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Updating build dependency versions to latest minor versions #847

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heuermh commented Oct 5, 2015

I updated several dependency versions to the latest minor version (and guava from 14.0.1 --> 18.0) hoping that the build would still be ok. Three unit tests fail:

$ mvn clean install
AlignmentRecordRDDFunctionsSuite:
...
- writing a small sorted file as SAM should produce the expected result *** FAILED ***
  "@HD  VN:1.[4]    SO:unsorted" did not equal "@HD VN:1.[5]    SO:unsorted" Line 1 differs.
  Expected:
  @HD   VN:1.4  SO:unsorted
  @SQ   SN:1    LN:1000
  @SQ   SN:3    LN:1000
  @SQ   SN:4    LN:2000
  @SQ   SN:chr2 LN:1000
  A 0   1   1   50  10M *   0   0   ACACACACAC  **********
  B 0   3   11  40  4M2I4M  *   0   0   ACACACACAC  **********
  C 0   4   1001    25  8M  *   0   0   ACACACAC    ********
  E 0   chr2    101 45  10M *   0   0   ACACACACAC  **********
  D 0   chr2    501 55  10M2S   *   0   0   ACACACACACAC    ************

  Actual:
  @HD   VN:1.5  SO:unsorted
  @SQ   SN:1    LN:1000
  @SQ   SN:3    LN:1000
  @SQ   SN:4    LN:2000
  @SQ   SN:chr2 LN:1000
  A 0   1   1   50  10M *   0   0   ACACACACAC  **********
  B 0   3   11  40  4M2I4M  *   0   0   ACACACACAC  **********
  C 0   4   1001    25  8M  *   0   0   ACACACAC    ********
  E 0   chr2    101 45  10M *   0   0   ACACACACAC  **********
  D 0   chr2    501 55  10M2S   *   0   0   ACACACACACAC    ************ (ADAMFunSuite.scala:44)
- writing unordered sam from unordered sam *** FAILED ***
  "@HD  VN:1.[4]    SO:unsorted" did not equal "@HD VN:1.[5]    SO:unsorted" Line 1 differs.
  Expected:
  @HD   VN:1.4  SO:unsorted
  @SQ   SN:GL000211.1   LN:166566   M5:GL000211.1
  @SQ   SN:GL000244.1   LN:39929    M5:GL000244.1
  @SQ   SN:chr22    LN:51304566 M5:CHR22
  @SQ   SN:14   LN:107349540    M5:14
  @RG   ID:SRR062634    SM:HG00096  CN:WUGSC    DS:SRP001294    LB:2845856850   PI:206  PL:ILLUMINA
  SRR062634.20563591    99  GL000211.1  100 0   100M    =   500 161 GGACAACATTCACCTTTAAAAGTTTATTGATCTTTTGTGACATGCACGTGGGTTCCCAGTAGCAAGAAACTAAAGGGTCGCAGGCCGGTTTCTGCTAATT    GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGFGGGGGGGFGGGGGEGGGGGGEFGFGGFGGGGFBGGGDE>EEECBCCEEC>E:A@=ADBCAB    X0:i:2  X1:i:0  XA:Z:14,-19792774,100M,0;   LB:Z:2845856850 MD:Z:0T0C0T0A0C0G0A1A0A0A1A0T3T0C0C1A0A0C1G0C1C1A0T0C0A0A0A0A0G0A1A0G0G0T0T0C0A0A0C0T0C0T0G1G0A0G1T0G1A0T0G0C0A0C1C0A1T0T0C0A0A0A0G0A0A0G0T0T0T1T0C0A0G0A0A0T1C0T1C0T0G0C0  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R
  SRR062634.20563591    147 GL000211.1  500 0   100M    =   100 -161    GCAAGAAACTAAAGGGTCGCAGGCCGGTTTCTGCTAATTTCTTTAATTCCAAGACAGTCTCAAATATTTTCTTATTAACTTCCTGGAGGGAGGCTTATCA    =DDFECDCFEDFEFFFEEFD:EF?FBFFFFBACEF?EGGGEDGGBGEGFGGGGGGFGGGGGGGGGFGGGGFFGGGGGGGFGGGGGGGGGGGGGGGGGGGG    X0:i:2  X1:i:0  XA:Z:14,+19792713,100M,0;   LB:Z:2845856850 MD:Z:0A0T0G0C0A0C1C0A1T0T0C0A0A0A0G0A0A0G0T0T0T1T0C0A0G0A0A0T1C0T1C0T0G0C0A0T0A0G0C0T0T3T0G0T2A0G0A1A1T0T0C2T2C0C0A0C0C0C1A0G0G1C2A0A0A1C0A0C0T0C1A0A0A1G2C0    RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R
