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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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I have had success installing jvarkit on Mac in the past, but now problems on CentOS #115

Closed bgphd closed 5 years ago

bgphd commented 5 years ago

Verify

There are 5 programs which provide 'java'.

Selection Command

1 java-1.7.0-openjdk.x86_64 (/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.191-2.6.15.4.el7_5.x86_64/jre/bin/java) 2 java-1.8.0-openjdk.x86_64 (/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-3.b13.el7_5.x86_64/jre/bin/java)

Enter to keep the current selection[+], or type selection number: 3 (ldc-1.12.0)[bgold@centos7 jvarkit]$ cd .. (ldc-1.12.0)[bgold@centos7 ~]$ rm -rf jvarkit (ldc-1.12.0)[bgold@centos7 ~]$ git clone "https://github.com/lindenb/jvarkit.git" Cloning into 'jvarkit'... remote: Enumerating objects: 34992, done. remote: Total 34992 (delta 0), reused 0 (delta 0), pack-reused 34992 Receiving objects: 100% (34992/34992), 11.82 MiB | 17.72 MiB/s, done. Resolving deltas: 100% (18016/18016), done. (ldc-1.12.0)[bgold@centos7 ~]$ export PATH=${JAVA_HOME}/bin:${PATH} (ldc-1.12.0)[bgold@centos7 ~]$ cd jvarkit (ldc-1.12.0)[bgold@centos7 jvarkit]$ make bamstats05 mkdir -p lib/com/github/samtools/htsjdk/2.15.0/ && curl -Lk -o "lib/com/github/samtools/htsjdk/2.15.0/htsjdk-2.15.0.jar" "http://central.maven.org/maven2/com/github/samtools/htsjdk/2.15.0/htsjdk-2.15.0.jar" % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 1573k 100 1573k 0 0 7929k 0 --:--:-- --:--:-- --:--:-- 7945k mkdir -p lib/commons-logging/commons-logging/1.1.1/ && curl -Lk -o "lib/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar" "http://central.maven.org/maven2/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar" % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 60686 100 60686 0 0 1102k 0 --:--:-- --:--:-- --:--:-- 1118k mkdir -p lib/gov/nih/nlm/ncbi/ngs-java/1.2.4/ && curl -Lk -o "lib/gov/nih/nlm/ncbi/ngs-java/1.2.4/ngs-java-1.2.4.jar" "http://central.maven.org/maven2/gov/nih/nlm/ncbi/ngs-java/1.2.4/ngs-java-1.2.4.jar" % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 74133 100 74133 0 0 1025k 0 --:--:-- --:--:-- --:--:-- 1034k mkdir -p lib/org/apache/commons/commons-compress/1.4.1/ && curl -Lk -o "lib/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar" "http://central.maven.org/maven2/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar" % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 235k 100 235k 0 0 2618k 0 --:--:-- --:--:-- --:--:-- 2648k mkdir -p lib/org/apache/commons/commons-jexl/2.1.1/ && curl -Lk -o "lib/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar" "http://central.maven.org/maven2/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar" % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 261k 100 261k 0 0 2906k 0 --:--:-- --:--:-- --:--:-- 2904k mkdir -p lib/org/tukaani/xz/1.5/ && curl -Lk -o "lib/org/tukaani/xz/1.5/xz-1.5.jar" "http://central.maven.org/maven2/org/tukaani/xz/1.5/xz-1.5.jar" % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 99555 100 99555 0 0 1578k 0 --:--:-- --:--:-- --:--:-- 1593k mkdir -p lib/org/xerial/snappy/snappy-java/1.1.4/ && curl -Lk -o "lib/org/xerial/snappy/snappy-java/1.1.4/snappy-java-1.1.4.jar" "http://central.maven.org/maven2/org/xerial/snappy/snappy-java/1.1.4/snappy-java-1.1.4.jar" % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 1470k 100 1470k 0 0 7380k 0 --:--:-- --:--:-- --:--:-- 7389k mkdir -p lib/com/beust/jcommander/1.64/ && curl -Lk -o "lib/com/beust/jcommander/1.64/jcommander-1.64.jar" "http://central.maven.org/maven2/com/beust/jcommander/1.64/jcommander-1.64.jar" % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 65585 100 65585 0 0 867k 0 --:--:-- --:--:-- --:--:-- 877k mkdir -p /home/bgold/jvarkit/dist/ rm -rf "/home/bgold/jvarkit/_tmp-2.15.0" mkdir -p /home/bgold/jvarkit/_tmp-2.15.0/META-INF/services echo "com.github.lindenb.jvarkit.annotproc.JVarkitAnnotationProcessor" > /home/bgold/jvarkit/_tmp-2.15.0/META-INF/services/javax.annotation.processing.Processor echo '### Printing javac version : it should be Oracle 1.8 (NOT OpenJDK). if Not, check your $${PATH}.'

