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conda-forge / openjdk-feedstock

A conda-smithy repository for openjdk.
BSD 3-Clause "New" or "Revised" License
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openjdk version #57

Closed YiweiZhu closed 2 years ago

YiweiZhu commented 5 years ago

Issue: I have installed openjdk 11.0.1 version in conda-forge channel, but when I check java -version, it shows the version is 1.8

(base) [zyw@localhost miniconda3]$ java -version openjdk version "1.8.0_191" OpenJDK Runtime Environment (build 1.8.0_191-b12) OpenJDK 64-Bit Server VM (build 25.191-b12, mixed mode)


Environment (conda list):

``` $ conda list # packages in environment at /data3/zyw/miniconda3: # # Name Version Build Channel _r-mutex 1.0.0 anacondar_1 apache-tomcat 7.0.88 0 birdhouse appdirs 1.4.3 py_1 conda-forge aragorn 1.2.38 h470a237_2 bioconda artemis 18.0.2 0 bioconda asn1crypto 0.24.0 py36_1003 conda-forge atomicwrites 1.3.0 py_0 conda-forge attrs 19.1.0 py_0 conda-forge barrnap 0.9 2 bioconda bcftools 1.9 h47928c2_2 bioconda bedtools 2.27.1 he860b03_3 bioconda binutils_impl_linux-64 2.28.1 had2808c_3 binutils_linux-64 7.2.0 had2808c_27 biopython 1.70 np112py36_1 bioconda blas 1.0 mkl blast 2.6.0 boost1.64_2 bioconda boost 1.64.0 py36_4 conda-forge boost-cpp 1.64.0 1 conda-forge bowtie2 2.3.4.3 py36he860b03_1 bioconda breseq 0.33.0 ha92aebf_0 bioconda bwa 0.7.17 h84994c4_5 bioconda bwidget 1.9.11 1 bzip2 1.0.6 h14c3975_1002 conda-forge ca-certificates 2019.3.9 hecc5488_0 conda-forge cairo 1.14.12 h80bd089_1005 conda-forge certifi 2019.3.9 py36_0 conda-forge cffi 1.12.2 py36hf0e25f4_1 conda-forge chardet 3.0.4 py36_1003 conda-forge circos 0.69.6 4 bioconda conda 4.6.8 py36_0 conda-forge conda-env 2.6.0 1 cryptography 2.6.1 py36h9d9f1b6_0 conda-forge curl 7.62.0 hbc83047_0 cycler 0.10.0 py_1 conda-forge dbus 1.13.2 h714fa37_1 diamond 0.8.36 hdbcaa40_3 bioconda emboss 6.6.0 h6debe1e_0 bioconda expat 2.2.5 hf484d3e_1002 conda-forge fastqc 0.11.8 1 bioconda filetype 1.0.5 py_0 conda-forge font-ttf-dejavu-sans-mono 2.37 h6964260_0 fontconfig 2.13.1 h2176d3f_1000 conda-forge freebayes 1.2.0 py36h56106d0_4 bioconda freetype 2.9.1 h94bbf69_1005 conda-forge gcc_impl_linux-64 7.2.0 habb00fd_3 gcc_linux-64 7.2.0 h550dcbe_27 gettext 0.19.8.1 h9745a5d_1001 conda-forge gfortran_impl_linux-64 7.2.0 hdf63c60_3 gfortran_linux-64 7.2.0 h550dcbe_27 giflib 5.1.7 h516909a_0 conda-forge glib 2.56.2 had28632_1001 conda-forge glimmerhmm 3.0.4 h2d50403_2 bioconda graphite2 1.3.13 hf484d3e_1000 conda-forge gst-plugins-base 1.14.0 hbbd80ab_1 gstreamer 1.14.0 hb453b48_1 gxx_impl_linux-64 7.2.0 hdf63c60_3 gxx_linux-64 7.2.0 h550dcbe_27 harfbuzz 1.9.0 he243708_1001 conda-forge hmmer 3.2.1 hf484d3e_1 bioconda htslib 1.9 h47928c2_5 bioconda icu 58.2 hf484d3e_1000 conda-forge idna 2.8 py36_1000 conda-forge infernal 1.1.2 h14c3975_2 bioconda intel-openmp 2019.1 144 joblib 0.13.2 py_0 conda-forge jpeg 9c h14c3975_1001 conda-forge kiwisolver 1.0.1 py36h6bb024c_1002 conda-forge libcurl 7.62.0 h20c2e04_0 libdeflate 1.0 h14c3975_1 bioconda libedit 3.1.20170329 h6b74fdf_2 libffi 3.2.1 hd88cf55_4 libgcc 7.2.0 h69d50b8_2 conda-forge libgcc-ng 8.2.0 hdf63c60_1 libgd 2.2.5 h0d07dcb_1005 conda-forge