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Whippet install issue with HttpParser #51

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AndrewLangvt opened this issue Sep 8, 2017 · 4 comments
Closed

Whippet install issue with HttpParser #51

AndrewLangvt opened this issue Sep 8, 2017 · 4 comments

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@AndrewLangvt
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I am having difficulty with the HttpParser build when trying to install Whippet.

julia> dependencies.jl 
INFO: Updating METADATA...
INFO: Updating IndexableBitVectors master...
INFO: Computing changes...
INFO: No packages to install, update or remove
Checking IndexableBitVectors ... Found version 0.1.2
Checking DataStructures ... Found version 0.6.1
Checking ArgParse ... Found version 0.5.0
Checking SuffixArrays ... Found version 0.1.0
Checking FMIndexes ... Found version 0.0.1
Checking IntArrays ... Found version 0.0.1
Checking IntervalTrees ... Found version 0.1.0
Checking Libz ... Found version 0.2.4
Checking StatsBase ... Found version 0.17.0
Checking Distributions ... Found version 0.13.0
Checking Glob ... Found version 1.1.1
Checking Bio ... Found version 0.4.7
Checking Requests ... Found version 0.5.1
INFO: Loading and precompiling dependencies... 
INFO: using DataStructures
INFO: using ArgParse
INFO: using Bio
WARNING: Method definition count() in module IterTools at deprecated.jl:49 overwritten in module Iterators at deprecated.jl:49.
WARNING: Method definition count(Number) in module IterTools at deprecated.jl:49 overwritten in module Iterators at deprecated.jl:49.
WARNING: Method definition count(Number, Number) in module IterTools at deprecated.jl:49 overwritten in module Iterators at deprecated.jl:49.
INFO: using FMIndexes
INFO: using IntArrays
INFO: using IntervalsTrees
INFO: using BufferedStreams
INFO: using Libz
INFO: using StatsBase
INFO: using Distributions
INFO: using Glob
INFO: using SuffixArrays
INFO: using Requests
ERROR: LoadError: HttpParser not properly installed. Please run
Pkg.build("HttpParser")
 in error(::String, ::String, ::Vararg{String,N}) at ./error.jl:22
 in include_from_node1(::String) at ./loading.jl:488
 in macro expansion; at ./none:2 [inlined]
 in anonymous at ./<missing>:?
 in eval(::Module, ::Any) at ./boot.jl:234
 in process_options(::Base.JLOptions) at ./client.jl:242
 in _start() at ./client.jl:321
while loading /home/al2025/.julia/v0.5/HttpParser/src/HttpParser.jl, in expression starting on line 9
ERROR: LoadError: Failed to precompile HttpParser to /home/al2025/.julia/lib/v0.5/HttpParser.ji.
 in compilecache(::String) at ./loading.jl:593
 in require(::Symbol) at ./loading.jl:393
 in include_from_node1(::String) at ./loading.jl:488
 in macro expansion; at ./none:2 [inlined]
 in anonymous at ./<missing>:?
 in eval(::Module, ::Any) at ./boot.jl:234
 in process_options(::Base.JLOptions) at ./client.jl:242
 in _start() at ./client.jl:321
while loading /home/al2025/.julia/v0.5/Requests/src/Requests.jl, in expression starting on line 17
ERROR: LoadError: Failed to precompile Requests to /home/al2025/.julia/lib/v0.5/Requests.ji.
 in compilecache(::String) at ./loading.jl:593
 in require(::Symbol) at ./loading.jl:422
 in include_from_node1(::String) at ./loading.jl:488
 in process_options(::Base.JLOptions) at ./client.jl:265
 in _start() at ./client.jl:321
while loading /pylon2/mc3bg6p/al2025/storage/Whippet.jl/dependencies.jl, in expression starting on line 70

I then attempted to build the package, but still no luck...

julia> Pkg.build("HttpParser")
INFO: Building HttpParser
INFO: Attempting to Create directory /home/al2025/.julia/v0.5/HttpParser/deps/downloads
INFO: Directory /home/al2025/.julia/v0.5/HttpParser/deps/downloads already created
INFO: Attempting to Create directory /home/al2025/.julia/v0.5/HttpParser/deps/downloads
INFO: Directory /home/al2025/.julia/v0.5/HttpParser/deps/downloads already created
INFO: Downloading file https://github.com/nodejs/http-parser/archive/v2.7.1.zip
INFO: Done downloading file https://github.com/nodejs/http-parser/archive/v2.7.1.zip
INFO: Attempting to Create directory /home/al2025/.julia/v0.5/HttpParser/deps
INFO: Directory /home/al2025/.julia/v0.5/HttpParser/deps already created
INFO: Path /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1 already created
INFO: Attempting to Create directory /home/al2025/.julia/v0.5/HttpParser/deps/usr/lib
INFO: Directory /home/al2025/.julia/v0.5/HttpParser/deps/usr/lib already created
INFO: Changing Directory to /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1
INFO: Changing Directory to /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1
INFO: Changing Directory to /home/al2025/.julia/v0.5/HttpParser/deps/src
INFO: Attempting to Create directory /home/al2025/.julia/v0.5/HttpParser/deps/usr/lib
INFO: Directory /home/al2025/.julia/v0.5/HttpParser/deps/usr/lib already created
INFO: Changing Directory to /home/al2025/.julia/v0.5/HttpParser/deps/src
==================================================================[ ERROR: HttpParser ]===================================================================

