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mitoClone2 #2158

Closed benstory closed 3 years ago

benstory commented 3 years ago

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bioc-issue-bot commented 3 years ago

Hi @benstory

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: mitoClone2
Type: Package
Title: Clonal population identification in single-cell RNA-seq data
        using mitochondrial and somatic mutations
LinkingTo: Rhtslib (>= 1.13.1)
Version: 0.99.0
Authors@R: c( person(given = "Benjamin", family = "Story", role = c("aut", "cre"), email = "story.benjamin@gmail.com"),
       person(given = "Lars", family = "Velten", role = "aut"),
       person(given = "Gregor", family = "Mönke", role = "aut") )
Description: This package primarily identifies variants in mitochondrial genomes from BAM alignment files; filters these variants to remove RNA editing events; estimates their evolutionary relationship (i.e. their phylogenetic tree); groups single cells into clones using a probabilistic approach; visualizes the mutations and provides context in relation to genomic annotations
License: GPLv3
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
biocViews: Annotation, DataImport, Genetics, SNP, Software, SingleCell,
        Alignment
Imports: reshape2, GenomicRanges, pheatmap, deepSNV, grDevices,
        graphics, stats, utils, S4Vectors, Rhtslib, parallel
Suggests: knitr, rmarkdown, Biostrings
RoxygenNote: 7.1.0
SystemRequirements: GNU make, SCITE (optional), PhISCS (optional)
Packaged: 2021-06-20 21:50:22 UTC; story
Depends: R (>= 4.0.0)
NeedsCompilation: yes
bioc-issue-bot commented 3 years ago

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bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/mitoClone2 to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: ba0696d1903162e48472d8637af31fcc6eab7ca9

bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/mitoClone2 to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 5b2ad0a48b077f54f954f7883f9eaf10a570ebac

bioc-issue-bot commented 3 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, 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/mitoClone2 to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 38f81505ccc4024bbb3101fa88a1f8d464506caa

bioc-issue-bot commented 3 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, 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/mitoClone2 to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 9129cc48ffca1aa57ea859ab9614621bbf716450

bioc-issue-bot commented 3 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, 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/mitoClone2 to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 052ec4c77c3d73ab289c6c3d117b5797ff7b55fa

bioc-issue-bot commented 3 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, 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/mitoClone2 to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 2c3f2c613a57cba6da1881a84ea6663925f80db4

bioc-issue-bot commented 3 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, 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/mitoClone2 to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: d4c67af75d0a303ede1b1d9ede465db794e7a763

bioc-issue-bot commented 3 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, 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/mitoClone2 to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

benstory commented 3 years ago

The package builds on the Mac/Linux machines but not the BioC Windows machine. However, it does build successfully on https://win-builder.r-project.org/.

The only Warning for the Linux/Mac build is related to the included source code from an external program (https://github.com/cbg-ethz/SCITE) and I would prefer not to edit any of their code as a matter of principle. Hervé suggested I include the software since it was so easy to compile - which is a great idea - rather than have the end-user download it on their own. Hopefully this is OK. Please let me know how I can move this process forward.

hpages commented 3 years ago

There was a file permission issue on our Windows builder. It should be addressed now. Please bump the version of the package to trigger a new build by the SPB. Thanks!

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 985cf20853f3706eb380b607960501a3f8e0abc8

bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/mitoClone2 to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

benstory commented 3 years ago

Hi Hérve thanks for looking into this, I was worried it was something on my end. Either way it was a good learning experience :)

@LiNk-NY, at this point I think the package is ready for review. The "WARNING" is related to an external software package included in the package (https://github.com/cbg-ethz/SCITE) and I am hesitant to edit their source code out of principle. Outside of that I'm ready to make any changes, that you deem necessary to the package, for acceptance to Bioconductor. I'm always easily available on the bioC slack if needed. Thanks. -Ben

LiNk-NY commented 3 years ago

Hi Ben, @benstory

Thank you for your submission. Please see the review below.

Regards, Marcel

mitoClone2 #2158

README

DESCRIPTION

NAMESPACE

R

vignettes

src

tests

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: e302cea0e8744869e01c6ce6dbab210d40d42d07

bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/mitoClone2 to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

benstory commented 3 years ago

Dear Marcel (@LiNk-NY),

Thank you for taking the time to review my submission. I have responded point-by-point to your concerns. Please let me know if everything is acceptable to you.

Best, Ben

Hi Ben, @benstory

Thank you for your submission. Please see the review below.

Regards, Marcel

mitoClone2 #2158

README

  • Please don't advertise your package as install-able from Bioconductor when it hasn't been accepted.

