Closed bioinformatist closed 4 years ago
Hi @bioinformatist
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: CrossICC
Type: Package
Title: An Iteractive Consensus Clustering Framework for Multi-platform Data Analysis
Version: 0.1.0
Description: Unsupervised clustering of high-throughput molecular profiling data is widely adopted for discovering cancer subtypes. However, cancer subtypes derived from a single dataset are not usually applicable across multiple datasets from different platforms. We previously published an iterative clustering algorithm to address the issue (see this paper), but its use was hampered due to lack of implementation. In this work, we presented CrossICC that was an R package implementation of this method. Moreover, many new features were added to improve the performance of the algorithm. Briefly, CrossICC utilizes an iterative strategy to derive the optimal gene set and cluster number from consensus similarity matrix generated by consensus clustering. CrossICC is able to deal with multiple cross platform datasets so that requires no between-dataset normalizations. This package also provides abundant functions to help users visualize the identified subtypes and evaluate the subtyping performance. Specially, many cancer-related analysis methods are embedded to facilitate the clinical translation of the identified cancer subtypes.
Authors@R: as.person(c(
"Yu Sun <sun_yu@mail.nankai.edu.cn> [aut, cre]",
"Qi Zhao <zhaoqi@sysucc.org.cn> [aut]"
))
License: file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: rmarkdown, testthat, knitr
RoxygenNote: 6.1.1
Imports: data.table,
methods,
ConsensusClusterPlus,
limma,
MergeMaid,
cluster,
pheatmap,
shiny,
RColorBrewer,
ggplot2,
shinydashboard,
shinyWidgets,
shinycssloaders,
DT,
ggthemes,
dplyr,
tibble
Depends: R (>= 2.10),
MASS,
Biobase
biocViews: Software
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
Before your package can be reviewed, it must satisfy the Bioconductor vignette guidelines. Please update your package and add a comment here when it satisfies this and all other Bioconductor guidelines.
@mtmorgan Hi, we finished the vignette and it seems all guidelines have been satisfied. Could you help us for further review? Thank you in advance.
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Dear Package contributor,
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Received a valid push; starting a build. Commits are:
0480369 version bumped
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: "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.
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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.
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Hi @bioinformatist ,
Please check this webpage for how to develop Bioconductor packages: https://bioconductor.org/developers/package-guidelines/
Please open the build report here and address all the ERRORS, WARNINGS, NOTES as appropriate. Most of the messages are clear to follow. Let me know if you have any specific questions concerning that.
For the vignette @mtmorgan has mentioned, you should at least add the Installation
section in the beginning (maybe after Introduction
)and sessionInfo()
section in the end. And If appropriate, we strongly encourage a table of contents. Look at this example for reference.
Please (try to) make single fix each time and commit with specific message. Remember to bump version when you feel some error/warnings are fixed so the building machine could catch all your commits with that version bump. Comment back here if you have any questions.
Best, Qian
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Dear Package contributor,
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Dear Package contributor,
This is the automated single package builder at bioconductor.org.
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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.
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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.
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Received a valid push; starting a build. Commits are:
0711f20 Label ssGSEA examples as donttest; some non-used c...
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: "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.
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Received a valid push; starting a build. Commits are:
4390d32 v0.99.10
Dear Package contributor,
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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.
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@Liubuntu Dear Qian, Our package seems can pass all check with no error and only few warning and notes. Could you help me for next step? Thank you in advance.
Yours, Sun
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: "ABNORMAL". 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:
62d26de v0.99.14
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: "ABNORMAL". 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:
b3c0ab0 back to R 3.6; fix import is from methods; v0.99.1...
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
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@mtmorgan @Liubuntu Also no warnings now 😄 Could you tell me what should I do next?
wait for your reviewer to review the package.
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