[Biopython-dev] Test suite failure

[Michiel de Hoon]

Dear all,

I am getting the errors below when running the Biopython tests on Mac OS X. This is with blast+ 2.2.23. The blast+ 2.2.24 installer fails on Mac OS X, so I don't know if the same problem would occur with that version. 

--Michiel

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ERROR: test_blastn (test_NCBI_BLAST_tools.CheckCompleteArgList)
Check all blastn arguments are supported
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Traceback (most recent call last):
  File "test_NCBI_BLAST_tools.py", line 220, in test_blastn
    self.check("blastn", Applications.NcbiblastnCommandline)
  File "test_NCBI_BLAST_tools.py", line 204, in check
    ",".join(sorted(missing))))
MissingExternalDependencyError: BLAST+ and Biopython out of sync. Your version of the NCBI BLAST+ tool blastn does not match what we are expecting. Please update your copy of Biopython, or report this issue if you are already using the latest version. (Exta args: -seqidlist; Missing: )

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ERROR: test_blastp (test_NCBI_BLAST_tools.CheckCompleteArgList)
Check all blastp arguments are supported
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Traceback (most recent call last):
  File "test_NCBI_BLAST_tools.py", line 216, in test_blastp
    self.check("blastp", Applications.NcbiblastpCommandline)
  File "test_NCBI_BLAST_tools.py", line 204, in check
    ",".join(sorted(missing))))
MissingExternalDependencyError: BLAST+ and Biopython out of sync. Your version of the NCBI BLAST+ tool blastp does not match what we are expecting. Please update your copy of Biopython, or report this issue if you are already using the latest version. (Exta args: -seqidlist; Missing: )

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ERROR: test_blastx (test_NCBI_BLAST_tools.CheckCompleteArgList)
Check all blastx arguments are supported
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Traceback (most recent call last):
  File "test_NCBI_BLAST_tools.py", line 212, in test_blastx
    self.check("blastx", Applications.NcbiblastxCommandline)
  File "test_NCBI_BLAST_tools.py", line 204, in check
    ",".join(sorted(missing))))
MissingExternalDependencyError: BLAST+ and Biopython out of sync. Your version of the NCBI BLAST+ tool blastx does not match what we are expecting. Please update your copy of Biopython, or report this issue if you are already using the latest version. (Exta args: -seqidlist; Missing: )

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ERROR: test_psiblast (test_NCBI_BLAST_tools.CheckCompleteArgList)
Check all psiblast arguments are supported
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Traceback (most recent call last):
  File "test_NCBI_BLAST_tools.py", line 232, in test_psiblast
    self.check("psiblast", Applications.NcbipsiblastCommandline)
  File "test_NCBI_BLAST_tools.py", line 204, in check
    ",".join(sorted(missing))))
MissingExternalDependencyError: BLAST+ and Biopython out of sync. Your version of the NCBI BLAST+ tool psiblast does not match what we are expecting. Please update your copy of Biopython, or report this issue if you are already using the latest version. (Exta args: -seqidlist; Missing: )

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ERROR: test_rpsblast (test_NCBI_BLAST_tools.CheckCompleteArgList)
Check all rpsblast arguments are supported
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Traceback (most recent call last):
  File "test_NCBI_BLAST_tools.py", line 236, in test_rpsblast
    self.check("rpsblast", Applications.NcbirpsblastCommandline)
  File "test_NCBI_BLAST_tools.py", line 204, in check
    ",".join(sorted(missing))))
MissingExternalDependencyError: BLAST+ and Biopython out of sync. Your version of the NCBI BLAST+ tool rpsblast does not match what we are expecting. Please update your copy of Biopython, or report this issue if you are already using the latest version. (Exta args: -seqidlist; Missing: )

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ERROR: test_rpstblastn (test_NCBI_BLAST_tools.CheckCompleteArgList)
Check all rpstblastn arguments are supported
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Traceback (most recent call last):
  File "test_NCBI_BLAST_tools.py", line 240, in test_rpstblastn
    self.check("rpstblastn", Applications.NcbirpstblastnCommandline)
  File "test_NCBI_BLAST_tools.py", line 204, in check
    ",".join(sorted(missing))))
MissingExternalDependencyError: BLAST+ and Biopython out of sync. Your version of the NCBI BLAST+ tool rpstblastn does not match what we are expecting. Please update your copy of Biopython, or report this issue if you are already using the latest version. (Exta args: -seqidlist; Missing: )

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ERROR: test_tblastn (test_NCBI_BLAST_tools.CheckCompleteArgList)
Check all tblastn arguments are supported
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Traceback (most recent call last):
  File "test_NCBI_BLAST_tools.py", line 228, in test_tblastn
    self.check("tblastn", Applications.NcbitblastnCommandline)
  File "test_NCBI_BLAST_tools.py", line 204, in check
    ",".join(sorted(missing))))
MissingExternalDependencyError: BLAST+ and Biopython out of sync. Your version of the NCBI BLAST+ tool tblastn does not match what we are expecting. Please update your copy of Biopython, or report this issue if you are already using the latest version. (Exta args: -db_soft_mask,-seqidlist; Missing: )

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ERROR: test_tblastx (test_NCBI_BLAST_tools.CheckCompleteArgList)
Check all tblastx arguments are supported
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Traceback (most recent call last):
  File "test_NCBI_BLAST_tools.py", line 224, in test_tblastx
    self.check("tblastx", Applications.NcbitblastxCommandline)
  File "test_NCBI_BLAST_tools.py", line 204, in check
    ",".join(sorted(missing))))
MissingExternalDependencyError: BLAST+ and Biopython out of sync. Your version of the NCBI BLAST+ tool tblastx does not match what we are expecting. Please update your copy of Biopython, or report this issue if you are already using the latest version. (Exta args: -db_soft_mask,-seqidlist; Missing: )

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