Installation problem #160

francicco · 2019-09-26T21:35:54Z

Hi,

I'm trying to install the jcvi package. Running the test analysis I got these errors:

(AllMapsEnv) [tk19812@bc4login1 ALLMAPS-testdata]$ ./run.sh 
22:33:31 [allmaps] A total of 120 markers written to `JM-2.bed`.
22:33:31 [allmaps] Weights file `weights.txt` found. Will not overwrite.
22:33:32 [base] Load file `JM-2.bed`
22:33:32 [allmaps] Map contains 120 markers in 2 linkage groups.
22:33:32 [allmaps] Retained 120 of 120 (100.0%) clean markers.
22:33:32 [base] Load file `weights.txt`
22:33:32 [base] Imported 2 records from `weights.txt`.
22:33:32 [allmaps] Map weights: dict_items([('JMFemale', 1), ('JMMale', 1)])
22:33:32 [allmaps] Linkage function: double-linkage
22:33:32 [allmaps] Partition LGs based on JMFemale
22:33:32 [base] Load file `scaffolds.fasta.sizes`
22:33:32 [allmaps] Working on JMMale-23|JMFemale-23 ...
22:33:32 [allmaps] Graph size: |V|=24, |E|=474.
22:33:32 [allmaps] concorde-TSP failed. Use default scaffold ordering.
22:33:32 [allmaps] Start EC round 0
22:33:32 [ec] GA setup: ngen=500 npop=100 cpus=16 seed=666
Current iteration 20: max_score=(71.0,)
Current iteration 40: max_score=(79.0,)
Current iteration 60: max_score=(83.0,)
Current iteration 80: max_score=(86.0,)
Current iteration 100: max_score=(87.0,)
Current iteration 120: max_score=(88.0,)
Current iteration 140: max_score=(88.0,)
Current iteration 160: max_score=(89.0,)
Current iteration 180: max_score=(89.0,)
Current iteration 200: max_score=(89.0,)
Current iteration 220: max_score=(89.0,)
Current iteration 240: max_score=(89.0,)
Current iteration 260: max_score=(89.0,)
Current iteration 280: max_score=(89.0,)
Current iteration 300: max_score=(89.0,)
Current iteration 320: max_score=(89.0,)
Current iteration 340: max_score=(89.0,)
Current iteration 360: max_score=(89.0,)
Current iteration 380: max_score=(89.0,)
Current iteration 400: max_score=(89.0,)
Current iteration 420: max_score=(89.0,)
Current iteration 440: max_score=(89.0,)
Current iteration 460: max_score=(89.0,)
Current iteration 480: max_score=(89.0,)
Current iteration 500: max_score=(89.0,)
Current iteration 520: max_score=(89.0,)
Current iteration 540: max_score=(89.0,)
Current iteration 560: max_score=(89.0,)
Current iteration 580: max_score=(89.0,)
Current iteration 600: max_score=(89.0,)
Current iteration 620: max_score=(89.0,)
Current iteration 640: max_score=(89.0,)
22:33:35 [allmaps] Fixed orientations for 1 scaffolds.
22:33:35 [allmaps] Current best fitness: (89.0,)
22:33:35 [allmaps] Start EC round 1
/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/deap/creator.py:141: RuntimeWarning: A class named 'FitnessMax' has already been created and it will be overwritten. Consider deleting previous creation of that class or rename it.
  RuntimeWarning)
/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/deap/creator.py:141: RuntimeWarning: A class named 'Individual' has already been created and it will be overwritten. Consider deleting previous creation of that class or rename it.
  RuntimeWarning)
22:33:35 [ec] GA setup: ngen=500 npop=100 cpus=16 seed=666
Current iteration 20: max_score=(89.0,)
Current iteration 40: max_score=(89.0,)
Current iteration 60: max_score=(89.0,)
Current iteration 80: max_score=(89.0,)
Current iteration 100: max_score=(89.0,)
Current iteration 120: max_score=(89.0,)
Current iteration 140: max_score=(89.0,)
Current iteration 160: max_score=(89.0,)
Current iteration 180: max_score=(89.0,)
Current iteration 200: max_score=(89.0,)
Current iteration 220: max_score=(89.0,)
