Bool,Tuple{Symbol},NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}}, ::typeof(HTTP.request), ::Type{MessageLayer{RetryLayer{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}}}, ::String, ::HTTP.URIs.URI, ::Array{Pair{SubString{String},SubString{String}},1}, ::String) at .\none:0 [7] (::getfield(HTTP, Symbol("#kw##request")))(::NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}, ::typeof(HTTP.request), ::Type{MessageLayer{RetryLayer{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}}}, ::String, ::HTTP.URIs.URI, ::Array{Pair{SubString{String},SubString{String}},1}, ::String) at .\none:0 [8] #request#1(::Int64, ::Bool, ::Base.Iterators.Pairs{Symbol,Bool,Tuple{Symbol},NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}}, ::typeof(HTTP.request), ::Type{RedirectLayer{MessageLayer{RetryLayer{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}}}}, ::String, ::HTTP.URIs.URI, ::Array{Pair{SubString{String},SubString{String}},1}, ::String) at C:\Users\Thor.julia\packages\HTTP\6Smhf\src\RedirectRequest.jl:24 [9] (::getfield(HTTP, Symbol("#kw##request")))(::NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}, ::typeof(HTTP.request), ::Type{RedirectLayer{MessageLayer{RetryLayer{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}}}}, ::String, ::HTTP.URIs.URI, ::Array{Pair{SubString{String},SubString{String}},1}, ::String) at .\none:0 [10] #request#5(::Array{Pair{SubString{String},SubString{String}},1}, ::String, ::Nothing, ::Base.Iterators.Pairs{Symbol,Bool,Tuple{Symbol},NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}}, ::typeof(HTTP.request), ::String, ::String, ::Array{Pair{SubString{String},SubString{String}},1}, ::Array{UInt8,1}) at C:\Users\Thor.julia\packages\HTTP\6Smhf\src\HTTP.jl:308 [11] #request at .\none:0 [inlined] (repeats 2 times) [12] #efetch#5 at C:\Users\Thor.julia\packages\BioServices\KPZxN\src\eutils.jl:126 [inlined] [13] #efetch at .\none:0 [inlined] (repeats 2 times) [14] get_pubmed_efetch_as_xml(::Array{Any,1}) at C:\Users\Thor\Documents\Machine Learning\Work\collect_data.jl:482 [15] main() at C:\Users\Thor\Documents\Machine Learning\Work\collect_data.jl:577 [16] top-level scope at C:\Users\Thor\Documents\Machine Learning\Work\collect_data.jl:613 [17] include at .\boot.jl:328 [inlined] [18] include_relative(::Module, ::String) at .\loading.jl:1094 [19] include(::Module, ::String) at .\Base.jl:31 [20] exec_options(::Base.JLOptions) at .\client.jl:295 [21] _start() at .\client.jl:464 caused by [exception 4] error compiling #sslconnection#18: error compiling global_sslconfig: error compiling #SSLConfig#46: could not load library "C:\Users\Thor.julia\packages\MbedTLS\a1JFn\deps\usr\bin\libmbedtls.dll" The specified procedure could not be found.

