TaskLogger error - Rmagic

[tallulandrews]

Describe the bug I can install and load Rmagic without errors, and I can import the "magic" python package without errors, but when I try to run the "magic" command I get the following error: Error in py_call_impl(callable, dots$args, dots$keywords) : AttributeError: 'TaskLogger' object has no attribute 'task'

Detailed traceback: File "/software/team218/TA/my_condastuff/anaconda3/envs/magic/lib/python3.8/site-packages/magic_impute-2.0.3-py3.8.egg/magic/magic.py", line 699, in fit_transform with _logger.task("MAGIC"):

System information: Python info: Python 3.8.1 | packaged by conda-forge | (default, Jan 5 2020, 20:58:18) [GCC 7.3.0] on linux magic.version <module 'magic.version' from '/software/team218/TA/my_condastuff/anaconda3/envs/magic/lib/python3.8/site-packages/magic_impute-2.0.3-py3.8.egg/magic/version.py'>

Output of magic.__version__:

If you are running MAGIC in R or Python, please run magic.__version__ and paste the results here.

You can do this with `python -c 'import magic; print(magic.__version__)'`

Output of pd.show_versions(): INSTALLED VERSIONS

commit : None python : 3.8.1.final.0 python-bits : 64 OS : Linux OS-release : 3.10.0-957.1.3.el7.x86_64 machine : x86_64 processor : x86_64 byteorder : little LC_ALL : None LANG : en_GB.utf8 LOCALE : en_GB.UTF-8

pandas : 1.0.0rc0 numpy : 1.18.1 pytz : 2019.3 dateutil : 2.8.1 pip : 19.3.1 setuptools : 45.0.0.post20200113 Cython : None pytest : None hypothesis : None sphinx : None blosc : None feather : None xlsxwriter : None lxml.etree : None html5lib : None pymysql : None psycopg2 : None jinja2 : None IPython : None pandas_datareader: None bs4 : None bottleneck : None fastparquet : None gcsfs : None lxml.etree : None matplotlib : 3.2.0rc1 numexpr : None odfpy : None openpyxl : None pandas_gbq : None pyarrow : None pytables : None pytest : None s3fs : None scipy : 1.4.1 sqlalchemy : None tables : None tabulate : None xarray : None xlrd : None xlwt : None xlsxwriter : None numba : None

``` If you are running MAGIC in R or Python, please run pd.show_versions() and paste the results here. You can do this with `python -c 'import pandas as pd; pd.show_versions()'` ```

Output of sessionInfo(): R version 3.5.3 (2019-03-11) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux

Matrix products: default BLAS: /software/R-3.5.3/lib64/R/lib/libRblas.so LAPACK: /software/R-3.5.3/lib64/R/lib/libRlapack.so

locale: [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=en_GB.utf8 LC_MESSAGES=C [7] LC_PAPER=en_GB.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C

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

other attached packages: [1] Rmagic_2.0.3 Matrix_1.2-17

loaded via a namespace (and not attached): [1] Rcpp_1.0.2 lattice_0.20-38 assertthat_0.2.1 crayon_1.3.4 [5] dplyr_0.8.3 R6_2.4.0 grid_3.5.3 jsonlite_1.6 [9] gtable_0.3.0 magrittr_1.5 scales_1.0.0 ggplot2_3.2.1 [13] pillar_1.4.2 rlang_0.4.0 lazyeval_0.2.2 reticulate_1.12 [17] tools_3.5.3 glue_1.3.1 purrr_0.3.2 munsell_0.5.0 [21] compiler_3.5.3 pkgconfig_2.0.2 colorspace_1.4-1 tidyselect_0.2.5 [25] tibble_2.1.3

``` If you are running MAGIC in R, please run sessionInfo() and paste the results here. You can do this with `R -e 'library(Rmagic); sessionInfo()'` ```

Output of reticulate::py_discover_config(required_module = "magic"):

python: /software/team218/TA/my_condastuff/anaconda3/envs/magic/bin/python libpython: /software/team218/TA/my_condastuff/anaconda3/envs/magic/lib/libpython3.8.so pythonhome: /software/team218/TA/my_condastuff/anaconda3/envs/magic:/software/team218/TA/my_condastuff/anaconda3/envs/magic version: 3.8.1 | packaged by conda-forge | (default, Jan 5 2020, 20:58:18) [GCC 7.3.0] numpy: /software/team218/TA/my_condastuff/anaconda3/envs/magic/lib/python3.8/site-packages/numpy-1.18.1-py3.8-linux-x86_64.egg/numpy numpy_version: 1.18.1 magic: /software/team218/TA/my_condastuff/anaconda3/envs/magic/lib/python3.8/site-packages/magic_impute-2.0.3-py3.8.egg/magic

python versions found: /software/team218/TA/my_condastuff/anaconda3/envs/magic/bin/python /usr/bin/python /usr/bin/python3

``` If you are running MAGIC in R, please run `reticulate::py_discover_config(required_module = "magic")` and paste the results here. You can do this with `R -e 'reticulate::py_discover_config(required_module = "magic")'` ```

Additional context Add any other context about the problem here.

[scottgigante]

It looks like you have the wrong version on tasklogger. Can you please run the following?

python -c 'import magic; print(magic.__version__)'
python -c 'import tasklogger; print(tasklogger.__version__)'

If tasklogger is less than version 1.0.0, you can resolve the issue with

pip install --user --upgrade tasklogger

[tallulandrews]

Thanks I couldn't figure out which package was the one that was out of date, that has resolved the issue.

Best, Tallulah

On Wed, Jan 15, 2020 at 12:53 PM Scott Gigante notifications@github.com wrote:

It looks like you have the wrong version on tasklogger. Can you please run the following?

python -c 'import magic; print(magic.version)' python -c 'import tasklogger; print(tasklogger.version)'

If tasklogger is less than version 1.0.0, you can resolve the issue with

pip install --user --upgrade tasklogger

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[scottgigante]

You're welcome!