Current iteration 240: max_score=(89.0,)
Current iteration 260: max_score=(89.0,)
Current iteration 280: max_score=(89.0,)
Current iteration 300: max_score=(89.0,)
Current iteration 320: max_score=(89.0,)
Current iteration 340: max_score=(89.0,)
Current iteration 360: max_score=(89.0,)
Current iteration 380: max_score=(89.0,)
Current iteration 400: max_score=(89.0,)
Current iteration 420: max_score=(89.0,)
Current iteration 440: max_score=(89.0,)
Current iteration 460: max_score=(89.0,)
Current iteration 480: max_score=(89.0,)
Current iteration 500: max_score=(89.0,)
22:33:37 [allmaps] No fitness improvement: (89.0,). Exit EC.
22:33:37 [allmaps] Dropped 0 minor scaffolds
>chr23 (JMMale-23|JMFemale-23) FINAL
scaffold_158? scaffold_1006? scaffold_382- scaffold_648? scaffold_829+ scaffold_642? scaffold_513+ scaffold_331? scaffold_150+ scaffold_80+ scaffold_43+ scaffold_129- scaffold_164+ scaffold_225? scaffold_148+ scaffold_95? scaffold_310+ scaffold_375+ scaffold_792? scaffold_1189+ scaffold_866? scaffold_821?
22:33:37 [allmaps] AGP file written to `JM-2.chr.agp`.
22:33:37 [allmaps] Tour file written to `JM-2.tour`.
22:33:37 [base] Load file `JM-2.chr.agp`
22:33:37 [base] Load file `scaffolds.fasta`
22:33:38 [agp] Write object chr23 to `JM-2.chr.fasta`
22:33:38 [agp] Target fasta written to `JM-2.chr.fasta`.
22:33:38 [base] Load file `JM-2.chr.agp`
22:33:38 [base] Load file `scaffolds.fasta.sizes`
22:33:38 [allmaps] Write unplaced AGP to `JM-2.unplaced.agp`.
22:33:38 [base] Load file `JM-2.unplaced.agp`
22:33:38 [base] Load file `scaffolds.fasta`
22:33:38 [agp] Target fasta written to `JM-2.unplaced.fasta`.
22:33:38 [base] cat JM-2.chr.agp JM-2.unplaced.agp >JM-2.agp
22:33:38 [base] cat JM-2.chr.fasta JM-2.unplaced.fasta >JM-2.fasta
22:33:38 [base] Load file `JM-2.agp`
22:33:38 [base] Load file `scaffolds.fasta.sizes`
22:33:38 [base] faSize -detailed /mnt/storage/scratch/tk19812/software/jcvi/ALLMAPS-testdata/JM-2.fasta >JM-2.fasta.sizes
22:33:38 [base] Load file `JM-2.fasta.sizes`
22:33:38 [chain] File written to `JM-2.chain`.
22:33:38 [base] liftOver -minMatch=1 JM-2.bed JM-2.chain JM-2.lifted.bed unmapped
Reading liftover chains
Mapping coordinates
22:33:38 [base] sort -k1,1 -k2,2n -k3,3n -k4,4 JM-2.lifted.bed -o JM-2.lifted.bed
22:33:38 [base] Load file `JM-2.bed`
22:33:38 [allmaps] Map contains 120 markers in 2 linkage groups.
22:33:38 [base] Load file `scaffolds.fasta.sizes`
22:33:38 [base] Load file `JM-2.chr.agp`
22:33:38 [base] Load file `JM-2.chr.agp`
22:33:38 [base] Load file `JM-2.lifted.bed`
22:33:38 [allmaps] Map contains 120 markers in 2 linkage groups.
22:33:38 [base] Load file `weights.txt`
22:33:38 [base] Imported 2 records from `weights.txt`.
22:33:38 [allmaps] Map weights: dict_items([('JMFemale', 1), ('JMMale', 1)])
22:33:38 [base] Load file `JM-2.agp`
22:33:38 [base] savefig failed. Reset usetex to False.
Failed to process string with tex because latex could not be found
22:33:38 [font_manager] findfont: Font family ['sans-serif'] not found. Falling back to DejaVu Sans.
22:33:38 [font_manager] findfont: Font family ['sans-serif'] not found. Falling back to DejaVu Sans.
Traceback (most recent call last):
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/texmanager.py", line 304, in _run_checked_subprocess
    stderr=subprocess.STDOUT)
  File "/mnt/storage/software/languages/anaconda/Anaconda3-2019.03/lib/python3.7/subprocess.py", line 395, in check_output
    **kwargs).stdout
  File "/mnt/storage/software/languages/anaconda/Anaconda3-2019.03/lib/python3.7/subprocess.py", line 472, in run
