Closed zhewa closed 5 years ago
Hi @zhewa
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: celda
Title: CEllular Latent Dirichlet Allocation
Version: 0.99.8
Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu", role = c("aut", "cre")),
person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
person("Yusuke", "Koga", email="ykoga07@bu.edu", role = c("aut")))
Description: celda leverages Bayesian hierarchical modeling to cluster genes,
cells, or both simultaneously from single cell sequencing data.
Depends:
R (>= 3.5),
SummarizedExperiment
Imports:
plyr,
foreach,
ggplot2,
RColorBrewer,
pheatmap,
grid,
scales,
gtable,
grDevices,
graphics,
matrixStats,
doParallel,
cluster,
digest,
gridExtra,
methods,
reshape2,
MAST,
GenomicRanges,
data.table,
Rcpp,
RcppEigen,
umap,
enrichR
Suggests:
testthat,
knitr,
roxygen2,
rmarkdown,
vcd,
corrplot,
Matrix,
biomaRt,
Rtsne,
covr,
M3DExampleData
LinkingTo: Rcpp, RcppEigen
VignetteBuilder: knitr
License: MIT
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0.9000
BugReports: https://github.com/definitelysean/celda/issues
biocViews: SingleCell, GeneExpression, Clustering, Sequencing, Bayesian
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Received a valid push; starting a build. Commits are:
93b80be update vignette, smaller simulated count matrix, c... 2fee690 Merge branch 'master' of https://github.com/campbi... 38eba10 version bump 9e40cee Merge pull request #72 from zhewa/master update v...
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
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Received a valid push; starting a build. Commits are:
92e3ef2 Merge pull request #62 from zhewa/devel merge mas... f5a4624 Merge branch 'master' of https://github.com/campbi... cef4a55 Merge pull request #69 from zhewa/devel merge mas... a6919cb Updating documentation. Fixes #71 0eaa63d Merging from compbiomed@devel cd3e60e Merge pull request #73 from definitelysean/devel ... 340fa92 update celda vignette b473475 version bump c5b5b6c Merge branch 'master' of https://github.com/campbi... 4082c4e Merge branch 'devel' of https://github.com/campbio... 1028f31 rewind simulateCells doc update. need a function r... d0252c3 fix geneSetEnrich function example error 69dd2cf lower bound for the total number of counts should ... 2ef3c28 fix an edge case where simulated cell has 0 count bf9aff7 rewind removal of ... in celda_C/G/CG f1ff31a Merge pull request #76 from zhewa/master Yusuke's...
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Received a valid push; starting a build. Commits are:
e69e750 temp fix to celda_G 'len' is not long enough to ac... 33b7cbd Merge branch 'master' of https://github.com/campbi... f8074b9 version bump 28e1724 remove library(celda) in geneSetEnrich example 58d2e12 fix testthat error c2c507d Merge pull request #83 from zhewa/master temporar...
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Received a valid push; starting a build. Commits are:
b42f118 reformat geneSetEnrich.R 88531e8 Reformat elbow.R b15c03a reformat matrixSums.R 12d56f3 reformat matrixSums.R file 843b346 reformat data.R. update data filenames 16dba6f Reformat plot_dr ac522b6 Updating diffExp.R and feature_selection.R for for... 1786be5 reformat diffExp.R d1c540a code style reformat initialize_clusters.R file fdf53f5 rename function names in R/initialize_clusters.R 25d7d3d Updating StateHeatmap.R for formatting. 59b64d6 code style reformat R/recursiveSplit.R 4b1d560 reformat R/celdaGridSearch.R 4d9072b Reformatting for model_performance.R 0b3c7f9 Reformat celda_functions.R, celda_heatmap.R 5a6c528 reformat celda_CG.R 1cb4a9e Fix vapply bug in .resampleCounts 6e06967 reformat celda_C.R 5a3007f Fixing missing line in diffExp.R 60acdef Reformatted all_generics.R d2e8abd reformat celda_G.R b26d22a Reformat 9c6ba64 Add periods to hidden functions in semi_pheatmap.R 2c8e7d4 Removal of set.seed statements. One was in a funct... 528aa60 reformat split_clusters.R dbb5ce7 Reformat test-celda-functions.R 990ed18 Merge branch 'reformat' of github.com:definitelyse... 8c8d2cf Updating test-recursiveSplit.R 3913d00 reformat decon.R 3cb4522 reformat test-celda_C.R 282f04c reformat test-celda_CG.R ae35c9b reformat test-celda_G.R cea7089 reformat test-decon.R 1cfdcd7 reformat test-intialize_cluster.R b785cc1 reformat test-matrixSums.R 5e9b618 reformat DecontX-analysis.Rmd 2f4e6c1 reformat celda-analysis.Rmd 51f06ec reformat celda-analysis.Rmd 61565eb Merge branch 'reformat' of https://github.com/Iris... 8253ef9 Merge branch 'reformat' of https://github.com/ykog... fd21661 Merge branch 'reformat' of https://github.com/defi... c6fc5e1 Merge pull request #86 from zhewa/reformat Reform... ca5fb59 review of reformatted files 5838050 update documentation 56c68c7 fix logLikelihood.celda_C/G/CG 25256e1 fix .setSeed 2e877ff fix function/variable names af4c3cb debug reformat 0d9510f Delete DecontX.Rd e945781 Add files via upload 0b4a650 Versioning untracked files ebed9a2 Delete DecontX.Rd 30fa811 update data .rda files acfdc7f incorporate recent changes to master to reformat 2c5d35b comment out some unit tests. only.pos -> onlyPos 62b36c7 version bump 7a24c5e celdaCGSim -> celdaCGSim in data.R dc0ddbb fix variables in unit tests ccc3c72 cores = 4 -> cores = 2 c2ae71e fix unit testx. put Rtsne to imports in DESCRIPTIO... bd39a87 fix unit tests. remove test-lintr.R a144fef fix example bugs 8ce2cf1 gix result is type 'double' vapply bug 863ef5a Merge pull request #100 from zhewa/reformat Refor... 08eb2b0 Merge branch 'master' of https://github.com/campbi... 7837192 reindent b2bf3b3 Merge branch 'master' of https://github.com/campbi... 6008044 Merge branch 'reformat' of github.com:zhewa/celda cfeb0d0 resolve conflict semi_pheatmap.R 0f49a79 update docs 3f6fb45 add lintr integration f7780d1 added inst/NEWS b6cf56a fix lints 9e57cf4 Merge pull request #103 from zhewa/master Complet...
