(inactive) ceRNAmiRNAfun

JohnMengChun commented 6 years ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Repository: https://github.com/JohnMengChun/ceRNAmiRNAfun

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bioc-issue-bot commented 6 years ago

Hi @JohnMengChun

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: ceRNAmiRNAfun
Type: Package
Title: A pakage of creating an algorithm of identifying microRNA-competing endogenous RNA triplets.
Version: 0.99.0
Author: c(
    person("Lin", "Wang", email = "judy79802002@gmail.com", role = c("cre", "aut")),
        person("Tzu-Pin", "Lu", email = "tplu@ntu.edu.tw", role = c("aut")),
        person("Meng-Chun.", "Wu", email ="r06849011@ntu.edu.tw", role = c("aut")))
Maintainer: Lin Wang <judy79802002@gmail.com>
        Tzu-Pin Lu <tplu@ntu.edu.tw>
        Meng-Chun Wu <r06849011@ntu.edu.tw>
Description: This alogorithm is used to identify the microRNA-competing endogenous RNA triplets, based on the random walk concept and sliding windows algorithm.
License: GPL-2
URL:
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
Imports:foreach,DNAcopy,mvtnorm,gridExtra,clusterGeneration,quantmod,psych,data.table,Rcpp,ggplot2,doParallel,rlang,stats,xts
Suggests: knitr
Depends: R (>= 3.4.4)
RoxygenNote: 6.1.0

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mtmorgan commented 6 years ago

There is no vignette with evaluated code chunks. This is required for all Bioconductor packages.

JohnMengChun commented 6 years ago

@mtmorgan Dear Mr.Morgan: Thank you for your comment, I will soon add the vignette to the package. How can I let you know when I finish new updating for your new checking?

thanks

mtmorgan commented 6 years ago

To let me know, post a comment just like the one above.

JohnMengChun commented 6 years ago

@mtmorgan Dear Mr.Morgan: Sorry for letting you wait so long. I have updated the vignette of my package, please give me any comments if there is a problem of that, thank you

mtmorgan commented 6 years ago

Hmm, most of the chunks are eval=FALSE, which defeats the purpose of the vignette; you reference paths on your own disk so obviously not portable.

JohnMengChun commented 6 years ago

@mtmorgan I see. But I have no idea how I can get the data reading protable? To assign the link to the github? Is it possible to give me the examples because I couldn't find it in the R packages file. thank you.

mtmorgan commented 6 years ago

Usually vignettes use small sample data sets that are distributed with the package in a folder /inst/extdata/... and the files are referenced in the vignette with system.file(package="<pkg>", "extdata", "..."). If the files are large (this is usually not necessary, the vignette is demonstrating functionality not performing a full analysis) then they can be included via a separate 'experiment data' package or in experiment hub. Try the first solution (data included in the package) first.

JohnMengChun commented 6 years ago

@mtmorgan thank you for the reply, I will give it a try.

JohnMengChun commented 6 years ago

@mtmorgan I have uploaded the new one version of vignette. Please check it. Thank you.

bioc-issue-bot commented 6 years ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

mtmorgan commented 6 years ago

@Kayla-Morrell I'll review this package...

bioc-issue-bot commented 6 years ago

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.

JohnMengChun commented 6 years ago

@mtmorgan I renamed my vignette, hope it would work, can you check my package again? Thank you

mtmorgan commented 6 years ago

Do you have the 'web hook' active? Did you bump the version of your package (to 0.99.1) to trigger an automatic build?

bioc-issue-bot commented 6 years ago

Received a valid push; starting a build. Commits are:

78fda36 Update DESCRIPTION

bioc-issue-bot commented 6 years ago

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.

JohnMengChun commented 5 years ago

@mtmorgan I think I bumped the version of my package to 0.99.1 to trigger an automatic build And oncemore, how can I deal with the problem of invalid UTF-8 encoding ? It is pretty annoying since my laptop is under window10 system.

mtmorgan commented 5 years ago

The version needs to be bumped (0.99.2, 0.99.3, ...) each time a change is pushed to the repository.