    with Popen(*popenargs, **kwargs) as process:
  File "/mnt/storage/software/languages/anaconda/Anaconda3-2019.03/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/mnt/storage/software/languages/anaconda/Anaconda3-2019.03/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'latex': 'latex'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/mnt/storage/home/tk19812/scratch/software/jcvi/jcvi/graphics/base.py", line 183, in savefig
    plt.savefig(figname, dpi=dpi, format=format)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/pyplot.py", line 722, in savefig
    res = fig.savefig(*args, **kwargs)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/figure.py", line 2180, in savefig
    self.canvas.print_figure(fname, **kwargs)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/backend_bases.py", line 2082, in print_figure
    **kwargs)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/backends/backend_pdf.py", line 2503, in print_pdf
    self.figure.draw(renderer)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/artist.py", line 38, in draw_wrapper
    return draw(artist, renderer, *args, **kwargs)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/figure.py", line 1709, in draw
    renderer, self, artists, self.suppressComposite)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/image.py", line 135, in _draw_list_compositing_images
    a.draw(renderer)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/artist.py", line 38, in draw_wrapper
    return draw(artist, renderer, *args, **kwargs)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/axes/_base.py", line 2607, in draw
    self._update_title_position(renderer)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/axes/_base.py", line 2549, in _update_title_position
    bb = ax.xaxis.get_tightbbox(renderer)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/axis.py", line 1164, in get_tightbbox
    self._update_label_position(renderer)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/axis.py", line 2014, in _update_label_position
    bboxes, bboxes2 = self._get_tick_boxes_siblings(renderer=renderer)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/axis.py", line 1999, in _get_tick_boxes_siblings
    tlb, tlb2 = axx.xaxis._get_tick_bboxes(ticks_to_draw, renderer)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/axis.py", line 1150, in _get_tick_bboxes
    for tick in ticks if tick.label1.get_visible()],
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/axis.py", line 1150, in <listcomp>
    for tick in ticks if tick.label1.get_visible()],
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/text.py", line 890, in get_window_extent
    bbox, info, descent = self._get_layout(self._renderer)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/text.py", line 291, in _get_layout
    ismath="TeX" if self.get_usetex() else False)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/backends/_backend_pdf_ps.py", line 47, in get_text_width_height_descent
    s, fontsize, renderer=self)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/texmanager.py", line 448, in get_text_width_height_descent
    dvifile = self.make_dvi(tex, fontsize)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/texmanager.py", line 338, in make_dvi
    texfile], tex)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/texmanager.py", line 308, in _run_checked_subprocess
    'found'.format(command[0])) from exc
RuntimeError: Failed to process string with tex because latex could not be found