Stacktrace: [1] #request#1(::Nothing, ::Type, ::Int64, ::Base.Iterators.Pairs{Symbol,Nothing,Tuple{Symbol},NamedTuple{(:iofunction,),Tuple{Nothing}}}, ::typeof(HTTP.request), ::Type{ConnectionPoolLayer{StreamLayer{Union{}}}}, ::HTTP.URIs.URI, ::HTTP.Messages.Request, ::String) at C:\Users\Thor.julia\packages\HTTP\6Smhf\src\ConnectionRequest.jl:41 [2] (::getfield(HTTP, Symbol("#kw##request")))(::NamedTuple{(:iofunction,),Tuple{Nothing}}, ::typeof(HTTP.request), ::Type{ConnectionPoolLayer{StreamLayer{Union{}}}}, ::HTTP.URIs.URI, ::HTTP.Messages.Request, ::String) at .\none:0 [3] #request#1(::Base.Iterators.Pairs{Symbol,Nothing,Tuple{Symbol},NamedTuple{(:iofunction,),Tuple{Nothing}}}, ::typeof(HTTP.request), ::Type{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}, ::HTTP.URIs.URI, ::Vararg{Any,N} where N) at C:\Users\Thor.julia\packages\HTTP\6Smhf\src\ExceptionRequest.jl:19 [4] (::getfield(HTTP, Symbol("#kw##request")))(::NamedTuple{(:iofunction,),Tuple{Nothing}}, ::typeof(HTTP.request), ::Type{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}, ::HTTP.URIs.URI, ::HTTP.Messages.Request, ::String) at .\none:0 [5] (::getfield(Base, Symbol("###50#51#53")){ExponentialBackOff,getfield(HTTP.RetryRequest, Symbol("##2#3")){Bool,HTTP.Messages.Request},typeof(HTTP.request)})(::Base.Iterators.Pairs{Symbol,Nothing,Tuple{Symbol},NamedTuple{(:iofunction,),Tuple{Nothing}}}, ::getfield(Base, Symbol("##50#52")){getfield(Base, Symbol("###50#51#53")){ExponentialBackOff,getfield(HTTP.RetryRequest, Symbol("##2#3")){Bool,HTTP.Messages.Request},typeof(HTTP.request)}}, ::Type, ::Vararg{Any,N} where N) at .\error.jl:249 [6] #request#1(::VersionNumber, ::String, ::Nothing, ::Nothing, ::Base.Iterators.Pairs{Symbol,Bool,Tuple{Symbol},NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}}, ::typeof(HTTP.request), ::Type{MessageLayer{RetryLayer{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}}}, ::String, ::HTTP.URIs.URI, ::Array{Pair{SubString{String},SubString{String}},1}, ::String) at .\none:0 [7] (::getfield(HTTP, Symbol("#kw##request")))(::NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}, ::typeof(HTTP.request), ::Type{MessageLayer{RetryLayer{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}}}, ::String, ::HTTP.URIs.URI, ::Array{Pair{SubString{String},SubString{String}},1}, ::String) at .