csabadaday
commented
3 years ago Hi Mattyboi123,
Ironically, the test module is the one that causes the most problems. :(
Could you tell me if this is from the "stable" version 1.0 or the newest commit? The "stable" version's (gulp) test module crashes on zsh but not on bash. I'd suggest you clone the newest commit and just use it, it should work on all Linux shells.
A simpler way would be to just not run the test script. Chances are, conan works just fine, it is the test script's interactions with Linux that fail.
Let me know if this helped and sorry for the inconvenience.
Csaba
Mattyboi123
Hello, I have just installed conan on a linux-breathing machine and ran the test.py script from the terminal. It found gromacs, mencoder and gnuplot OK (after I installed them) but seems not to find any of the .dat files (although they are present) subsequently it fails to pass the test and suggests that conan will not run at all.
Here is the complete (long) output
Welcome to the CONAN test script. Fingers crossed! Checking for gmx_2019...FOUND Checking for mencoder...FOUND Checking for gnuplot...FOUND This file doesn't exist at all: aggregate/local_interactions.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/local_interactions.dat, file_b: aggregate/local_interactions.dat, errors:-1 This file doesn't exist at all: aggregate/time_mdmat_rmsd.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/time_mdmat_rmsd.dat, file_b: aggregate/time_mdmat_rmsd.dat, errors:-1 This file doesn't exist at all: aggregate/timeline.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/timeline.dat, file_b: aggregate/timeline.dat, errors:-1 This file doesn't exist at all: aggregate/native_contacts.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/native_contacts.dat, file_b: aggregate/native_contacts.dat, errors:-1 This file doesn't exist at all: aggregate/mdmat_average_rmsf.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/mdmat_average_rmsf.dat, file_b: aggregate/mdmat_average_rmsf.dat, errors:-1 This file doesn't exist at all: matrices/00010.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00010.dat, file_b: matrices/00010.dat, errors:-1 This file doesn't exist at all: matrices/00008.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00008.dat, file_b: matrices/00008.dat, errors:-1 This file doesn't exist at all: matrices/00000.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00000.dat, file_b: matrices/00000.dat, errors:-1 This file doesn't exist at all: matrices/00006.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00006.dat, file_b: matrices/00006.dat, errors:-1 This file doesn't exist at all: matrices/00005.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00005.dat, file_b: matrices/00005.dat, errors:-1 This file doesn't exist at all: matrices/00002.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00002.dat, file_b: matrices/00002.dat, errors:-1 This file doesn't exist at all: matrices/00001.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00001.dat, file_b: matrices/00001.dat, errors:-1 This file doesn't exist at all: matrices/00009.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00009.dat, file_b: matrices/00009.dat, errors:-1 This file doesn't exist at all: matrices/00003.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00003.dat, file_b: matrices/00003.dat, errors:-1 This file doesn't exist at all: matrices/00007.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00007.dat, file_b: matrices/00007.dat, errors:-1 This file doesn't exist at all: matrices/00004.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00004.dat, file_b: matrices/00004.dat, errors:-1 Test 1: I/O, Result: FAILED Removing files from old tests... This file doesn't exist at all: aggregate/pearson_data_obs_1.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/pearson_data_obs_1.dat, file_b: aggregate/pearson_data_obs_1.dat, errors:-1 This file doesn't exist at all: aggregate/pearson_map_density.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/pearson_map_density.dat, file_b: aggregate/pearson_map_density.dat, errors:-1 This file doesn't exist at all: aggregate/pearson_data.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/pearson_data.dat, file_b: aggregate/pearson_data.dat, errors:-1 Test 2: Correlation analysis... FAILED This file doesn't exist at all: cluster_trj/rmsd_interframe.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/rmsd_interframe.dat, file_b: cluster_trj/rmsd_interframe.dat, errors:-1 This file doesn't exist at all: cluster_trj/2/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/2/assignment.dat, file_b: cluster_trj/2/assignment.dat, errors:-1 This file doesn't exist at all: cluster_trj/2/cluster1/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/2/cluster1/lifetime.dat, file_b: cluster_trj/2/cluster1/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/2/cluster1/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/2/cluster1/average_map.dat, file_b: cluster_trj/2/cluster1/average_map.dat, errors:-1 This file doesn't exist at all: cluster_trj/2/cluster0/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/2/cluster0/lifetime.dat, file_b: cluster_trj/2/cluster0/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/2/cluster0/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/2/cluster0/average_map.dat, file_b: cluster_trj/2/cluster0/average_map.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/assignment.dat, file_b: cluster_trj/3/assignment.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster1/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster1/lifetime.dat, file_b: cluster_trj/3/cluster1/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster1/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster1/average_map.dat, file_b: cluster_trj/3/cluster1/average_map.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster0/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster0/lifetime.dat, file_b: cluster_trj/3/cluster0/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster0/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster0/average_map.dat, file_b: cluster_trj/3/cluster0/average_map.