  SRR062634.5613583 99  GL000244.1  200 0   100M    =   600 158 TGCAGGCCGGTTTCTGCTAATTTCTTTAATTCCAAGACAGTCTCAATTATTTTCTTATTAACTTCCTGGAGGGAGGCTTATCATTCTCTCTTTTGGATGA    GGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDEGEFEGDCEEEBF?DDEEGDGEEEGE=ABB?    X0:i:2  X1:i:0  XA:Z:14,-19792696,100M,2;   LB:Z:2845856850 MD:Z:0A0A0G0T0T0T1T0C0A0G0A0A0T1C0T1C0T0G0C0A0T0A0G0C0T0T3T0G0T2A0G0A1A1T0T0C0A1T2C0C0A0C0C0C1A0G0G1C2A0A0A1C0A0C0T0C1A0A0A1G2C0A0C0A0G0G0C0A0G0A2C0C1C0A1  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:2  SM:i:0  XM:i:2  XO:i:0  XT:A:R
  SRR062634.5613583 147 GL000244.1  600 0   100M    =   200 -158    TAACTTCCTGGAGGGAGGCTTATCATTCTCTCTTTTGGATGATTCTAAGTACCAGCTAAAATACAGCTATCATTCATTTTCCTTGATTTGGGAGCCTAAT    @E=EAEEEEGF?EEGEGFFEDBGEGFGGGGFGFFGFGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG    X0:i:2  X1:i:0  XA:Z:14,+19792638,100M,0;   LB:Z:2845856850 MD:Z:0A0G0G1C2A0A0A1C0A0C0T0C1A0A0A1G2C0A0C0A0G0G0C0A0G0A2C0C1C0A1A0A0A0G1G0T0A0T0T0T0C0A0A0A1C0T0G0G0T1C0A0T0C1A0A0G0G0A0A1G0A3A0G0C0T0C1G1T1A1T0G0A0A0T0G0C0  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R
  SRR062634.11091461    99  chr22   16050471    0   100M    =   16050505    134 CAAGTAGTAGTGCCATAATTACCAAACATAAAGCCAACTGAGATGCCCAAAGGGGGCCACTCTCCTTGCTTTTCCTCCTTTTTAGAGGATTTATTTCCCA    GGGGGFFFFFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGFGGEGGEFEEBEEECFEEEBEFBACDBEEEEEACC?AAAA7=5::59BBBCB6/=CA    X0:i:2  X1:i:0  XA:Z:14,-19792431,100M,0;   LB:Z:2845856850 MD:Z:1T1C0A1A0A2A1T0T0T1T1C0A1A1T0G0C0T0C0A1T0C0A0A0A0G0G0A0A0A0G1T1C0A0A1T0C0T1T0A0A1A0T0G0A0A1C1A0C0A0T0A1C0A0C0A0A0A0G0A0A0G3C0T0C0A0A1A2C2C0T0G0T0C0    RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R
  SRR062634.11091461    147 chr22   16050505    0   100M    =   16050471    -134    CAACTGAGATGCCCAAAGGGGGCCACTCTCCTTGCTTTTCCTCCTTTTTAGAGGATTTATTTCCCATTTTTCTTAAAAAGGAAGAACAAACTGTGCCCTA    =@@?CCCD?@DCDCC@CEFEEGEEEFFFFDEFEGAGGFGGGGGGGGGGGGGFGGGGGFGGDGEGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGG    X0:i:2  X1:i:0  XA:Z:14,+19792397,100M,0;   LB:Z:2845856850 MD:Z:0A0G0G0A0A0A0G1T1C0A0A1T0C0T1T0A0A1A0T0G0A0A1C1A0C0A0T0A1C0A0C0A0A0A0G0A0A0G3C0T0C0A0A1A2C2C0T0G0T0C0C0A0G2G3C0G0T0G0A0A0G1T0G0T0T0T0T0C0T1T1C1A0A0C1  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R
  SRR062634.6859057 163 14  16050606    37  100M    =   16050680    174 GGTTTACTGTGTCAGAACAGAGTGTGCCGATTGTGGTCAGGACTCCATAGCATTTCACCATTGAGTTATTTCCGCCCCCTTACGTGTCTCTCTTCAGCGG    GFFGGGGGGGGGGFGGGGGGGGGGGGGGGFGGGBGGCGGGDDEFFGEEFFGFEGEEEEEEEGFEGEEEEDEFEEEEEEE=DBCCBCCCCCACCAC,A@??    X0:i:1  X1:i:0  LB:Z:2845856850 MD:Z:0A1G0C1T1A0A0G1C0A0C0T0C0G0A1A0T0C1C1A1T0T0G0C0A1A0T0T0C0T1C0A1A0A0A0G1G0T0A0T0T1C0A0A1A1T0G0G0T0C0C2C0A0A0A0A0G0A0A0A0G0G0T1C1A0T1C1G0G0G0A0G0A1A1A0T1C0  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:37 XM:i:0  XO:i:0  XT:A:U
  SRR062634.6859057 83  14  16050680    36  100M    =   16050606    -174    CCCCCTTACGTGTCTCTCTTCAGCGGTCTATTATCTCCAAGAGGGCATAAAACACTGAGTAAACAGCTCTTTTATATGTGTTTCCTGGATGAGCCTTCTT    9<5=;;A7B<?A?A?AABB:C:CC=CACE?DDCCD@EEFEEFEFEFGFGGGEGEGGGGGGGEGFGEGGGGFGGGGGGGGGEGGGGGGGGGGGGGFGFGGG    X0:i:2  X1:i:0  XA:Z:14,+19792222,100M,0;   LB:Z:2845856850 MD:Z:0A0A0G0G0T1C1A0T1C1G0G0G0A0G0A1A1A0T1C0A0T0A0C0A1C0A1A0A0A2A0G0T0T0T1T0C1G2T0T3T0C2G0T0T0T0T0T0A0T0G1G0A1G2A1T1C0C0T0T2C0C0A0C0C0A0T0A0G0G1C1  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R