\none:0 [8] #request#1(::Int64, ::Bool, ::Base.Iterators.Pairs{Symbol,Bool,Tuple{Symbol},NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}}, ::typeof(HTTP.request), ::Type{RedirectLayer{MessageLayer{RetryLayer{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}}}}, ::String, ::HTTP.URIs.URI, ::Array{Pair{SubString{String},SubString{String}},1}, ::String) at C:\Users\Thor.julia\packages\HTTP\6Smhf\src\RedirectRequest.jl:24 [9] (::getfield(HTTP, Symbol("#kw##request")))(::NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}, ::typeof(HTTP.request), ::Type{RedirectLayer{MessageLayer{RetryLayer{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}}}}, ::String, ::HTTP.URIs.URI, ::Array{Pair{SubString{String},SubString{String}},1}, ::String) at .\none:0 [10] #request#5(::Array{Pair{SubString{String},SubString{String}},1}, ::String, ::Nothing, ::Base.Iterators.Pairs{Symbol,Bool,Tuple{Symbol},NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}}, ::typeof(HTTP.request), ::String, ::String, ::Array{Pair{SubString{String},SubString{String}},1}, ::Array{UInt8,1}) at C:\Users\Thor.julia\packages\HTTP\6Smhf\src\HTTP.jl:308 [11] #request at .\none:0 [inlined] (repeats 2 times) [12] #efetch#5 at C:\Users\Thor.julia\packages\BioServices\KPZxN\src\eutils.jl:126 [inlined] [13] #efetch at .\none:0 [inlined] (repeats 2 times) [14] get_pubmed_efetch_as_xml(::Array{Any,1}) at C:\Users\Thor\Documents\Machine Learning\Work\collect_data.jl:482 [15] main() at C:\Users\Thor\Documents\Machine Learning\Work\collect_data.jl:577 [16] top-level scope at C:\Users\Thor\Documents\Machine Learning\Work\collect_data.jl:613 [17] include at .\boot.jl:328 [inlined] [18] include_relative(::Module, ::String) at .\loading.jl:1094 [19] include(::Module, ::String) at .\Base.jl:31 [20] exec_options(::Base.JLOptions) at .\client.jl:295 [21] _start() at .\client.jl:464 caused by [exception 3] error compiling global_sslconfig: error compiling #SSLConfig#46: could not load library "C:\Users\Thor.julia\packages\MbedTLS\a1JFn\deps\usr\bin\libmbedtls.dll" The specified procedure could not be found.

