could not load library "C:\Users\Thor\.julia\packages\MbedTLS\a1JFn\deps\usr\bin\libmbedtls.dll"

[anthonyagudelox3]

Hey, I am trying to use a function in the BioServices.jl package, efetch() which utilizes MbedTLS.jl. When I run efetch I get the following error and says could not load library "C:\Users\Thor.julia\packages\MbedTLS\a1JFn\deps\usr\bin\libmbedtls.dll":

Stacktrace:
[1] #request#1(::Nothing, ::Type, ::Int64, ::Base.Iterators.Pairs{Symbol,Nothing,Tuple{Symbol},NamedTuple{(:iofunction,),Tuple{Nothing}}}, ::typeof(HTTP.request), ::Type{HTTP.ConnectionRequest.ConnectionPoolLayer{HTTP.StreamRequest.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{HTTP.ConnectionRequest.ConnectionPoolLayer{HTTP.StreamRequest.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{HTTP.ExceptionRequest.ExceptionLayer{HTTP.ConnectionRequest.ConnectionPoolLayer{HTTP.StreamRequest.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{HTTP.ExceptionRequest.ExceptionLayer{HTTP.ConnectionRequest.ConnectionPoolLayer{HTTP.StreamRequest.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{HTTP.MessageRequest.MessageLayer{HTTP.RetryRequest.RetryLayer{HTTP.ExceptionRequest.ExceptionLayer{HTTP.ConnectionRequest.ConnectionPoolLayer{HTTP.StreamRequest.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{HTTP.MessageRequest.MessageLayer{HTTP.RetryRequest.RetryLayer{HTTP.ExceptionRequest.ExceptionLayer{HTTP.ConnectionRequest.ConnectionPoolLayer{HTTP.StreamRequest.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{HTTP.RedirectRequest.RedirectLayer{HTTP.MessageRequest.MessageLayer{HTTP.RetryRequest.RetryLayer{HTTP.ExceptionRequest.ExceptionLayer{HTTP.ConnectionRequest.ConnectionPoolLayer{HTTP.StreamRequest.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{HTTP.RedirectRequest.RedirectLayer{HTTP.MessageRequest.MessageLayer{HTTP.RetryRequest.RetryLayer{HTTP.ExceptionRequest.ExceptionLayer{HTTP.ConnectionRequest.ConnectionPoolLayer{HTTP.StreamRequest.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] top-level scope at REPL[6]:1
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.

I am running julia 1.2.0
on a Windows 10 machine and the following packages installed:

"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"

[anthonyagudelox3]

Is anyone watching?

[kescobo]

Hi Anthony - Sorry no one has replied to you. I'm afraid I won't be much help fixing the issue, but have you tried building MbedTLS itself? In the REPL, just do ] build MbedTLS.

[anthonyagudelox3]

Hi Anthony - Sorry no one has replied to you. I'm afraid I won't be much help fixing the issue, but have you tried building MbedTLS itself? In the REPL, just do ] build MbedTLS.

Hey Kevin- No worries, and I have tried building MbedTLS. Building the package works fine.

[kescobo]

Ok, that's good - does this solve the original issue, or do you still end up with the same error?

[anthonyagudelox3]

Unfortunately, I still end up with the same issue.

[kescobo]

:-( I'm afraid I don't have a good idea where to go next (not a windows user). What's the actual error message (just above the stack trace)?

Might also be helpful to share the actual query (if you can), I can see if I get some other error on mac/linux that might be illuminating.

[anthonyagudelox3]

The actual error is:

ERROR: LoadError: error compiling #getconnection: 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.