  Actual:
  @HD   VN:1.5  SO:unsorted
  @SQ   SN:GL000211.1   LN:166566   M5:GL000211.1
  @SQ   SN:GL000244.1   LN:39929    M5:GL000244.1
  @SQ   SN:chr22    LN:51304566 M5:CHR22
  @SQ   SN:14   LN:107349540    M5:14
  @RG   ID:SRR062634    SM:HG00096  CN:WUGSC    DS:SRP001294    LB:2845856850   PI:206  PL:ILLUMINA
  SRR062634.20563591    99  GL000211.1  100 0   100M    =   500 161 GGACAACATTCACCTTTAAAAGTTTATTGATCTTTTGTGACATGCACGTGGGTTCCCAGTAGCAAGAAACTAAAGGGTCGCAGGCCGGTTTCTGCTAATT    GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGFGGGGGGGFGGGGGEGGGGGGEFGFGGFGGGGFBGGGDE>EEECBCCEEC>E:A@=ADBCAB    X0:i:2  X1:i:0  XA:Z:14,-19792774,100M,0;   LB:Z:2845856850 MD:Z:0T0C0T0A0C0G0A1A0A0A1A0T3T0C0C1A0A0C1G0C1C1A0T0C0A0A0A0A0G0A1A0G0G0T0T0C0A0A0C0T0C0T0G1G0A0G1T0G1A0T0G0C0A0C1C0A1T0T0C0A0A0A0G0A0A0G0T0T0T1T0C0A0G0A0A0T1C0T1C0T0G0C0  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R
  SRR062634.20563591    147 GL000211.1  500 0   100M    =   100 -161    GCAAGAAACTAAAGGGTCGCAGGCCGGTTTCTGCTAATTTCTTTAATTCCAAGACAGTCTCAAATATTTTCTTATTAACTTCCTGGAGGGAGGCTTATCA    =DDFECDCFEDFEFFFEEFD:EF?FBFFFFBACEF?EGGGEDGGBGEGFGGGGGGFGGGGGGGGGFGGGGFFGGGGGGGFGGGGGGGGGGGGGGGGGGGG    X0:i:2  X1:i:0  XA:Z:14,+19792713,100M,0;   LB:Z:2845856850 MD:Z:0A0T0G0C0A0C1C0A1T0T0C0A0A0A0G0A0A0G0T0T0T1T0C0A0G0A0A0T1C0T1C0T0G0C0A0T0A0G0C0T0T3T0G0T2A0G0A1A1T0T0C2T2C0C0A0C0C0C1A0G0G1C2A0A0A1C0A0C0T0C1A0A0A1G2C0    RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R
  SRR062634.5613583 99  GL000244.1  200 0   100M    =   600 158 TGCAGGCCGGTTTCTGCTAATTTCTTTAATTCCAAGACAGTCTCAATTATTTTCTTATTAACTTCCTGGAGGGAGGCTTATCATTCTCTCTTTTGGATGA    GGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDEGEFEGDCEEEBF?DDEEGDGEEEGE=ABB?    X0:i:2  X1:i:0  XA:Z:14,-19792696,100M,2;   LB:Z:2845856850 MD:Z:0A0A0G0T0T0T1T0C0A0G0A0A0T1C0T1C0T0G0C0A0T0A0G0C0T0T3T0G0T2A0G0A1A1T0T0C0A1T2C0C0A0C0C0C1A0G0G1C2A0A0A1C0A0C0T0C1A0A0A1G2C0A0C0A0G0G0C0A0G0A2C0C1C0A1  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:2  SM:i:0  XM:i:2  XO:i:0  XT:A:R
  SRR062634.5613583 147 GL000244.1  600 0   100M    =   200 -158    TAACTTCCTGGAGGGAGGCTTATCATTCTCTCTTTTGGATGATTCTAAGTACCAGCTAAAATACAGCTATCATTCATTTTCCTTGATTTGGGAGCCTAAT    @E=EAEEEEGF?EEGEGFFEDBGEGFGGGGFGFFGFGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG    X0:i:2  X1:i:0  XA:Z:14,+19792638,100M,0;   LB:Z:2845856850 MD:Z:0A0G0G1C2A0A0A1C0A0C0T0C1A0A0A1G2C0A0C0A0G0G0C0A0G0A2C0C1C0A1A0A0A0G1G0T0A0T0T0T0C0A0A0A1C0T0G0G0T1C0A0T0C1A0A0G0G0A0A1G0A3A0G0C0T0C1G1T1A1T0G0A0A0T0G0C0  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R
  SRR062634.11091461    99  chr22   16050471    0   100M    =   16050505    134 CAAGTAGTAGTGCCATAATTACCAAACATAAAGCCAACTGAGATGCCCAAAGGGGGCCACTCTCCTTGCTTTTCCTCCTTTTTAGAGGATTTATTTCCCA    GGGGGFFFFFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGFGGEGGEFEEBEEECFEEEBEFBACDBEEEEEACC?AAAA7=5::59BBBCB6/=CA    X0:i:2  X1:i:0  XA:Z:14,-19792431,100M,0;   LB:Z:2845856850 MD:Z:1T1C0A1A0A2A1T0T0T1T1C0A1A1T0G0C0T0C0A1T0C0A0A0A0G0G0A0A0A0G1T1C0A0A1T0C0T1T0A0A1A0T0G0A0A1C1A0C0A0T0A1C0A0C0A0A0A0G0A0A0G3C0T0C0A0A1A2C2C0T0G0T0C0    RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R
