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bioFAM / MOFA

Multi-Omics Factor Analysis
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Error in py_call_impl(callable, dots$args, dots$keywords) #24

Closed CarlBrunius closed 5 years ago

CarlBrunius commented 5 years ago

Hi, New to MOFA and super excited to try it out :)

I am installing/running CLL tutorial for the 1st time. Must warn: I speak R pretty OK, but am a total python illiterate.

Installation of python part was nightmarish. Suggest easier installation tutorial (e.g. install pip like this; install python like this with links to such sites). Several error messages during installation. Googled for tips and tricks. Manual tweaks for installing python package dependencies. Added --user flag to most installation steps. Finally, exited installation without error messages

R installation however flawless.

Running thru CLL tutorial: All steps up to and including prepareMOFA() OK

When running MOFAobject <- runMOFA(MOFAobject) I get error message:

Error in py_call_impl(callable, dots$args, dots$keywords) : AttributeError: 'list' object has no attribute 'copy' In addition: Warning message: In if (class(mofa) == "try-error") { :

With traceback:

4.
stop(structure(list(message = "AttributeError: 'list' object has no attribute 'copy'", 
    call = py_call_impl(callable, dots$args, dots$keywords), 
    cppstack = structure(list(file = "", line = -1L, stack = c("1   reticulate.so                       0x000000011fe89f9b _ZN4Rcpp9exceptionC2EPKcb + 219", 
    "2   reticulate.so                       0x000000011fe90a35 _ZN4Rcpp4stopERKNSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEE + 53",  ... 
3.
set_data at entry_point.py#90
2.
mofa_entrypoint$set_data(data = unname(lapply(object@TrainData, 
    function(x) r_to_py(t(x))))) 
1.
runMOFA(MOFAobject)

I guess something not quite right with python installation anyway?

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.2

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] bindrcpp_0.2.2   MOFAtools_0.99.0

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.12.0 reticulate_1.10             beeswarm_0.2.3             
 [4] tidyselect_0.2.5            corrplot_0.84               purrr_0.2.5                
 [7] reshape2_1.4.3              rhdf5_2.26.2                lattice_0.20-38            
[10] colorspace_1.4-0            stats4_3.5.1                yaml_2.2.0                 
[13] rlang_0.3.1                 pillar_1.3.1                glue_1.3.0                 
[16] BiocParallel_1.16.5         BiocGenerics_0.28.0         RColorBrewer_1.1-2         
[19] matrixStats_0.54.0          GenomeInfoDbData_1.2.0      foreach_1.4.4              
[22] bindr_0.1.1                 plyr_1.8.4                  stringr_1.3.1              
[25] zlibbioc_1.28.0             munsell_0.5.0               gtable_0.2.0               
[28] codetools_0.2-16            Biobase_2.42.0              IRanges_2.16.0             
[31] doParallel_1.0.14           MultiAssayExperiment_1.8.1  GenomeInfoDb_1.18.1        
[34] vipor_0.4.5                 parallel_3.5.1              Rcpp_1.0.0                 
[37] scales_1.0.0                DelayedArray_0.8.0          S4Vectors_0.20.1           
[40] jsonlite_1.6                XVector_0.22.0              ggplot2_3.1.0              
[43] stringi_1.2.4               dplyr_0.7.8                 ggrepel_0.8.0              
[46] cowplot_0.9.4               GenomicRanges_1.34.0        grid_3.5.1                 
[49] tools_3.5.1                 bitops_1.0-6                magrittr_1.5               
[52] RCurl_1.95-4.11             lazyeval_0.2.1              tibble_2.0.1               
[55] crayon_1.3.4                pkgconfig_2.0.2             pheatmap_1.0.12            
[58] Matrix_1.2-15               ggbeeswarm_0.6.0            assertthat_0.2.0           
[61] rstudioapi_0.9.0            iterators_1.0.10            Rhdf5lib_1.4.2             
[64] R6_2.3.0                    compiler_3.5.1

Best wishes, Carl

rargelaguet commented 5 years ago

Hi Carl, Thanks for the feedback. I uploaded the python package to pypi so it should be easier to install by pip install mofapy. I will update the README file now. Can you try if it works?

The error is a bug I actually introduced 30min ago. Can you pull the last commit and install again the R package?

Thanks!

CarlBrunius commented 5 years ago

Hi, thx!

Terminal output from PyPI installation:

emp-235-92:~ carlbru$ pip install mofapy
Requirement already satisfied: mofapy in ./Library/Python/2.7/lib/python/site-packages (1.0)
Requirement already satisfied: pandas in ./Library/Python/2.7/lib/python/site-packages (from mofapy) (0.23.4)
Requirement already satisfied: scipy in ./Library/Python/2.7/lib/python/site-packages (from mofapy) (1.2.0)
Requirement already satisfied: numpy in ./Library/Python/2.7/lib/python/site-packages (from mofapy) (1.16.0)
Requirement already satisfied: sklearn in ./Library/Python/2.7/lib/python/site-packages (from mofapy) (0.0)
Requirement already satisfied: argparse in ./Library/Python/2.7/lib/python/site-packages (from mofapy) (1.4.0)
Requirement already satisfied: h5py in ./Library/Python/2.7/lib/python/site-packages (from mofapy) (2.9.0)
Requirement already satisfied: pytz>=2011k in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from pandas->mofapy) (2013.7)
Requirement already satisfied: python-dateutil>=2.5.0 in ./Library/Python/2.7/lib/python/site-packages (from pandas->mofapy) (2.7.5)
Requirement already satisfied: scikit-learn in ./Library/Python/2.7/lib/python/site-packages (from sklearn->mofapy) (0.20.2)
Requirement already satisfied: six in ./Library/Python/2.7/lib/python/site-packages (from h5py->mofapy) (1.12.0)

