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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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Problems while installing vcffilterjdk #82

Closed muhammadsohailraza closed 7 years ago

muhammadsohailraza commented 7 years ago

Subject of the issue

I am trying to install vcffilterjdk module of jvakit. During installation, i am encountering some errors.

ERROR:

18 errors make: *** [vcffilterjdk] Error 1

Please help me resolve this

Your environment

recent directly cloned by GIT *java version "1.8.0_45" the value of ${JAVA_HOME}: /software/biosoft/software/jdk1.8/jdk1.8.0_45/bin/java :

Steps to reproduce

i used following commands to install: cd jvarkit git pull origin master make vcffilterjdk

Complete Error log

[sohail@login2 jvarkit]$ make vcffilterjdk
make: Warning: File `jfx.mk' has modification time 2e+03 s in the future
mkdir -p /share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/
echo "package com.github.lindenb.jvarkit.util.htsjdk;" > /share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo '@javax.annotation.Generated("jvarkit")' >> /share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo 'public class HtsjdkVersion{ private HtsjdkVersion(){}' >> /share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo 'public static String getVersion() {return "2.9.1";}' >> /share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo -n 'public static String getDate() {return "' >> /share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java &&  date | tr -d '\n' >> /share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java && echo ')";}' >> /share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo 'public static String getHash() {return "2.9.1";}' >> /share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo 'public static String getHome() {return "lib/com/github/samtools/htsjdk/2.9.1/htsjdk-2.9.1.jar";}' >> /share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo 'public static String getJavadocUrl(Class<?> clazz) {return "https://samtools.github.io/htsjdk/javadoc/htsjdk/"+clazz.getName().replaceAll("\\.","/")+".html";}' >> /share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo '}'  >> /share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java
echo " COMPILING vcffilterjdk "
COMPILING vcffilterjdk
rm -f /share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/_tmp-2.9.1/markdown.flag
mkdir -p /share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/_tmp-2.9.1/META-INF /share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/dist 
mkdir -p /share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/_tmp-2.9.1/com/github/lindenb/jvarkit/tools/vcffilterjs/
cp -v "/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java" "/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/_tmp-2.9.1/com/github/lindenb/jvarkit/tools/vcffilterjs/"
`/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java' -> `/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/_tmp-2.9.1/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java'
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 1.8.0_45
compile
javac -J-Djvarkit.libs.jars='lib/com/github/samtools/htsjdk/2.9.1/htsjdk-2.9.1.jar:lib/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar:lib/gov/nih/nlm/ncbi/ngs-java/1.2.4/ngs-java-1.2.4.jar:lib/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar:lib/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar:lib/org/tukaani/xz/1.5/xz-1.5.jar:lib/org/xerial/snappy/snappy-java/1.0.3-rc3/snappy-java-1.0.3-rc3.jar:lib/com/beust/jcommander/1.64/jcommander-1.64.jar' -J-Djvarkit.main.class='com.github.lindenb.jvarkit.tools.vcffilterjs.VcfFilterJdk' -J-Djvarkit.this.dir='/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/' -processorpath /share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/dist/annotproc.jar -d /share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/_tmp-2.9.1 -g -classpath "lib/com/github/samtools/htsjdk/2.9.1/htsjdk-2.9.1.jar:lib/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar:lib/gov/nih/nlm/ncbi/ngs-java/1.2.4/ngs-java-1.2.4.jar:lib/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar:lib/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar:lib/org/tukaani/xz/1.5/xz-1.5.jar:lib/org/xerial/snappy/snappy-java/1.0.3-rc3/snappy-java-1.0.3-rc3.jar:lib/com/beust/jcommander/1.64/jcommander-1.64.jar" -sourcepath /share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/java:/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/generated-sources/java /share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java /share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java
/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java:166: error: unmappable character for encoding ASCII
java -jar dist/vcffilterjdk.jar -e 'return variant.getGenotypes().stream().filter(G->G.hasAD() && java.util.Arrays.stream(G.getAD()).skip(1).filter(AD->AD>10)??????.findAny().isPresent??????()).findAny().isPres??????ent();' 