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/texmanager.py", line 304, in _run_checked_subprocess
    stderr=subprocess.STDOUT)
  File "/mnt/storage/software/languages/anaconda/Anaconda3-2019.03/lib/python3.7/subprocess.py", line 395, in check_output
    **kwargs).stdout
  File "/mnt/storage/software/languages/anaconda/Anaconda3-2019.03/lib/python3.7/subprocess.py", line 472, in run
    with Popen(*popenargs, **kwargs) as process:
  File "/mnt/storage/software/languages/anaconda/Anaconda3-2019.03/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/mnt/storage/software/languages/anaconda/Anaconda3-2019.03/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'latex': 'latex'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/mnt/storage/software/languages/anaconda/Anaconda3-2019.03/lib/python3.7/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/mnt/storage/software/languages/anaconda/Anaconda3-2019.03/lib/python3.7/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/mnt/storage/home/tk19812/scratch/software/jcvi/jcvi/assembly/allmaps.py", line 1872, in <module>
    main()
  File "/mnt/storage/home/tk19812/scratch/software/jcvi/jcvi/assembly/allmaps.py", line 828, in main
    p.dispatch(globals())
  File "/mnt/storage/home/tk19812/scratch/software/jcvi/jcvi/apps/base.py", line 100, in dispatch
    globals[action](sys.argv[2:])
  File "/mnt/storage/home/tk19812/scratch/software/jcvi/jcvi/assembly/allmaps.py", line 1526, in path
    "--figsize={0}".format(opts.figsize)])
  File "/mnt/storage/home/tk19812/scratch/software/jcvi/jcvi/assembly/allmaps.py", line 1868, in plotall
    plot(xargs + [seqid])
  File "/mnt/storage/home/tk19812/scratch/software/jcvi/jcvi/assembly/allmaps.py", line 1843, in plot
    savefig(image_name, dpi=iopts.dpi, iopts=iopts)
  File "/mnt/storage/home/tk19812/scratch/software/jcvi/jcvi/graphics/base.py", line 189, in savefig
    plt.savefig(figname, dpi=dpi)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/pyplot.py", line 722, in savefig
    res = fig.savefig(*args, **kwargs)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/figure.py", line 2180, in savefig
    self.canvas.print_figure(fname, **kwargs)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/backend_bases.py", line 2082, in print_figure
    **kwargs)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/backends/backend_pdf.py", line 2503, in print_pdf
    self.figure.draw(renderer)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/artist.py", line 38, in draw_wrapper
    return draw(artist, renderer, *args, **kwargs)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/figure.py", line 1709, in draw
    renderer, self, artists, self.suppressComposite)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/image.py", line 135, in _draw_list_compositing_images
    a.draw(renderer)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/artist.py", line 38, in draw_wrapper
    return draw(artist, renderer, *args, **kwargs)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/axes/_base.py", line 2647, in draw
    mimage._draw_list_compositing_images(renderer, self, artists)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/image.py", line 135, in _draw_list_compositing_images
    a.draw(renderer)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/artist.py", line 38, in draw_wrapper
    return draw(artist, renderer, *args, **kwargs)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/text.py", line 714, in draw
    mtext=mtext)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/backends/backend_pdf.py", line 1893, in draw_tex
    dvifile = texmanager.make_dvi(s, fontsize)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/texmanager.py", line 338, in make_dvi
    texfile], tex)
  File "/mnt/storage/scratch/tk19812/software/jcvi/AllMapsEnv/lib/python3.7/site-packages/matplotlib/texmanager.py", line 308, in _run_checked_subprocess
    'found'.format(command[0])) from exc
RuntimeError: Failed to process string with tex because latex could not be found