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

Where request_str being:

request_str = [7683506, 21273794, 20502278, 12837696, 9671894, 10910540, 1726111, 12925463, 14977895, 8354293, 21126967, 11874162, 11196419, 19856865, 14711867, 11077942, 19369394, 10071840, 17653692, 24052503, 19828801, 22875049, 1756527, 21094951, 21392146, 1641273, 7562289, 8157019, 11149114, 19588439, 20526778, 21056307, 9988814, 15678510, 20071566, 16856062, 17921123, 11474660, 17728088, 19803911, 16510632, 10321674, 22654787, 304806, 9751753, 15818055, 22491902, 22414880, 17377412, 23920104, 9458929, 9175950, 16837240, 11339911, 12439489, 24368157, 21197428, 16251172, 18724063, 22009856, 11912289, 10070119, 17314118, 11529543, 12865310, 17686002, 9124602, 11406028, 12148961, 21093581, 21166684, 15131465, 12427391, 19571582, 20510913, 17095552, 16497715, 22243792, 17395122, 18987014, 20618699, 23889750, 17675357, 19282364, 1797514, 12839290, 10378403, 16446602, 18450898, 11285060, 17055193, 3777985, 11293640, 17401502, 15695923, 9470905, 12439523, 12827239, 16792994, 10709119, 17439630, 20192887, 11373920, 19338208, 18185082, 17143058, 20172976, 22958386, 16936265, 17468132, 21294065, 3292100, 6351537, 7694463, 10544751, 21212851, 7597092, 10765604, 23485951, 12756873, 21815258, 14759308, 23841577, 17900453, 18851856, 15956731, 12671173, 15538630, 21382466, 23772774, 15177670, 21801864, 18674658, 21656057, 20308837, 19718578, 12526770, 18166549, 23359489, 2238843, 20452493, 23666920, 19336370, 9065108, 15353504, 16263773, 17855451, 13009470, 17074544, 24335141, 16936247, 19099817, 21338666, 24288432, 11433084, 20570286, 24709930, 11673754, 22682000, 798269, 12904590, 16157128, 19521336, 16357110, 23972758, 11703405, 24439811, 18838246, 15809210, 20069051, 8040778, 22044007, 16679958, 23194157, 24124699, 12496176, 4717441, 18317236, 21447942, 23307787, 21975772, 21643846, 17368647, 11815549, 20234144, 1614456, 7643957, 20003277, 20495079, 15507966, 23942554, 1302425, 1773923, 15764963, 12478992, 9593950, 1349050, 12367822, 11158594, 12763109, 9002665, 19234164, 1403464, 15493717, 14671170, 16276336, 12915475, 12169829, 17449701, 8835397, 17667860, 15163335, 9183569, 22421261, 23828585, 17443204, 19144956, 20177288, 23651728, 2591339, 8238198, 10782394, 16938879, 24225293, 19515978, 19309286, 20419149, 10471825, 16580281, 11035337, 11861414, 23236705, 9160976, 118051, 21034609, 21701445, 17119993, 10469778, 24188066, 18754838, 17446182, 781206, 9595363, 8917583, 11520397, 15718365, 19446788, 14723749, 21883885, 15703196, 16652108, 20420200, 9240577, 2364907, 9357932, 10926289, 16510184, 17136231, 19106236, 23529685, 23295978, 15214004, 17127271, 19026292, 16982938, 16202930, 17703185, 17339775, 10909993, 16356438, 7538729, 10576642, 21960125, 12050275, 18568888, 16238543, 21659962, 22568870, 22676722, 8680517, 17711923, 15867044, 17703412, 15745646, 18276950, 15232008, 22355322, 23161670, 24923732, 8886630, 15733276, 22744848, 9528914, 12904319, 22426431, 17344923, 24518760, 3029767, 11935406, 17428554]

[kescobo]

Alright, the good news is that your code works fine on my mac.

The bad news is that's the end of the help I can offer. I'm tagging the contributors to the EUtils package - maybe they have an idea? @mirestrepo @fernandogelin @mcmcgrath13 @ibacher

[anthonyagudelox3]

Alright, the good news is that your code works fine on my mac.

The bad news is that's the end of the help I can offer. I'm tagging the contributors to the EUtils package - maybe they have an idea? @mirestrepo @fernandogelin @mcmcgrath13 @ibacher

Thanks for the help Kevin! Hopefully we can figure out why it is not working on my windows machine.

[anthonyagudelox3]

So I was able to get the function to work on a coworkers mac as well. So it looks like the function does not work for Windows unfortunately. Do you know of any way to get it up and running on Windows?

[kescobo]

I have no idea, hopefully someone else will chime in...

[stevengj]

Is there an error message when you do build MbedTLS at the pkg> prompt?