                                                                                                                                                              ^
/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java:166: error: unmappable character for encoding ASCII
java -jar dist/vcffilterjdk.jar -e 'return variant.getGenotypes().stream().filter(G->G.hasAD() && java.util.Arrays.stream(G.getAD()).skip(1).filter(AD->AD>10)??????.findAny().isPresent??????()).findAny().isPres??????ent();' 
                                                                                                                                                               ^
/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java:166: error: unmappable character for encoding ASCII
java -jar dist/vcffilterjdk.jar -e 'return variant.getGenotypes().stream().filter(G->G.hasAD() && java.util.Arrays.stream(G.getAD()).skip(1).filter(AD->AD>10)??????.findAny().isPresent??????()).findAny().isPres??????ent();' 
                                                                                                                                                                ^
/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java:166: error: unmappable character for encoding ASCII
java -jar dist/vcffilterjdk.jar -e 'return variant.getGenotypes().stream().filter(G->G.hasAD() && java.util.Arrays.stream(G.getAD()).skip(1).filter(AD->AD>10)??????.findAny().isPresent??????()).findAny().isPres??????ent();' 
                                                                                                                                                                 ^
/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java:166: error: unmappable character for encoding ASCII
java -jar dist/vcffilterjdk.jar -e 'return variant.getGenotypes().stream().filter(G->G.hasAD() && java.util.Arrays.stream(G.getAD()).skip(1).filter(AD->AD>10)??????.findAny().isPresent??????()).findAny().isPres??????ent();' 
                                                                                                                                                                  ^
/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java:166: error: unmappable character for encoding ASCII
java -jar dist/vcffilterjdk.jar -e 'return variant.getGenotypes().stream().filter(G->G.hasAD() && java.util.Arrays.stream(G.getAD()).skip(1).filter(AD->AD>10)??????.findAny().isPresent??????()).findAny().isPres??????ent();' 
                                                                                                                                                                   ^
/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java:166: error: unmappable character for encoding ASCII
java -jar dist/vcffilterjdk.jar -e 'return variant.getGenotypes().stream().filter(G->G.hasAD() && java.util.Arrays.stream(G.getAD()).skip(1).filter(AD->AD>10)??????.findAny().isPresent??????()).findAny().isPres??????ent();' 
                                                                                                                                                                                        ^
/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java:166: error: unmappable character for encoding ASCII
java -jar dist/vcffilterjdk.jar -e 'return variant.getGenotypes().stream().filter(G->G.hasAD() && java.util.Arrays.stream(G.getAD()).skip(1).filter(AD->AD>10)??????.findAny().isPresent??????()).findAny().isPres??????ent();' 
                                                                                                                                                                                         ^
/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java:166: error: unmappable character for encoding ASCII
java -jar dist/vcffilterjdk.jar -e 'return variant.getGenotypes().stream().filter(G->G.hasAD() && java.util.Arrays.stream(G.getAD()).skip(1).filter(AD->AD>10)??????.findAny().isPresent??????()).findAny().isPres??????ent();' 
                                                                                                                                                                                          ^
/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java:166: error: unmappable character for encoding ASCII
java -jar dist/vcffilterjdk.jar -e 'return variant.getGenotypes().stream().filter(G->G.hasAD() && java.util.Arrays.stream(G.getAD()).skip(1).filter(AD->AD>10)??????.findAny().isPresent??????()).findAny().isPres??????ent();' 
                                                                                                                                                                                           ^
/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java:166: error: unmappable character for encoding ASCII
java -jar dist/vcffilterjdk.jar -e 'return variant.getGenotypes().stream().filter(G->G.hasAD() && java.util.Arrays.stream(G.getAD()).skip(1).filter(AD->AD>10)??????.findAny().isPresent??????()).findAny().isPres??????ent();' 
