Closed ulexis99 closed 5 years ago
rargelaguet
commented
5 years ago Definitely looks good, and running the same exact code in my laptop works. Sometimes a problem is that Rstudio needs to be restarted after installing mofapy package. Did you do this?
Also, can you check that the following folder contains entry_point.py?
~/bin/python/envs/env_MOFA/lib/python3.6/site-packages/mofapy/core
ulexis99
commented
5 years ago Thank you for your reply!
First, yes I restarted Rstudio after installing mofapy, because I read a similar suggestion from another thread of Q&A. Also, I installed another R to test if the above code works on it, but I got the same error.
Next, I checked ~/bin/python/envs/env_MOFA/lib/python3.6/site-packages/mofapy/core as you suggested and I found that entry_point.py is there. Please have a look at the following ls result.
I would thank you for any more suggestions!
Gene
~/bin/python/envs/env_MOFA/lib/python3.6/site-packages/mofapy/core$ ls -1 BayesNet.py build_model.py distributions.py entry_point.py init_nodes.py init.py mixed_nodes.py multiview_nodes.py nodes.py nongaussian_nodes.py pycache simulate.py updates.py utils.py variational_nodes.py
ulexis99
commented
5 years ago I think that I've got this issue resolved. I set up another Rstudio in a different cloud platform and I could pass the step that I had stumbled on previously.
However, I have another error when I was running runMOFA. I will create another issue.
dfermin
commented
4 years ago Sorry to revive this issue but I'm having this same error. Restarting R doesn't help. I'm not using RStudio just the command line on RHEL 7.
Here is my check of the python code:
> library(MOFA)
> library(MOFAdata)
> library(reticulate)
> use_condaenv(condaenv="py36", required=TRUE)
> py_config()
python: /home/dfermin/anaconda3/envs/py36/bin/python
libpython: /home/dfermin/anaconda3/envs/py36/lib/libpython3.6m.so
pythonhome: /home/dfermin/anaconda3/envs/py36:/home/dfermin/anaconda3/envs/py36
version: 3.6.7 | packaged by conda-forge | (default, Jul 2 2019, 02:18:42) [GCC 7.3.0]
numpy: /home/dfermin/anaconda3/envs/py36/lib/python3.6/site-packages/numpy
numpy_version: 1.17.0
NOTE: Python version was forced by use_python functionEverything works fine until I try to run MOFA:
MOFAObject <- runMOFA(MOFAObject)
Error in py_get_attr_impl(x, name, silent) :
AttributeError: module 'mofapy' has no attribute 'core.entry_point'Any suggestions what I can do to fix this?
Here is my session info in case it helps:
R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Workstation 7.7 (Maipo)
Matrix products: default
BLAS: /opt/microsoft/ropen/3.5.3/lib64/R/lib/libRblas.so
LAPACK: /opt/microsoft/ropen/3.5.3/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] reticulate_1.12 MOFAdata_1.1.0 MOFA_1.1.1 RevoUtils_11.0.3 nvimcom_0.9-83 RevoUtilsMath_11.0.0
loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.12.0 beeswarm_0.2.3 tidyselect_0.2.5 corrplot_0.84 purrr_0.3.3 reshape2_1.4.3 rhdf5_2.26.2 lattice_0.20-38 colorspace_1.4-1
[10] stats4_3.5.3 rlang_0.4.1 pillar_1.4.2 glue_1.3.1 BiocParallel_1.16.6 BiocGenerics_0.28.0 RColorBrewer_1.1-2 matrixStats_0.54.0 GenomeInfoDbData_1.2.0
[19] foreach_1.5.1 plyr_1.8.4 stringr_1.4.0 zlibbioc_1.28.0 munsell_0.5.0 gtable_0.3.0 codetools_0.2-16 Biobase_2.42.0 IRanges_2.16.0
[28] doParallel_1.0.15 MultiAssayExperiment_1.8.3 GenomeInfoDb_1.18.2 vipor_0.4.5 parallel_3.5.3 Rcpp_1.0.2 scales_1.0.0 DelayedArray_0.8.0 S4Vectors_0.20.1
[37] jsonlite_1.6 XVector_0.22.0 ggplot2_3.2.1 stringi_1.4.3 dplyr_0.8.3 ggrepel_0.8.0 cowplot_0.9.4 GenomicRanges_1.34.0 grid_3.5.3
[46] tools_3.5.3 bitops_1.0-6 magrittr_1.5 RCurl_1.95-4.12 lazyeval_0.2.2 tibble_2.1.3 crayon_1.3.4 pkgconfig_2.0.3 pheatmap_1.0.12
[55] Matrix_1.2-17 ggbeeswarm_0.6.0 assertthat_0.2.1 iterators_1.0.12 Rhdf5lib_1.4.3 R6_2.4.0 compiler_3.5.3Hi Damian,
everything looks good. Are you pointing to the right python executable? Try doing import mofapy in the python terminal that you are pointing to (/home/dfermin/anaconda3/envs/py36/bin/python). If it doesn't work, can you contact me via the Slack channel (link in the README)? We will need an interactive chat to debug this
dfermin
commented
4 years ago Okay I can get it to run with two changes:
First I need to use R 3.6.0
Second I need to use use_python("/home/dfermin/anaconda3/envs/py36/bin/python", required=TRUE).
I'm not sure what's different between the 2 versions of R but things go without a hitch using 3.6
Thanks!
dfermin
commented
4 years ago Okay... Spoke too soon. After exiting out of R and restarting it I get back to the same error:
> py_config()
python: /home/dfermin/anaconda3/envs/py36/bin/python
libpython: /home/dfermin/anaconda3/envs/py36/lib/libpython3.6m.so
pythonhome: /home/dfermin/anaconda3/envs/py36:/home/dfermin/anaconda3/envs/py36
version: 3.6.7 | packaged by conda-forge | (default, Jul 2 2019, 02:18:42) [GCC 7.3.0]
numpy: /home/dfermin/anaconda3/envs/py36/lib/python3.6/site-packages/numpy
numpy_version: 1.17.0
mofapy: /home/dfermin/anaconda3/envs/py36/lib/python3.6/site-packages/mofapy
> MOFAObject <- prepareMOFA(
+ MOFAObject,
+ DataOptions=DataOptions,
+ ModelOptions=ModelOptions,
+ TrainOptions=TrainOptions)
Checking data options...
Checking training options...
Checking model options...
> MOFAObject <- runMOFA(MOFAObject)
[1] "No output file provided, using a temporary file..."
Error in py_get_attr_impl(x, name, silent) :
AttributeError: module 'mofapy' has no attribute 'core.entry_point'Is there anyway to debug this on my end?
Damian
Hi,
I know that someone else already posted a similar issue and got his issue answered by you. I am posting mine because I tried to resolve the issue as suggested, but my attempt was not successful. I appreciate any of your help.
Let me explain what I did.
Computing environment: Linux CentOS 6.3
Python and condaenv: Anaconda was used to install python and create a conda environemnt for the use of mofapy through the R pakcage 'reticulate'. Conda environment was created as follows on the linux command line.
R: R 3.4.3 is run on Rstudio. MOFA, MOFAdata, and reticulate packages are installed. Python is being used as follows. The followings are on the R command.
Then, I try to test MOFA on the CLL data as follows.
Interestingly, when I run import("mofapy"), no errors were returned; thus, mofapy is actually imported. Do you have any idea or comment on the issue that I have?
Thank you!
Gene