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster2/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster2/lifetime.dat, file_b: cluster_trj/3/cluster2/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster2/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster2/average_map.dat, file_b: cluster_trj/3/cluster2/average_map.dat, errors:-1 This file doesn't exist at all: cluster_trj/1/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/1/assignment.dat, file_b: cluster_trj/1/assignment.dat, errors:-1 This file doesn't exist at all: cluster_trj/1/cluster0/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/1/cluster0/lifetime.dat, file_b: cluster_trj/1/cluster0/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/1/cluster0/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/1/cluster0/average_map.dat, file_b: cluster_trj/1/cluster0/average_map.dat, errors:-1 Test 3: Framewise cluster analysis.... FAILED This file doesn't exist at all: cluster_res/lifetime/2/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/lifetime/2/assignment.dat, file_b: cluster_res/lifetime/2/assignment.dat, errors:-1 This file doesn't exist at all: cluster_res/lifetime/3/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/lifetime/3/assignment.dat, file_b: cluster_res/lifetime/3/assignment.dat, errors:-1 This file doesn't exist at all: cluster_res/lifetime/1/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/lifetime/1/assignment.dat, file_b: cluster_res/lifetime/1/assignment.dat, errors:-1 This file doesn't exist at all: cluster_res/distance/2/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/distance/2/assignment.dat, file_b: cluster_res/distance/2/assignment.dat, errors:-1 This file doesn't exist at all: cluster_res/distance/3/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/distance/3/assignment.dat, file_b: cluster_res/distance/3/assignment.dat, errors:-1 This file doesn't exist at all: cluster_res/distance/1/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/distance/1/assignment.dat, file_b: cluster_res/distance/1/assignment.dat, errors:-1 Test 4: Residue-wise cluster analysis.... FAILED This file doesn't exist at all: blocking/block_out.txt. This probably means that CONAN could not run at all. file_a: correct_output/blocking/block_out.txt, file_b: blocking/block_out.txt, errors:-1 Test 5: Blocking analysis.... FAILED This file doesn't exist at all: pca/pc.9.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.9.dat, file_b: pca/pc.9.dat, errors:-1 This file doesn't exist at all: pca/pc.10.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.10.dat, file_b: pca/pc.10.dat, errors:-1 This file doesn't exist at all: pca/pca_output.txt. This probably means that CONAN could not run at all. file_a: correct_output/pca/pca_output.txt, file_b: pca/pca_output.txt, errors:-1 This file doesn't exist at all: pca/pc.5.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.5.dat, file_b: pca/pc.5.dat, errors:-1 This file doesn't exist at all: pca/pc.3.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.3.dat, file_b: pca/pc.3.dat, errors:-1 This file doesn't exist at all: pca/pca_projections.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pca_projections.dat, file_b: pca/pca_projections.dat, errors:-1 This file doesn't exist at all: pca/pc.6.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.6.dat, file_b: pca/pc.6.dat, errors:-1 This file doesn't exist at all: pca/pc.8.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.8.dat, file_b: pca/pc.8.dat, errors:-1 This file doesn't exist at all: pca/pc.4.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.4.dat, file_b: pca/pc.4.dat, errors:-1 This file doesn't exist at all: pca/pc.2.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.2.dat, file_b: pca/pc.2.dat, errors:-1 This file doesn't exist at all: pca/pc.1.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.1.dat, file_b: pca/pc.1.dat, errors:-1 This file doesn't exist at all: pca/pc.7.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.7.dat, file_b: pca/pc.7.dat, errors:-1 Test 6: Principal component analysis.... FAILED This file doesn't exist at all: matrices/00005_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00005_dr.prev.dat, file_b: matrices/00005_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00002_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00002_dr.prev.dat, file_b: matrices/00002_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00006_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00006_dr.prev.dat, file_b: matrices/00006_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00010.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00010.dat, file_b: matrices/00010.dat, errors:-1 This file doesn't exist at all: matrices/00001_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00001_dr.init.dat, file_b: matrices/00001_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00001_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00001_dr.prev.dat, file_b: matrices/00001_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00005_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00005_dr.init.dat, file_b: matrices/00005_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00010_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00010_dr.prev.dat, file_b: matrices/00010_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00004_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00004_dr.prev.dat, file_b: matrices/00004_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00004_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00004_dr.init.dat, file_b: matrices/00004_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00008.