bioc-issue-bot
commented
5 years ago Received a valid push; starting a build. Commits are:
1d666c9 Trigger build
Closed ptrebulle closed 5 years ago
bioc-issue-bot
commented
5 years ago Received a valid push; starting a build. Commits are:
1d666c9 Trigger build
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: "TIMEOUT, 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 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: "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.
ptrebulle
commented
5 years ago @Kayla-Morrell I tried to bumped again but the error remains for Linux and MacOS. Windows is working properly.
Kayla-Morrell
commented
5 years ago I was able to get your package build/checked/installed on my local Mac without any errors/warnings. As long as that keeps working I'll be able to accept your package. We have been experiencing some connectivity problems so that's probably the reason why. Just a couple more points/comments...
- [x] REQUIRED: In Data Requirement section, the citation does not render correctly.
- [x] REQUIRED: Under User guide - 4.2 Predict gene state/gene expression level from a condition specific experiment using a linear model, there needs to be a data("iMM904") command or PredictedGeneState() won't execute.
- [x] REQUIRED:Under 4.3 Simulations, the code needs to be executable. The user should be able to copy the corresponding commands into an R session and get the same results. Since the Simulation1 variable is defined in the beginning of your vignette in the 'r setup' chunk of R code. The user does not have this code provided in the vignette so if they were to run the command you provide under 4.3 Simulations, they would get an error Error: object 'Simulation1' not found. (You do however define Simulation1 later on in the vignette - section 4.3.1, so maybe this line of code belongs down with that section.)
Thank you for adding the Simulation() code so that the user can run the vignette, but you need to add metabolites definition so that the code can run.
- [x] SUGGESTION: Under Section 4.4.5 Constraining the model according to gene expression, TF KO or OV, gene KO or OV to run various FBA using sybil, I think this section of code should end with a print out of sol so that the user knows what it looks like (like done in section 4.4).
- [x] REQUIRED: The package "rBayesianOptimization" should be added to the Suggests packages in your DESCRIPTION file.
- [x] CLARIFICATION: We prefer to have all chunks of code to be evaluated. What is the reason to have the code in Section 4.4.5 and Section 4.6 have eval=FALSE?
- [x] REQUIRED: Avoid the use of direct slot access with '@' in the example code. Accessor methods should be created and utilized instead.
R files
- [x] REQUIRED: For data.R, 'SC_EXP_DATA' the '@source' url should not have \url{} around the url. Instead use '<' url '>'.
Right idea with the '<>' but try removing the spaces so that it is <url>.
General Package Development
These notes come from R CMD BiocCheck
- [ ] SUGGESTION:
If possible, use vapply() instead of sapply(). This was found in ODToGenes: [...]
- [x] SUGGESTION:
Avoid using 1:..., use seq_len() or seq_along(). Found in files:
CoregfluxFunctions.R, line 147 FVAFunctions.R, line 36 ODToGenes.R, line 485 ODToGenes.R, line 526
bioc-issue-bot
commented
5 years ago Received a valid push; starting a build. Commits are:
0dd0327 Remove space
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". 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.
ptrebulle
commented
5 years ago Hih @Kayla-Morrell , I changed the last few point you mentionned !
It seems like the connectivity issue has been solved for now but since I turned back some part of the vignette to eval = TRUE in a previous push, the R CMD Check takes more than 5 min on OS X and Windows leading to a warning message. Let me know if it is ok to leave it that way.
bioc-issue-bot
commented
5 years ago Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.
Thank you for contributing to Bioconductor!
mtmorgan
commented
5 years ago The master branch of your GitHub repository has been added to Bioconductor's git repository.
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