SurfR - Githubissues

auroramaurizio commented 1 year ago

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ococrook commented 11 months ago

Hi @auroramaurizio

Did you recieved and respond to a review from Peter? I cant see anything explicit above but dont want to make you do work you have already done? In the meantime. The package is welll put together and like the vignette

[ ] It worth stating the R dependency
[ ] Is the uncommented code needed? Usually best to delete this to avoid confusion
[ ] Really worth having a comphrehensive .readme so that that someone can understand if they are interested in the package before loading it? What does tha package do exactly.

Thanks, Olly

auroramaurizio commented 11 months ago

Hi @ococrook, I haven't received a package review yet. Thank you for your advice. I will address the points you mentioned and get back to you!

Best, Aurora

bioc-issue-bot commented 11 months ago

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bioc-issue-bot commented 11 months ago

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The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): SurfR_0.99.17.tar.gz

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auroramaurizio commented 11 months ago

Dear @ococrook, I bumped the new package version addressing your points, in particular, I:

cleaned the code, removing commented lines
added the README.md
stated the R dependency in the README.md

Thank you, let me know how it looks now! Aurora

ococrook commented 11 months ago

Thanks Aurura, trying to make may way through the package but I get stuck in the vignette

> # Download metadata from GEO
> mGSE121810 <- GEOmetadata(GSE = "GSE121810")

Warning: cannot open file 'GSE121810_series_matrix.txt.gz': No such file or directoryError in file(file, "rt") : cannot open the connection

Some comments on the R code:

[ ] You have some contructions like 5:N, we generally recommend using something like seq_along, seq_int etc.
[ ] Still examples of code with comments that are likely to cause confusion: e.g. `grouped <- exploded %>%

dplyr::group_by(GeneID) %>%

dplyr::summarise(temp = toString(term)) %>%

dplyr::ungroup()

group_by(GeneID) %>% summarise(temp = toString(term)) %>% ungroup()`
[ ] Is this sequence going backwards? as.factor(dim(pathways.dataframe)[1]:1) Im a bit confused as to what this coded is intneded to do.
[ ] Try to be consistent with white spaces, espcially after columns or operations
[ ] I'm not sure whats happening here, did you redefine log and then use the base log again? `log <- sort(list.files("log/", pattern = "*.xlsx"))

---- surfy database versioning ----

if (!Surfy_version %in% c("log", "new")) { stop("The specified database version is not available. \n Choose between log or new") }

if (length(log)>0 & Surfy_version == "log") { ST <- read.xlsx(xlsxFile = paste0(".log/", log[length(log)]), startRow = 1) }`
[ ] I would stick with <- for assignment note sure why you switch to using = for some functions?
[ ] I usually don't advise to use as.factor and suggest to convert to a factor more explicity with factor specificying the levels you expect
[ ] You have lots of imports in the description are these necessary?

I think the R code in general could be cleaned up but I'm very happy with the documentation and vignette (once I can getting working)

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auroramaurizio commented 11 months ago

Thank you @ococrook for your careful code revision.

I'm sorry to hear that you are having problems in the vignette with the GEOmetadata function. Most probably you are facing the Rhdf5lib Mac Iconway builder issue reported here https://github.com/Bioconductor/BBS/issues/245#issuecomment-1721605029. hpages clearly defines the problem and the steps to solve it. This issue is also the reason why SurfR fails the Mac check on the Iconway buidler but i.e. runs successfully on our Mac laptops https://github.com/Bioconductor/Contributions/issues/3105#issuecomment-1713954422. Hope you'll manage to fix it!
All the functions should be cleared from code commented lines now.
I removed the line "as.factor(dim(pathways.dataframe)[1]:1)" from the "Enrichment_barplot" function. It wasn't used.
I spotted some instances like 1:... where seq_len(), seq_along(), etc. would fit better and used these constructs.
In the Gene2SProtein function we allow the user to select the version of the Surfy data frame he wishes to use. In other words, to decide if he wants to use an xlsx table already downloaded from Surfy's URL or to download it again, choosing between "log" and "newest" Surfy_version. The line "log <- sort(list.files("log/", pattern = "*.xlsx"))" screens the ".log/" directory and lists in "log" all the xlsx files present in the directory in the variable "log". To avoid confusion I renamed the variable log as log_list.
I improved code styling: commas now always have a space after, spaces are present around infix operators, I always use double quotes, etc.
I stuck with <- for assignments
I replaced as.factor with factor.
I agree there are quite a few imports. The package aims to allow the user to perform an end-to-end protein annotation analysis from data retrieval to DGE, meta-analysis, annotation, plotting, etc., and each of these steps requires dedicated packages

