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{bio}[foss/2017a] Trinity 2.4.0 (REVIEW)#4973

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boegel merged 5 commits intoeasybuilders:developfrom
hajgato:Trinit240
Aug 8, 2017
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{bio}[foss/2017a] Trinity 2.4.0 (REVIEW)#4973
boegel merged 5 commits intoeasybuilders:developfrom
hajgato:Trinit240

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@hajgato hajgato commented Aug 3, 2017

intel/2017a fails with inchworm
similar errors like:

GCCcore/6.3.0/bin/../include/c++/6.3.0/bits/stl_multimap.h(972): note: this candidate was rejected because at least one template argument could not be deduced
      operator==(const multimap<_Key, _Tp, _Compare, _Alloc>& __x,
      ^

I did not have time to look into more details into the problem, bit it might be intel 17.0 compiler problem/C++ incompatibility
See https://software.intel.com/en-us/forums/intel-c-compiler/topic/703133

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hajgato commented Aug 3, 2017

The actual error is:

./analysis/sequenceUtil.cc(53): error: no operator "==" matches these operands
            operand types are: std::ifstream == int
    if (fileReader == 0) { // couldn't open file
                   ^

@verdurin verdurin added this to the 3.4.0 milestone Aug 3, 2017
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verdurin commented Aug 3, 2017

Test report by @verdurin
SUCCESS
Build succeeded for 13 out of 13 (5 easyconfigs in this PR)
ca005.camp.thecrick.org - Linux centos linux 7.3.1611, Intel(R) Xeon(R) CPU E5-2640 v3 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/7fc973d10d46a8f980b1b29cc7ae156b for a full test report.

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verdurin previously requested changes Aug 4, 2017
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Comment thread easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-GCCcore-6.3.0.eb
toolchainopts = {'pic': True}

sources = ['%(namelower)s-%(version)s-src.zip']
source_urls = ['http://download.sourceforge.net/bowtie-bio/']
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@hajgato please add a checksum here

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added

Comment thread easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2017a.eb
toolchainopts = {'pic': True, 'cstd': 'gnu++98'}

sources = ['%(namelower)s-%(version)s-source.zip']
source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')]
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Again, checksum here please.

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added

Comment thread easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb
toolchainopts = {'optarch': True}

source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/archive/']
sources = ['%(name)s-v%(version)s.tar.gz']
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Checksum, please.

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added

Comment thread easybuild/easyconfigs/t/tbb/tbb-2017_U6-GCCcore-6.3.0.eb
toolchain = {'name': 'GCCcore', 'version': '6.3.0'}

source_urls = ['https://github.com/01org/tbb/archive/']
sources = ['%(version)s.tar.gz']
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And a checksum here too, please.

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added

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hajgato commented Aug 4, 2017

@verdurin Is it a new policy that we add checksums everywhere?

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verdurin commented Aug 4, 2017

@hajgato yes it is - I was caught out initially as well

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hajgato commented Aug 4, 2017

@verdurin It will be fun to make Perl, Python, R, etc. modules ;)

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hajgato commented Aug 4, 2017
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checksums added

boegel
boegel requested changes Aug 7, 2017
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Comment thread easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb Outdated
name = 'Trinity'
version = '2.4.0'
java = 'Java'
javaver = '1.8.0_121'
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@hajgato no need for this, you can use %(javaver)s:

dependencies = [
    ('Java', '1.8.0_121', '', True),
    ('ant', '1.10.1', '-Java-%(javaver)s', True),

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@boegel done!

boegel
boegel requested changes Aug 8, 2017
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Comment thread easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb Outdated
]

dependencies = [
(java, javaver, '', True),
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@boegel boegel Aug 8, 2017

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@hajgato You missed a spot, this should be:

('Java', '1.8.0_121', '', True),

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@boegel done (Sorry its too morning...)

Balazs Hajgato added 2 commits August 8, 2017 09:53
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boegel commented Aug 8, 2017

Test report by @boegel
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in this PR)
node2107.delcatty.os - Linux centos linux 7.3.1611, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/1c44eb2c3505e48749365af9e3f0bf88 for a full test report.

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boegel commented Aug 8, 2017

Test report by @boegel
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in this PR)
node2421.golett.os - Linux centos linux 7.3.1611, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 2.7.5
See https://gist.github.com/09aabc691120226c44df0945f856fdf5 for a full test report.

@boegel boegel dismissed verdurin’s stale review August 8, 2017 15:51

remarks have been tackled

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boegel commented Aug 8, 2017

Going in, thanks @hajgato!

@boegel boegel merged commit 28f8a62 into easybuilders:develop Aug 8, 2017
@boegel boegel mentioned this pull request Aug 8, 2017
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@hajgato hajgato deleted the Trinit240 branch February 12, 2018 13:17
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