New pull of MOFA package (MOFAtools_0.99.0)

> devtools::install_github("bioFAM/MOFA", subdir="MOFAtools")
Downloading GitHub repo bioFAM/MOFA@master
Skipping 15 packages ahead of CRAN: Biobase, BiocGenerics, BiocParallel, DelayedArray, GenomeInfoDb, GenomeInfoDbData, GenomicRanges, IRanges, MultiAssayExperiment, rhdf5, Rhdf5lib, S4Vectors, SummarizedExperiment, XVector, zlibbioc
✔  checking for file ‘/private/var/folders/2r/zlfvsylj481_1f153mph_644b3ydvg/T/RtmpZ6a7f3/remotes5943dbf218d/bioFAM-MOFA-b310386/MOFAtools/DESCRIPTION’ ...
─  preparing ‘MOFAtools’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘MOFAtools_0.99.0.tar.gz’ (1.5s)
   Warning: invalid uid value replaced by that for user 'nobody'
   Warning: invalid gid value replaced by that for user 'nobody'

* installing *source* package ‘MOFAtools’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MOFAtools)
> MOFAobject <- runMOFA(MOFAobject)
[1] "No output file provided, using a temporary file..."

    ###########################################################
    ###                 __  __  ___  _____ _                ### 
    ###                |  \/  |/ _ \|  ___/ \               ### 
    ###                | |\/| | | | | |_ / _ \              ### 
    ###                | |  | | |_| |  _/ ___ \             ### 
    ###                |_|  |_|\___/|_|/_/   \_\            ### 
    ###                                                     ###
    ########################################################### 

Loaded view 0 with 200 samples and 310 features...
Loaded view 1 with 200 samples and 4248 features...
Loaded view 2 with 200 samples and 5000 features...
Loaded view 3 with 200 samples and 69 features...

##############################################
## Doing sanity checks and parsing the data ##
##############################################

Error in py_call_impl(callable, dots$args, dots$keywords) : 
  AttributeError: 'list' object has no attribute 'copy' 
4.
stop(structure(list(message = "AttributeError: 'list' object has no attribute 'copy'", 
    call = py_call_impl(callable, dots$args, dots$keywords), 
    cppstack = structure(list(file = "", line = -1L, stack = c("1   reticulate.so                       0x0000000121bb9f9b _ZN4Rcpp9exceptionC2EPKcb + 219", 
    "2   reticulate.so                       0x0000000121bc0a35 _ZN4Rcpp4stopERKNSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEE + 53",  ... 
3.
set_data at entry_point.py#90
2.
mofa_entrypoint$set_data(data = unname(lapply(object@TrainData, 
    function(x) r_to_py(t(x))))) 
1.
rargelaguet commented 5 years ago

Could you re-install the python package from github and try again?

CarlBrunius commented 5 years ago

Let me get back to you in a few hours...

CarlBrunius commented 5 years ago

python installation using pip install git+git://github.com/bioFAM/MOFA --upgrade -> Rolling back uninstall of mofapy

However, with the --user flag -> success :)

carlbru$ pip install git+git://github.com/bioFAM/MOFA --upgrade --user
Collecting git+git://github.com/bioFAM/MOFA
  Cloning git://github.com/bioFAM/MOFA to /private/var/folders/2r/zlfvsylj481_1f153mph_644b3ydvg/T/pip-req-build-6KatHF
Requirement already satisfied, skipping upgrade: pandas in ./Library/Python/2.7/lib/python/site-packages (from mofapy==1.1) (0.23.4)
Requirement already satisfied, skipping upgrade: scipy in ./Library/Python/2.7/lib/python/site-packages (from mofapy==1.1) (1.2.0)
Requirement already satisfied, skipping upgrade: numpy in ./Library/Python/2.7/lib/python/site-packages (from mofapy==1.1) (1.16.0)
Requirement already satisfied, skipping upgrade: sklearn in ./Library/Python/2.7/lib/python/site-packages (from mofapy==1.1) (0.0)
Requirement already satisfied, skipping upgrade: argparse in ./Library/Python/2.7/lib/python/site-packages (from mofapy==1.1) (1.4.0)
Requirement already satisfied, skipping upgrade: h5py in ./Library/Python/2.7/lib/python/site-packages (from mofapy==1.1) (2.9.0)
Requirement already satisfied, skipping upgrade: pytz>=2011k in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from pandas->mofapy==1.1) (2013.7)
Requirement already satisfied, skipping upgrade: python-dateutil>=2.5.0 in ./Library/Python/2.7/lib/python/site-packages (from pandas->mofapy==1.1) (2.7.5)
Requirement already satisfied, skipping upgrade: scikit-learn in ./Library/Python/2.7/lib/python/site-packages (from sklearn->mofapy==1.1) (0.20.2)
Requirement already satisfied, skipping upgrade: six in ./Library/Python/2.7/lib/python/site-packages (from h5py->mofapy==1.1) (1.12.0)
Installing collected packages: mofapy
  Found existing installation: mofapy 1.0
    Uninstalling mofapy-1.0:
      Successfully uninstalled mofapy-1.0
  Running setup.py install for mofapy ... done
Successfully installed mofapy-1.1

RunMOFA() now seems to work:

...
Iteration 1227: time=0.40 ELBO=-3129248.31, deltaELBO=0.0996, Factors=10
Converged!

###########################################
## Training finished, processing results ##
###########################################
rargelaguet commented 5 years ago

Great, thanks for the confirmation. If you want personalised help on interpreting your model, don't hesitate to reach me via the Slack channel