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Received a valid push; starting a build. Commits are:
2fa37b1 delete ./NEWS 8180d2a Merge branch 'master' of https://github.com/campbi... 22ad839 remove pheatmap import 17d62e3 version bump. update NEWS aeb951b fix example in geneSetEnrich d47b038 Merge pull request #104 from zhewa/master Fix Bio...
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Hi @Kayla-Morrell
I think our package celda is now passing the BiocCheck with minimal warning and notes and is ready for your review. The only warning in the latest build report is the use of set.seed
:
* WARNING: Remove set.seed usage in R code
Found in R/ directory functions:
.setSeed()
As mentioned in our previous submission, this is a feature we would like to include in our package. We employed a strategy that "We could allow the user to set the ‘seed’ argument to NULL and then the calls to ‘set.seed()’ will be bypassed with ‘if’ statements." Please let us know if you have any suggestions.
Thank you, Zhe
Hi @zhewa,
We require that set.seed()
not be included inside functions. The user should set the seed outside the function if they choose to do so. Please make the necessary changes.
Best, Kayla
Hi @Kayla-Morrell
Sorry, I think I did not make myself clear. A major reason why we use set.seed()
in our package is we want to maintain reproducibility. The more detailed explanation is here: https://github.com/Bioconductor/Contributions/issues/910#issuecomment-433493355. We would really appreciate it if you can read through it and take a look at the issue from our point of view.
Also, in this comment https://github.com/Bioconductor/Contributions/issues/910#issuecomment-433964386, @dvantwisk already approved our solution to the use of set.seed()
in our package. Is this no longer an option anymore? If not, we might need to re-evaluate our options.
Thank you, Zhe
Received a valid push; starting a build. Commits are:
b04e08a Text labels for clusters in t-SNE plots Adds abil... dab0022 Merge pull request #95 from definitelysean/devel ... 372b08f Merge branch 'master' of https://github.com/campbi... dcb0ea7 resolve conflict in plot_dr.R 518ac77 Merge pull request #96 from zhewa/devel Devel 977ae3a fix division by 0 error in fastNormProp 57b334d stop if division by 0 f3f1710 Merge branch 'master' of https://github.com/campbi... ad22169 Merge pull request #108 from zhewa/devel Merge re... 27fcd64 fix lints de558ee Merge branch 'devel' of https://github.com/campbio... ba5d4d5 fix remaining lints 5a9d62b version bump 2d29e04 Merge pull request #109 from zhewa/master Fix lin...
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On one or more platforms, the build results were: "TIMEOUT, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
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Dear Package contributor,
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Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "TIMEOUT, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
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Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
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Hi @zhewa,
I have read over the previous discussion and understand your concerns. However, after talking over this issue with @mtmorgan and my other colleagues, the set.seed()
feature you have within your function is not acceptable. Please make the necessary changes.
Best, Kayla
Received a valid push; starting a build. Commits are:
75664a2 remove seed & .setSeed 501d7a5 comment out unused codes 440164f update documentation 464b785 update vignette to explicitly ask for set.seed for... f031bb7 ) fc0f302 fix division by 0 error b677736 remove setting seeds in test 3134ca6 remove LogLikelihood test in celda_G e22fd7a remove featureModuleTable unit test ba036d3 version bump 2ce539e Merge pull request #118 from zhewa/master remove ...
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Hi @Kayla-Morrell
Thank you for taking the time to read over the previous discussion. We gave some more thoughts about the use of set.seed()
and decided to remove them from our package. Please let us know if any more changes are needed.
Thank you
Received a valid push; starting a build. Commits are:
92ca710 sapply -> vapply d5d2c47 Merge branch 'master' of https://github.com/campbi... d45035a version bump 131939b Merge pull request #123 from zhewa/master sapply ...
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This is a re-submission of the package celda. The original submission is here: #910