The enimpute from zhangxf-ccnu

DCA error

Hello,

I'm running into issues with running DCA when it's trying to save the latent representation.
Error in count.imputed.individual[, , k] <- DCA.EnImpute(count, normtype = DCA.normtype, : number of items to replace is not a multiple of replacement length

Thanks

Fail to run with Seurat v3/Magic v2

For a tool depending of many tools it need to be keep updated to be useful.

With Seurat updated to version 3 it fail to run due to deprecated options in 'CreateSeuratObject' part.

Error in Seurat::CreateSeuratObject(count, normalization.method = "LogNormalize") : 
  unused argument (normalization.method = "LogNormalize")`

Magic fail with

Argument k is deprecated. Using knn instead.
Argument alpha is deprecated. Using decay instead.
Error in py_call_impl(callable, dots$args, dots$keywords) : 
  TypeError: __init__() got an unexpected keyword argument 'knn_max'

I can't make it work with dca. This might be me.

library(reticulate)
conda_list(conda = "$APATH/anaconda3/condabin/conda") 
system("conda activate DCA")
use_condaenv(condaenv = "DCA",conda = "$APATH/anaconda3/condabin/conda",required = F)
conda_python(envname = "DCA", conda = "$APATH/anaconda3/condabin/conda")

With system('which dca') I get $APATH/anaconda3/bin/dca

But executing it

$APATH/anaconda3/lib/python3.7/site-packages/tensorflow/python/framework/dtypes.py:516: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint8 = np.dtype([("qint8", np.int8, 1)])
$APATH/anaconda3/lib/python3.7/site-packages/tensorflow/python/framework/dtypes.py:517: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint8 = np.dtype([("quint8", np.uint8, 1)])
$APATH/anaconda3/lib/python3.7/site-packages/tensorflow/python/framework/dtypes.py:518: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint16 = np.dtype([("qint16", np.int16, 1)])
$APATH/anaconda3/lib/python3.7/site-packages/tensorflow/python/framework/dtypes.py:519: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint16 = np.dtype([("quint16", np.uint16, 1)])
$APATH/anaconda3/lib/python3.7/site-packages/tensorflow/python/framework/dtypes.py:520: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint32 = np.dtype([("qint32", np.int32, 1)])
$APATH/anaconda3/lib/python3.7/site-packages/tensorflow/python/framework/dtypes.py:525: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  np_resource = np.dtype([("resource", np.ubyte, 1)])
$APATH/anaconda3/lib/python3.7/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:541: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint8 = np.dtype([("qint8", np.int8, 1)])
$APATH/anaconda3/lib/python3.7/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:542: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint8 = np.dtype([("quint8", np.uint8, 1)])
$APATH/anaconda3/lib/python3.7/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:543: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint16 = np.dtype([("qint16", np.int16, 1)])
$APATH/anaconda3/lib/python3.7/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:544: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint16 = np.dtype([("quint16", np.uint16, 1)])
$APATH/anaconda3/lib/python3.7/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:545: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint32 = np.dtype([("qint32", np.int32, 1)])
$APATH/anaconda3/lib/python3.7/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:550: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  np_resource = np.dtype([("resource", np.ubyte, 1)])
Traceback (most recent call last):
  File "$APATH/anaconda3/bin/dca", line 10, in <module>
    sys.exit(main())
  File "$APATH/anaconda3/lib/python3.7/site-packages/dca/__main__.py", line 147, in main
    from . import train
  File "$APATH/anaconda3/lib/python3.7/site-packages/dca/train.py", line 23, in <module>
    from . import io
  File "$APATH/anaconda3/lib/python3.7/site-packages/dca/io.py", line 24, in <module>
    import scipy as sp
  File "$APATH/anaconda3/lib/python3.7/site-packages/scipy/__init__.py", line 156, in <module>
    from . import fft
  File "$APATH/anaconda3/lib/python3.7/site-packages/scipy/fft/__init__.py", line 81, in <module>
    from ._helper import next_fast_len
  File "$APATH/anaconda3/lib/python3.7/site-packages/scipy/fft/_helper.py", line 4, in <module>
    from . import _pocketfft
  File "$APATH/anaconda3/lib/python3.7/site-packages/scipy/fft/_pocketfft/__init__.py", line 3, in <module>
    from .basic import *
  File "$APATH/anaconda3/lib/python3.7/site-packages/scipy/fft/_pocketfft/basic.py", line 8, in <module>
    from . import pypocketfft as pfft
ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by $APATH/anaconda3/lib/python3.7/site-packages/scipy/fft/_pocketfft/pypocketfft.cpython-37m-x86_64-linux-gnu.so)
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file './DCA_result/result/mean.tsv': No such file or directory

count.imputed.individual[, , k] number of items to replace is not a multiple of replacement length

After making changes in EnImpute, it run properly with the Test data provided by the package. However, I get this error with the real dataset. Any help to resolve this is appreciated.

dca: Saving denoised expression...
dca: Saving latent representations...
/home/subudhak/.local/lib/python3.8/site-packages/tensorflow/python/keras/engine/training.py:2323: UserWarning: `Model.state_updates` will be removed in a future version. This property should not be used in TensorFlow 2.0, as `updates` are applied automatically.
  warnings.warn('`Model.state_updates` will be removed in a future version. '
Error in count.imputed.individual[, , k] <- DCA.EnImpute(count, normtype = DCA.normtype,  : 
  number of items to replace is not a multiple of replacement length
In addition: Warning message:
In asMethod(object) :
  sparse->dense coercion: allocating vector of size 1.9 GiB
Error in fetch(key) : 
  lazy-load database '/home/subudhak/R/x86_64-pc-linux-gnu-library/4.3/EnImpute/help/EnImpute.rdb' is corrupt

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DCA error

Fail to run with Seurat v3/Magic v2

count.imputed.individual[, , k] number of items to replace is not a multiple of replacement length

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