libgfortran-ng 7.2.0 hdf63c60_3 conda-forge libiconv 1.15 h14c3975_1004 conda-forge libidn11 1.34 h1cef754_0 conda-forge libpng 1.6.36 h84994c4_1000 conda-forge libssh2 1.8.0 h90d6eec_1004 conda-forge libstdcxx-ng 8.2.0 hdf63c60_1 libtiff 4.0.10 h648cc4a_1001 conda-forge libuuid 2.32.1 h14c3975_1000 conda-forge libwebp 1.0.2 h576950b_1 conda-forge libxcb 1.13 h14c3975_1002 conda-forge libxml2 2.9.8 h143f9aa_1005 conda-forge matplotlib 2.2.3 py36h8e2386c_0 conda-forge minced 0.3.2 0 bioconda miniasm 0.3_r179 ha92aebf_0 bioconda minimap2 2.16 h84994c4_1 bioconda mkl 2018.0.3 1 mmtf-python 1.1.2 py_0 conda-forge mock 2.0.0 py36_1001 conda-forge more-itertools 4.3.0 py36_1000 conda-forge msgpack-python 0.6.1 py36h6bb024c_0 conda-forge ncbi-genome-download 0.2.9 py36_0 bioconda ncurses 6.1 he6710b0_1 numpy 1.12.1 py36he24570b_1 olefile 0.46 py_0 conda-forge openjdk 11.0.1 h14c3975_1014 conda-forge openssl 1.1.1b h14c3975_1 conda-forge pandas 0.24.2 py36hf484d3e_0 conda-forge pango 1.40.14 hf0c64fd_1003 conda-forge parallel 20190122 0 conda-forge patsy 0.5.1 py_0 conda-forge pbr 5.1.3 py_0 conda-forge pcre 8.43 he6710b0_0 perl 5.26.2 h14c3975_1002 conda-forge perl-app-cpanminus 1.7044 pl526_1 bioconda perl-autoloader 5.74 pl526_2 bioconda perl-bioperl 1.6.924 4 bioconda perl-business-isbn 3.004 pl526_0 bioconda perl-business-isbn-data 20140910.003 pl526_0 bioconda perl-carp 1.38 pl526_2 bioconda perl-clone 0.41 pl526h470a237_0 bioconda perl-config-general 2.63 pl526_0 bioconda perl-constant 1.33 pl526_1 bioconda perl-data-dumper 2.173 pl526_0 bioconda perl-devel-symdump 2.18 pl526_1 bioconda perl-digest-hmac 1.03 pl526_3 bioconda perl-digest-perl-md5 1.9 pl526_1 bioconda perl-dynaloader 1.25 pl526_1 bioconda perl-encode 2.88 pl526_1 bioconda perl-encode-locale 1.05 pl526_6 bioconda perl-exporter 5.72 pl526_1 bioconda perl-exporter-tiny 0.042 1 bioconda perl-extutils-makemaker 7.34 pl526_3 bioconda perl-file-listing 6.04 0 bioconda perl-file-path 2.15 pl526_0 bioconda perl-file-temp 0.2304 pl526_2 bioconda perl-font-ttf 1.06 pl526_0 bioconda perl-gd 2.70 pl526he941832_0 bioconda perl-html-parser 3.72 pl526h2d50403_4 bioconda perl-html-tagset 3.20 pl526_3 bioconda perl-http-cookies 6.01 0 bioconda perl-http-daemon 6.01 0 bioconda perl-http-date 6.02 pl526_3 bioconda perl-http-message 6.11 0 bioconda perl-http-negotiate 6.01 0 bioconda perl-io-html 1.001 pl526_2 bioconda perl-io-socket-ssl 2.024 0 bioconda perl-io-string 1.08 pl526_3 bioconda perl-libwww-perl 6.15 0 bioconda perl-list-moreutils 0.428 pl526_1 bioconda perl-list-moreutils-xs 0.428 pl526_0 bioconda perl-lwp-mediatypes 6.02 pl526_3 bioconda perl-math-bezier 0.01 pl526_1 bioconda perl-math-round 0.07 pl526_1 bioconda perl-math-vecstat 0.08 pl526_1 bioconda perl-mime-base64 3.15 pl526_1 bioconda perl-module-implementation 0.09 pl526_2 bioconda perl-module-runtime 0.016 pl526_0 bioconda perl-net-http 6.09 0 bioconda perl-net-ssleay 1.74 0 bioconda perl-ntlm 1.09 1 bioconda perl-number-format 1.75 pl526_3 bioconda perl-params-validate 1.29 pl526h470a237_0 bioconda perl-parent 0.236 pl526_1 bioconda perl-pathtools 3.73 h470a237_2 bioconda perl-readonly 2.05 pl526_0 bioconda perl-regexp-common 2017060201 pl526_0 bioconda perl-scalar-list-utils 