LoadError: could not spawn setenv(`make -j8 -C http-parser-2.7.1 library`,String["PATH=/home/al2025/linuxbrew/.linuxbrew/Cellar/gcc/5.3.0/bin:/home/al2025/linuxbrew/.linuxbrew/bin/python3:/home/al2025/kallisto_linux-v0.43.1:/home/al2025/salmon-0.8.2/bin:/home/al2025/linuxbrew/.linuxbrew/sbin:/home/al2025/linuxbrew/.linuxbrew/bin:/usr/lib64/qt-3.3/bin:/opt/intel/advisor_2017.1.3.510716/bin64:/opt/intel/vtune_amplifier_xe_2017.3.0.510739/bin64:/opt/intel/inspector_2017.1.3.510645/bin64:/opt/intel/itac/2017.3.030/intel64/bin:/opt/intel//itac/2017.3.030/intel64/bin:/opt/intel//clck/2017.2.019/bin/intel64:/opt/intel/compilers_and_libraries_2017.4.196/linux/bin/intel64:/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin:/opt/intel/debugger_2017/gdb/intel64_mic/bin:/opt/packages/slurm/17.02.5/bin:/opt/packages/allocations:/opt/packages/interact/bin:/usr/lib64/ccache:/usr/local/bin:/bin:/usr/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/puppet/bin:/opt/packages/slash2/psc/sbin:/opt/intel/parallel_studio_xe_2017.4.056/bin:/opt/puppetlabs/bin:/home/al2025/.rvm/bin:/home/al2025/.local/bin:/home/al2025/bin:/home/al2025/transrate-1.0.3-linux-x86_64:/home/al2025/augustus-3.2.3/home/al2025/augustus-3.2.3/bin:/home/al2025/BUSCO_v1.22:/home/al2025/usr/lib:/home/al2025/transfuse-0.5.0-linux-x86_64:/home/al2025/ncbi-blast-2.5.0+/bin:/home/al2025/SPAdes-3.9.0-Linux/bin:/home/al2025/STAR-2.5.3a/bin/Linux_x86_64:/pylon2/mc3bg6p/al2025/storage/julia-f4c6c9d4bb/bin","VTUNE_AMPLIFIER_XE_2017_DIR=/opt/intel/vtune_amplifier_xe_2017.3.0.510739","QTDIR=/usr/lib64/qt-3.3","MPS_LD_PRELOAD=libmps.so","LD_LIBRARY_PATH=/opt/intel/itac/2017.3.030/mic/slib:/opt/intel/itac/2017.3.030/intel64/slib:/opt/intel//itac/2017.3.030/mic/slib:/opt/intel//itac/2017.3.030/intel64/slib:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64_lin:/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/lib:/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/mic/lib:/opt/intel/compilers_and_libraries_2017.4.196/linux/ipp/lib/intel64:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64_lin:/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin:/opt/intel/compilers_and_libraries_2017.4.196/linux/tbb/lib/intel64/gcc4.7:/opt/intel/debugger_2017/iga/lib:/opt/intel/debugger_2017/libipt/intel64/lib:/opt/intel/compilers_and_libraries_2017.4.196/linux/daal/lib/intel64_lin:/opt/intel/compilers_and_libraries_2017.4.196/linux/daal/../tbb/lib/intel64_lin/gcc4.4/home/al2025/salmon-0.8.2/lib","GLOBUS_LOCATION=/usr","MANPATH=/home/al2025/linuxbrew/.linuxbrew/share/man:/opt/intel//itac/2017.3.030/man:/opt/intel/man/common:/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/man:/opt/intel/documentation_2017/en/debugger//gdb-ia/man/:/opt/intel/documentation_2017/en/debugger//gdb-mic/man/:/opt/intel/documentation_2017/en/debugger//gdb-igfx/man/:/opt/packages/slurm/17.02.5/share/man:/usr/local/man:/usr/share/man:/opt/packages/slash2/psc/man:","MODULEPATH=:/opt/modulefiles","NLSPATH=/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64/locale/%l_%t/%N:/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/locale/%l_%t/%N:/opt/intel/debugger_2017/gdb/intel64_mic/share/locale/%l_%t/%N:/opt/intel/debugger_2017/gdb/intel64/share/locale/%l_%t/%N","PROJECT=/pylon2/mc3bg6p/al2025","MIC_LIBRARY_PATH=/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/mic/lib:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64_lin_mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin_mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/tbb/lib/mic","VT_SLIB_DIR=/opt/intel//itac/2017.3.030/intel64/slib","MPS_STAT_ENABLE_IDLE_VAL=1","USER=al2025","CPLUS_INCLUDE_PATH=/opt/intel//clck/2017.2.019/include","INSPECTOR_2017_DIR=/opt/intel/inspector_2017.1.3.510645","IPPROOT=/opt/intel/compilers_and_libraries_2017.4.196/linux/ipp","CPATH=/opt/intel/compilers_and_libraries_2017.4.196/linux/ipp/include:/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/include:/opt/intel/compilers_and_libraries_2017.4.196/linux/tbb/include:/opt/intel/compilers_and_libraries_2017.4.196/linux/daal/include","MPS_STAT_ENABLE_IDLE=I_MPI_PVAR_IDLE","LESSOPEN=||/usr/bin/lesspipe.sh %s","SHELL=/usr/psc/shells/bash","INTEL_PYTHONHOME=/opt/intel/debugger_2017/python/intel64/","INTEL_LICENSE_FILE=/opt/intel/licenses:/opt/intel/licenses:/root/intel/licenses:/opt/intel/licenses:/opt/intel/compilers_and_libraries_2017.4.196/linux/licenses:/opt/intel/licenses:/opt/intel//clck/2017.2.019/licenses:/opt/intel/licenses:/Users/Shared/Library/Application Support/Intel/Licenses","CLASSPATH=/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/lib/mpi.jar:/opt/intel/compilers_and_libraries_2017.4.196/linux/daal/lib/daal.jar","DAALROOT=/opt/intel/compilers_and_libraries_2017.4.196/linux/daal","QTLIB=/usr/lib64/qt-3.3/lib","SSH_CLIENT=132.177.238.70 25884 2222","SSH_TTY=/dev/pts/12","TERM=xterm-256color","TBBROOT=/opt/intel/compilers_and_libraries_2017.4.196/linux/tbb","HOME=/home/al2025","HOSTNAME=br006.pvt.bridges.psc.edu","LIBRARY_PATH=/opt/intel//clck/2017.2.019/lib/intel64:/opt/intel/compilers_and_libraries_2017.4.196/linux/ipp/lib/intel64:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64_lin:/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin:/opt/intel/compilers_and_libraries_2017.4.196/linux/tbb/lib/intel64/gcc4.7:/opt/intel/compilers_and_libraries_2017.4.196/linux/daal/lib/intel64_lin:/opt/intel/compilers_and_libraries_2017.4.196/linux/daal/../tbb/lib/intel64_lin/gcc4.4","QTINC=/usr/lib64/qt-3.3/include","MYPROXY_SERVER=myproxy.xsede.org,myproxy.psc.xsede.org","CLCK_ROOT=/opt/intel//clck/2017.2.019","VT_ARCH=intel64","MPS_KMP_FORKJOIN_FRAMES_MODE=3","HISTSIZE=1000","GLOBUS_TCP_SOURCE_RANGE=50000,51000","MPS_STAT_LEVEL=5","GDB_CROSS=/opt/intel/debugger_2017/gdb/intel64_mic/bin/gdb-mic","MPS_STAT_DIR_POSTFIX=_%D-%T","MPS_STAT_MESSAGES=1","VT_MPI=impi4","LANG=en_US.UTF-8","SHLVL=1","LOADEDMODULES=psc_path/1.1:slurm/17.02.5:intel/17.4","MPS_INTEL_LIBITTNOTIFY64=libmps.so","VT_ROOT=/opt/intel//itac/2017.3.030","LOGNAME=al2025","OLDPWD=/pylon2/mc3bg6p/al2025/storage","XDG_RUNTIME_DIR=/run/user/57241","_LMFILES_=/opt/modulefiles/psc_path/1.1:/opt/modulefiles/slurm/17.02.5:/opt/modulefiles/intel/17.4","AUTOJUMP_SOURCED=1","INFOPATH=/home/al2025/linuxbrew/.linuxbrew/share/info:/opt/intel/documentation_2017/en/debugger//gdb-ia/info/:/opt/intel/documentation_2017/en/debugger//gdb-mic/info/:/opt/intel/documentation_2017/en/debugger//gdb-igfx/info/","SCRATCH=/pylon5/mc3bg6p/al2025","QT_GRAPHICSSYSTEM_CHECKED=1","_=/pylon2/mc3bg6p/al2025/storage/julia-f4c6c9d4bb/bin/julia","CVS_RSH=ssh","VT_LIB_DIR=/opt/intel//itac/2017.3.030/intel64/lib","VT_ADD_LIBS=-ldwarf -lelf -lvtunwind -lm -lpthread","PWD=/pylon2/mc3bg6p/al2025/storage/Whippet.jl","MODULESHOME=/usr/share/Modules","I_MPI_ROOT=/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi","PYTHONPATH=/opt/intel/advisor_2017.1.3.510716/pythonapi","BASH_FUNC_module()=() {  eval `/usr/bin/modulecmd bash \$*`\n}","SSH_CONNECTION=132.177.238.70 25884 128.182.108.57 2222","AUTOJUMP_ERROR_PATH=/home/al2025/.local/share/autojump/errors.log","MYPROXY_SERVER_PORT=7512","OPENBLAS_NUM_THREADS=8","SONAME=libhttp_parser.so","MPM_LAUNCHER=/opt/intel/debugger_2017/mpm/mic/bin/start_mpm.sh","HISTCONTROL=ignoredups","GDBSERVER_MIC=/opt/intel/debugger_2017/gdb/targets/mic/bin/gdbserver","ADVISOR_2017_DIR=/opt/intel/advisor_2017.1.3.510716","MAIL=/var/spool/mail/al2025","XDG_SESSION_ID=7820","TMOUT=604800","MPS_TOOL_ROOT=/opt/intel/itac/2017.3.030","GLOBUS_TCP_PORT_RANGE=50000,51000","MIC_LD_LIBRARY_PATH=/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/mic/lib:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/ipp/lib/mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64_lin_mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin_mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/tbb/lib/mic","LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:","MKLROOT=/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl","OPENBLAS_MAIN_FREE=1"]): not a directory (ENOTDIR)
while loading /home/al2025/.julia/v0.5/HttpParser/deps/build.jl, in expression starting on line 71