                                                                                                                                                                                            ^
/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java:166: error: unmappable character for encoding ASCII
java -jar dist/vcffilterjdk.jar -e 'return variant.getGenotypes().stream().filter(G->G.hasAD() && java.util.Arrays.stream(G.getAD()).skip(1).filter(AD->AD>10)??????.findAny().isPresent??????()).findAny().isPres??????ent();' 
                                                                                                                                                                                             ^
/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java:166: error: unmappable character for encoding ASCII
java -jar dist/vcffilterjdk.jar -e 'return variant.getGenotypes().stream().filter(G->G.hasAD() && java.util.Arrays.stream(G.getAD()).skip(1).filter(AD->AD>10)??????.findAny().isPresent??????()).findAny().isPres??????ent();' 
                                                                                                                                                                                                                  ^
/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java:166: error: unmappable character for encoding ASCII
java -jar dist/vcffilterjdk.jar -e 'return variant.getGenotypes().stream().filter(G->G.hasAD() && java.util.Arrays.stream(G.getAD()).skip(1).filter(AD->AD>10)??????.findAny().isPresent??????()).findAny().isPres??????ent();' 
                                                                                                                                                                                                                   ^
/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java:166: error: unmappable character for encoding ASCII
java -jar dist/vcffilterjdk.jar -e 'return variant.getGenotypes().stream().filter(G->G.hasAD() && java.util.Arrays.stream(G.getAD()).skip(1).filter(AD->AD>10)??????.findAny().isPresent??????()).findAny().isPres??????ent();' 
                                                                                                                                                                                                                    ^
/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java:166: error: unmappable character for encoding ASCII
java -jar dist/vcffilterjdk.jar -e 'return variant.getGenotypes().stream().filter(G->G.hasAD() && java.util.Arrays.stream(G.getAD()).skip(1).filter(AD->AD>10)??????.findAny().isPresent??????()).findAny().isPres??????ent();' 
                                                                                                                                                                                                                     ^
/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java:166: error: unmappable character for encoding ASCII
java -jar dist/vcffilterjdk.jar -e 'return variant.getGenotypes().stream().filter(G->G.hasAD() && java.util.Arrays.stream(G.getAD()).skip(1).filter(AD->AD>10)??????.findAny().isPresent??????()).findAny().isPres??????ent();' 
                                                                                                                                                                                                                      ^
/share_bio/unisvx3/zengchq_group/sohail/softwares/J/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcffilterjs/VcfFilterJdk.java:166: error: unmappable character for encoding ASCII
java -jar dist/vcffilterjdk.jar -e 'return variant.getGenotypes().stream().filter(G->G.hasAD() && java.util.Arrays.stream(G.getAD()).skip(1).filter(AD->AD>10)??????.findAny().isPresent??????()).findAny().isPres??????ent();' 
                                                                                                                                                                                                                       ^
18 errors
make: *** [vcffilterjdk] Error 1
lindenb commented 7 years ago

my bad, there are some unicode characters hidden in the code comment. Many thanks for pointing this out. Strangely, it compiles on gith and on my machine. Give me a few minutes, I'll try to fix see.

lindenb commented 7 years ago

Ok, thanks again for the warning, I hope I've fixed all the encoding problem: https://github.com/lindenb/jvarkit/commit/68254c69b027a9ce81d8b211447f1c0bf02dc626

can you try again please ?

muhammadsohailraza commented 7 years ago

i tried the command, it prompts following message,

cd jvarkit git pull origin master fatal: Reading from helper 'git-remote-https' failed

my server has properly online connection, can you please check?

Thanks!

lindenb commented 7 years ago

Reading from helper 'git-remote-https' failed

no idea, i would say , it's a problem with git/github.

I would suggest to reinstall from scratch ?

muhammadsohailraza commented 7 years ago

It's okay now.. Installed successfully.. Thanks!