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4.1.2.0: build fails: unmappable character for encoding ASCII #5934

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yurivict opened this issue May 11, 2019 · 0 comments · Fixed by #5936
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4.1.2.0: build fails: unmappable character for encoding ASCII #5934

yurivict opened this issue May 11, 2019 · 0 comments · Fixed by #5936
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:compileJava/usr/ports/biology/gatk/work/gatk-4.1.2.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandOddsRatio.java:106: error: unmappable character for encoding ASCII
 * SOR = ln(5.7284) + ln(0.2385) ??? ln(0.7559) = 1.7454427755 + (-1.433) ??? (-0.2798) = 0.592
                                 ^
/usr/ports/biology/gatk/work/gatk-4.1.2.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandOddsRatio.java:106: error: unmappable character for encoding ASCII
 * SOR = ln(5.7284) + ln(0.2385) ??? ln(0.7559) = 1.7454427755 + (-1.433) ??? (-0.2798) = 0.592
                                  ^
/usr/ports/biology/gatk/work/gatk-4.1.2.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandOddsRatio.java:106: error: unmappable character for encoding ASCII
 * SOR = ln(5.7284) + ln(0.2385) ??? ln(0.7559) = 1.7454427755 + (-1.433) ??? (-0.2798) = 0.592
                                   ^
/usr/ports/biology/gatk/work/gatk-4.1.2.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandOddsRatio.java:106: error: unmappable character for encoding ASCII
 * SOR = ln(5.7284) + ln(0.2385) ??? ln(0.7559) = 1.7454427755 + (-1.433) ??? (-0.2798) = 0.592
                                                                          ^
/usr/ports/biology/gatk/work/gatk-4.1.2.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandOddsRatio.java:106: error: unmappable character for encoding ASCII
 * SOR = ln(5.7284) + ln(0.2385) ??? ln(0.7559) = 1.7454427755 + (-1.433) ??? (-0.2798) = 0.592
                                                                           ^
/usr/ports/biology/gatk/work/gatk-4.1.2.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandOddsRatio.java:106: error: unmappable character for encoding ASCII
 * SOR = ln(5.7284) + ln(0.2385) ??? ln(0.7559) = 1.7454427755 + (-1.433) ??? (-0.2798) = 0.592
                                                                            ^
/usr/ports/biology/gatk/work/gatk-4.1.2.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2.java:137: error: unmappable character for encoding ASCII
 * Specifically, the mode sets <nobr>???-initial-tumor-lod</nobr> to 0, <nobr>???-tumor-lod-to-emit</nobr> to 0, <nobr>--af-of-alleles-not-in-resource</nobr> to
                                     ^
/usr/ports/biology/gatk/work/gatk-4.1.2.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2.java:137: error: unmappable character for encoding ASCII
 * Specifically, the mode sets <nobr>???-initial-tumor-lod</nobr> to 0, <nobr>???-tumor-lod-to-emit</nobr> to 0, <nobr>--af-of-alleles-not-in-resource</nobr> to
                                      ^
/usr/ports/biology/gatk/work/gatk-4.1.2.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2.java:137: error: unmappable character for encoding ASCII
 * Specifically, the mode sets <nobr>???-initial-tumor-lod</nobr> to 0, <nobr>???-tumor-lod-to-emit</nobr> to 0, <nobr>--af-of-alleles-not-in-resource</nobr> to
                                       ^
/usr/ports/biology/gatk/work/gatk-4.1.2.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2.java:137: error: unmappable character for encoding ASCII
 * Specifically, the mode sets <nobr>???-initial-tumor-lod</nobr> to 0, <nobr>???-tumor-lod-to-emit</nobr> to 0, <nobr>--af-of-alleles-not-in-resource</nobr> to
                                                                              ^
/usr/ports/biology/gatk/work/gatk-4.1.2.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2.java:137: error: unmappable character for encoding ASCII
 * Specifically, the mode sets <nobr>???-initial-tumor-lod</nobr> to 0, <nobr>???-tumor-lod-to-emit</nobr> to 0, <nobr>--af-of-alleles-not-in-resource</nobr> to
                                                                               ^
/usr/ports/biology/gatk/work/gatk-4.1.2.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2.java:137: error: unmappable character for encoding ASCII
 * Specifically, the mode sets <nobr>???-initial-tumor-lod</nobr> to 0, <nobr>???-tumor-lod-to-emit</nobr> to 0, <nobr>--af-of-alleles-not-in-resource</nobr> to

FreeBSD 11.2 amd64
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Remove non-ascii chars from javadoc. broadinstitute/gatk
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@yurivict @lbergelson