==========================================================================================================================================================

=====================================================================[ BUILD ERRORS ]=====================================================================

WARNING: HttpParser had build errors.

 - packages with build errors remain installed in /home/al2025/.julia/v0.5
 - build the package(s) and all dependencies with `Pkg.build("HttpParser")`
 - build a single package by running its `deps/build.jl` script

==========================================================================================================================================================

julia>

Any thoughts on where I'm going wrong here? I'm quite new to Julia, so it may be a very simple issue...
@timbitz
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Owner

timbitz commented Sep 8, 2017

Hey, I am away on honeymoon until 9/12 without a computer. So not sure how much I can help now.

That being said, it is possible the original error message might be useful. One way to get this is to just start from scratch: 'rm -rf /home/al2025/.julia/v0.5' and open julia and try Pkg.add("Requests")

@AndrewLangvt
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Author

so I tried a complete removal of julia, reinstall of v0.5, and ended up with a hangup on HttpParser again...

[al2025@br006 Whippet.jl]$ julia dependencies.jl 
INFO: Initializing package repository /home/al2025/.julia/v0.5
INFO: Cloning METADATA from https://github.com/JuliaLang/METADATA.jl
INFO: Updating METADATA...
INFO: Computing changes...
INFO: No packages to install, update or remove
Checking IndexableBitVectors ... Trying to install IndexableBitVectors ...
INFO: Cloning cache of Compat from https://github.com/JuliaLang/Compat.jl.git
INFO: Cloning cache of IndexableBitVectors from https://github.com/BioJulia/IndexableBitVectors.jl.git
INFO: Installing Compat v0.31.0
INFO: Installing IndexableBitVectors v0.1.2
INFO: Package database updated
INFO: Checking out IndexableBitVectors master...
INFO: Pulling IndexableBitVectors latest master...
INFO: No packages to install, update or remove
Checking DataStructures ... Trying to install DataStructures ...
INFO: Cloning cache of DataStructures from https://github.com/JuliaCollections/DataStructures.jl.git
INFO: Installing DataStructures v0.6.1
INFO: Package database updated
Checking ArgParse ... Trying to install ArgParse ...
INFO: Cloning cache of ArgParse from https://github.com/carlobaldassi/ArgParse.jl.git
INFO: Cloning cache of TextWrap from https://github.com/carlobaldassi/TextWrap.jl.git
INFO: Installing ArgParse v0.5.0
INFO: Installing TextWrap v0.2.0
INFO: Package database updated
Checking SuffixArrays ... Trying to install SuffixArrays ...
INFO: Cloning cache of SuffixArrays from https://github.com/quinnj/SuffixArrays.jl.git
INFO: Installing SuffixArrays v0.1.0
INFO: Package database updated
Checking FMIndexes ... Trying to install FMIndexes ...
INFO: Cloning cache of FMIndexes from https://github.com/BioJulia/FMIndexes.jl.git
INFO: Cloning cache of IntArrays from https://github.com/bicycle1885/IntArrays.jl.git
INFO: Cloning cache of WaveletMatrices from https://github.com/BioJulia/WaveletMatrices.jl.git
INFO: Installing FMIndexes v0.0.1
INFO: Installing IntArrays v0.0.1
INFO: Installing WaveletMatrices v0.1.0
INFO: Package database updated
Checking IntArrays ... Found version 0.0.1
Checking IntervalTrees ... Trying to install IntervalTrees ...
INFO: Cloning cache of IntervalTrees from https://github.com/BioJulia/IntervalTrees.jl.git
INFO: Installing IntervalTrees v0.3.0
INFO: Package database updated
Checking Libz ... Trying to install Libz ...
INFO: Cloning cache of BufferedStreams from https://github.com/BioJulia/BufferedStreams.jl.git
INFO: Cloning cache of Libz from https://github.com/BioJulia/Libz.jl.git
INFO: Installing BufferedStreams v0.3.3
INFO: Installing Libz v0.2.4
INFO: Package database updated
Checking StatsBase ... Trying to install StatsBase ...
INFO: Cloning cache of SpecialFunctions from https://github.com/JuliaMath/SpecialFunctions.jl.git
INFO: Cloning cache of StatsBase from https://github.com/JuliaStats/StatsBase.jl.git
INFO: Installing SpecialFunctions v0.2.0
INFO: Installing StatsBase v0.17.0
INFO: Package database updated
Checking Distributions ... Trying to install Distributions ...
INFO: Cloning cache of BinDeps from https://github.com/JuliaLang/BinDeps.jl.git
INFO: Cloning cache of Calculus from https://github.com/johnmyleswhite/Calculus.jl.git
INFO: Cloning cache of Distributions from https://github.com/JuliaStats/Distributions.jl.git
INFO: Cloning cache of PDMats from https://github.com/JuliaStats/PDMats.jl.git
INFO: Cloning cache of QuadGK from https://github.com/JuliaMath/QuadGK.jl.git
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gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c qnbeta.c -o qnbeta.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c fsign.c -o fsign.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c dcauchy.c -o dcauchy.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c dpois.c -o dpois.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c d1mach.c -o d1mach.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c rexp.c -o rexp.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c rgamma.c -o rgamma.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c qnbinom.c -o qnbinom.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c df.c -o df.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c pchisq.c -o pchisq.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c dhyper.c -o dhyper.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c pf.c -o pf.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c qnchisq.c -o qnchisq.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c fmin2.c -o fmin2.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c chebyshev.c -o chebyshev.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c bessel_k.c -o bessel_k.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c qexp.c -o qexp.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c lgamma.c -o lgamma.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c ftrunc.c -o ftrunc.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c gamma_cody.c -o gamma_cody.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c fprec.c -o fprec.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c dgamma.c -o dgamma.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c rweibull.c -o rweibull.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c pgeom.c -o pgeom.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c bd0.c -o bd0.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c pnchisq.c -o pnchisq.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c dnf.c -o dnf.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c qbinom.c -o qbinom.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c gammalims.c -o gammalims.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c pexp.c -o pexp.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c pbinom.c -o pbinom.