Stacktrace: [1] #request#1(::Nothing, ::Type, ::Int64, ::Base.Iterators.Pairs{Symbol,Nothing,Tuple{Symbol},NamedTuple{(:iofunction,),Tuple{Nothing}}}, ::typeof(HTTP.request), ::Type{ConnectionPoolLayer{StreamLayer{Union{}}}}, ::HTTP.URIs.URI, ::HTTP.Messages.Request, ::String) at C:\Users\Thor.julia\packages\HTTP\6Smhf\src\ConnectionRequest.jl:41 [2] (::getfield(HTTP, Symbol("#kw##request")))(::NamedTuple{(:iofunction,),Tuple{Nothing}}, ::typeof(HTTP.request), ::Type{ConnectionPoolLayer{StreamLayer{Union{}}}}, ::HTTP.URIs.URI, ::HTTP.Messages.Request, ::String) at .\none:0 [3] #request#1(::Base.Iterators.Pairs{Symbol,Nothing,Tuple{Symbol},NamedTuple{(:iofunction,),Tuple{Nothing}}}, ::typeof(HTTP.request), ::Type{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}, ::HTTP.URIs.URI, ::Vararg{Any,N} where N) at C:\Users\Thor.julia\packages\HTTP\6Smhf\src\ExceptionRequest.jl:19 [4] (::getfield(HTTP, Symbol("#kw##request")))(::NamedTuple{(:iofunction,),Tuple{Nothing}}, ::typeof(HTTP.request), ::Type{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}, ::HTTP.URIs.URI, ::HTTP.Messages.Request, ::String) at .\none:0 [5] (::getfield(Base, Symbol("###50#51#53")){ExponentialBackOff,getfield(HTTP.RetryRequest, Symbol("##2#3")){Bool,HTTP.Messages.Request},typeof(HTTP.request)})(::Base.Iterators.Pairs{Symbol,Nothing,Tuple{Symbol},NamedTuple{(:iofunction,),Tuple{Nothing}}}, ::getfield(Base, Symbol("##50#52")){getfield(Base, Symbol("###50#51#53")){ExponentialBackOff,getfield(HTTP.RetryRequest, Symbol("##2#3")){Bool,HTTP.Messages.Request},typeof(HTTP.request)}}, ::Type, ::Vararg{Any,N} where N) at .\error.jl:249 [6] #request#1(::VersionNumber, ::String, ::Nothing, ::Nothing, ::Base.Iterators.Pairs{Symbol,Bool,Tuple{Symbol},NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}}, ::typeof(HTTP.request), ::Type{MessageLayer{RetryLayer{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}}}, ::String, ::HTTP.URIs.URI, ::Array{Pair{SubString{String},SubString{String}},1}, ::String) at .\none:0 [7] (::getfield(HTTP, Symbol("#kw##request")))(::NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}, ::typeof(HTTP.request), ::Type{MessageLayer{RetryLayer{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}}}, ::String, ::HTTP.URIs.URI, ::Array{Pair{SubString{String},SubString{String}},1}, ::String) at .\none:0 [8] #request#1(::Int64, ::Bool, ::Base.Iterators.Pairs{Symbol,Bool,Tuple{Symbol},NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}}, ::typeof(HTTP.request), ::Type{RedirectLayer{MessageLayer{RetryLayer{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}}}}, ::String, ::HTTP.URIs.URI, ::Array{Pair{SubString{String},SubString{String}},1}, ::String) at C:\Users\Thor.julia\packages\HTTP\6Smhf\src\RedirectRequest.jl:24 [9] (::getfield(HTTP, Symbol("#kw##request")))(::NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}, ::typeof(HTTP.request), ::Type{RedirectLayer{MessageLayer{RetryLayer{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}}}}, ::String, ::HTTP.URIs.URI, ::Array{Pair{SubString{String},SubString{String}},1}, ::String) at .\none:0 [10] #request#5(::Array{Pair{SubString{String},SubString{String}},1}, ::String, ::Nothing, ::Base.Iterators.Pairs{Symbol,Bool,Tuple{Symbol},NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}}, ::typeof(HTTP.request), ::String, ::String, ::Array{Pair{SubString{String},SubString{String}},1}, ::Array{UInt8,1}) at C:\Users\Thor.julia\packages\HTTP\6Smhf\src\HTTP.jl:308 [11] #request at .\none:0 [inlined] (repeats 2 times) [12] #efetch#5 at C:\Users\Thor.julia\packages\BioServices\KPZxN\src\eutils.jl:126 [inlined] [13] #efetch at .\none:0 [inlined] (repeats 2 times) [14] get_pubmed_efetch_as_xml(::Array{Any,1}) at C:\Users\Thor\Documents\Machine Learning\Work\collect_data.jl:482 [15] main() at C:\Users\Thor\Documents\Machine Learning\Work\collect_data.jl:577 [16] top-level scope at C:\Users\Thor\Documents\Machine Learning\Work\collect_data.jl:613 [17] include at .\boot.jl:328 [inlined] [18] include_relative(::Module, ::String) at .\loading.jl:1094 [19] include(::Module, ::String) at .\Base.jl:31 [20] exec_options(::Base.JLOptions) at .\client.jl:295 [21] _start() at .\client.jl:464 caused by [exception 2] error compiling #SSLConfig#46: could not load library "C:\Users\Thor.julia\packages\MbedTLS\a1JFn\deps\usr\bin\libmbedtls.dll" The specified procedure could not be found.

