Description
I build picard in an apptainer container using ubuntu 22.04.
I use gradle that I installed first with sdk, this resulted in an error (-like?) behaviour, when i den installed picard.
So I downloaded binaries of gradle, but I get the same messags.
It then says at the end that the build is fine. But is it?
Here are the messages:
Welcome to Gradle 8.5!
Here are the highlights of this release:
- Support for running on Java 21
- Faster first use with Kotlin DSL
- Improved error and warning messages
For more details see https://docs.gradle.org/8.5/release-notes.html
Starting a Gradle Daemon (subsequent builds will be faster)
Task :compileJava
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:178: error: unmappable character (0xE2) for encoding US-ASCII
"Output is generated in the form of a ???molten??? (one row per comparison) CrosscheckMetric " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:178: error: unmappable character (0x80) for encoding US-ASCII
"Output is generated in the form of a ???molten??? (one row per comparison) CrosscheckMetric " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:178: error: unmappable character (0x9C) for encoding US-ASCII
"Output is generated in the form of a ???molten??? (one row per comparison) CrosscheckMetric " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:178: error: unmappable character (0xE2) for encoding US-ASCII
"Output is generated in the form of a ???molten??? (one row per comparison) CrosscheckMetric " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:178: error: unmappable character (0x80) for encoding US-ASCII
"Output is generated in the form of a ???molten??? (one row per comparison) CrosscheckMetric " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:178: error: unmappable character (0x9D) for encoding US-ASCII
"Output is generated in the form of a ???molten??? (one row per comparison) CrosscheckMetric " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:181: error: unmappable character (0xE2) for encoding US-ASCII
"a severe Loss of Heterozygosity (LOH) with high purity???this could otherwise lead to a " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:181: error: unmappable character (0x80) for encoding US-ASCII
"a severe Loss of Heterozygosity (LOH) with high purity???this could otherwise lead to a " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:181: error: unmappable character (0x94) for encoding US-ASCII
"a severe Loss of Heterozygosity (LOH) with high purity???this could otherwise lead to a " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:204: error: unmappable character (0xE2) for encoding US-ASCII
"In some cases, the groups collected may not have any observations (???reads??? for BAM files, or ???calls??? for VCF files) " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:204: error: unmappable character (0x80) for encoding US-ASCII
"In some cases, the groups collected may not have any observations (???reads??? for BAM files, or ???calls??? for VCF files) " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:204: error: unmappable character (0x98) for encoding US-ASCII
"In some cases, the groups collected may not have any observations (???reads??? for BAM files, or ???calls??? for VCF files) " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:204: error: unmappable character (0xE2) for encoding US-ASCII
"In some cases, the groups collected may not have any observations (???reads??? for BAM files, or ???calls??? for VCF files) " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:204: error: unmappable character (0x80) for encoding US-ASCII
"In some cases, the groups collected may not have any observations (???reads??? for BAM files, or ???calls??? for VCF files) " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:204: error: unmappable character (0x99) for encoding US-ASCII
"In some cases, the groups collected may not have any observations (???reads??? for BAM files, or ???calls??? for VCF files) " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:204: error: unmappable character (0xE2) for encoding US-ASCII
"In some cases, the groups collected may not have any observations (???reads??? for BAM files, or ???calls??? for VCF files) " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:204: error: unmappable character (0x80) for encoding US-ASCII
"In some cases, the groups collected may not have any observations (???reads??? for BAM files, or ???calls??? for VCF files) " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:204: error: unmappable character (0x98) for encoding US-ASCII
"In some cases, the groups collected may not have any observations (???reads??? for BAM files, or ???calls??? for VCF files) " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:204: error: unmappable character (0xE2) for encoding US-ASCII
"In some cases, the groups collected may not have any observations (???reads??? for BAM files, or ???calls??? for VCF files) " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:204: error: unmappable character (0x80) for encoding US-ASCII
"In some cases, the groups collected may not have any observations (???reads??? for BAM files, or ???calls??? for VCF files) " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:204: error: unmappable character (0x99) for encoding US-ASCII
"In some cases, the groups collected may not have any observations (???reads??? for BAM files, or ???calls??? for VCF files) " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:219: error: unmappable character (0xE2) for encoding US-ASCII
"the tool will return a ???zero???. However, an error will be logged and the tool will return EXIT_CODE_WHEN_NO_VALID_CHECKS " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:219: error: unmappable character (0x80) for encoding US-ASCII
"the tool will return a ???zero???. However, an error will be logged and the tool will return EXIT_CODE_WHEN_NO_VALID_CHECKS " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:219: error: unmappable character (0x98) for encoding US-ASCII
"the tool will return a ???zero???. However, an error will be logged and the tool will return EXIT_CODE_WHEN_NO_VALID_CHECKS " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:219: error: unmappable character (0xE2) for encoding US-ASCII
"the tool will return a ???zero???. However, an error will be logged and the tool will return EXIT_CODE_WHEN_NO_VALID_CHECKS " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:219: error: unmappable character (0x80) for encoding US-ASCII
"the tool will return a ???zero???. However, an error will be logged and the tool will return EXIT_CODE_WHEN_NO_VALID_CHECKS " +
^
/opt/picard/src/main/java/picard/fingerprint/CrosscheckFingerprints.java:219: error: unmappable character (0x99) for encoding US-ASCII
"the tool will return a ???zero???. However, an error will be logged and the tool will return EXIT_CODE_WHEN_NO_VALID_CHECKS " +
^
/opt/picard/src/main/java/picard/analysis/AlignmentSummaryMetrics.java:204: error: unmappable character (0xE2) for encoding US-ASCII
* The fraction of read pairs with a mapping quality (MAPQ) ??? 20 that are identified as chimeric by and any of the
^
/opt/picard/src/main/java/picard/analysis/AlignmentSummaryMetrics.java:204: error: unmappable character (0x89) for encoding US-ASCII
* The fraction of read pairs with a mapping quality (MAPQ) ??? 20 that are identified as chimeric by and any of the
^
/opt/picard/src/main/java/picard/analysis/AlignmentSummaryMetrics.java:204: error: unmappable character (0xA5) for encoding US-ASCII
* The fraction of read pairs with a mapping quality (MAPQ) ??? 20 that are identified as chimeric by and any of the
^
/opt/picard/src/main/java/picard/analysis/CollectAlignmentSummaryMetrics.java:73: error: unmappable character (0xE2) for encoding US-ASCII
- Read pairs with a mapping quality (MAPQ) is ??? 20 are classified as chimeric if any of the following criteria are met:
^
/opt/picard/src/main/java/picard/analysis/CollectAlignmentSummaryMetrics.java:73: error: unmappable character (0x89) for encoding US-ASCII - Read pairs with a mapping quality (MAPQ) is ??? 20 are classified as chimeric if any of the following criteria are met:
^
/opt/picard/src/main/java/picard/analysis/CollectAlignmentSummaryMetrics.java:73: error: unmappable character (0xA5) for encoding US-ASCII - Read pairs with a mapping quality (MAPQ) is ??? 20 are classified as chimeric if any of the following criteria are met:
^
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
BUILD SUCCESSFUL in 42s
4 actionable tasks: 4 executed