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MetfragLib failed to install by #106

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SivanXW opened this issue Nov 18, 2022 · 2 comments
Open

MetfragLib failed to install by #106

SivanXW opened this issue Nov 18, 2022 · 2 comments

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@SivanXW
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SivanXW commented Nov 18, 2022 •
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Hi prof,
I tried to install MetfragLib and MetfragCL on Linux (CentOS) following the MetFrag relaunched tutorial. But when running "mvn clean install -pl MetFragLib -am", some errors occured:

[ERROR] /root/MetFragRelaunched/MetFragLib/src/main/java/de/ipbhalle/metfraglib/parameter/ClassNames.java:[32,39] cannot find symbol symbol: class OnlineChemSpiderDatabase location: package de.ipbhalle.metfraglib.database [ERROR] /root/MetFragRelaunched/MetFragLib/src/main/java/de/ipbhalle/metfraglib/parameter/ClassNames.java:[33,39] cannot find symbol symbol: class OnlineChemSpiderRestDatabase location: package de.ipbhalle.metfraglib.database [ERROR] /root/MetFragRelaunched/MetFragLib/src/main/java/de/ipbhalle/metfraglib/parameter/ClassNames.java:[38,39] cannot find symbol symbol: class OnlinePubChemDatabase location: package de.ipbhalle.metfraglib.database [ERROR] /root/MetFragRelaunched/MetFragLib/src/main/java/de/ipbhalle/metfraglib/database/OnlineExtendedPubChemDatabase.java:[21,52] cannot find symbol symbol: class OnlinePubChemDatabase

Also, it seems that there are some problems connecting to ChemSpider as mentioned in #96 and #97. I wonder is there a way to deal with this problem now?

Thanks for your kind help.
Sivan
@sneumann
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sneumann commented Nov 18, 2022 via email

@SivanXW
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SivanXW commented Nov 18, 2022 •
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It works!! Cannot express my appreciation!

In addtion, previously when I tried to use
# java -jar MetFragCommandLine-VERSION-jar-with-dependencies.jar [parameter file]
to install MetFragCL (with java version 19.0), using the jar downloaded from "https://github.com/ipb-halle/MetFragRelaunched/releases/tag/v.2.5.0",
errors came out like:

16:42:17.074 ERROR HelloWorld - Parameter file is missing! 16:42:17.086 ERROR HelloWorld - ParameterFile='path_to_parameterfile'

I fail to find the similar error in through Internet. Is this error due to the jar package or the missing of some dependencies?
Really thanks for your kind help!

Hi, I think your errors are a symptom of not being able to download some dependencies further up in your output. can you try mvn -Dhttps.protocols=TLSv1.2 -f MetFragRelaunched clean package -pl MetFragLib -pl MetFragWeb -am -DskipTests Yours, Steffen I blame Android for the brevity and typos
…
________________________________ From: SivanXW @.> Sent: Friday, November 18, 2022 3:21:19 AM To: ipb-halle/MetFragRelaunched @.> Cc: Subscribed @.> Subject: [ipb-halle/MetFragRelaunched] MetfragLib failed to install by (Issue #106) Hi prof, I tried to install MetfragLib and MetfragCL on Linux (CentOS) following the MetFrag relaunched tutorial. But when running "mvn clean install -pl MetFragLib -am", some errors occured: [ERROR] /root/MetFragRelaunched/MetFragLib/src/main/java/de/ipbhalle/metfraglib/parameter/ClassNames.java:[32,39] cannot find symbol symbol: class OnlineChemSpiderDatabase location: package de.ipbhalle.metfraglib.database [ERROR] /root/MetFragRelaunched/MetFragLib/src/main/java/de/ipbhalle/metfraglib/parameter/ClassNames.java:[33,39] cannot find symbol symbol: class OnlineChemSpiderRestDatabase location: package de.ipbhalle.metfraglib.database [ERROR] /root/MetFragRelaunched/MetFragLib/src/main/java/de/ipbhalle/metfraglib/parameter/ClassNames.java:[38,39] cannot find symbol symbol: class OnlinePubChemDatabase location: package de.ipbhalle.metfraglib.database [ERROR] /root/MetFragRelaunched/MetFragLib/src/main/java/de/ipbhalle/metfraglib/database/OnlineExtendedPubChemDatabase.java:[21,52] cannot find symbol symbol: class OnlinePubChemDatabase It seems that there are some problems connecting to ChemSpider as mentioned in #96https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fipb-halle%2FMetFragRelaunched%2Fissues%2F96&data=05%7C01%7C%7C0bd629437a0248b0bf5c08dac90b952e%7C0934ee6c2a574efd80a9fc003defef4e%7C0%7C0%7C638043348835017566%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=4YKo1F2hIbnhlJ2%2F2krYrdZX1KDi5JpRnMzc5%2BAt%2B4o%3D&reserved=0 and #97https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fipb-halle%2FMetFragRelaunched%2Fissues%2F97&data=05%7C01%7C%7C0bd629437a0248b0bf5c08dac90b952e%7C0934ee6c2a574efd80a9fc003defef4e%7C0%7C0%7C638043348835017566%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ECWGY7Tn477rkftY9RRDT%2F4Z0FbGdNASizaSP15a2hM%3D&reserved=0. I wonder is there a way to deal with this problem now? Thanks for your kind help. Sivan — Reply to this email directly, view it on GitHubhttps://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fipb-halle%2FMetFragRelaunched%2Fissues%2F106&data=05%7C01%7C%7C0bd629437a0248b0bf5c08dac90b952e%7C0934ee6c2a574efd80a9fc003defef4e%7C0%7C0%7C638043348835172752%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=vwtd9ZF5pCJ8YDHRyaapwIax6aMfiPQ56ZmToe57OaA%3D&reserved=0, or unsubscribehttps://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAABPWOOE3IVBYEA4F4L6RNLWI3RZ7ANCNFSM6AAAAAASEALYKM&data=05%7C01%7C%7C0bd629437a0248b0bf5c08dac90b952e%7C0934ee6c2a574efd80a9fc003defef4e%7C0%7C0%7C638043348835172752%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Vj4ySbP2dbFKQKKNVYAdZFK1pRP997QYnQbPBwtVJ0I%3D&reserved=0. You are receiving this because you are subscribed to this thread.Message ID: @.>

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@sneumann @SivanXW