Stacktrace: [1] #request#1(::Nothing, ::Type, ::Int64, ::Base.Iterators.Pairs{Symbol,Nothing,Tuple{Symbol},NamedTuple{(:iofunction,),Tuple{Nothing}}}, ::typeof(HTTP.request), ::Type{ConnectionPoolLayer{StreamLayer{Union{}}}}, ::HTTP.URIs.URI, ::HTTP.Messages.Request, ::String) at C:\Users\Thor.julia\packages\HTTP\6Smhf\src\ConnectionRequest.jl:41 [2] (::getfield(HTTP, Symbol("#kw##request")))(::NamedTuple{(:iofunction,),Tuple{Nothing}}, ::typeof(HTTP.request), ::Type{ConnectionPoolLayer{StreamLayer{Union{}}}}, ::HTTP.URIs.URI, ::HTTP.Messages.Request, ::String) at .\none:0 [3] #request#1(::Base.Iterators.Pairs{Symbol,Nothing,Tuple{Symbol},NamedTuple{(:iofunction,),Tuple{Nothing}}}, ::typeof(HTTP.request), ::Type{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}, ::HTTP.URIs.URI, ::Vararg{Any,N} where N) at C:\Users\Thor.julia\packages\HTTP\6Smhf\src\ExceptionRequest.jl:19 [4] (::getfield(HTTP, Symbol("#kw##request")))(::NamedTuple{(:iofunction,),Tuple{Nothing}}, ::typeof(HTTP.request), ::Type{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}, ::HTTP.URIs.URI, ::HTTP.Messages.Request, ::String) at .\none:0 [5] (::getfield(Base, Symbol("###50#51#53")){ExponentialBackOff,getfield(HTTP.RetryRequest, Symbol("##2#3")){Bool,HTTP.Messages.Request},typeof(HTTP.request)})(::Base.Iterators.Pairs{Symbol,Nothing,Tuple{Symbol},NamedTuple{(:iofunction,),Tuple{Nothing}}}, ::getfield(Base, Symbol("##50#52")){getfield(Base, Symbol("###50#51#53")){ExponentialBackOff,getfield(HTTP.RetryRequest, Symbol("##2#3")){Bool,HTTP.Messages.Request},typeof(HTTP.request)}}, ::Type, ::Vararg{Any,N} where N) at .\error.jl:249 [6] #request#1(::VersionNumber, ::String, ::Nothing, ::Nothing, ::Base.Iterators.Pairs{Symbol,Bool,Tuple{Symbol},NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}}, ::typeof(HTTP.request), ::Type{MessageLayer{RetryLayer{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}}}, ::String, ::HTTP.URIs.URI, ::Array{Pair{SubString{String},SubString{String}},1}, ::String) at .\none:0 [7] (::getfield(HTTP, Symbol("#kw##request")))(::NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}, ::typeof(HTTP.request), ::Type{MessageLayer{RetryLayer{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}}}, ::String, ::HTTP.URIs.URI, ::Array{Pair{SubString{String},SubString{String}},1}, ::String) at .\none:0 [8] #request#1(::Int64, ::Bool, ::Base.Iterators.Pairs{Symbol,Bool,Tuple{Symbol},NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}}, ::typeof(HTTP.request), ::Type{RedirectLayer{MessageLayer{RetryLayer{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}}}}, ::String, ::HTTP.URIs.URI, ::Array{Pair{SubString{String},SubString{String}},1}, ::String) at C:\Users\Thor.julia\packages\HTTP\6Smhf\src\RedirectRequest.jl:24 [9] (::getfield(HTTP, Symbol("#kw##request")))(::NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}, ::typeof(HTTP.request), ::Type{RedirectLayer{MessageLayer{RetryLayer{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}}}}, ::String, ::HTTP.URIs.URI, ::Array{Pair{SubString{String},SubString{String}},1}, ::String) at .\none:0 [10] #request#5(::Array{Pair{SubString{String},SubString{String}},1}, ::String, ::Nothing, ::Base.Iterators.Pairs{Symbol,Bool,Tuple{Symbol},NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}}, ::typeof(HTTP.request), ::String, ::String, ::Array{Pair{SubString{String},SubString{String}},1}, ::Array{UInt8,1}) at C:\Users\Thor.julia\packages\HTTP\6Smhf\src\HTTP.jl:308 [11] #request at .\none:0 [inlined] (repeats 2 times) [12] #efetch#5 at C:\Users\Thor.julia\packages\BioServices\KPZxN\src\eutils.jl:126 [inlined] [13] #efetch at .\none:0 [inlined] (repeats 2 times) [14] get_pubmed_efetch_as_xml(::Array{Any,1}) at C:\Users\Thor\Documents\Machine Learning\Work\collect_data.jl:482 [15] main() at C:\Users\Thor\Documents\Machine Learning\Work\collect_data.jl:577 [16] top-level scope at C:\Users\Thor\Documents\Machine Learning\Work\collect_data.jl:613 [17] include at .\boot.jl:328 [inlined] [18] include_relative(::Module, ::String) at .\loading.jl:1094 [19] include(::Module, ::String) at .\Base.jl:31 [20] exec_options(::Base.JLOptions) at .\client.jl:295 [21] _start() at .\client.jl:464 caused by [exception 1] could not load library "C:\Users\Thor.julia\packages\MbedTLS\a1JFn\deps\usr\bin\libmbedtls.dll" The specified procedure could not be found.

