Closed AndrewLangvt closed 6 years ago
timbitz
commented
6 years ago 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
commented
6 years ago 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
INFO: Cloning cache of Rmath from https://github.com/JuliaStats/Rmath.jl.git
INFO: Cloning cache of SHA from https://github.com/staticfloat/SHA.jl.git
INFO: Cloning cache of StatsFuns from https://github.com/JuliaStats/StatsFuns.jl.git
INFO: Cloning cache of URIParser from https://github.com/JuliaWeb/URIParser.jl.git
INFO: Installing BinDeps v0.6.0
INFO: Installing Calculus v0.2.2
INFO: Installing Distributions v0.13.0
INFO: Installing PDMats v0.7.0
INFO: Installing QuadGK v0.1.3
INFO: Installing Rmath v0.2.0
INFO: Installing SHA v0.3.3
INFO: Installing StatsFuns v0.5.0
INFO: Installing URIParser v0.2.0
INFO: Building Rmath
INFO: Attempting to Create directory /home/al2025/.julia/v0.5/Rmath/deps/downloads
INFO: Downloading file https://github.com/JuliaLang/Rmath-julia/archive/v0.2.0.tar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 129 0 129 0 0 1066 0 --:--:-- --:--:-- --:--:-- 1162
100 155k 100 155k 0 0 741k 0 --:--:-- --:--:-- --:--:-- 741k
INFO: Done downloading file https://github.com/JuliaLang/Rmath-julia/archive/v0.2.0.tar.gz
INFO: Attempting to Create directory /home/al2025/.julia/v0.5/Rmath/deps/src
INFO: Attempting to Create directory /home/al2025/.julia/v0.5/Rmath/deps
INFO: Directory /home/al2025/.julia/v0.5/Rmath/deps already created
INFO: Attempting to Create directory /home/al2025/.julia/v0.5/Rmath/deps/usr/lib
INFO: Changing Directory to /home/al2025/.julia/v0.5/Rmath/deps/src/Rmath-julia-0.2.0
make -C src
make[1]: Entering directory `/home/al2025/.julia/v0.5/Rmath/deps/src/Rmath-julia-0.2.0/src'
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
make[1]: Leaving directory `/home/al2025/.julia/v0.5/Rmath/deps/src/Rmath-julia-0.2.0/src'
INFO: Changing Directory to /home/al2025/.julia/v0.5/Rmath/deps/src/Rmath-julia-0.2.0
INFO: Package database updated
Checking Glob ... Trying to install Glob ...
INFO: Cloning cache of Glob from https://github.com/vtjnash/Glob.jl.git
INFO: Installing Glob v1.1.1
INFO: Package database updated
Checking Bio ... Trying to install Bio ...
INFO: Cloning cache of AutoHashEquals from https://github.com/andrewcooke/AutoHashEquals.jl.git
INFO: Cloning cache of BGZFStreams from https://github.com/BioJulia/BGZFStreams.jl.git
INFO: Cloning cache of Bio from https://github.com/BioJulia/Bio.jl.git
INFO: Cloning cache of Blosc from https://github.com/stevengj/Blosc.jl.git
INFO: Cloning cache of ColorTypes from https://github.com/JuliaGraphics/ColorTypes.jl.git
INFO: Cloning cache of Colors from https://github.com/JuliaGraphics/Colors.jl.git
INFO: Cloning cache of Combinatorics from https://github.com/JuliaMath/Combinatorics.jl.git
INFO: Cloning cache of DiffBase from https://github.com/JuliaDiff/DiffBase.jl.git
INFO: Cloning cache of EzXML from https://github.com/bicycle1885/EzXML.jl.git
INFO: Cloning cache of FileIO from https://github.com/JuliaIO/FileIO.jl.git
INFO: Cloning cache of FixedPointNumbers from https://github.com/JuliaMath/FixedPointNumbers.jl.git
INFO: Cloning cache of ForwardDiff from https://github.com/JuliaDiff/ForwardDiff.jl.git
INFO: Cloning cache of GZip from https://github.com/JuliaIO/GZip.jl.git
INFO: Cloning cache of HDF5 from https://github.com/JuliaIO/HDF5.jl.git
INFO: Cloning cache of IterTools from https://github.com/JuliaCollections/IterTools.jl.git
INFO: Cloning cache of Iterators from https://github.com/JuliaCollections/Iterators.jl.git
INFO: Cloning cache of JLD from https://github.com/JuliaIO/JLD.jl.git
INFO: Cloning cache of LegacyStrings from https://github.com/JuliaArchive/LegacyStrings.jl.git
INFO: Cloning cache of LightGraphs from https://github.com/JuliaGraphs/LightGraphs.jl.git
INFO: Cloning cache of LightXML from https://github.com/JuliaIO/LightXML.jl.git
INFO: Cloning cache of NaNMath from https://github.com/mlubin/NaNMath.jl.git
INFO: Cloning cache of ParserCombinator from https://github.com/andrewcooke/ParserCombinator.jl.git
INFO: Cloning cache of Polynomials from https://github.com/JuliaMath/Polynomials.jl.git
INFO: Cloning cache of Reexport from https://github.com/simonster/Reexport.jl.git
INFO: Cloning cache of Roots from https://github.com/JuliaMath/Roots.jl.git
INFO: Installing AutoHashEquals v0.1.2
INFO: Installing BGZFStreams v0.1.4
INFO: Installing Bio v0.4.7
INFO: Installing Blosc v0.3.0
INFO: Installing ColorTypes v0.5.2
INFO: Installing Colors v0.7.4
INFO: Installing Combinatorics v0.4.1
INFO: Installing DiffBase v0.1.0
INFO: Installing EzXML v0.4.5
INFO: Installing FileIO v0.5.1
INFO: Installing FixedPointNumbers v0.3.9
INFO: Installing ForwardDiff v0.4.2
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
% Total % Received % Xferd Average Speed Time Time Time Current
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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 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 ]===============================================================
LoadError: could not spawn setenv(`make -j8 -C http-parser-2.7.1 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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 70At 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 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:/pylon2/mc3bg6p/al2025/storage/cash_v2.1.0-alpha1","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 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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
commented
6 years ago 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:
https://github.com/JuliaWeb/HttpParser.jl/issues/69
https://github.com/JunoLab/atom-julia-client/issues/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
commented
6 years ago 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!
I am having difficulty with the HttpParser build when trying to install Whippet.
I then attempted to build the package, but still no luck...
Any thoughts on where I'm going wrong here? I'm quite new to Julia, so it may be a very simple issue...