Hello,
I have run into a quite strange problem.
I am trying to use scBio::CPM through CATD. This pipeline relies on conda to install and manage packages.
However, the pipeline fails at the CPM() step due to the following error: unused argument (typeTransformation = TRUE).
I checked, the conda package installed is bioconda r-scbio (https://anaconda.org/bioconda/r-scbio), version 0.1.4. From the recipe of this package, it is built using the code from https://github.com/amitfrish/scBio/archive/refs/tags/0.1.4.tar.gz
I checked, in this code the function CPM() does not have the typeTransformation argument.
However, the code at https://github.com/amitfrish/scBio/releases/download/0.1.4/scBio_0.1.4.tar.gz does have the extra CPM typeTransformation argument. In fact, the release notes at https://github.com/amitfrish/scBio/releases/tag/0.1.4 state "We added the option to use cell type predictions transformation into fractions in the case of absolute cell type deconvolution.", but it seems that the archives (https://github.com/amitfrish/scBio/archive/refs/tags/0.1.4.zip and https://github.com/amitfrish/scBio/archive/refs/tags/0.1.4.tar.gz) have not been updated.
Could you please update the archives, so that the code source with tag 0.1.4 is consistent between release and archive?
As a side note, the CRAN version of scBio does have the typeTransformation argument.
Thanks in advance,
Best,
Theo
Hello,
I have run into a quite strange problem.
I am trying to use
scBio::CPMthrough CATD. This pipeline relies on conda to install and manage packages.However, the pipeline fails at the CPM() step due to the following error:
unused argument (typeTransformation = TRUE).I checked, the conda package installed is bioconda
r-scbio(https://anaconda.org/bioconda/r-scbio), version 0.1.4. From the recipe of this package, it is built using the code from https://github.com/amitfrish/scBio/archive/refs/tags/0.1.4.tar.gzI checked, in this code the function
CPM()does not have thetypeTransformationargument.However, the code at https://github.com/amitfrish/scBio/releases/download/0.1.4/scBio_0.1.4.tar.gz does have the extra CPM
typeTransformationargument. In fact, the release notes at https://github.com/amitfrish/scBio/releases/tag/0.1.4 state "We added the option to use cell type predictions transformation into fractions in the case of absolute cell type deconvolution.", but it seems that the archives (https://github.com/amitfrish/scBio/archive/refs/tags/0.1.4.zip and https://github.com/amitfrish/scBio/archive/refs/tags/0.1.4.tar.gz) have not been updated.Could you please update the archives, so that the code source with tag 0.1.4 is consistent between release and archive?
As a side note, the CRAN version of scBio does have the
typeTransformationargument.Thanks in advance,
Best,
Theo