  SRR062634.11091461    147 chr22   16050505    0   100M    =   16050471    -134    CAACTGAGATGCCCAAAGGGGGCCACTCTCCTTGCTTTTCCTCCTTTTTAGAGGATTTATTTCCCATTTTTCTTAAAAAGGAAGAACAAACTGTGCCCTA    =@@?CCCD?@DCDCC@CEFEEGEEEFFFFDEFEGAGGFGGGGGGGGGGGGGFGGGGGFGGDGEGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGG    X0:i:2  X1:i:0  XA:Z:14,+19792397,100M,0;   LB:Z:2845856850 MD:Z:0A0G0G0A0A0A0G1T1C0A0A1T0C0T1T0A0A1A0T0G0A0A1C1A0C0A0T0A1C0A0C0A0A0A0G0A0A0G3C0T0C0A0A1A2C2C0T0G0T0C0C0A0G2G3C0G0T0G0A0A0G1T0G0T0T0T0T0C0T1T1C1A0A0C1  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R
  SRR062634.6859057 163 14  16050606    37  100M    =   16050680    174 GGTTTACTGTGTCAGAACAGAGTGTGCCGATTGTGGTCAGGACTCCATAGCATTTCACCATTGAGTTATTTCCGCCCCCTTACGTGTCTCTCTTCAGCGG    GFFGGGGGGGGGGFGGGGGGGGGGGGGGGFGGGBGGCGGGDDEFFGEEFFGFEGEEEEEEEGFEGEEEEDEFEEEEEEE=DBCCBCCCCCACCAC,A@??    X0:i:1  X1:i:0  LB:Z:2845856850 MD:Z:0A1G0C1T1A0A0G1C0A0C0T0C0G0A1A0T0C1C1A1T0T0G0C0A1A0T0T0C0T1C0A1A0A0A0G1G0T0A0T0T1C0A0A1A1T0G0G0T0C0C2C0A0A0A0A0G0A0A0A0G0G0T1C1A0T1C1G0G0G0A0G0A1A1A0T1C0  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:37 XM:i:0  XO:i:0  XT:A:U
  SRR062634.6859057 83  14  16050680    36  100M    =   16050606    -174    CCCCCTTACGTGTCTCTCTTCAGCGGTCTATTATCTCCAAGAGGGCATAAAACACTGAGTAAACAGCTCTTTTATATGTGTTTCCTGGATGAGCCTTCTT    9<5=;;A7B<?A?A?AABB:C:CC=CACE?DDCCD@EEFEEFEFEFGFGGGEGEGGGGGGGEGFGEGGGGFGGGGGGGGGEGGGGGGGGGGGGGFGFGGG    X0:i:2  X1:i:0  XA:Z:14,+19792222,100M,0;   LB:Z:2845856850 MD:Z:0A0A0G0G0T1C1A0T1C1G0G0G0A0G0A1A1A0T1C0A0T0A0C0A1C0A1A0A0A2A0G0T0T0T1T0C1G2T0T3T0C2G0T0T0T0T0T0A0T0G1G0A1G2A1T1C0C0T0T2C0C0A0C0C0A0T0A0G0G1C1  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R (ADAMFunSuite.scala:44)
- writing ordered sam from unordered sam *** FAILED ***
  "@HD  VN:1.[4]    SO:unsorted" did not equal "@HD VN:1.[5]    SO:unsorted" Line 1 differs.
  Expected:
  @HD   VN:1.4  SO:unsorted
  @SQ   SN:14   LN:107349540    M5:14
  @SQ   SN:GL000211.1   LN:166566   M5:GL000211.1
  @SQ   SN:GL000244.1   LN:39929    M5:GL000244.1
  @SQ   SN:chr22    LN:51304566 M5:CHR22
  @RG   ID:SRR062634    SM:HG00096  CN:WUGSC    DS:SRP001294    LB:2845856850   PI:206  PL:ILLUMINA
  SRR062634.6859057 163 14  16050606    37  100M    =   16050680    174 GGTTTACTGTGTCAGAACAGAGTGTGCCGATTGTGGTCAGGACTCCATAGCATTTCACCATTGAGTTATTTCCGCCCCCTTACGTGTCTCTCTTCAGCGG    GFFGGGGGGGGGGFGGGGGGGGGGGGGGGFGGGBGGCGGGDDEFFGEEFFGFEGEEEEEEEGFEGEEEEDEFEEEEEEE=DBCCBCCCCCACCAC,A@??    X0:i:1  X1:i:0  LB:Z:2845856850 MD:Z:0A1G0C1T1A0A0G1C0A0C0T0C0G0A1A0T0C1C1A1T0T0G0C0A1A0T0T0C0T1C0A1A0A0A0G1G0T0A0T0T1C0A0A1A1T0G0G0T0C0C2C0A0A0A0A0G0A0A0A0G0G0T1C1A0T1C1G0G0G0A0G0A1A1A0T1C0  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:37 XM:i:0  XO:i:0  XT:A:U
  SRR062634.6859057 83  14  16050680    36  100M    =   16050606    -174    CCCCCTTACGTGTCTCTCTTCAGCGGTCTATTATCTCCAAGAGGGCATAAAACACTGAGTAAACAGCTCTTTTATATGTGTTTCCTGGATGAGCCTTCTT    9<5=;;A7B<?A?A?AABB:C:CC=CACE?DDCCD@EEFEEFEFEFGFGGGEGEGGGGGGGEGFGEGGGGFGGGGGGGGGEGGGGGGGGGGGGGFGFGGG    X0:i:2  X1:i:0  XA:Z:14,+19792222,100M,0;   LB:Z:2845856850 MD:Z:0A0A0G0G0T1C1A0T1C1G0G0G0A0G0A1A1A0T1C0A0T0A0C0A1C0A1A0A0A2A0G0T0T0T1T0C1G2T0T3T0C2G0T0T0T0T0T0A0T0G1G0A1G2A1T1C0C0T0T2C0C0A0C0C0A0T0A0G0G1C1  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R