1.45 pl526h470a237_3 bioconda perl-set-intspan 1.19 pl526_1 bioconda perl-statistics-basic 1.6611 pl526_2 bioconda perl-svg 2.84 pl526_0 bioconda perl-test-more 1.001002 pl526_1 bioconda perl-text-format 0.59 pl526_2 bioconda perl-threaded 5.22.0 13 bioconda perl-time-hires 1.9758 pl526_0 bioconda perl-time-local 1.28 pl526_1 bioconda perl-time-piece 1.27 pl526_1 bioconda perl-try-tiny 0.30 pl526_1 bioconda perl-uri 1.76 pl526_0 bioconda perl-www-robotrules 6.02 0 bioconda perl-xml-namespacesupport 1.11 0 bioconda perl-xml-parser 2.44 4 bioconda perl-xml-sax 0.99 0 bioconda perl-xml-sax-base 1.08 0 bioconda perl-xml-sax-expat 0.51 0 bioconda perl-xml-simple 2.22 0 bioconda perl-xsloader 0.24 pl526_0 bioconda perl-yaml 1.27 pl526_0 bioconda pillow 5.3.0 py36h00a061d_1000 conda-forge pilon 1.23 0 bioconda pip 19.0.3 py36_0 conda-forge pixman 0.34.0 h14c3975_1003 conda-forge pluggy 0.9.0 py_0 conda-forge prodigal 2.6.3 1 bioconda prokka 1.13 0 bioconda pthread-stubs 0.4 h14c3975_1001 conda-forge py 1.8.0 py_0 conda-forge pyahocorasick 1.4.0 py36h14c3975_0 conda-forge pycosat 0.6.3 py36h14c3975_1001 conda-forge pycparser 2.19 py36_1 conda-forge pyfaidx 0.5.5.2 py_0 bioconda pyopenssl 19.0.0 py36_0 conda-forge pyparsing 2.3.1 py_0 conda-forge pyqt 5.6.0 py36h13b7fb3_1008 conda-forge pysocks 1.6.8 py36_1002 conda-forge pytest 4.3.1 py36_0 conda-forge python 3.6.8 h0371630_0 python-dateutil 2.8.0 py_0 conda-forge pytz 2018.9 py_0 conda-forge qt 5.6.3 h8bf5577_3 quast 5.0.2 py36pl526ha92aebf_0 bioconda r-base 3.4.3 h9bb98a2_5 racon 1.3.2 he941832_0 bioconda raxml 8.2.12 h470a237_0 bioconda readline 7.0 h7b6447c_5 reportlab 3.5.13 py36hbd3ef63_1000 conda-forge requests 2.21.0 py36_1000 conda-forge rgi 4.2.2 py36ha92aebf_1 bioconda ruamel_yaml 0.15.71 py36h14c3975_1000 conda-forge samclip 0.2 1 bioconda samtools 1.9 h91753b0_5 bioconda scipy 1.1.0 py36hd20e5f9_0 seaborn 0.9.0 py_0 conda-forge seqtk 1.3 h84994c4_1 bioconda setuptools 40.8.0 py36_0 conda-forge simplejson 3.8.1 py36_0 bioconda sip 4.18.1 py36hf484d3e_1000 conda-forge six 1.12.0 py36_1000 conda-forge snippy 4.0.2 0 bioconda snp-sites 2.4.1 ha92aebf_0 bioconda snpeff 4.3.1t 2 bioconda spades 3.13.0 0 bioconda sqlite 3.26.0 h7b6447c_0 statsmodels 0.9.0 py36h3010b51_1000 conda-forge tbb 2019.4 h6bb024c_0 conda-forge tbl2asn 25.6 3 bioconda tk 8.6.8 hbc83047_0 tktable 2.10 h14c3975_0 tornado 6.0.1 py36h14c3975_0 conda-forge trimmomatic 0.38 1 bioconda unicycler 0.4.7 py36hdbcaa40_0 bioconda urllib3 1.24.1 py36_1000 conda-forge vcflib 1.0.0_rc2 h56106d0_2 bioconda vt 2015.11.10 he941832_3 bioconda wheel 0.33.1 py36_0 conda-forge xorg-kbproto 1.0.7 h14c3975_1002 conda-forge xorg-libice 1.0.9 h14c3975_1004 conda-forge xorg-libsm 1.2.3 h4937e3b_1000 conda-forge xorg-libx11 1.6.7 h14c3975_1000 conda-forge xorg-libxau 1.0.9 h14c3975_0 conda-forge xorg-libxdmcp 1.1.2 h14c3975_1007 conda-forge xorg-libxext 1.3.3 h14c3975_1004 conda-forge xorg-libxrender 0.9.10 h14c3975_1002 conda-forge xorg-renderproto 0.11.1 h14c3975_1002 conda-forge xorg-xextproto 7.3.0 h14c3975_1002 conda-forge xorg-xproto 7.0.31 h14c3975_1007 conda-forge xz 5.2.4 h14c3975_4 yaml 0.1.7 had09818_2 zlib 1.2.11 h7b6447c_3 ```


Details about conda and system ( conda info ):

