Kayla-Morrell
commented
4 years ago Hello @selcenari - Thank you for making the necessary changes. I have some additional notes before accepting the package. Please see them below.
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[ ] REQUIRED: For the NEWS file, thank you for changing to the correct file format. However, the information in the file is not formatted correctly so when I render the NEWS file nothing is shown. Please see https://bioconductor.org/developers/package-guidelines/#news for proper formatting.
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[ ] REQUIRED: In the basic_usage vignette, lines 77-82, 88-92, and 100-103 need to be shown to the user (echo = TRUE) or else the user won't be able to reproduce what you have done in lines 111-117.
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[ ] REQUIRED: We have our build systems set up in a specific way, as you can see in the details of the build report. This does not include using --no-build-vignettes. We need as much code as possible to be eval = TRUE to insure vignettes are working properly. The major offender of this is the mirtarbase_example vignette as much of this code is set to eval = FALSE. Upon further investigation of the code in the vignette I may have a potential solution to help speed up the build of this vignette. Starting at line 175,
system.time(TCGA_E9_A1N5_mirnagene %>%
priming_graph(competing_count = gene_expression, miRNA_count = total_read))
user system elapsed
3.009 0.410 3.459This part of the function only about 3.5 seconds to run.
> system.time(TCGA_E9_A1N5_mirnagene %>%
priming_graph(competing_count = gene_expression, miRNA_count = total_read) %>%
update_how(node_name = "HIST1H3H", how = 30))
user system elapsed
3.232 0.605 3.874Adding the next part of the code only adds about 0.4 of a second. Then the lengthy part of the code...
> system.time(TCGA_E9_A1N5_mirnagene %>%
priming_graph(competing_count = gene_expression, miRNA_count = total_read) %>%
update_how(node_name = "HIST1H3H", how = 30) %>%
simulate(20))
user system elapsed
95.245 10.596 107.258Every time you call this simulate() function you are adding about 103 seconds (or almost 2 minutes) of run time. Then in lines 189-193 you repeat the same code. So my thought was to save this chunk of code to a variable so you only do the calculation once, like so:
> tst <- TCGA_E9_A1N5_mirnagene %>%
priming_graph(competing_count = gene_expression, miRNA_count = total_read) %>%
update_how(node_name = "HIST1H3H", how = 30) %>%
simulate(20)
Warning message:
In priming_graph(., competing_count = gene_expression, miRNA_count = total_read) :
First column is processed as competing and the second as miRNA.
> tst %>% find_iteration(plot=TRUE)
> system.time(tst %>% find_iteration(plot=TRUE))
user system elapsed
15.815 0.381 16.402I would suggest avoid repeating the same code over and over, especially if it takes time to run. Try simplifying code where you can and it may save you some time in the build step (this can be used in any of the vignettes to help speed up the build time as much as possible).
Let me know if you need clarification in any way.
Best, Kayla
bioc-issue-bot
selcenari
mtmorgan
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