Aurora

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lshep commented 10 months ago

R CMD check

[ ] @auroramaurizio It looks like there were still ERROR in the linux build report unrelated to the one mentioned above on MAC. It may have just been temporary but when I run it manually on the builder


> dbs
[1] "GO_Biological_Process_2021" "WikiPathways_2016"         
[3] "MSigDB_Hallmark_2020"      
>  up_genes <- c("RUNX1", "DLK1", "TOP2A", "EPCAM", "GATA1", "KDR")
dfList[["fdr_up"]] <- enrichR::enrichr(up_genes, dbs)

Must specify at least one of url or handle

dw_genes <- c("CD275", "COL1A1", "COL1A2","LUM", "SOX9") dfList[["fdr_down"]] <- enrichR::enrichr(dw_genes, dbs)

Must specify at least one of url or handle

Enrichment_barplot(dfList, enrich.databases = dbs, p_adj = 0.01, num_term = 5, cond = "UP") Error in Enrichment_barplot(dfList, enrich.databases = dbs, p_adj = 0.01, : Selected Enrich databases not present in your enrichment analysis. In addition: Warning message: In Enrichment_barplot(dfList, enrich.databases = dbs, p_adj = 0.01, : GO_Biological_Process_2021WikiPathways_2016MSigDB_Hallmark_2020not present in your Enrichment analysis. Enrichment_barplot(dfList, enrich.databases = dbs, p_adj = 0.01, num_term = 5, cond = "DOWN") Error in Enrichment_barplot(dfList, enrich.databases = dbs, p_adj = 0.01, : Selected Enrich databases not present in your enrichment analysis. In addition: Warning message: In Enrichment_barplot(dfList, enrich.databases = dbs, p_adj = 0.01, : GO_Biological_Process_2021WikiPathways_2016MSigDB_Hallmark_2020not present in your Enrichment analysis.


**BiocCheck**
- [ ] The R version WARNING should also be corrected;  we can not verify that this will work on such an outdated version of R.  

- [ ] avoiding `cat` and use `message` instead so users that don't want verbose output can suppressMessages. Found in

cat() in R/Enrichment.R (line 66, column 5) cat() in R/Enrichment.R (line 74, column 5) cat() in R/Enrichment.R (line 91, column 5)


- [ ] Please explain why the suppressWarnings are justified

suppressWarnings() in R/Annotate_SPID.R (line 156, column 3) suppressWarnings() in R/SVenn.R (line 41, column 3)

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auroramaurizio commented 10 months ago

Dear @lshep, Thank you for your attention to SurfR package. I'm sorry to hear you got an ERROR on your manual linux build. I can confidently say the ERROR you are facing now is due to a temporary connection problem with the EnrichR database. If it happens I re-run the command after a few minutes (1, 2 minutes) and the connection with EnrichR is re-established. I now added a line in the vignette about this potential temporary issue.

The automatic linux builds and checks on nebbiolo2 of SurfR_0.99.20.tar.gz, but also SurfR_0.99.19.tar.gz, SurfR_0.99.18.tar.gz etc. were all successful. I can assure we also tested it on our linux cluster and 4 different MacOS laptops and it worked well without any errors. If It may be helpful I can send the session info of each.

We tested the package on R versions 4.1 and greater. I now explicitly report all tested versions (4.1, 4.2, and 4.3) in the README. I do not get an Rversion warning, unfortunately, I can not reproduce it.

I replaced cat with message in R/Enrichment.R (line 66, line 74, line 91).

I removed suppressWarnings() in SVenn function, while I kept it in Annotate_SPID. I added a comment above suppressWarnings() in Annotate_SPID to provide context to the user and justify its usage.

Thank you, Aurora

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lshep commented 10 months ago

Unfortunately it seems to be consistently ERRORing. Is there any way to make the package more dependable or able to fail out gracefully if the connection cannot be established.

Because there are data objects R during the build stage will automatically add an R version because of incompatiblity with pervious version saved objects. To fix this ERROR please put the following in the DESCRIPTION R (>= 4.3.0) in the Depends field.

Thank you for the other changes.

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auroramaurizio commented 10 months ago

Dear @lshep, thank you for your advice. I added the Depends field in DESCRIPTION, fixed the issue with the failing function and now the check on the nebbiolo2 linux builder is successful.

Aurora

ococrook commented 9 months ago

Sorry for the delay here, could you add the bioconductor install instruction. Could you also trigger a new build? I would like to see whats happening there more recently.

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SurfR #3105

dplyr::group_by(GeneID) %>%

dplyr::summarise(temp = toString(term)) %>%

dplyr::ungroup()

---- surfy database versioning ----