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c pnbeta.c -o pnbeta.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c sign.c -o sign.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c polygamma.c -o polygamma.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c runif.c -o runif.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c lgammacor.c -o lgammacor.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c rmultinom.c -o rmultinom.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c dnchisq.c -o dnchisq.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c pnbinom.c -o pnbinom.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c qf.c -o qf.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c qtukey.c -o qtukey.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c bessel_i.c -o bessel_i.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c qunif.c -o qunif.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c fround.c -o fround.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c pnf.c -o pnf.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c expm1.c -o expm1.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c phyper.c -o phyper.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c dchisq.c -o dchisq.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c rnorm.c -o rnorm.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c cospi.c -o cospi.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c imax2.c -o imax2.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c pnt.c -o pnt.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c ptukey.c -o ptukey.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c qweibull.c -o qweibull.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c wilcox.c -o wilcox.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c callback.c -o callback.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c dt.c -o dt.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c qbeta.c -o qbeta.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c mlutils.c -o mlutils.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c pbeta.c -o pbeta.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c dweibull.c -o dweibull.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c rgeom.c -o rgeom.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c dlogis.c -o dlogis.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c dnbeta.c -o dnbeta.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c lbeta.c -o lbeta.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c rf.c -o rf.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c qgamma.c -o qgamma.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c toms708.c -o toms708.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c rt.c -o rt.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c rcauchy.c -o rcauchy.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c signrank.c -o signrank.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c pgamma.c -o pgamma.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c dbinom.c -o dbinom.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c qcauchy.c -o qcauchy.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c rlogis.c -o rlogis.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c qt.c -o qt.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c gamma.c -o gamma.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c pcauchy.c -o pcauchy.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c rhyper.c -o rhyper.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c qnorm.c -o qnorm.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c dbeta.c -o dbeta.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c qgeom.c -o qgeom.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c beta.c -o beta.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c qlogis.c -o qlogis.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c pt.c -o pt.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c imin2.c -o imin2.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c dnt.c -o dnt.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c dexp.c -o dexp.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c plogis.c -o plogis.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c qhyper.c -o qhyper.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c punif.c -o punif.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c rlnorm.c -o rlnorm.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c pnorm.c -o pnorm.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c rnbinom.c -o rnbinom.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c rbeta.c -o rbeta.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c rpois.c -o rpois.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c bessel_y.c -o bessel_y.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c ppois.c -o ppois.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c dgeom.c -o dgeom.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c bessel_j.c -o bessel_j.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c qlnorm.c -o qlnorm.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c plnorm.c -o plnorm.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c choose.c -o choose.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c qnt.c -o qnt.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c log1p.c -o log1p.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c rnchisq.c -o rnchisq.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c qnf.c -o qnf.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c dnorm.c -o dnorm.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c rbinom.c -o rbinom.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c pweibull.c -o pweibull.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c dunif.c -o dunif.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c rchisq.c -o rchisq.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c dlnorm.c -o dlnorm.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c stirlerr.c -o stirlerr.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c fmax2.c -o fmax2.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c qpois.c -o qpois.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c dnbinom.c -o dnbinom.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c qchisq.c -o qchisq.o
gcc  -Wall -O3 -fPIC -DMATHLIB_STANDALONE   -std=gnu99 -I../include -DNDEBUG -c i1mach.c -o i1mach.o
rm -f libRmath-julia.so
gcc   -shared -o libRmath-julia.so qnbeta.o fsign.o dcauchy.o dpois.o d1mach.o rexp.o rgamma.o qnbinom.o df.o pchisq.o dhyper.o pf.o qnchisq.o fmin2.o chebyshev.o bessel_k.o qexp.o lgamma.o ftrunc.o gamma_cody.o fprec.o dgamma.o rweibull.o pgeom.o bd0.o pnchisq.o dnf.o qbinom.o gammalims.o pexp.o pbinom.o pnbeta.o sign.o polygamma.o runif.o lgammacor.o rmultinom.o dnchisq.o pnbinom.o qf.o qtukey.o bessel_i.o qunif.o fround.o pnf.o expm1.o phyper.o dchisq.o rnorm.o cospi.o imax2.o pnt.o ptukey.o qweibull.o wilcox.o callback.o dt.o qbeta.o mlutils.o pbeta.o dweibull.o rgeom.o dlogis.o dnbeta.o lbeta.o rf.o qgamma.o toms708.o rt.o rcauchy.o signrank.o pgamma.o dbinom.o qcauchy.o rlogis.o qt.o gamma.o pcauchy.o rhyper.o qnorm.o dbeta.o qgeom.o beta.o qlogis.o pt.o imin2.o dnt.o dexp.o plogis.o qhyper.o punif.o rlnorm.o pnorm.o rnbinom.o rbeta.o rpois.o bessel_y.o ppois.o dgeom.o bessel_j.o qlnorm.o plnorm.o choose.o qnt.o log1p.o rnchisq.o qnf.o dnorm.o rbinom.o pweibull.o dunif.o rchisq.o dlnorm.o stirlerr.o fmax2.o qpois.o dnbinom.o qchisq.o i1mach.o