The problem in your vignette is that you have used non-ASCII characters to represent special symbols. I did

> tools::showNonASCIIfile("introduction_to_ceRNAmiRNAfun.Rmd")
87: pairinformation<e3><80><80><e3><80><80>miRNA<e3><80><80><e3><80><80>genelist
88: Row1<e3><80><80><e3><80><80><e3><80><80><e3><80><80><e3><80><80><e3><80><80><e3><80><80><e3><80><80><e3><80><80>A      <e3><80><80>geneA1,geneA2<e2><80><a6>
89: Row2<e3><80><80><e3><80><80><e3><80><80><e3><80><80><e3><80><80><e3><80><80><e3><80><80><e3><80><80><e3><80><80>B      <e3><80><80>geneB1,geneB2<e2><80><a6>
90: Row3<e3><80><80><e3><80><80><e3><80><80><e3><80><80><e3><80><80><e3><80><80><e3><80><80><e3><80><80><e3><80><80>C      <e3><80><80>geneC1,geneC2
97: <e3><80><80>        miRNA
98: Row1<e3><80><80><e3><80><80><e3><80><80>A
99: Row2<e3><80><80><e3><80><80><e3><80><80>B
100: Row3<e3><80><80><e3><80><80><e3><80><80>C
110: To demonstrate the usage of the ceRNAmiRNAfun package, the package contains 475 paired miRNA and gene lung cancer samples. As for dictionary data, there are 137 paired miRNA and corresponding gene data in a list form, and miRNA_total data has the first column of the dictionary data of the miRNA<e2><80><99>s names.

all of those <e2><80><99> and similar are problematic. I see: '...' printed as a single character, maybe you want to use three separate '.'; use of a 'fancy' apostrophe, rather than a plain apostrophe in miRNA's, use of a M-width space ' ' rather than a plain space. I guess each of these are examples of whatever editor you are using trying to be 'helpful' and make your text look 'pretty' or 'smart'; the solution is to turn off these features of your editor, or to use an editor that does not try to be helpful in this way, or to override the suggestions that the editor makes.

mtmorgan commented 5 years ago

Oops, pressed the wrong button...

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

2ea7c7f Update DESCRIPTION

JohnMengChun commented 5 years ago

@mtmorgan thank you for the reply, I have corrected the encoding part, and also updated the version of the description. please let me know if there is any problem

bioc-issue-bot commented 5 years ago

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, 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.

mtmorgan commented 5 years ago

The current problem in the DESCRIPTION file is that the field is called Authors@R, not Author@R. With the Authors@R field set, you do not need the Maintainer: field.

Also remember that the 'best practice' is to build and check your package locally, before pushing the commit and waiting to see errors in our build system

R CMD build ceRNAmiRNAfun
R CMD check ceRNAmiRNAfun_0.99.2.tar.gz

or similar, e.g., within R, devtools::check("ceRNAmiRNAfun")

JohnMengChun commented 5 years ago

@mtmorgan I think I have already uploaded the new file, please check it. And furthermore, I have some questions I don't understand in my R CMD check 1.I would like to know where are the "codoc" and "documentation" that I can check my data. The warnings are as followed:

checking for code/documentation mismatches ... WARNING Data codoc mismatches from documentation object 'gene_sam': Variables in data frame 'gene_sam'

2.Are we necessary to use the Rtools to build a package? Because I followed the website installation, but I still got the same warnings.

The warning is as followed: WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/

Please give me some hints, thank you

mtmorgan commented 5 years ago

The 'VERSION BUMP REQUIRED' tag indicates that you pushed changes, but did not increment the version of your package in the DESCRIPTION file, to 0.99.3. If you want to build your package before checking (recommended), then yes, you need Rtools installed. You can also check the package without building, but that will result in misleading warnings.

'codoc' is trying to say that your code defines a function or object in one way, but the documentation is different, i.e., a 'code / documentation' mismatch. When the warning mentions documentation object 'gene_sam', it means that the problem is in the man/gene_sam.Rd file. Instructions for documenting data objects are found in Writing R Extensions https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Documenting-data-sets .

mtmorgan commented 5 years ago

The 'version bump required' tag has been present for 21 days; do you plan to update your package?

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

7329152 Update DESCRIPTION

JohnMengChun commented 5 years ago

@mtmorgan Sorry I was a little busy last two weeks and still had some error message I didn't know how to solve in my package check. I already bumped a new version of my description, please check it. But there are still some warnings in my check, I will do that within this week. Sorry to bother you so far.

bioc-issue-bot commented 5 years ago

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, 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.

mtmorgan commented 5 years ago

Will you be updating your package to pass the checks, or shall we mark this issue as 'inactive'?

JohnMengChun commented 5 years ago

@mtmorgan Sorry for the late update I want to update the package, but I was stuck by the errors I had The one of them was the Rtools installation.

I used install.packages("Rtools") in R version 3.5.1 but it didn't work as the following error occurred: Warning in install.packages : package ‘Rtools’ is not available (for R version 3.5.1)

How can I fix it to finish my procedure of building packages

Thank you

mtmorgan commented 5 years ago

Rtools is not an R package. It is software required to compile R software. See https://cran.r-project.org/bin/windows/Rtools/ .