Stacktrace: [1] #request#1(::Nothing, ::Type, ::Int64, ::Base.Iterators.Pairs{Symbol,Nothing,Tuple{Symbol},NamedTuple{(:iofunction,),Tuple{Nothing}}}, ::typeof(HTTP.request), ::Type{ConnectionPoolLayer{StreamLayer{Union{}}}}, ::HTTP.URIs.URI, ::HTTP.Messages.Request, ::String) at C:\Users\Thor.julia\packages\HTTP\6Smhf\src\ConnectionRequest.jl:41 [2] (::getfield(HTTP, Symbol("#kw##request")))(::NamedTuple{(:iofunction,),Tuple{Nothing}}, ::typeof(HTTP.request), ::Type{ConnectionPoolLayer{StreamLayer{Union{}}}}, ::HTTP.URIs.URI, ::HTTP.Messages.Request, ::String) at .\none:0 [3] #request#1(::Base.Iterators.Pairs{Symbol,Nothing,Tuple{Symbol},NamedTuple{(:iofunction,),Tuple{Nothing}}}, ::typeof(HTTP.request), ::Type{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}, ::HTTP.URIs.URI, ::Vararg{Any,N} where N) at C:\Users\Thor.julia\packages\HTTP\6Smhf\src\ExceptionRequest.jl:19 [4] (::getfield(HTTP, Symbol("#kw##request")))(::NamedTuple{(:iofunction,),Tuple{Nothing}}, ::typeof(HTTP.request), ::Type{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}, ::HTTP.URIs.URI, ::HTTP.Messages.Request, ::String) at .\none:0 [5] (::getfield(Base, Symbol("###50#51#53")){ExponentialBackOff,getfield(HTTP.RetryRequest, Symbol("##2#3")){Bool,HTTP.Messages.Request},typeof(HTTP.request)})(::Base.Iterators.Pairs{Symbol,Nothing,Tuple{Symbol},NamedTuple{(:iofunction,),Tuple{Nothing}}}, ::getfield(Base, Symbol("##50#52")){getfield(Base, Symbol("###50#51#53")){ExponentialBackOff,getfield(HTTP.RetryRequest, Symbol("##2#3")){Bool,HTTP.Messages.Request},typeof(HTTP.request)}}, ::Type, ::Vararg{Any,N} where N) at .\error.jl:249 [6] #request#1(::VersionNumber, ::String, ::Nothing, ::Nothing, ::Base.Iterators.Pairs{Symbol,Bool,Tuple{Symbol},NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}}, ::typeof(HTTP.request), ::Type{MessageLayer{RetryLayer{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}}}, ::String, ::HTTP.URIs.URI, ::Array{Pair{SubString{String},SubString{String}},1}, ::String) at .\none:0 [7] (::getfield(HTTP, Symbol("#kw##request")))(::NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}, ::typeof(HTTP.request), ::Type{MessageLayer{RetryLayer{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}}}, ::String, ::HTTP.URIs.URI, ::Array{Pair{SubString{String},SubString{String}},1}, ::String) at .\none:0 [8] #request#1(::Int64, ::Bool, ::Base.Iterators.Pairs{Symbol,Bool,Tuple{Symbol},NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}}, ::typeof(HTTP.request), ::Type{RedirectLayer{MessageLayer{RetryLayer{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}}}}, ::String, ::HTTP.URIs.URI, ::Array{Pair{SubString{String},SubString{String}},1}, ::String) at C:\Users\Thor.julia\packages\HTTP\6Smhf\src\RedirectRequest.jl:24 [9] (::getfield(HTTP, Symbol("#kw##request")))(::NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}, ::typeof(HTTP.request), ::Type{RedirectLayer{MessageLayer{RetryLayer{ExceptionLayer{ConnectionPoolLayer{StreamLayer{Union{}}}}}}}}, ::String, ::HTTP.URIs.URI, ::Array{Pair{SubString{String},SubString{String}},1}, ::String) at .\none:0 [10] #request#5(::Array{Pair{SubString{String},SubString{String}},1}, ::String, ::Nothing, ::Base.Iterators.Pairs{Symbol,Bool,Tuple{Symbol},NamedTuple{(:retry_non_idempotent,),Tuple{Bool}}}, ::typeof(HTTP.request), ::String, ::String, ::Array{Pair{SubString{String},SubString{String}},1}, ::Array{UInt8,1}) at C:\Users\Thor.julia\packages\HTTP\6Smhf\src\HTTP.jl:308 [11] #request at .\none:0 [inlined] (repeats 2 times) [12] #efetch#5 at C:\Users\Thor.julia\packages\BioServices\KPZxN\src\eutils.jl:126 [inlined] [13] #efetch at .\none:0 [inlined] (repeats 2 times) [14] get_pubmed_efetch_as_xml(::Array{Any,1}) at C:\Users\Thor\Documents\Machine Learning\Work\collect_data.jl:482 [15] main() at C:\Users\Thor\Documents\Machine Learning\Work\collect_data.jl:577 [16] top-level scope at C:\Users\Thor\Documents\Machine Learning\Work\collect_data.jl:613 [17] include at .\boot.jl:328 [inlined] [18] include_relative(::Module, ::String) at .\loading.jl:1094 [19] include(::Module, ::String) at .\Base.jl:31 [20] exec_options(::Base.JLOptions) at .\client.jl:295 [21] _start() at .\client.jl:464