``` $ conda info active environment : base active env location : /data3/zyw/miniconda3 shell level : 1 user config file : /data3/zyw/.condarc populated config files : /data3/zyw/.condarc conda version : 4.6.8 conda-build version : not installed python version : 3.6.8.final.0 base environment : /data3/zyw/miniconda3 (writable) channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://conda.anaconda.org/bioconda/linux-64 https://conda.anaconda.org/bioconda/noarch https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/free/linux-64 https://repo.anaconda.com/pkgs/free/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /data3/zyw/miniconda3/pkgs /data3/zyw/.conda/pkgs envs directories : /data3/zyw/miniconda3/envs /data3/zyw/.conda/envs platform : linux-64 user-agent : conda/4.6.8 requests/2.21.0 CPython/3.6.8 Linux/3.10.0-514.10.2.el7.x86_64 centos/7.1.1503 glibc/2.17 UID:GID : 1010:1011 netrc file : None offline mode : False ```
edisongustavo commented 5 years ago

You shouldn't install it on the base environment.

For me this worked:

$ conda create -n give-me-java openjdk=11
$ conda activate give-me-java
$ java -version
openjdk version "1.8.0_192"
OpenJDK Runtime Environment (Zulu 8.33.0.1-linux64) (build 1.8.0_192-b01)
OpenJDK 64-Bit Server VM (Zulu 8.33.0.1-linux64) (build 25.192-b01, mixed mode)