Any help to fix it?
Thanks a lot
F

The text was updated successfully, but these errors were encountered:

tanghaibao · 2019-09-27T03:52:56Z

@francicco

This is perhaps the most asked issue for this repo.

Try google on how to install Latex (it was only an optional requirement before when ALLMAPS was developed a few years ago, however, matplotlib has changed its way to interact with latex in recent versions, so it's emitting this error).

Please take a look at Get LaTeX for various options for each major OS. For example, on Debian-like Linux OS you can often do:

sudo apt-get install -y texlive texlive-latex-extra texlive-latex-recommended

Haibao

francicco · 2019-09-27T08:45:48Z

Hi Haibao,

I fixed that but apparently the syntax of the new version is changed. I used to execute these commands:

python -m jcvi.compara.synteny depth --histogram $SPECIES.$REFSP.anchors
python -m jcvi.assembly.syntenypath bed $SPECIES.$REFSP.anchors -o $SPECIES.synteny.bed
python -m jcvi.assembly.allmaps mergebed $SPECIES.synteny.bed -o $SPECIES.scaff.bed
python -m jcvi.assembly.allmaps path --cpus=$THREADS --links=100 --renumber --ngen=1000 $SPECIES.scaff.bed $ASSEMBLY.fasta

for example, the first command (synteny depth) returns this error:

/mnt/storage/home/tk19812/scratch/software/jcvi/jcvi/compara/synteny.py:10: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
  from collections import Iterable, defaultdict
09:44:47 [blast] Fall back to Python implementation of BlastLine
09:44:47 [synteny] Assuming --qbed=Haoe.bed --sbed=Hmel.bed
09:44:47 [base] Load file `Haoe.bed`
09:44:47 [base] Load file `Hmel.bed`
09:44:47 [base] Load file `Haoe.Hmel.anchors`
Genome Haoe depths:
Depth 0: 12,545 of 22,225 (56.4%)
Depth 1: 9,680 of 22,225 (43.6%)
Genome Hmel depths:
Depth 0: 8,164 of 19,480 (41.9%)
Depth 1: 10,764 of 19,480 (55.3%)
Depth 2: 496 of 19,480 (2.5%)
Depth 3: 46 of 19,480 (0.2%)
Depth 4: 6 of 19,480 (0.0%)
Depth 5: 4 of 19,480 (0.0%)
Traceback (most recent call last):
  File "/mnt/storage/software/languages/anaconda/Anaconda3-2019.03/lib/python3.7/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/mnt/storage/software/languages/anaconda/Anaconda3-2019.03/lib/python3.7/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/mnt/storage/home/tk19812/scratch/software/jcvi/jcvi/compara/synteny.py", line 1550, in <module>
    main()
  File "/mnt/storage/home/tk19812/scratch/software/jcvi/jcvi/compara/synteny.py", line 487, in main
    p.dispatch(globals())
  File "/mnt/storage/home/tk19812/scratch/software/jcvi/jcvi/apps/base.py", line 100, in dispatch
    globals[action](sys.argv[2:])
  File "/mnt/storage/home/tk19812/scratch/software/jcvi/jcvi/compara/synteny.py", line 1350, in depth
    xmax = opts.xmax or max(4, max(dsq.keys() + dss.keys()))
TypeError: unsupported operand type(s) for +: 'dict_keys' and 'dict_keys'

Any help?
Thank you
F

* [compara] Fix py37 regression in synteny.depth() (#160), add tests * [CI] Update .travis.yml to see if osx supports non-generic install * [CI] Update osx generic ENV * [CI] osx tests not triggered

tanghaibao · 2019-09-27T16:37:11Z

@francicco

Thanks for reporting the issue. As I am starting to move the repo to Python 3, we are expecting a number of bugs, and this is one of them. I think I have fixed the issue in 7150682 and have added tests.

Please pull from the repo and see if the issues persist.

Thanks,
Haibao

DieTANG · 2020-01-17T08:34:07Z

Hi, Haibao,
I have the latex errors when I running the test analysis
RuntimeError: Failed to process string with tex because latex could not be found
I installed latex by pip install latex but not working.
I have no sudo authority, and using python3.7, what can I do to fix this bug?
Thanks!

ShawnWx2019 · 2020-03-06T12:44:21Z

Hi Prof. Tang
I have installed MacTex on MacOS, but it still not work, with

20:20:54 [base] savefig failed. Reset usetex to False.
[Errno 2] No such file or directory: 'latex'
---
OSError: [Errno 2] No such file or directory: 'latex'

and the dotplot pdf file was broken. Do you have any suggestion？
Thanks！

tanghaibao · 2020-03-06T15:15:43Z

@DieTANG

You are missing LaTex, which can be installed here.

@ShawnWx2019

Not sure what the problem is but that's what you need. You should be able to run latex --help in your terminal after installation, otherwise, the plotting will not work.