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INFO: Installing GZip v0.3.0
INFO: Installing HDF5 v0.8.5
INFO: Downgrading IntervalTrees: v0.3.0 => v0.1.0
INFO: Installing IterTools v0.1.0
INFO: Installing Iterators v0.3.1
INFO: Installing JLD v0.6.11
INFO: Installing LegacyStrings v0.2.2
INFO: Installing LightGraphs v0.7.7
INFO: Installing LightXML v0.5.0
INFO: Installing NaNMath v0.2.6
INFO: Installing ParserCombinator v1.7.11
INFO: Installing Polynomials v0.1.6
INFO: Installing Reexport v0.0.3
INFO: Installing Roots v0.4.1
INFO: Building EzXML
INFO: Building Rmath
INFO: Building Blosc
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100   122    0   122    0     0    927      0 --:--:-- --:--:-- --:--:--   931
100  667k  100  667k    0     0  1384k      0 --:--:-- --:--:-- --:--:-- 1384k
Compiling libblosc...
gcc -I. -DBLOSC_SHARED_LIBRARY -DSHUFFLE_AVX2_ENABLED -DSHUFFLE_SSE2_ENABLED -fPIC -O3 -pthread -std=gnu99 -DHAVE_LZ4 -I../internal-complibs/lz4-1.7.5 -c -o bitshuffle-generic.o bitshuffle-generic.c
gcc -I. -DBLOSC_SHARED_LIBRARY -DSHUFFLE_AVX2_ENABLED -DSHUFFLE_SSE2_ENABLED -fPIC -O3 -pthread -std=gnu99 -DHAVE_LZ4 -I../internal-complibs/lz4-1.7.5 -c -o shuffle-generic.o shuffle-generic.c
gcc -I. -DBLOSC_SHARED_LIBRARY -DSHUFFLE_AVX2_ENABLED -DSHUFFLE_SSE2_ENABLED -fPIC -O3 -pthread -std=gnu99 -DHAVE_LZ4 -I../internal-complibs/lz4-1.7.5 -c -o shuffle.o shuffle.c
gcc -I. -DBLOSC_SHARED_LIBRARY -DSHUFFLE_AVX2_ENABLED -DSHUFFLE_SSE2_ENABLED -fPIC -O3 -pthread -std=gnu99 -DHAVE_LZ4 -I../internal-complibs/lz4-1.7.5 -c -o blosclz.o blosclz.c
gcc -I. -DBLOSC_SHARED_LIBRARY -DSHUFFLE_AVX2_ENABLED -DSHUFFLE_SSE2_ENABLED -fPIC -O3 -pthread -std=gnu99 -DHAVE_LZ4 -I../internal-complibs/lz4-1.7.5 -c -o blosc.o blosc.c
gcc -I. -DBLOSC_SHARED_LIBRARY -DSHUFFLE_AVX2_ENABLED -DSHUFFLE_SSE2_ENABLED -fPIC -O3 -pthread -std=gnu99 -DHAVE_LZ4 -I../internal-complibs/lz4-1.7.5 -c -o ../internal-complibs/lz4-1.7.5/lz4.o ../internal-complibs/lz4-1.7.5/lz4.c
gcc -I. -DBLOSC_SHARED_LIBRARY -DSHUFFLE_AVX2_ENABLED -DSHUFFLE_SSE2_ENABLED -fPIC -O3 -pthread -std=gnu99 -DHAVE_LZ4 -I../internal-complibs/lz4-1.7.5 -c -o ../internal-complibs/lz4-1.7.5/lz4hc.o ../internal-complibs/lz4-1.7.5/lz4hc.c
echo "building with AVX2"
building with AVX2
gcc -I. -DBLOSC_SHARED_LIBRARY -DSHUFFLE_AVX2_ENABLED -DSHUFFLE_SSE2_ENABLED -fPIC -O3 -pthread -std=gnu99 -DHAVE_LZ4 -I../internal-complibs/lz4-1.7.5 -mavx2 -c -o bitshuffle-avx2.o bitshuffle-avx2.c
gcc -I. -DBLOSC_SHARED_LIBRARY -DSHUFFLE_AVX2_ENABLED -DSHUFFLE_SSE2_ENABLED -fPIC -O3 -pthread -std=gnu99 -DHAVE_LZ4 -I../internal-complibs/lz4-1.7.5 -mavx2 -c -o shuffle-avx2.o shuffle-avx2.c
echo "building without AVX2"
building without AVX2
gcc -I. -DBLOSC_SHARED_LIBRARY -DSHUFFLE_AVX2_ENABLED -DSHUFFLE_SSE2_ENABLED -fPIC -O3 -pthread -std=gnu99 -DHAVE_LZ4 -I../internal-complibs/lz4-1.7.5 -msse2 -c -o bitshuffle-sse2.o bitshuffle-sse2.c
gcc -I. -DBLOSC_SHARED_LIBRARY -DSHUFFLE_AVX2_ENABLED -DSHUFFLE_SSE2_ENABLED -fPIC -O3 -pthread -std=gnu99 -DHAVE_LZ4 -I../internal-complibs/lz4-1.7.5 -msse2 -c -o shuffle-sse2.o shuffle-sse2.c
gcc -fPIC -O3 -pthread -std=gnu99 -DHAVE_LZ4 -I../internal-complibs/lz4-1.7.5 -shared bitshuffle-generic.o shuffle-generic.o shuffle.o blosclz.o blosc.o ../internal-complibs/lz4-1.7.5/lz4.o ../internal-complibs/lz4-1.7.5/lz4hc.o bitshuffle-avx2.o shuffle-avx2.o bitshuffle-sse2.o shuffle-sse2.o -o ../../libblosc.so
INFO: Building HDF5
INFO: Building LightXML
INFO: Package database updated
Checking Requests ... Trying to install Requests ...
INFO: Cloning cache of Codecs from https://github.com/dcjones/Codecs.jl.git
INFO: Cloning cache of HttpCommon from https://github.com/JuliaWeb/HttpCommon.jl.git
INFO: Cloning cache of HttpParser from https://github.com/JuliaWeb/HttpParser.jl.git
INFO: Cloning cache of JSON from https://github.com/JuliaIO/JSON.jl.git
INFO: Cloning cache of MbedTLS from https://github.com/JuliaWeb/MbedTLS.jl.git
INFO: Cloning cache of Requests from https://github.com/JuliaWeb/Requests.jl.git
INFO: Installing Codecs v0.3.0
INFO: Installing HttpCommon v0.3.0
INFO: Installing HttpParser v0.3.0
INFO: Installing JSON v0.13.0
INFO: Installing MbedTLS v0.4.5
INFO: Installing Requests v0.5.1
INFO: Building HttpParser
INFO: Attempting to Create directory /home/al2025/.julia/v0.5/HttpParser/deps/downloads
INFO: Attempting to Create directory /home/al2025/.julia/v0.5/HttpParser/deps/downloads
INFO: Directory /home/al2025/.julia/v0.5/HttpParser/deps/downloads already created
INFO: Downloading file https://github.com/nodejs/http-parser/archive/v2.7.1.zip
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100   123    0   123    0     0   1161      0 --:--:-- --:--:-- --:--:--  1171
100 55365  100 55365    0     0   288k      0 --:--:-- --:--:-- --:--:--  983k
INFO: Done downloading file https://github.com/nodejs/http-parser/archive/v2.7.1.zip
INFO: Attempting to Create directory /home/al2025/.julia/v0.5/HttpParser/deps
INFO: Directory /home/al2025/.julia/v0.5/HttpParser/deps already created
Archive:  /home/al2025/.julia/v0.5/HttpParser/deps/downloads/v2.7.1.zip
feae95a3a69f111bc1897b9048d9acbc290992f9
   creating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/.gitignore  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/.mailmap  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/.travis.yml  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/AUTHORS  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/LICENSE-MIT  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/Makefile  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/README.md  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/bench.c  
   creating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/contrib/
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/contrib/parsertrace.c  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/contrib/url_parser.c  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/http_parser.c  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/http_parser.gyp  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/http_parser.h  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/test.c  
INFO: Attempting to Create directory /home/al2025/.julia/v0.5/HttpParser/deps/usr/lib
INFO: Changing Directory to /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1
INFO: Changing Directory to /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1
INFO: Changing Directory to /home/al2025/.julia/v0.5/HttpParser/deps/src
INFO: Attempting to Create directory /home/al2025/.julia/v0.5/HttpParser/deps/usr/lib
INFO: Directory /home/al2025/.julia/v0.5/HttpParser/deps/usr/lib already created
INFO: Changing Directory to /home/al2025/.julia/v0.5/HttpParser/deps/src
===============================================================[ ERROR: HttpParser ]===============================================================