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00008.dat, file_b: matrices/00008.dat, errors:-1 This file doesn't exist at all: matrices/00009_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00009_dr.prev.dat, file_b: matrices/00009_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00010_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00010_dr.init.dat, file_b: matrices/00010_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00000.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00000.dat, file_b: matrices/00000.dat, errors:-1 This file doesn't exist at all: matrices/00007_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00007_dr.init.dat, file_b: matrices/00007_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00003_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00003_dr.prev.dat, file_b: matrices/00003_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00006.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00006.dat, file_b: matrices/00006.dat, errors:-1 This file doesn't exist at all: matrices/00005.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00005.dat, file_b: matrices/00005.dat, errors:-1 This file doesn't exist at all: matrices/00007_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00007_dr.prev.dat, file_b: matrices/00007_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00002.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00002.dat, file_b: matrices/00002.dat, errors:-1 This file doesn't exist at all: matrices/00001.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00001.dat, file_b: matrices/00001.dat, errors:-1 This file doesn't exist at all: matrices/00009_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00009_dr.init.dat, file_b: matrices/00009_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00006_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00006_dr.init.dat, file_b: matrices/00006_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00008_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00008_dr.init.dat, file_b: matrices/00008_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00008_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00008_dr.prev.dat, file_b: matrices/00008_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00009.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00009.dat, file_b: matrices/00009.dat, errors:-1 This file doesn't exist at all: matrices/00003.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00003.dat, file_b: matrices/00003.dat, errors:-1 This file doesn't exist at all: matrices/00003_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00003_dr.init.dat, file_b: matrices/00003_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00007.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00007.dat, file_b: matrices/00007.dat, errors:-1 This file doesn't exist at all: matrices/00004.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00004.dat, file_b: matrices/00004.dat, errors:-1 This file doesn't exist at all: matrices/00002_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00002_dr.init.dat, file_b: matrices/00002_dr.init.dat, errors:-1 Test 7: Rereading of sparse files.... FAILED This file doesn't exist at all: aggregate/time_mdmat_rmsd.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/time_mdmat_rmsd.dat, file_b: aggregate/time_mdmat_rmsd.dat, errors:-1 This file doesn't exist at all: aggregate/total_interactions.y.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/total_interactions.y.dat, file_b: aggregate/total_interactions.y.dat, errors:-1 This file doesn't exist at all: aggregate/timeline.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/timeline.dat, file_b: aggregate/timeline.dat, errors:-1 This file doesn't exist at all: aggregate/native_contacts.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/native_contacts.dat, file_b: aggregate/native_contacts.dat, errors:-1 This file doesn't exist at all: aggregate/mdmat_average_rmsf.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/mdmat_average_rmsf.dat, file_b: aggregate/mdmat_average_rmsf.dat, errors:-1 This file doesn't exist at all: aggregate/total_interactions.x.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/total_interactions.x.dat, file_b: aggregate/total_interactions.x.dat, errors:-1 This file doesn't exist at all: matrices/00010.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00010.dat, file_b: matrices/00010.dat, errors:-1 This file doesn't exist at all: matrices/00008.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00008.dat, file_b: matrices/00008.dat, errors:-1 This file doesn't exist at all: matrices/00000.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00000.dat, file_b: matrices/00000.dat, errors:-1 This file doesn't exist at all: matrices/00006.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00006.dat, file_b: matrices/00006.dat, errors:-1 This file doesn't exist at all: matrices/00005.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00005.dat, file_b: matrices/00005.dat, errors:-1 This file doesn't exist at all: matrices/00002.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00002.dat, file_b: matrices/00002.dat, errors:-1 This file doesn't exist at all: matrices/00001.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00001.dat, file_b: matrices/00001.dat, errors:-1 This file doesn't exist at all: matrices/00009.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00009.dat, file_b: matrices/00009.dat, errors:-1 This file doesn't exist at all: matrices/00003.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00003.dat, file_b: matrices/00003.dat, errors:-1 This file doesn't exist at all: matrices/00007.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00007.dat, file_b: matrices/00007.dat, errors:-1 This file doesn't exist at all: matrices/00004.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00004.dat, file_b: matrices/00004.dat, errors:-1 Test 8: Asymmetric mode.... FAILED 7 test(s) failed. The output of the failed tests has been preserved. It is possible that the deviations are minor. The failures are in the following folders: 2_Pearson 3_ClusterTraj 4_ClusterRes 5_Blocking 6_PCA 7_Reread 8_Asymmetric