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Reviewer 1 : Package Is Too Big, 73M?

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Answers to comments of Reviewer 1 (CMEA package https://github.com/isarnassiri/CMEA) 1. Package is too big: 73M. That's because it contains big data sets of experimental data. The source tarball of a Bioconductor software package should occupy less than 4MB on disk. Please check our package guidelines (at ) and make sure CMEA satisfies them. One way to reduce the size is to move all the experimental data to a separate data experiment package. Let's call this solution 1. If the data is not too big, another way to reduce the size of the package is to explicitly download the data in the examples or vignette. Let's call this solution 2. Answer: We moved the files of complete experimental data to a separate data experiment package, and used …show more content…

4. None of your functions have arguments. The input they take is unclear. Some of it seems to come from some user defined variables (e.g. number_of_features for Cell_Morphology_Enrichment_Analysis()). But they also seem to take as input some files produced by other functions. This is very poor software design. Besides, none of this is documented. This makes the package barely usable. Answer: The name of functions were revised. We added arguments with comprehensive explanations. All functions return the R objects to the global environment after running them. 5. One consequence of this design is that I can't run the example in the man page of the Ranking_Cell_Morphological_features() function: > library(CMEA) > example(Ranking_Cell_Morphological_features) R_C_M_> { R_C_M_+ data(Transcriptomic_Profile) R_C_M_+ data(Cell_Morphology_Profile) R_C_M_+ TOP=20 R_C_M_+ Ranking_Cell_Morphological_features() R_C_M_+ } Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file '/home/hpages/R/R-3.4.r72630/library/CMEA/TP_subset.txt': No such file or directory That's probably because it requires other things from other examples to run before it. All the examples should work independently. Answer: Revised. All the examples work independently, and return the R objects to the global environment after running them. Some of your functions

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