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-lelf -lvtunwind -lm -lpthread","PWD=/pylon2/mc3bg6p/al2025/storage/Whippet.jl","MODULESHOME=/usr/share/Modules","I_MPI_ROOT=/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi","PYTHONPATH=/opt/intel/advisor_2017.1.3.510716/pythonapi","BASH_FUNC_module()=() {  eval `/usr/bin/modulecmd bash \$*`\n}","SSH_CONNECTION=132.177.238.67 32946 128.182.108.57 2222","AUTOJUMP_ERROR_PATH=/home/al2025/.local/share/autojump/errors.log","MYPROXY_SERVER_PORT=7512","OPENBLAS_NUM_THREADS=8","SONAME=libhttp_parser.so","MPM_LAUNCHER=/opt/intel/debugger_2017/mpm/mic/bin/start_mpm.sh","HISTCONTROL=ignoredups","GDBSERVER_MIC=/opt/intel/debugger_2017/gdb/targets/mic/bin/gdbserver","ADVISOR_2017_DIR=/opt/intel/advisor_2017.1.3.510716","MAIL=/var/spool/mail/al2025","XDG_SESSION_ID=2778","TMOUT=604800","MPS_TOOL_ROOT=/opt/intel/itac/2017.3.030","GLOBUS_TCP_PORT_RANGE=50000,51000","MIC_LD_LIBRARY_PATH=/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/mic/lib:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/ipp/lib/mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64_lin_mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin_mic:/opt/intel/compilers_and_libraries_2017.4.196/linux/tbb/lib/mic","LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:","MKLROOT=/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl","OPENBLAS_MAIN_FREE=1"]): not a directory (ENOTDIR)
while loading /home/al2025/.julia/v0.5/HttpParser/deps/build.jl, in expression starting on line 71