  SRR062634.20563591    99  GL000211.1  100 0   100M    =   500 161 GGACAACATTCACCTTTAAAAGTTTATTGATCTTTTGTGACATGCACGTGGGTTCCCAGTAGCAAGAAACTAAAGGGTCGCAGGCCGGTTTCTGCTAATT    GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGFGGGGGGGFGGGGGEGGGGGGEFGFGGFGGGGFBGGGDE>EEECBCCEEC>E:A@=ADBCAB    X0:i:2  X1:i:0  XA:Z:14,-19792774,100M,0;   LB:Z:2845856850 MD:Z:0T0C0T0A0C0G0A1A0A0A1A0T3T0C0C1A0A0C1G0C1C1A0T0C0A0A0A0A0G0A1A0G0G0T0T0C0A0A0C0T0C0T0G1G0A0G1T0G1A0T0G0C0A0C1C0A1T0T0C0A0A0A0G0A0A0G0T0T0T1T0C0A0G0A0A0T1C0T1C0T0G0C0  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R
  SRR062634.20563591    147 GL000211.1  500 0   100M    =   100 -161    GCAAGAAACTAAAGGGTCGCAGGCCGGTTTCTGCTAATTTCTTTAATTCCAAGACAGTCTCAAATATTTTCTTATTAACTTCCTGGAGGGAGGCTTATCA    =DDFECDCFEDFEFFFEEFD:EF?FBFFFFBACEF?EGGGEDGGBGEGFGGGGGGFGGGGGGGGGFGGGGFFGGGGGGGFGGGGGGGGGGGGGGGGGGGG    X0:i:2  X1:i:0  XA:Z:14,+19792713,100M,0;   LB:Z:2845856850 MD:Z:0A0T0G0C0A0C1C0A1T0T0C0A0A0A0G0A0A0G0T0T0T1T0C0A0G0A0A0T1C0T1C0T0G0C0A0T0A0G0C0T0T3T0G0T2A0G0A1A1T0T0C2T2C0C0A0C0C0C1A0G0G1C2A0A0A1C0A0C0T0C1A0A0A1G2C0    RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R
  SRR062634.5613583 99  GL000244.1  200 0   100M    =   600 158 TGCAGGCCGGTTTCTGCTAATTTCTTTAATTCCAAGACAGTCTCAATTATTTTCTTATTAACTTCCTGGAGGGAGGCTTATCATTCTCTCTTTTGGATGA    GGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDEGEFEGDCEEEBF?DDEEGDGEEEGE=ABB?    X0:i:2  X1:i:0  XA:Z:14,-19792696,100M,2;   LB:Z:2845856850 MD:Z:0A0A0G0T0T0T1T0C0A0G0A0A0T1C0T1C0T0G0C0A0T0A0G0C0T0T3T0G0T2A0G0A1A1T0T0C0A1T2C0C0A0C0C0C1A0G0G1C2A0A0A1C0A0C0T0C1A0A0A1G2C0A0C0A0G0G0C0A0G0A2C0C1C0A1  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:2  SM:i:0  XM:i:2  XO:i:0  XT:A:R
  SRR062634.5613583 147 GL000244.1  600 0   100M    =   200 -158    TAACTTCCTGGAGGGAGGCTTATCATTCTCTCTTTTGGATGATTCTAAGTACCAGCTAAAATACAGCTATCATTCATTTTCCTTGATTTGGGAGCCTAAT    @E=EAEEEEGF?EEGEGFFEDBGEGFGGGGFGFFGFGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG    X0:i:2  X1:i:0  XA:Z:14,+19792638,100M,0;   LB:Z:2845856850 MD:Z:0A0G0G1C2A0A0A1C0A0C0T0C1A0A0A1G2C0A0C0A0G0G0C0A0G0A2C0C1C0A1A0A0A0G1G0T0A0T0T0T0C0A0A0A1C0T0G0G0T1C0A0T0C1A0A0G0G0A0A1G0A3A0G0C0T0C1G1T1A1T0G0A0A0T0G0C0  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R
  SRR062634.11091461    99  chr22   16050471    0   100M    =   16050505    134 CAAGTAGTAGTGCCATAATTACCAAACATAAAGCCAACTGAGATGCCCAAAGGGGGCCACTCTCCTTGCTTTTCCTCCTTTTTAGAGGATTTATTTCCCA    GGGGGFFFFFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGFGGEGGEFEEBEEECFEEEBEFBACDBEEEEEACC?AAAA7=5::59BBBCB6/=CA    X0:i:2  X1:i:0  XA:Z:14,-19792431,100M,0;   LB:Z:2845856850 MD:Z:1T1C0A1A0A2A1T0T0T1T1C0A1A1T0G0C0T0C0A1T0C0A0A0A0G0G0A0A0A0G1T1C0A0A1T0C0T1T0A0A1A0T0G0A0A1C1A0C0A0T0A1C0A0C0A0A0A0G0A0A0G3C0T0C0A0A1A2C2C0T0G0T0C0    RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R
  SRR062634.11091461    147 chr22   16050505    0   100M    =   16050471    -134    CAACTGAGATGCCCAAAGGGGGCCACTCTCCTTGCTTTTCCTCCTTTTTAGAGGATTTATTTCCCATTTTTCTTAAAAAGGAAGAACAAACTGTGCCCTA    =@@?CCCD?@DCDCC@CEFEEGEEEFFFFDEFEGAGGFGGGGGGGGGGGGGFGGGGGFGGDGEGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGG    X0:i:2  X1:i:0  XA:Z:14,+19792397,100M,0;   LB:Z:2845856850 MD:Z:0A0G0G0A0A0A0G1T1C0A0A1T0C0T1T0A0A1A0T0G0A0A1C1A0C0A0T0A1C0A0C0A0A0A0G0A0A0G3C0T0C0A0A1A2C2C0T0G0T0C0C0A0G2G3C0G0T0G0A0A0G1T0G0T0T0T0T0C0T1T1C1A0A0C1  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R