JohnMengChun commented 5 years ago

＠mtmorgan 1.Thank you for your reply, I installed Rtools from the website for several times before, and also check it really exists in my R directory, but still cannot work The following message still exists: WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding: https://cran.rstudio.com/bin/windows/Rtools/

Is it possible for another problem to occur even if Rtools indeed in the directory?

another similar problem is I exactly put 2 of my png files under the folder inst but the following message still exists: Files in the 'vignettes' directory but no files in 'inst/doc': 'pics/plotp.png', 'pics/workflow_ceRNAmiRNAfun.png'

I tried some solutions on the website, but it didn't work :https://stackoverflow.com/questions/42670800/r-check-warning-files-in-the-vignettes-directory-but-no-files-in-inst-doc

Can you give me some hints?

I used Win10, version3.5.1 Rstudio to compile I was stuck here and couldn't find the solutions for a while.

Thank you so much for the reply.

mtmorgan commented 5 years ago

Rtools needs to be installed on the system PATH, so your Rtools is not installed correctly. But to back up, why are you trying to install Rtools, which is typically required to only to install packages that have compiled (C or Fortran) code?

JohnMengChun commented 5 years ago

@mtmorgan you mean Rtools is not necessary in my case?(I don't use C or Fortune in my command) because the error message shows up below the checking result every time when I test the package

mtmorgan commented 5 years ago

I see, I reviewed the comment history here. Yes you want to install Rtools to build and check your package. So the problem is that Rtools is not installed correctly. You should install Rtools in a path WITHOUT spaces. When you install Rtools it asks you if you want to add the tools to your system PATH. You should answer Yes, but then also confirm after installation that the PATH (it is a Windows system environment variable) is set correctly; one way to do this is to ensure that in a new DOS or PowerShell terminal the command gcc --version returns correctly.

JohnMengChun commented 5 years ago

@mtmorgan Thank you for you comments, but it still failed I did what you said(in a no-spaced path and answer yes) and tried installing all different combinations of Rtools installation, but it still couldn't find my path I am just wondering if it is a problem with devtools based on this (https://github.com/r-lib/devtools/issues/1772) because I got the error when I ran a command devtools::find_rtools()

And one more thing , I hope to know how to deal with the problem as well, also the problem I cannot figure out where the problem is.

I exactly put 2 of my png files under the folder inst but the following message still exists: Files in the 'vignettes' directory but no files in 'inst/doc': 'pics/plotp.png', 'pics/workflow_ceRNAmiRNAfun.png' I tried some solutions on the website, but it didn't work :https://stackoverflow.com/questions/42670800/r-check-warning-files-in-the-vignettes-directory-but-no-files-in-inst-doc

mtmorgan commented 5 years ago

Build and install packages from the command line rather than using devtools. In this way problems with devtools are avoided.

Commit your most recent changes and trigger a build; I will provide detailed comments from that.

JohnMengChun commented 5 years ago

@mtmorgan ok, I am doing my best and will upload a new version in these two days, thank you

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

fe04b59 Update DESCRIPTION

bioc-issue-bot commented 5 years ago

Received a valid push; starting a build. Commits are:

dc3e717 Update DESCRIPTION

bioc-issue-bot commented 5 years ago

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, 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.

bioc-issue-bot commented 5 years ago

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, 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.

mtmorgan commented 5 years ago

It looks like you're still struggling to get this package in order. I suggest we close this issue so that you can work on it independently. When you are ready, let me know and we will re-open and review it.

JohnMengChun commented 5 years ago

@mtmorgan Dear mtmorgan: I want to reupload my package here, what should I do to eliminate the inactive label?

Please let me know, thanks

mtmorgan commented 5 years ago

Please make sure the web hook is still in place, and increment the version of your package to trigger a new build.

JohnMengChun commented 5 years ago

Ok, thank you, I will upload it in recent days By the way, is that any quick way to delete some of the folders of old version folder? what I know so far is only delete file by file, which takes some time

mtmorgan commented 5 years ago

I don't understand your question, maybe you could show what you are doing now that takes some time.

JohnMengChun commented 5 years ago

Uh..It's a little difficult to show.. Roughly speaking, in my package ceRNAmiRNAfun, I have 8 folders, but when I want to delete the whole folder, I should go into the folder and delete the file, rather than the whole folder. Is it possible to accelerate the procedure?

Bioconductor / Contributions

(inactive) ceRNAmiRNAfun #875