Matplotlib's LaTeX support requires a working LaTeX installation, dvipng (which may be included with your LaTeX installation), and Ghostscript (GPL Ghostscript 9.0 or later is required). The executables for these external dependencies must all be located on your PATH.

Haibao

ShawnWx2019 · 2020-03-06T22:41:08Z

Hi prof. Tang
Thanks for your reply, it is really weird,

First, I tried latex --help, nothing happend, than I completely uninstalled MacTex followed the Uninstalling TeX steps and reinstalled MacTex, the latex --help worked;
Second, I removed the jcvi conda env than reinstalled jcvi with pip:

pip install jcvi

Finally Jcvi worked.
Thank you again.
best wishes.

Qiaojilim · 2020-05-22T02:10:35Z

@francicco
hello, could you give me some hint about how did you solve the latex problem? I meet with the same issue on my mac os system. appreciate it

Lim

ShawnWx2019 · 2020-05-22T02:18:47Z

@francicco
hello, could you give me some hint about how did you solve the latex problem? I meet with the same issue on my mac os system. appreciate it

Lim
I record the solution in：
My blog

Qiaojilim · 2020-05-22T02:50:23Z

@francicco
hello, could you give me some hint about how did you solve the latex problem? I meet with the same issue on my mac os system. appreciate it

Lim
I record the solution in：
My blog

@ShawnWx2019
Thanks a lot, will check that soon. Nice day
:-)

Qiaojilim · 2020-05-22T03:34:38Z

@francicco
hello, could you give me some hint about how did you solve the latex problem? I meet with the same issue on my mac os system. appreciate it
Lim
I record the solution in：
My blog

@ShawnWx2019
Thanks a lot, will check that soon. Nice day
:-)

I just figured out my issue. My sol is to add my executable MacTex to my PATH. Then it works perfectly. Thanks for your reply

ShawnWx2019 · 2020-05-22T07:20:32Z

@francicco
hello, could you give me some hint about how did you solve the latex problem? I meet with the same issue on my mac os system. appreciate it
Lim
I record the solution in：
My blog

@ShawnWx2019
Thanks a lot, will check that soon. Nice day
:-)

I just figured out my issue. My sol is to add my executable MacTex to my PATH. Then it works perfectly. Thanks for your reply

Thanks！

tanghaibao added a commit that referenced this issue Sep 27, 2019

[compara] Fix py37 regression in synteny.depth() (#160), add tests

313aa2a

tanghaibao mentioned this issue Oct 19, 2019

error while running jcvi.compara.catalog ortholog #164

Closed

tanghaibao pinned this issue Jun 9, 2020

ITEliteCCY mentioned this issue Aug 20, 2020

Hi, Haibao, #287

Closed

tanghaibao closed this as completed Oct 27, 2020

tanghaibao unpinned this issue Oct 27, 2020

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Installation problem #160

Installation problem #160

francicco commented Sep 26, 2019

tanghaibao commented Sep 27, 2019

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tanghaibao commented Sep 27, 2019

DieTANG commented Jan 17, 2020

ShawnWx2019 commented Mar 6, 2020

tanghaibao commented Mar 6, 2020 •

edited

ShawnWx2019 commented Mar 6, 2020

Qiaojilim commented May 22, 2020

ShawnWx2019 commented May 22, 2020

Qiaojilim commented May 22, 2020

Qiaojilim commented May 22, 2020

ShawnWx2019 commented May 22, 2020

Installation problem #160

Installation problem #160

Comments

francicco commented Sep 26, 2019

tanghaibao commented Sep 27, 2019

francicco commented Sep 27, 2019

tanghaibao commented Sep 27, 2019

DieTANG commented Jan 17, 2020

ShawnWx2019 commented Mar 6, 2020

tanghaibao commented Mar 6, 2020 • edited

ShawnWx2019 commented Mar 6, 2020

Qiaojilim commented May 22, 2020

ShawnWx2019 commented May 22, 2020

Qiaojilim commented May 22, 2020

Qiaojilim commented May 22, 2020

ShawnWx2019 commented May 22, 2020

tanghaibao commented Mar 6, 2020 •

edited