Closed ghost closed 8 years ago
TransGirlCodes
commented
8 years ago Hmm this looks like some stream is opened to /dev/null - so basically stuff that's written out is deleted. But I believe that on Windows, /dev/null doesn't exist, because it's a Linux / OSX thing. This looks like something wrong with the Interval Collections.
TransGirlCodes
commented
8 years ago Can I ask how did you install Bio.jl? Because the test file you are running (Bio/test/intervals/TestIntervals.jl), no longer exist, as all test files we have no are called runtests.jl. If you added Bio by using Pkg.add("Bio") it may be your problem is solved by checking out the latest master branch, because the version in Julia' package manager METADATA is somewhat out of date.
ghost
commented
8 years ago @Ward9250 So you mean I should use Pkg.update() to update the (Bio) package?
ghost
commented
8 years ago yeah... I use Pkg.add("Bio") to install the BIo package
TransGirlCodes
commented
8 years ago I would remove Bio as you currently have it, using Pkg.rm("Bio"), then install it through cloning: Pkg.clone("https://github.com/BioJulia/Bio.jl.git") This will give you the very latest state of the master.
ghost
commented
8 years ago Or Pkg.clone("https://github.com/BioJulia/Bio.jl.git") ?
TransGirlCodes
commented
8 years ago Yep that's the one!
ghost
commented
8 years ago Still error...
INFO: Computing test dependencies for Bio... INFO: Cloning cache of BaseTestNext from git://github.com/JuliaCI/BaseTestNext.jl.git INFO: Installing BaseTestNext v0.2.1 INFO: Installing YAML v0.1.10 INFO: Testing Bio Test Summary: | Pass Total Alignments | 301 301 Test Summary: | Pass Total PairwiseAlignment | 204 204 Test Summary: | Pass Total Interval | 6 6 Test Summary: | Pass Total IntervalCollection | 7 7 Test Summary: | Pass Total Alphanumeric Sorting | 8 8 Test Summary: | Pass Total IntervalStream | 15 15 Cloning into 'C:\Users\Miller.julia\v0.4\Bio\test\BioFmtSpecimens'... Test Summary: | Pass Total Interval Parsing | 14 14 BED → BigBed → BED round-trip: Error During Test Got an exception of type ArgumentError outside of a @test ArgumentError: ensureroom failed, IOBuffer is not writeable in ensureroom at iobuffer.jl:175 in write at iobuffer.jl:319 in write at io.jl:54 in write at C:\Users\Miller.julia\v0.4\Bio\src\intervals\bigbed.jl:300 in bigbed_write_index at C:\Users\Miller.julia\v0.4\Bio\src\intervals\bigbed.jl:1443 in write_bigbed_bigwig at C:\Users\Miller.julia\v0.4\Bio\src\intervals\bigbed.jl:1811 [inlined code] from C:\Users\Miller.julia\v0.4\Bio\test\intervals/runtests.jl:460 in anonymous at no file:0 in include at boot.jl:261 in include_from_node1 at loading.jl:320 [inlined code] from C:\Users\Miller.julia\v0.4\Bio\test\runtests.jl:27 in anonymous at no file:0 in include at boot.jl:261 in include_from_node1 at loading.jl:320 in process_options at client.jl:280 in _start at client.jl:378 BigBed Intersection: Error During Test Got an exception of type ArgumentError outside of a @test ArgumentError: ensureroom failed, IOBuffer is not writeable in ensureroom at iobuffer.jl:175 in write_sub at iobuffer.jl:299 in flushbuffer! at C:\Users\Miller.julia\v0.4\BufferedStreams\src\bufferedoutputstream.jl:39 in close at C:\Users\Miller.julia\v0.4\BufferedStreams\src\bufferedoutputstream.jl:121 in writebytes at C:\Users\Miller.julia\v0.4\Libz\src\sink.jl:144 in flushbuffer! at C:\Users\Miller.julia\v0.4\BufferedStreams\src\bufferedoutputstream.jl:39 in close at C:\Users\Miller.julia\v0.4\BufferedStreams\src\bufferedoutputstream.jl:121 