Error in py_call_impl(callable, dots$args, dots$keywords)
CarlBrunius opened this issue · 6 comments
CarlBrunius commented
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
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
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$set_data(data = unname(lapply(object@TrainData,
function(x) r_to_py(t(x)))))
1.
rargelaguet commented
Could you re-install the python package from github and try again?
CarlBrunius commented
Let me get back to you in a few hours...
CarlBrunius commented
python installation using pip install git+git://github.com/bioFAM/MOFA --upgrade -> Rolling back uninstall of mofapy
However, with the --user flag -> success :)
carlbru$ 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
Great, thanks for the confirmation.
If you want personalised help on interpreting your model, don't hesitate to reach me via the Slack channel