===================================================================================================================================================
INFO: Building MbedTLS
Using system libraries...

=================================================================[ BUILD ERRORS ]==================================================================

WARNING: HttpParser had build errors.

 - packages with build errors remain installed in /home/al2025/.julia/v0.5
 - build the package(s) and all dependencies with `Pkg.build("HttpParser")`
 - build a single package by running its `deps/build.jl` script

===================================================================================================================================================
INFO: Package database updated
INFO: Loading and precompiling dependencies... 
INFO: using DataStructures
INFO: using ArgParse
INFO: using Bio
WARNING: Method definition count() in module Iterators at deprecated.jl:49 overwritten in module IterTools at deprecated.jl:49.
WARNING: Method definition count(Number) in module Iterators at deprecated.jl:49 overwritten in module IterTools at deprecated.jl:49.
WARNING: Method definition count(Number, Number) in module Iterators at deprecated.jl:49 overwritten in module IterTools at deprecated.jl:49.
WARNING: Method definition count() in module IterTools at deprecated.jl:49 overwritten in module Iterators at deprecated.jl:49.
WARNING: Method definition count(Number) in module IterTools at deprecated.jl:49 overwritten in module Iterators at deprecated.jl:49.
WARNING: Method definition count(Number, Number) in module IterTools at deprecated.jl:49 overwritten in module Iterators at deprecated.jl:49.
INFO: using FMIndexes

WARNING: deprecated syntax "call(::Type{IntArray{w,T}}, ...)".
Use "(::Type{IntArray{w,T}})(...)" instead.

WARNING: deprecated syntax "call(::Type{IntArray{w,T}}, ...)".
Use "(::Type{IntArray{w,T}})(...)" instead.

WARNING: deprecated syntax "call(::Type{IntArray{w,T}}, ...)".
Use "(::Type{IntArray{w,T}})(...)" instead.

WARNING: deprecated syntax "call(::Type{IntArray{w,T}}, ...)".
Use "(::Type{IntArray{w,T}})(...)" instead.

WARNING: deprecated syntax "call(::Type{IntArray{w,T}}, ...)".
Use "(::Type{IntArray{w,T}})(...)" instead.

WARNING: deprecated syntax "call(::Type{IntArray{w,T,n}}, ...)".
Use "(::Type{IntArray{w,T,n}})(...)" instead.

WARNING: deprecated syntax "call(::Type{IntArray{w,T,n}}, ...)".
Use "(::Type{IntArray{w,T,n}})(...)" instead.

WARNING: deprecated syntax "call(::Type{IntVector{w,T}}, ...)".
Use "(::Type{IntVector{w,T}})(...)" instead.

WARNING: deprecated syntax "call(::Type{IntVector{w,T}}, ...)".
Use "(::Type{IntVector{w,T}})(...)" instead.

WARNING: deprecated syntax "call(::Type{IntVector{w,T}}, ...)".
Use "(::Type{IntVector{w,T}})(...)" instead.

WARNING: deprecated syntax "call(::Type{IntVector{w,T}}, ...)".
Use "(::Type{IntVector{w,T}})(...)" instead.

WARNING: deprecated syntax "call(::Type{IntMatrix{w,T}}, ...)".
Use "(::Type{IntMatrix{w,T}})(...)" instead.

WARNING: deprecated syntax "call(::Type{IntMatrix{w,T}}, ...)".
Use "(::Type{IntMatrix{w,T}})(...)" instead.

WARNING: deprecated syntax "call(::Type{IntMatrix{w,T}}, ...)".
Use "(::Type{IntMatrix{w,T}})(...)" instead.

WARNING: deprecated syntax "call(::Type{IntMatrix{w,T}}, ...)".
Use "(::Type{IntMatrix{w,T}})(...)" instead.

WARNING: deprecated syntax "call(::Type{WaveletMatrix{w}}, ...)".
Use "(::Type{WaveletMatrix{w}})(...)" instead.

WARNING: deprecated syntax "call(::Core.kwftype(Type{WaveletMatrix{w}}), ...)".
Use "(::Core.kwftype(Type{WaveletMatrix{w}}))(...)" instead.

WARNING: deprecated syntax "call(::Type{WaveletMatrix}, ...)".
Use "(::Type{WaveletMatrix})(...)" instead.

WARNING: deprecated syntax "call(::Type{WaveletMatrix}, ...)".
Use "(::Type{WaveletMatrix})(...)" instead.
WARNING: Base.ASCIIString is deprecated, use String instead.
  likely near /home/al2025/.julia/v0.5/FMIndexes/src/FMIndexes.jl:480
WARNING: Base.ASCIIString is deprecated, use String instead.
  likely near /home/al2025/.julia/v0.5/FMIndexes/src/FMIndexes.jl:480
WARNING: Base.ASCIIString is deprecated, use String instead.
  likely near /home/al2025/.julia/v0.5/FMIndexes/src/FMIndexes.jl:480
WARNING: Base.ASCIIString is deprecated, use String instead.
  likely near /home/al2025/.julia/v0.5/FMIndexes/src/FMIndexes.jl:481
INFO: using IntArrays
INFO: using IntervalsTrees
INFO: using BufferedStreams
INFO: using Libz
INFO: using StatsBase
INFO: using Distributions
INFO: using Glob
INFO: using SuffixArrays
INFO: using Requests
ERROR: LoadError: HttpParser not properly installed. Please run
Pkg.build("HttpParser")
 in error(::String, ::String, ::Vararg{String,N}) at ./error.jl:22
 in include_from_node1(::String) at ./loading.jl:488
 in macro expansion; at ./none:2 [inlined]
 in anonymous at ./<missing>:?
 in eval(::Module, ::Any) at ./boot.jl:234
 in process_options(::Base.JLOptions) at ./client.jl:242
 in _start() at ./client.jl:321
while loading /home/al2025/.julia/v0.5/HttpParser/src/HttpParser.jl, in expression starting on line 9
ERROR: LoadError: Failed to precompile HttpParser to /home/al2025/.julia/lib/v0.5/HttpParser.ji.
 in compilecache(::String) at ./loading.jl:593
 in require(::Symbol) at ./loading.jl:393
 in include_from_node1(::String) at ./loading.jl:488
 in macro expansion; at ./none:2 [inlined]
 in anonymous at ./<missing>:?
 in eval(::Module, ::Any) at ./boot.jl:234
 in process_options(::Base.JLOptions) at ./client.jl:242
 in _start() at ./client.jl:321
while loading /home/al2025/.julia/v0.5/Requests/src/Requests.jl, in expression starting on line 17
ERROR: LoadError: Failed to precompile Requests to /home/al2025/.julia/lib/v0.5/Requests.ji.
 in compilecache(::String) at ./loading.jl:593
 in require(::Symbol) at ./loading.jl:422
 in include_from_node1(::String) at ./loading.jl:488
 in process_options(::Base.JLOptions) at ./client.jl:265
 in _start() at ./client.jl:321
while loading /pylon2/mc3bg6p/al2025/storage/Whippet.jl/dependencies.jl, in expression starting on line 70