[kescobo]

I asked that earlier - seems it built fine

[aviks]

I can confirm that this works for rme in Windows 10, with MbedTLS 0.7.0

Some troubleshooting ideas:

I presume you have checked that the dll exists in that location: C:\Users\Thor\.julia\packages\MbedTLS\a1JFn\deps\usr\bin\libmbedtls.dll ?

On the Julia prompt, could you try using Libdl; dlopen("C:\Users\Thor\.julia\packages\MbedTLS\a1JFn\deps\usr\bin\libmbedtls.dll") . What is the output?

Just to check if this is a problem with a particular site (doesn't seem so, but still, to verify) can you do: using HTTP; HTTP.get("https://google.com")

Can you check the dll using dependency walker?

[quinnj]

Those are good ideas from @aviks. Another idea would be to add/download https://github.com/JuliaBinaryWrappers/MbedTLS_jll.jl and see if the problem still exists there (this would involve ccall-ing the function in question yourself).

[anthonyagudelox3]

julia> dlopen("C:\Users\Thor.julia\packages\MbedTLS\a1JFn\deps\usr\bin\libmbedtls.dll")
ERROR: syntax: invalid escape sequence
Stacktrace:
[1] top-level scope at REPL[3]:0

I can confirm that this works for rme in Windows 10, with MbedTLS 0.7.0

Some troubleshooting ideas:

I presume you have checked that the dll exists in that location: C:\Users\Thor\.julia\packages\MbedTLS\a1JFn\deps\usr\bin\libmbedtls.dll ?

On the Julia prompt, could you try using Libdl; dlopen("C:\Users\Thor\.julia\packages\MbedTLS\a1JFn\deps\usr\bin\libmbedtls.dll") . What is the output?

Just to check if this is a problem with a particular site (doesn't seem so, but still, to verify) can you do: using HTTP; HTTP.get("https://google.com")

Can you check the dll using dependency walker?

I checked to see if the if the problem is site specific and HTTP.get("https://google.com") works fine.

As for dlopen("C:\Users\Thor.julia\packages\MbedTLS\a1JFn\deps\usr\bin\libmbedtls.dll") it gives the following error:

dlopen("C:\Users\Thor.julia\packages\MbedTLS\a1JFn\deps\usr\bin")
ERROR: syntax: invalid escape sequence
Stacktrace:
[1] top-level scope at REPL[3]:0

I also tried dependency walker and I get the following error when I attempt to open the dll file:

Error: At least one required implicit or forwarded dependency was not found.
Error: At least one module has an unresolved import due to a missing export function in an implicitly dependent module.
Error: A circular dependency was detected.
Warning: At least one delay-load dependency module was not found.
Warning: At least one module has an unresolved import due to a missing export function in a delay-load dependent module.

[anthonyagudelox3]

I can confirm that this works for rme in Windows 10, with MbedTLS 0.7.0

Some troubleshooting ideas:

I presume you have checked that the dll exists in that location: C:\Users\Thor\.julia\packages\MbedTLS\a1JFn\deps\usr\bin\libmbedtls.dll ?

On the Julia prompt, could you try using Libdl; dlopen("C:\Users\Thor\.julia\packages\MbedTLS\a1JFn\deps\usr\bin\libmbedtls.dll") . What is the output?

Just to check if this is a problem with a particular site (doesn't seem so, but still, to verify) can you do: using HTTP; HTTP.get("https://google.com")

Can you check the dll using dependency walker?

[stevengj]

Use

dlopen(raw"C:\Users\Thor.julia\packages\MbedTLS\a1JFn\deps\usr\bin\libmbedtls.dll")

so that the backslashes aren't treated as escapes.

[anthonyagudelox3]

Okay so running dlopen(raw"C:\Users\Thor.julia\packages\MbedTLS\a1JFn\deps\usr\bin\libmbedtls.dll") gives:

julia> dlopen(raw"C:\Users\Thor.julia\packages\MbedTLS\a1JFn\deps\usr\bin\libmbedtls.dll")
Ptr{Nothing} @0x0000000000d50000

[anthonyagudelox3]

It looks like the using MbedTLS 0.7.0 on Julia v1.4.0 over Julia v1.1.1 seems to resolve the issue.