  Actual:
  @HD   VN:1.5  SO:unsorted
  @SQ   SN:14   LN:107349540    M5:14
  @SQ   SN:GL000211.1   LN:166566   M5:GL000211.1
  @SQ   SN:GL000244.1   LN:39929    M5:GL000244.1
  @SQ   SN:chr22    LN:51304566 M5:CHR22
  @RG   ID:SRR062634    SM:HG00096  CN:WUGSC    DS:SRP001294    LB:2845856850   PI:206  PL:ILLUMINA
  SRR062634.6859057 163 14  16050606    37  100M    =   16050680    174 GGTTTACTGTGTCAGAACAGAGTGTGCCGATTGTGGTCAGGACTCCATAGCATTTCACCATTGAGTTATTTCCGCCCCCTTACGTGTCTCTCTTCAGCGG    GFFGGGGGGGGGGFGGGGGGGGGGGGGGGFGGGBGGCGGGDDEFFGEEFFGFEGEEEEEEEGFEGEEEEDEFEEEEEEE=DBCCBCCCCCACCAC,A@??    X0:i:1  X1:i:0  LB:Z:2845856850 MD:Z:0A1G0C1T1A0A0G1C0A0C0T0C0G0A1A0T0C1C1A1T0T0G0C0A1A0T0T0C0T1C0A1A0A0A0G1G0T0A0T0T1C0A0A1A1T0G0G0T0C0C2C0A0A0A0A0G0A0A0A0G0G0T1C1A0T1C1G0G0G0A0G0A1A1A0T1C0  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:37 XM:i:0  XO:i:0  XT:A:U
  SRR062634.6859057 83  14  16050680    36  100M    =   16050606    -174    CCCCCTTACGTGTCTCTCTTCAGCGGTCTATTATCTCCAAGAGGGCATAAAACACTGAGTAAACAGCTCTTTTATATGTGTTTCCTGGATGAGCCTTCTT    9<5=;;A7B<?A?A?AABB:C:CC=CACE?DDCCD@EEFEEFEFEFGFGGGEGEGGGGGGGEGFGEGGGGFGGGGGGGGGEGGGGGGGGGGGGGFGFGGG    X0:i:2  X1:i:0  XA:Z:14,+19792222,100M,0;   LB:Z:2845856850 MD:Z:0A0A0G0G0T1C1A0T1C1G0G0G0A0G0A1A1A0T1C0A0T0A0C0A1C0A1A0A0A2A0G0T0T0T1T0C1G2T0T3T0C2G0T0T0T0T0T0A0T0G1G0A1G2A1T1C0C0T0T2C0C0A0C0C0A0T0A0G0G1C1  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R
  SRR062634.20563591    99  GL000211.1  100 0   100M    =   500 161 GGACAACATTCACCTTTAAAAGTTTATTGATCTTTTGTGACATGCACGTGGGTTCCCAGTAGCAAGAAACTAAAGGGTCGCAGGCCGGTTTCTGCTAATT    GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGFGGGGGGGFGGGGGEGGGGGGEFGFGGFGGGGFBGGGDE>EEECBCCEEC>E:A@=ADBCAB    X0:i:2  X1:i:0  XA:Z:14,-19792774,100M,0;   LB:Z:2845856850 MD:Z:0T0C0T0A0C0G0A1A0A0A1A0T3T0C0C1A0A0C1G0C1C1A0T0C0A0A0A0A0G0A1A0G0G0T0T0C0A0A0C0T0C0T0G1G0A0G1T0G1A0T0G0C0A0C1C0A1T0T0C0A0A0A0G0A0A0G0T0T0T1T0C0A0G0A0A0T1C0T1C0T0G0C0  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R
  SRR062634.20563591    147 GL000211.1  500 0   100M    =   100 -161    GCAAGAAACTAAAGGGTCGCAGGCCGGTTTCTGCTAATTTCTTTAATTCCAAGACAGTCTCAAATATTTTCTTATTAACTTCCTGGAGGGAGGCTTATCA    =DDFECDCFEDFEFFFEEFD:EF?FBFFFFBACEF?EGGGEDGGBGEGFGGGGGGFGGGGGGGGGFGGGGFFGGGGGGGFGGGGGGGGGGGGGGGGGGGG    X0:i:2  X1:i:0  XA:Z:14,+19792713,100M,0;   LB:Z:2845856850 MD:Z:0A0T0G0C0A0C1C0A1T0T0C0A0A0A0G0A0A0G0T0T0T1T0C0A0G0A0A0T1C0T1C0T0G0C0A0T0A0G0C0T0T3T0G0T2A0G0A1A1T0T0C2T2C0C0A0C0C0C1A0G0G1C2A0A0A1C0A0C0T0C1A0A0A1G2C0    RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R
  SRR062634.5613583 99  GL000244.1  200 0   100M    =   600 158 TGCAGGCCGGTTTCTGCTAATTTCTTTAATTCCAAGACAGTCTCAATTATTTTCTTATTAACTTCCTGGAGGGAGGCTTATCATTCTCTCTTTTGGATGA    GGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDEGEFEGDCEEEBF?DDEEGDGEEEGE=ABB?    X0:i:2  X1:i:0  XA:Z:14,-19792696,100M,2;   LB:Z:2845856850 MD:Z:0A0A0G0T0T0T1T0C0A0G0A0A0T1C0T1C0T0G0C0A0T0A0G0C0T0T3T0G0T2A0G0A1A1T0T0C0A1T2C0C0A0C0C0C1A0G0G1C2A0A0A1C0A0C0T0C1A0A0A1G2C0A0C0A0G0G0C0A0G0A2C0C1C0A1  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:2  SM:i:0  XM:i:2  XO:i:0  XT:A:R
  SRR062634.5613583 147 GL000244.1  600 0   100M    =   200 -158    TAACTTCCTGGAGGGAGGCTTATCATTCTCTCTTTTGGATGATTCTAAGTACCAGCTAAAATACAGCTATCATTCATTTTCCTTGATTTGGGAGCCTAAT    @E=EAEEEEGF?EEGEGFFEDBGEGFGGGGFGFFGFGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG    X0:i:2  X1:i:0  XA:Z:14,+19792638,100M,0;   LB:Z:2845856850 MD:Z:0A0G0G1C2A0A0A1C0A0C0T0C1A0A0A1G2C0A0C0A0G0G0C0A0G0A2C0C1C0A1A0A0A0G1G0T0A0T0T0T0C0A0A0A1C0T0G0G0T1C0A0T0C1A0A0G0G0A0A1G0A3A0G0C0T0C1G1T1A1T0G0A0A0T0G0C0  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R
  SRR062634.11091461    99  chr22   16050471    0   100M    =   16050505    134 CAAGTAGTAGTGCCATAATTACCAAACATAAAGCCAACTGAGATGCCCAAAGGGGGCCACTCTCCTTGCTTTTCCTCCTTTTTAGAGGATTTATTTCCCA    GGGGGFFFFFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGFGGEGGEFEEBEEECFEEEBEFBACDBEEEEEACC?AAAA7=5::59BBBCB6/=CA    X0:i:2  X1:i:0  XA:Z:14,-19792431,100M,0;   LB:Z:2845856850 MD:Z:1T1C0A1A0A2A1T0T0T1T1C0A1A1T0G0C0T0C0A1T0C0A0A0A0G0G0A0A0A0G1T1C0A0A1T0C0T1T0A0A1A0T0G0A0A1C1A0C0A0T0A1C0A0C0A0A0A0G0A0A0G3C0T0C0A0A1A2C2C0T0G0T0C0    RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R
  SRR062634.11091461    147 chr22   16050505    0   100M    =   16050471    -134    CAACTGAGATGCCCAAAGGGGGCCACTCTCCTTGCTTTTCCTCCTTTTTAGAGGATTTATTTCCCATTTTTCTTAAAAAGGAAGAACAAACTGTGCCCTA    =@@?CCCD?@DCDCC@CEFEEGEEEFFFFDEFEGAGGFGGGGGGGGGGGGGFGGGGGFGGDGEGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGG    X0:i:2  X1:i:0  XA:Z:14,+19792397,100M,0;   LB:Z:2845856850 MD:Z:0A0G0G0A0A0A0G1T1C0A0A1T0C0T1T0A0A1A0T0G0A0A1C1A0C0A0T0A1C0A0C0A0A0A0G0A0A0G3C0T0C0A0A1A2C2C0T0G0T0C0C0A0G2G3C0G0T0G0A0A0G1T0G0T0T0T0T0C0T1T1C1A0A0C1  RG:Z:SRR062634  XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  XT:A:R (ADAMFunSuite.scala:44)
...
Run completed in 53 seconds, 421 milliseconds.
Total number of tests run: 363
Suites: completed 51, aborted 0
Tests: succeeded 360, failed 3, canceled 0, ignored 0, pending 0
*** 3 TESTS FAILED ***
.parquet.hadoop.InternalParquetRecordReader: RecordReader initialized will read a total of 81 records.
Oct 5, 2015 12:39:35 PM INFO: org.apache.parquet.hadoop.InternalParquetRecordReader: at row 0. reading next block
Oct 5, 2015 12:39:35 PM INFO: org.apache.parquet.hadoop.InternalParquetRecordReader: block read in memory in 2 ms. row count = 81
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] ADAM_2.10 .......................................... SUCCESS [  4.858 s]
[INFO] ADAM_2.10: Core .................................... FAILURE [02:10 min]
[INFO] ADAM_2.10: APIs for Java ........................... SKIPPED
[INFO] ADAM_2.10: CLI ..................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 02:15 min
[INFO] Finished at: 2015-10-05T12:39:46-05:00
[INFO] Final Memory: 54M/735M
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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/959/