in bigbed_write_blocks at C:\Users\Miller.julia\v0.4\Bio\src\intervals\bigbed.jl:1044 in write_bigbed_bigwig at C:\Users\Miller.julia\v0.4\Bio\src\intervals\bigbed.jl:1800 [inlined code] from C:\Users\Miller.julia\v0.4\Bio\test\intervals/runtests.jl:481 in anonymous at no file:0 in include at boot.jl:261 in include_from_node1 at loading.jl:320 [inlined code] from C:\Users\Miller.julia\v0.4\Bio\test\runtests.jl:27 in anonymous at no file:0 in include at boot.jl:261 in include_from_node1 at loading.jl:320 in process_options at client.jl:280 in _start at client.jl:378 Test Summary: | Error Total BigBed | 2 2 BED → BigBed → BED round-trip | 1 1 BigBed Intersection | 1 1 ERROR: LoadError: LoadError: Some tests did not pass: 0 passed, 0 failed, 2 errored. in finish at C:\Users\Miller.julia\v0.4\BaseTestNext\src\BaseTestNext.jl:385 [inlined code] from C:\Users\Miller.julia\v0.4\BaseTestNext\src\BaseTestNext.jl:559 in anonymous at no file:0 in include at boot.jl:261 in include_from_node1 at loading.jl:320 [inlined code] from C:\Users\Miller.julia\v0.4\Bio\test\runtests.jl:27 in anonymous at no file:0 in include at boot.jl:261 in include_from_node1 at loading.jl:320 in process_options at client.jl:280 in _start at client.jl:378 while loading C:\Users\Miller.julia\v0.4\Bio\test\intervals/runtests.jl, in expression starting on line 448 while loading C:\Users\Miller.julia\v0.4\Bio\test\runtests.jl, in expression starting on line 26 =================================[ ERROR: Bio ]=================================
failed process: Process('C:\Users\Miller\AppData\Local\Julia-0.4.5\bin\julia' --check-bounds=yes --code-coverage=none --color=no 'C:\Users\Miller\.julia\v0.4\Bio\test\runtests.jl', ProcessExited(1)) [1]
INFO: Removing BaseTestNext v0.2.1 INFO: Removing YAML v0.1.10 Bio had test errors in error at base\error.jl:21
TransGirlCodes
commented
8 years ago Ah ok, so the bigbed error(s) is something we know about and it is on our radar to fix, but you can see from the output that tests for Bio.Align, Bio.Seq, and intervals is working. So Yes at this stage the tests do fail, but we know about this error, and you are up to date, everything else works and tests successfully.
ghost
commented
8 years ago Ok Thank you so much. Hope you will fix it successfully. Besh wishes...I will try later and close it now.
TransGirlCodes
commented
8 years ago This will only be a problem for you if you wanted to do things with bed files/data.
I don't know what's wrong.Please help me.
Pkg.test("Bio")
INFO: Computing test dependencies for Bio... INFO: Installing YAML v0.1.10 INFO: Testing Bio
WARNING: deprecated syntax "{}" at C:\Users\Miller.julia\v0.4\Switch\src\Switch.jl:8. Use "[]" instead.
WARNING: deprecated syntax "{}" at C:\Users\Miller.julia\v0.4\Switch\src\Switch.jl:9. Use "[]" instead.
WARNING: deprecated syntax "{}" at C:\Users\Miller.julia\v0.4\Switch\src\Switch.jl:21. Use "[]" instead.
WARNING: deprecated syntax "{}" at C:\Users\Miller.julia\v0.4\Switch\src\Switch.jl:30. Use "[]" instead.
WARNING: deprecated syntax "{}" at C:\Users\Miller.julia\v0.4\Switch\src\Switch.jl:44. Use "[]" instead.
WARNING: deprecated syntax "{}" at C:\Users\Miller.julia\v0.4\Switch\src\Switch.jl:61. Use "[]" instead. IntervalCollection
failed process: Process(
'C:\Users\Miller\AppData\Local\Julia-0.4.5\bin\julia' --check-bounds=yes --code-coverage=none --color=no 'C:\Users\Miller\.julia\v0.4\Bio\test\runtests.jl', ProcessExited(1)) [1]INFO: Removing YAML v0.1.10
Bio had test errors in error at base\error.jl:21