SyntaxError: invalid syntax

[ponomarevsy]

Hello,

This error most likely the result of the updated bioconda directory structure:

» ./easy_update.py R-3.4.0-goolf-1.7.20.eb
File "./easy_update.py", line 286 '%s/data/experiment/packages.json' % (base_path, biocver)] ^ SyntaxError: invalid syntax

Looking inside file "./easy_update.py", line 286:

def read_bioconductor_pacakges(self):
        """ read the Bioconductor package list into bio_data dict
        """
        base_path = 'https://bioconductor.org/packages/json/'
        bioc_urls = ['%s/bioc/packages.json' % (base_path, biocver),
                     '%s/data/annotation/packages.json' % (base_path, biocver,)
                     '%s/data/experiment/packages.json' % (base_path, biocver)]
        self.bioc_data = {}
        for url in bioc_urls:
            try:
                response = urllib2.urlopen(url)
            except IOError as e:
                print 'URL request: ', url
                sys.exit(e)
...

What would the correct (new) bioconda path should be? Thank you in advance!

[ponomarevsy]

Ok, I've made some progress here, but now getting a different error:

def read_bioconductor_pacakges(self): """ read the Bioconductor package list into bio_data dict """ base_path = "https://bioconductor.org/packages/release"

bioc_urls = ['%s/bioc/packages.json' % (base_path, biocver),

    #             '%s/data/annotation/packages.json' % (base_path, biocver,)
    #             '%s/data/experiment/packages.json' % (base_path, biocver)]

bioc_urls = ["%s/BiocViews.html#___Software/packages.json" % (base_path, biocver), "%s/BiocViews.html#___AnnotationData/packages.json" % (base_path, biocver), "%s/BiocViews.html#___ExperimentData/packages.json" % (base_path, biocver)] self.bioc_data = {} for url in bioc_urls: try: response = urllib2.urlopen(url)

» ./easy_update.py R-3.4.0-goolf-1.7.20.eb --verbose Traceback (most recent call last): File "./easy_update.py", line 502, in module = R(sys.argv[1], add_packages, package, verbose=vflag) TypeError: init() got multiple values for keyword argument 'verbose'

[fizwit]

I need to push a new version. The path versions for Biocondutor have been updated.

[ponomarevsy]

And that will happen when???

[fizwit]

uploaded new version, much improved please tryit.