Build result: FAILURE

GitHub pull request #847 of commit 19f3bad automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains 5430ce6e0320aa56c3bf939d0f15318b10ba8bb1 # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision 5430ce6e0320aa56c3bf939d0f15318b10ba8bb1 (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 5430ce6e0320aa56c3bf939d0f15318b10ba8bb1First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Oct 5, 2015

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/959/

Build result: FAILURE

GitHub pull request #847 of commit 19f3bad automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains 5430ce6e0320aa56c3bf939d0f15318b10ba8bb1 # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision 5430ce6e0320aa56c3bf939d0f15318b10ba8bb1 (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 5430ce6e0320aa56c3bf939d0f15318b10ba8bb1First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Those are just header version issues because the htsjdk version changed. If you update the unittest collateral, this should go away.

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fnothaft commented Oct 5, 2015

Those are just header version issues because the htsjdk version changed. If you update the unittest collateral, this should go away.

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Ah right, I assume since those were handcrafted .sam files, there'd be no harm in manually updating the version number? Running them through samtools view -h version 1.2 keeps the version number intact.

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heuermh commented Oct 5, 2015

Ah right, I assume since those were handcrafted .sam files, there'd be no harm in manually updating the version number? Running them through samtools view -h version 1.2 keeps the version number intact.

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Yeah, I would just manually update them.

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fnothaft commented Oct 5, 2015

Yeah, I would just manually update them.

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ok, then I get farther

- Standard FlagStat test *** FAILED ***
  java.lang.IllegalStateException: Cannot set value to a final field 'org.bdgenomics.adam.cli.FlagStatArgs.inputPath'.
  at org.kohsuke.args4j.spi.Setters.create(Setters.java:32)
  at org.kohsuke.args4j.ClassParser.parse(ClassParser.java:38)
  at org.kohsuke.args4j.CmdLineParser.<init>(CmdLineParser.java:94)
  at org.kohsuke.args4j.CmdLineParser.<init>(CmdLineParser.java:69)
  at org.bdgenomics.utils.cli.Args4j$.apply(Args4j.scala:35)
  at org.bdgenomics.adam.cli.FlagStatSuite$$anonfun$1.apply$mcV$sp(FlagStatSuite.scala:36)
  at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply$mcV$sp(SparkFunSuite.scala:97)
  at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:93)
  at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:93)
  at org.scalatest.Transformer$$anonfun$apply$1.apply$mcV$sp(Transformer.scala:22)
  ...

Looks like I jumped too far ahead with args4j.

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heuermh commented Oct 5, 2015

ok, then I get farther

- Standard FlagStat test *** FAILED ***
  java.lang.IllegalStateException: Cannot set value to a final field 'org.bdgenomics.adam.cli.FlagStatArgs.inputPath'.
  at org.kohsuke.args4j.spi.Setters.create(Setters.java:32)
  at org.kohsuke.args4j.ClassParser.parse(ClassParser.java:38)
  at org.kohsuke.args4j.CmdLineParser.<init>(CmdLineParser.java:94)
  at org.kohsuke.args4j.CmdLineParser.<init>(CmdLineParser.java:69)
  at org.bdgenomics.utils.cli.Args4j$.apply(Args4j.scala:35)
  at org.bdgenomics.adam.cli.FlagStatSuite$$anonfun$1.apply$mcV$sp(FlagStatSuite.scala:36)
  at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply$mcV$sp(SparkFunSuite.scala:97)
  at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:93)
  at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:93)
  at org.scalatest.Transformer$$anonfun$apply$1.apply$mcV$sp(Transformer.scala:22)
  ...

Looks like I jumped too far ahead with args4j.

@heuermh heuermh changed the title from Updating build dependency versions to latest minor version, fails unit tests to Updating build dependency versions to latest minor versions Oct 5, 2015

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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

GitHub pull request #847 of commit e6ce184 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains 22a204a627fd75fe7919955210074aa84eabbc0d # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision 22a204a627fd75fe7919955210074aa84eabbc0d (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 22a204a627fd75fe7919955210074aa84eabbc0dFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Test FAILed.
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Build result: FAILURE

GitHub pull request #847 of commit e6ce184 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains 22a204a627fd75fe7919955210074aa84eabbc0d # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision 22a204a627fd75fe7919955210074aa84eabbc0d (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 22a204a627fd75fe7919955210074aa84eabbc0dFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Bugger, servo-core went JDK8-only as of version 0.11.0

AlignmentRecordRDDFunctionsSuite:
*** RUN ABORTED ***
  java.lang.UnsupportedClassVersionError: com/netflix/servo/tag/Tags : Unsupported major.minor version 52.0
  at java.lang.ClassLoader.defineClass1(Native Method)
  at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
  at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
  at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
  at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
  at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
  at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
  at java.security.AccessController.doPrivileged(Native Method)
  at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
  at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
  ...
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heuermh commented Oct 5, 2015

Bugger, servo-core went JDK8-only as of version 0.11.0

AlignmentRecordRDDFunctionsSuite:
*** RUN ABORTED ***
  java.lang.UnsupportedClassVersionError: com/netflix/servo/tag/Tags : Unsupported major.minor version 52.0
  at java.lang.ClassLoader.defineClass1(Native Method)
  at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
  at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
  at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
  at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
  at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
  at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
  at java.security.AccessController.doPrivileged(Native Method)
  at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
  at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
  ...
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Test FAILed.
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Build result: FAILURE

GitHub pull request #847 of commit 21901e7 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains 9ff0c01 # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision 9ff0c01 (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 9ff0c01e1ffa7f03be73a32db12aa38a4ad74542First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Oct 5, 2015

Test FAILed.
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Build result: FAILURE

GitHub pull request #847 of commit 21901e7 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains 9ff0c01 # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision 9ff0c01 (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 9ff0c01e1ffa7f03be73a32db12aa38a4ad74542First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Grrr. Guava version mismatch

AlignmentRecordRDDFunctionsSuite:
- sorting reads
- characterizeTags counts integer tag values correctly
- withTag returns only those records which have the appropriate tag
- withTag, when given a tag name that doesn't exist in the input, returns an empty RDD
- characterizeTagValues counts distinct values of a tag
*** RUN ABORTED ***
  java.lang.IllegalAccessError: tried to access method com.google.common.base.Stopwatch.<init>()V from class org.apache.hadoop.mapreduce.lib.input.FileInputFormat
  at org.apache.hadoop.mapreduce.lib.input.FileInputFormat.getSplits(FileInputFormat.java:379)
  at org.seqdoop.hadoop_bam.AnySAMInputFormat.getSplits(AnySAMInputFormat.java:219)
  at org.apache.spark.rdd.NewHadoopRDD.getPartitions(NewHadoopRDD.scala:95)
  at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:219)
  at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:217)
  at scala.Option.getOrElse(Option.scala:120)
  at org.apache.spark.rdd.RDD.partitions(RDD.scala:217)
  at org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:32)
  at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:219)
  at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:217)
Member