At this point, I tried your above suggestion of removing the v0.5 folder, and then running Pkg.add("Requests") in julia....

julia> Pkg.add("Requests")
INFO: Initializing package repository /home/al2025/.julia/v0.5
INFO: Cloning METADATA from https://github.com/JuliaLang/METADATA.jl
INFO: Installing BinDeps v0.6.0
INFO: Installing BufferedStreams v0.3.3
INFO: Installing Codecs v0.3.0
INFO: Installing Compat v0.31.0
INFO: Installing HttpCommon v0.3.0
INFO: Installing HttpParser v0.3.0
INFO: Installing JSON v0.13.0
INFO: Installing Libz v0.2.4
INFO: Installing MbedTLS v0.4.5
INFO: Installing Requests v0.5.1
INFO: Installing SHA v0.3.3
INFO: Installing URIParser v0.2.0
INFO: Building HttpParser
INFO: Attempting to Create directory /home/al2025/.julia/v0.5/HttpParser/deps/downloads
INFO: Attempting to Create directory /home/al2025/.julia/v0.5/HttpParser/deps/downloads
INFO: Directory /home/al2025/.julia/v0.5/HttpParser/deps/downloads already created
INFO: Downloading file https://github.com/nodejs/http-parser/archive/v2.7.1.zip
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   123    0   123    0     0    922      0 --:--:-- --:--:-- --:--:--   924
100 55365  100 55365    0     0   253k      0 --:--:-- --:--:-- --:--:--  253k
INFO: Done downloading file https://github.com/nodejs/http-parser/archive/v2.7.1.zip
INFO: Attempting to Create directory /home/al2025/.julia/v0.5/HttpParser/deps
INFO: Directory /home/al2025/.julia/v0.5/HttpParser/deps already created
Archive:  /home/al2025/.julia/v0.5/HttpParser/deps/downloads/v2.7.1.zip
feae95a3a69f111bc1897b9048d9acbc290992f9
   creating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/.gitignore  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/.mailmap  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/.travis.yml  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/AUTHORS  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/LICENSE-MIT  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/Makefile  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/README.md  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/bench.c  
   creating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/contrib/
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/contrib/parsertrace.c  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/contrib/url_parser.c  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/http_parser.c  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/http_parser.gyp  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/http_parser.h  
  inflating: /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1/test.c  
INFO: Attempting to Create directory /home/al2025/.julia/v0.5/HttpParser/deps/usr/lib
INFO: Changing Directory to /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1
INFO: Changing Directory to /home/al2025/.julia/v0.5/HttpParser/deps/src/http-parser-2.7.1
INFO: Changing Directory to /home/al2025/.julia/v0.5/HttpParser/deps/src
INFO: Attempting to Create directory /home/al2025/.julia/v0.5/HttpParser/deps/usr/lib
INFO: Directory /home/al2025/.julia/v0.5/HttpParser/deps/usr/lib already created
INFO: Changing Directory to /home/al2025/.julia/v0.5/HttpParser/deps/src
===============================================================[ ERROR: HttpParser ]===============================================================

LoadError: could not spawn setenv(`make -j8 -C http-parser-2.7.1 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not a directory (ENOTDIR)
while loading /home/al2025/.julia/v0.5/HttpParser/deps/build.jl, in expression starting on line 71

===================================================================================================================================================
INFO: Building MbedTLS
Using system libraries...

=================================================================[ BUILD ERRORS ]==================================================================

WARNING: HttpParser had build errors.

 - packages with build errors remain installed in /home/al2025/.julia/v0.5
 - build the package(s) and all dependencies with `Pkg.build("HttpParser")`
 - build a single package by running its `deps/build.jl` script

===================================================================================================================================================
INFO: Package database updated

julia>

I'm wondering if this is an issue in some friction between linuxbrew (which is what I used to set up a good portion of my bioinformatic tools) and julia. Any thoughts now that the original error is up here?

@timbitz
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timbitz commented Sep 12, 2017

Hi @AndrewLangvt,

I can't reproduce the error, and since it is setenv and path/directory related, its possible that there might be something going on with your local environment, though I'm not sure what.
...
After a bit of searching. It looks like your not a directory (ENOTDIR) error has been seen before:
JuliaWeb/HttpParser.jl#69
JunoLab/atom-julia-client#366

I think the conclusion there was that the issue was system/environment specific since the errors didn't occur on travis. So not super helpful, and I am not sure how to suggest a fix. Can you try another user on the same machine or a different machine entirely? Perhaps opening an issue to the upstream package would produce some more specific suggestions?

NOTE: When I update Whippet.jl to Julia v0.6 (there are some significant syntax changes in v0.6 and so updating Whippet has been dependent on some other packages catching up first), I will look into the possibility of deprecating Requests.jl and HttpParser.jl in place of the newer HTTP.jl julian version.

@AndrewLangvt
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Thanks @timbitz I have opened an issue with the HttpParser.jl repo. I appreciate your help with this, and look forward to the new version of Whippet.jl!

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