Your Environment

Package Version used: 0.3.2
Julia Version used: 1.2
Operating System and version (desktop or mobile): Windows 10

"CSV" => v"0.5.14" "TextAnalysis" => v"0.6.0" "BioMedQuery" => v"0.6.4" "Atom" => v"0.10.1" "Juno" => v"0.7.2" "Conda" => v"1.3.0" "HTTP" => v"0.8.7" "DecFP" => v"0.4.8" "LinearAlgebra" => nothing "Missings" => v"0.4.3" "ScikitLearn" => v"0.5.1" "BioServices" => v"0.3.2" "StatsBase" => v"0.32.0" "VariantVisualization" => v"0.4.0" "Tables" => v"0.2.11" "EzXML" => v"0.9.4" "MbedTLS" => v"0.7.0" "Languages" => v"0.4.2" "DataFrames" => v"0.19.4" "Printf" => nothing "MySQL" => v"0.7.1" "LightXML" => v"0.8.1"

Nov 27 '19 16:11 anthonyagudelox3

Is anyone watching?

Mar 19 '20 18:03 anthonyagudelox3

Also this seems to be an issue only on Windows as efetch seems to be working on Mac.

Mar 19 '20 18:03 anthonyagudelox3

Huh... I thought I responded to this issue a couple of weeks ago, sorry! Unfortunately, my only contribution was to say that I could reproduce it. Don't know the solution :-(

Mar 20 '20 15:03 kescobo

Hey Kevin, you did reply I was trying to see if I could get the attention of someone on the Eutils package in BioServices. I was wondering what would be the best way to go about this?

Mar 20 '20 16:03 anthonyagudelox3

Oh, I see. Glad I'm not going crazy 😆. You should reference the other thread.

I don't have a good answer - not sure this package has any dedicated maintainers. @BenJWard Do you know who we should ping about this?

Mar 20 '20 20:03 kescobo

@anthonyagudelox3, can you upgrade MbedTLS?

Mar 21 '20 11:03 CiaranOMara

@CiaranOMara

I have added the link to the issue posted on the MbedTLS page. https://github.com/JuliaLang/MbedTLS.jl/issues/211#issue-529571394

I have tried updating MbedTLS is seems to still be giving issues.

Mar 23 '20 14:03 anthonyagudelox3

Hi - I'm supposed to be the dedicated maintainer. Sorry for all the silence. I however no longer find the time to give it the love it needs 😞. I have been trying to recruit. .... @aguang is willing to help out. Can we add them as a maintainer?

Mar 27 '20 12:03 mirestrepo

@ibacher was also interested at some point... If he is still interested, I'd say the more maintainers the merrier.

Mar 27 '20 12:03 mirestrepo

@mirestrepo Unfortunately, do to some changes in the scope of what I do, I don't think I really have enough time to take on maintaining this project.

Mar 27 '20 16:03 ibacher