heuermh commented Oct 5, 2015

Grrr. Guava version mismatch

AlignmentRecordRDDFunctionsSuite:
- sorting reads
- characterizeTags counts integer tag values correctly
- withTag returns only those records which have the appropriate tag
- withTag, when given a tag name that doesn't exist in the input, returns an empty RDD
- characterizeTagValues counts distinct values of a tag
*** RUN ABORTED ***
  java.lang.IllegalAccessError: tried to access method com.google.common.base.Stopwatch.<init>()V from class org.apache.hadoop.mapreduce.lib.input.FileInputFormat
  at org.apache.hadoop.mapreduce.lib.input.FileInputFormat.getSplits(FileInputFormat.java:379)
  at org.seqdoop.hadoop_bam.AnySAMInputFormat.getSplits(AnySAMInputFormat.java:219)
  at org.apache.spark.rdd.NewHadoopRDD.getPartitions(NewHadoopRDD.scala:95)
  at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:219)
  at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:217)
  at scala.Option.getOrElse(Option.scala:120)
  at org.apache.spark.rdd.RDD.partitions(RDD.scala:217)
  at org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:32)
  at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:219)
  at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:217)
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Upgrading guava past version 16.0.1 is blocked by
https://issues.apache.org/jira/browse/HADOOP-10101

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heuermh commented Oct 7, 2015

Upgrading guava past version 16.0.1 is blocked by
https://issues.apache.org/jira/browse/HADOOP-10101

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Test FAILed.
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Build result: FAILURE

GitHub pull request #847 of commit a21a02f automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains a5c1468 # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision a5c1468 (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f a5c1468950f2b5abf11e24e53b4b4516d81dc9a5First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Build result: FAILURE

GitHub pull request #847 of commit a21a02f automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains a5c1468 # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision a5c1468 (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f a5c1468950f2b5abf11e24e53b4b4516d81dc9a5First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Build result: FAILURE

GitHub pull request #847 of commit a446b0b automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains c99a355 # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision c99a355 (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f c99a3555ee8cd60a142d6bc4e52f012a4cf0eeffFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Test FAILed.
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Build result: FAILURE

GitHub pull request #847 of commit a446b0b automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains c99a355 # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision c99a355 (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f c99a3555ee8cd60a142d6bc4e52f012a4cf0eeffFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Jenkins, retest this please.

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fnothaft commented Oct 7, 2015

Jenkins, retest this please.

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Test PASSed.

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Test PASSed.

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This change looks good, but let's hold on merging it until after 0.18.0.

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fnothaft commented Oct 9, 2015

This change looks good, but let's hold on merging it until after 0.18.0.

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I agree.

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heuermh commented Oct 9, 2015

I agree.

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Test FAILed.
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Build result: FAILURE

[...truncated 16 lines...] > git rev-list c99a355 # timeout=10Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.2.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.3.1,centosTriggering ADAM-prb ? 1.0.4,2.10,1.2.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.2.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 1.0.4,2.11,1.2.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosADAM-prb ? 2.3.0,2.11,1.2.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result FAILUREADAM-prb ? 1.0.4,2.10,1.2.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 1.0.4,2.11,1.2.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.4.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Test FAILed.
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Build result: FAILURE

[...truncated 16 lines...] > git rev-list c99a355 # timeout=10Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.2.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.3.1,centosTriggering ADAM-prb ? 1.0.4,2.10,1.2.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.2.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 1.0.4,2.11,1.2.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosADAM-prb ? 2.3.0,2.11,1.2.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result FAILUREADAM-prb ? 1.0.4,2.10,1.2.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 1.0.4,2.11,1.2.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.4.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Jenkins, test this please.

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fnothaft commented Oct 10, 2015

Jenkins, test this please.

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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/996/

Build result: FAILURE

GitHub pull request #847 of commit 0f621e7 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains d53322c # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision d53322c (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f d53322c > git rev-list 9413aea # timeout=10Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Oct 10, 2015

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/996/

Build result: FAILURE

GitHub pull request #847 of commit 0f621e7 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains d53322c # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision d53322c (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f d53322c > git rev-list 9413aea # timeout=10Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Jenkins, test this please.

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fnothaft commented Oct 10, 2015

Jenkins, test this please.

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Test PASSed.
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Test PASSed.

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Test PASSed.
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Test PASSed.

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Test FAILed.
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Build result: FAILURE

GitHub pull request #847 of commit f31cfa3 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains 90bd871 # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision 90bd871 (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 90bd871 > git rev-list d53322c # timeout=10Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Oct 27, 2015

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/1005/

Build result: FAILURE

GitHub pull request #847 of commit f31cfa3 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains 90bd871 # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision 90bd871 (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 90bd871 > git rev-list d53322c # timeout=10Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Jenkins, retest this please.

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heuermh commented Oct 27, 2015

Jenkins, retest this please.

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Test PASSed.
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Test PASSed.

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Test PASSed.
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Test PASSed.

@heuermh heuermh added this to the 0.18.2 milestone Nov 2, 2015

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Test FAILed.
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Build result: FAILURE

GitHub pull request #847 of commit 4b71d0e automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains d982a8a9d36f1d6c221846988e12f05b0494c4e6 # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision d982a8a9d36f1d6c221846988e12f05b0494c4e6 (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f d982a8a9d36f1d6c221846988e12f05b0494c4e6 > git rev-list 90bd871 # timeout=10Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Nov 4, 2015

Test FAILed.
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Build result: FAILURE

GitHub pull request #847 of commit 4b71d0e automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/847/merge^{commit} # timeout=10 > git branch -a --contains d982a8a9d36f1d6c221846988e12f05b0494c4e6 # timeout=10 > git rev-parse remotes/origin/pr/847/merge^{commit} # timeout=10Checking out Revision d982a8a9d36f1d6c221846988e12f05b0494c4e6 (origin/pr/847/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f d982a8a9d36f1d6c221846988e12f05b0494c4e6 > git rev-list 90bd871 # timeout=10Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Jenkins, retest this please.

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heuermh commented Nov 4, 2015

Jenkins, retest this please.

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Test PASSed.
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Test PASSed.

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Test PASSed.
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Test PASSed.

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Thanks @heuermh! I've committed this as 295fb5c.

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fnothaft commented Nov 10, 2015

Thanks @heuermh! I've committed this as 295fb5c.

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@heuermh heuermh deleted the heuermh:dependency-versions branch Nov 10, 2015

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Thanks!

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heuermh commented Nov 10, 2015

Thanks!

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