Closed federicogiorgi closed 7 years ago
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@nturaga I implemented all the changes you suggested.
There is nothing I can do about the single warning, which seems to be on the server side: "Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11)."
Also, 9 lines (0%) are not indented with multiples of 4 spaces, but those are man pages automatically generated by roxygen2.
Hi @federicogiorgi
I'll review your package again soon. But you need to fix a couple of things before that.
Your formatting seems to have disappeared entirely on your R code.
vobj
in vulcan, is a list containing samples, peak counts, and
other data.frames, why not describe the contents of the list in the
man pages.
Please update the man
pages, to be more informative, wherever else needed.
Thanks @nturaga. OK give me some time to manually fix every single line. The tidy_source function from formatR cannot at the same time force line length below 80 columns and transform indentation in multiples of 4 white spaces, for some reason. Ha, I've spent 90% of this package time on formatting indentation, no jokes :-)
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@nturaga I have updated the man pages with extra info and reformatted the indentation of the source code :-) Again, I get this single server-side (I think) warning: "Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11)."
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@nturaga and all: I implemented all the suggested fixes, the package is ready for your inspection :-)
@lshep @mtmorgan @nturaga All the suggested fixes have been fixed a few weeks ago, the package is ready for your inspection :-)
I'll have your second-review done by mid next week.
Any news on the second review? :-)
Consider adding
importFrom("graphics", "abline", "grid", "layout", "legend", "lines",
"par", "plot", "points", "rect", "text")
importFrom("stats", "ks.test", "pchisq", "pnorm", "pt", "qnorm", "qt",
"rnorm", "setNames")
importFrom("utils", "read.csv", "setTxtProgressBar", "txtProgressBar")
Also needed are
importFrom("GenomicRanges", "GRanges")
importFrom("S4Vectors", "Rle")
Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 33 object(s) are initialized. Maybe
they are part of a data set loaded with data(), or perhaps part
of an object referenced in with() or within().
object (function)
Rle (average_fragment_length)
lines (average_fragment_length)
abline (average_fragment_length)
legend (average_fragment_length)
pt (corr2p)
pchisq (fisherp)
qt (p2corr)
qnorm (p2z)
ks.test (pareto.fit)
e2s (plot_gsea)
layout (plot_gsea)
par (plot_gsea)
plot (plot_gsea)
rect (plot_gsea)
abline (plot_gsea)
text (plot_gsea)
grid (plot_gsea)
lines (plot_gsea)
legend (plot_gsea)
qnorm (rea)
plot (textplot2)
points (textplot2)
lines (textplot2)
text (textplot2)
colorpanel (val2col)
GRanges (vulcan.annotate)
read.csv (vulcan.import)
exprs (vulcan.normalize)
setNames (vulcan.pathways)
rnorm (vulcan.pathways)
txtProgressBar (vulcan.pathways)
setTxtProgressBar (vulcan.pathways)
pnorm (z2p)
Many place where you remove objects in the middle of the function eg: rm(rawmat)
vulcan.R, l 67, l, 82.
This is not needed, if you are rewrinting the object, by creating a new matric in l71.
In vulcan.R,
232 ### Fix data types as needed
233 for (j in seq_len(ncol(rawcounts))) {
234 rawcounts[, j] <- as.numeric(rawcounts[, j])
235 }
236 rawcounts <- as.matrix(rawcounts)
237
238 for (j in seq_len(ncol(rpkms))) {
239 rpkms[, j] <- as.numeric(rpkms[, j])
240 }
241 rpkms <- as.matrix(rpkms)
can be replaced with,
rawcounts = matrix(as.numeric(rawcounts), nrow(rawcounts))
rpkms = matrix(as.numeric(rpkms), nrow(rpkms))
dist_calc
in vulcan.R. Lot of repeating code chunks.Received a valid push; starting a build. Commits are:
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@nturaga Thank you for your review! I implemented the suggested changes
@federicogiorgi
Your package times out in the build report because R CMD check takes more than 10 mins on the mac builder. Please fix this issue.
Otherwise, your package looks in good shape for acceptance.
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@nturaga not sure why the R CMD Check times out on the Mac server. It didn't before, and the recent changes I've made to the package were formalities in the code. On our Mac, it takes ~3minutes. Any suggestion?
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