What if the kpsewhich command for MCscan error is missing?
Editor to share with you what to do about the missing kpsewhich command of MCscan error report. I believe most people don't know much about it, so share this article for your reference. I hope you will gain a lot after reading this article. Let's learn about it together.
Missing kpsewhich command causes jcvi to report an error
Recently, the installation of jcvi under linux system for collinear analysis is smooth, but there are always errors at run time.
MCscan error message:
File "/ biosoft/python/Python-v2.7.11/lib/python2.7/site-packages/jcvi/graphics/dotplot.py", line 357, in dotplot_main title=opts.title, stdpf= (not opts.nostdpf) File "/ biosoft/python/Python-v2.7.11/lib/python2.7/site-packages/jcvi/graphics/dotplot.py", line 235, in dotplot sepcolor=sepcolor, minfont=minfont Stdpf=stdpf) File "/ biosoft/python/Python-v2.7.11/lib/python2.7/site-packages/jcvi/graphics/dotplot.py", line 79, in plot_breaks_and_labels th = TextHandler (fig) File "/ biosoft/python/Python-v2.7.11/lib/python2.7/site-packages/jcvi/graphics/base.py", line 51 In _ init__ self.build_height_array (fig) File "/ biosoft/python/Python-v2.7.11/lib/python2.7/site-packages/jcvi/graphics/base.py", line 65, in build_height_array w, h = TextHandler.get_text_width_height (fig, size=i) File "/ biosoft/python/Python-v2.7.11/lib/python2.7/site-packages/jcvi/graphics/base.py", line 57 In get_text_width_height tp = mpl.textpath.TextPath ((0init__ usetex=usetex 0), txt, size=size, usetex=usetex) File "/ biosoft/python/Python-v2.7.11/lib/python2.7/site-packages/matplotlib/textpath.py", line 450, in _ _ init__ usetex=usetex) File "/ biosoft/python/Python-v2.7.11/lib/python2.7/site-packages/matplotlib/textpath.py", line 530, in text_get_vertices_codes verts Codes = text_to_path.get_text_path (prop, s, usetex=True) File "/ biosoft/python/Python-v2.7.11/lib/python2.7/site-packages/matplotlib/textpath.py", line 152, in get_text_path glyph_info, glyph_map, rects = self.get_glyphs_tex (prop, s) File "/ biosoft/python/Python-v2.7.11/lib/python2.7/site-packages/matplotlib/textpath.py", line 305 In get_glyphs_tex dviread.find_tex_file ('pdftex.map') File "/ biosoft/python/Python-v2.7.11/lib/python2.7/site-packages/matplotlib/dviread.py", line 1045, in find_tex_file stderr=subprocess.PIPE) File "/ biosoft/python/Python-v2.7.11/lib/python2.7/site-packages/subprocess32.py", line 614, in _ _ init__ restore_signals Start_new_session) File "/ biosoft/python/Python-v2.7.11/lib/python2.7/site-packages/subprocess32.py", line 1393, in _ execute_child raise child_exception_type (errno_num, err_msg) OSError: [Errno 2] No such file or directory: 'kpsewhich'
After searching the query, we know that it is caused by the missing kpsewhich command in linux, so install the command as follows:
Sudo yum install tetex-latex tetex-doc tetex-fontssudo yum install texlive tex-live-latex
After installation, run again and pass smoothly.
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