Printing javac version : it should be Oracle 1.8 (NOT OpenJDK). if Not, check your $${PATH}.

javac -version javac 9.0.4

compile

javac -d /home/bgold/jvarkit/_tmp-2.15.0 -sourcepath /home/bgold/jvarkit/src/main/java:/home/bgold/jvarkit/src/main/generated-sources/java /home/bgold/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java jar cvf /home/bgold/jvarkit/dist/annotproc.jar -C /home/bgold/jvarkit/_tmp-2.15.0 . added manifest ignoring entry META-INF/ adding: META-INF/services/(in = 0) (out= 0)(stored 0%) adding: META-INF/services/javax.annotation.processing.Processor(in = 64) (out= 59)(deflated 7%) adding: com/(in = 0) (out= 0)(stored 0%) adding: com/github/(in = 0) (out= 0)(stored 0%) adding: com/github/lindenb/(in = 0) (out= 0)(stored 0%) adding: com/github/lindenb/jvarkit/(in = 0) (out= 0)(stored 0%) adding: com/github/lindenb/jvarkit/annotproc/(in = 0) (out= 0)(stored 0%) adding: com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.class(in = 12374) (out= 5529)(deflated 55%) adding: com/github/lindenb/jvarkit/annotproc/IncludeSourceInJar.class(in = 424) (out= 258)(deflated 39%) adding: com/github/lindenb/jvarkit/util/(in = 0) (out= 0)(stored 0%) adding: com/github/lindenb/jvarkit/util/log/(in = 0) (out= 0)(stored 0%) adding: com/github/lindenb/jvarkit/util/log/Logger$Level.class(in = 1232) (out= 604)(deflated 50%) adding: com/github/lindenb/jvarkit/util/log/Logger$Builder.class(in = 2017) (out= 953)(deflated 52%) adding: com/github/lindenb/jvarkit/util/log/Logger$DefaultLogger.class(in = 1382) (out= 664)(deflated 51%) adding: com/github/lindenb/jvarkit/util/log/Logger$KnimeLogger.class(in = 3159) (out= 1423)(deflated 54%) adding: com/github/lindenb/jvarkit/util/log/Logger$1.class(in = 877) (out= 513)(deflated 41%) adding: com/github/lindenb/jvarkit/util/log/Logger.class(in = 3469) (out= 1419)(deflated 59%) adding: com/github/lindenb/jvarkit/util/jcommander/(in = 0) (out= 0)(stored 0%) adding: com/github/lindenb/jvarkit/util/jcommander/Program.class(in = 767) (out= 448)(deflated 41%) rm -rf "/home/bgold/jvarkit/_tmp-2.15.0" echo "### COMPILING bamstats05 ######"

COMPILING bamstats05

rm -f /home/bgold/jvarkit/_tmp-2.15.0/markdown.flag mkdir -p /home/bgold/jvarkit/_tmp-2.15.0/META-INF /home/bgold/jvarkit/dist mkdir -p /home/bgold/jvarkit/_tmp-2.15.0/com/github/lindenb/jvarkit/tools/bamstats04/ cp -v "/home/bgold/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/bamstats04/BamStats05.java" "/home/bgold/jvarkit/_tmp-2.15.0/com/github/lindenb/jvarkit/tools/bamstats04/" ‘/home/bgold/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/bamstats04/BamStats05.java’ -> ‘/home/bgold/jvarkit/_tmp-2.15.0/com/github/lindenb/jvarkit/tools/bamstats04/BamStats05.java’ echo '### Printing javac version : it should be Oracle 1.8 (you should avoid OpenJDK). if Not, check your ${PATH}.'

Printing javac version : it should be Oracle 1.8 (you should avoid OpenJDK). if Not, check your ${PATH}.

javac -version 2> bamstats05.jdkversion && cat bamstats05.jdkversion && grep -E '1.8.[0-9_]+' bamstats05.jdkversion && rm bamstats05.jdkversion javac 9.0.4 make: *** [bamstats05] Error 1 (ldc-1.12.0)[bgold@centos7 jvarkit]$

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lindenb commented 5 years ago 
export PATH=${JAVA_HOME}/bin:${PATH}

what is the value of JAVA_HOME ? if it's empty, it won't work.

try: 

export PATH=/usr/java/jdk1.8.0_162/jre/bin:${PATH}
bgphd commented 5 years ago

That worked!!!!

thanks, and sorry to be a pest.

Bert

On Sat, Nov 10, 2018 at 3:56 AM Pierre Lindenbaum notifications@github.com wrote:

export PATH=${JAVA_HOME}/bin:${PATH}

what is the value of JAVA_HOME ? if it's empty, it won't work.

try:

export PATH=/usr/java/jdk1.8.0_162/jre/bin:${PATH}

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/lindenb/jvarkit/issues/115#issuecomment-437578800, or mute the thread https://github.com/notifications/unsubscribe-auth/Ap77L9QFUt-PsgHVexDZoaLqWVdFWqrZks5utr7jgaJpZM4YXzsf .

-- Bert Gold, PhD, FACMGG, CGMB Clinical Molecular Geneticist BillionToOne at StartX 2627 Hanover Street Palo Alto, CA 94304 USA CELL: 302-507-1827