Open hks5august opened 2 months ago
Hi @hks5august
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: CPSM
Type: Package
Title: CPSM: Cancer patient survival model
Version: 0.99.0
Authors@R: c(person("Harpreet", "Kaur", email = "hks04180@gmail.com",
role = c("aut", "cre"),
comment = c(ORCID = "0000-0003-0421-8341")),
person("Pijush", "Das", email = "topijush@gmail.com",
role = c("aut")),
person("Uma", "Shankavaram" , email = "uma@mail.nih.gov",
role = c("aut")))
Description: The CPSM package provides a comprehensive computational pipeline
for predicting the survival probability of cancer patients. It
offers a series of steps including data processing, splitting
data into training and test subsets, and normalization of data.
The package enables the selection of significant features based on
univariate survival analysis and generates a LASSO prognostic
index score. It supports the development of predictive models for
survival probability using various features and provides
visualization tools to draw survival curves based on predicted
survival probabilities. Additionally, SPM includes functionalities
for generating bar plots that depict the predicted mean and median
survival times of patients, making it a versatile tool for
survival analysis in cancer research.
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Imports:
SummarizedExperiment,
grDevices,
Rcpp ,
MASS ,
dplyr ,
reshape2 ,
survival ,
survminer ,
ggplot2 ,
MTLR ,
SurvMetrics ,
pec ,
glmnet ,
ggfortify ,
rms ,
preprocessCore ,
survivalROC ,
ROCR ,
Hmisc ,
Matrix ,
svglite,
stats,
utils
Suggests:
knitr,
rmarkdown,
testthat (>= 3.0.0)
URL: https://github.com/hks5august/CPSM/
BugReports: https://github.com/hks5august/CPSM/issues
VignetteBuilder: knitr
Config/testthat/edition: 3
biocViews: GeneExpression, Normalization
Please don't use the export pattern to export all functions. Please list exported function explicitly and avoid exporting internal/helper functions. Please also rename the vignette file to something more distinct. (Likely the name of the package) to avoid naming conflicts with other loaded packages. Currently without specifying your package the mixOmics vignette would open instead
> library(CPSM)
> vignette("vignette")
starting httpd help server ... done
Warning message:
vignette 'vignette' found more than once,
using the one found in '/home/lorikern/R-Libraries/R4.4-Bioc3.20/mixOmics/doc'
There is a error in the tests
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(SurvPredPipe)
Error in library(SurvPredPipe) :
there is no package called 'SurvPredPipe'
SurvPredPipe does not appear to be on CRAN or Bioconductor and cannot be used in your package. All dependencies must be on CRAN or Bioconductor. I see you import SummarizedExperiment but currently don't see it utilized. Given the data is samples and features with expression values, it seems appropriate that your functions should work with a SummarizedExperiment and that this should be shown in perhaps a secondary vignette rather than utilizing data.frames.
may we expect updates soon?
Thank you for reaching out to me. Yes, I am working on it. Hopefully, soon everything will works fine.
On Tue, Sep 24, 2024 at 1:42 PM lshep @.***> wrote:
may we expect updates soon?
— Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/3518#issuecomment-2371920647, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALEXFF7ZELN5XTURZUJ7ZJLZYGQA7AVCNFSM6AAAAABMU4HKZ6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNZRHEZDANRUG4 . You are receiving this because you were mentioned.Message ID: @.***>
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