FIXED

DESCRIPTION

  • Update the R version to >= 4.1.0 which corresponds to the current devel version.

FIXED

  • Include BugReports and URL fields that point to GitHub

FIXED

  • Use whole sentences in the Description field. BiocCheck will flag short Description fields by checking for ..

FIXED

  • Remove the LazyData: true or set to false.

FIXED

I had to move all the objects from the ‘data’ folder to ‘extdata’ and now load them explicitly. This results in a warning on build but ultimately I do really not want those objects facing the user. Happy to hear any suggestions.

NAMESPACE

  • Looks good.

THANK YOU

R

  • Use character indices rather than numeric ones for more robust code.

KINDA FIXED

In all reasonable cases, in some cases the numeric index makes sense.

  • Include all options in the argument, e.g., what = c("alleleRatio", "ternary"), and then use match.arg() inside the function to obtain one.

FIXED

  • Avoid using @ in the package code. You should have formal extractor functions for your class.

KINDA FIXED

_Add a few more accessors functions for use in the vignettes and examples. Within the internal code certain slots don’t necessarily need to be available to the end user. This is especially true for the recursive code chunks within functionstree.R. I removed all ‘@’ usage in vignettes and examples and also replaced those within the code (when accessor was available).

  • Avoid using system calls in plotTree. That code may not be portable to all platforms. Separate the plotting and saving functionality. Do not save files for the user by default.

FIXED

(removed entire function)

  • Consider using reticulate or basilisk rather than system calls to python.

FIXED

(removed it)

  • Does Rsamtools have the functionality that you are looking for? This is preferred over system("which samtools")

FIXED

(removed samtools call and added instructions for user to run python code externally and import through R)

  • Reduce repetitive coding by using conditional inputs in ggplot, e.g., legend.pos <- if (showLegend) "top" else "none"

FIXED

  • Please follow up with the Notes from BiocCheck::BiocCheck(), current count:

KINDA FIXED

I dropped the number of notes down to 8. At least 3 of them are not correct. The major thing has to do with line numbers for functions etc… I used RStudio to clean up how the actual code looks... and it looks a bit better. Not sure how to wrap the lines for the manual pages, maybe I need to do that manually?

  • Minor: the new("mutationsCalls", ...) should be the last call in the constructor

FIXED

  • Save the output of GRanges(sites) and re-use it in mutationCallsFromCohort.

FIXED

This parameter is not necessarily supposed to be reused across functions (e.g. user wants to investigate a subset of their data). Also, it is now clarified that the parameter can take both a character or GRanges object as input.

vignettes

  • Restrict text to an 80-character width limit. It makes it easier to review and maintain.

FIXED

I added a knitr option to force wrapping at 70-characters. Hopefully this solves the issue.

  • Avoid using @ access and provide formal accessor and replacement functions.

FIXED

  • Your example datasets in the vignette should be minimal enough to allow the demonstration of function use. Avoid providing code that takes more than 1 minute to run in the vignette.

KINDA FIXED

See below discussion of SCITE. I limited it to one experimental example but the run itself still takes about 2 minutes.

  • Provide a sessionInfo section at the end of the vignette.

FIXED

  • Avoid downloading data from a link.

FIXED

Removed all external links to data

  • Keep examples from publications (Ludwig et. al) in a separate repository. The main focus of the vignettes should be to demonstrate the functionality of the package rather than reproducing a real-world analysis. If you wish, you can create a workflow package to that end.

FIXED

I tried to cut down the size of everything in the vignette. The recreation of the Ludwig data is just an ideal dataset used to showcase the package. The type of data analysis done in this example is exactly what the package was designed to do. Anyway I removed all the repetitive exact figure creation at the end. I trimmed the vignette down to be shorter, faster, and more for focused on demonstrating functional aspects of the package.

src

  • We would prefer that you do not include external software with your package. Perhaps you can instruct users to use that software independently of yours and your package can optionally work with the output of the SCITE software? For the time being we can't accept your package with the SCITEpkg code inside of it.

NOT FIXED

I think that including the SCITE code as part of this R package is extremely valuable. I would imagine that the vast majority of Windows R users would be severely hamstrung when it comes to installing/compiling external software on their own and thus by having it pre-bundled and compiled with the R package – we make it extremely accessible to all. The SCITE software is step 3 in a very important 4-step process that is the raison d’être of this package. Before including it, I originally asked what to do about external dependencies on the Bioconductor Slack and was advised by Hérve Pagès to include the software to be compiled when the package is installed and then Mike Smith helped me create the Makefile to do just that. Then others had to fix the build server in order to help further. It is a bit confusing at this point to hear that this is not acceptable. In the package guidelines (#11) it is suggested that including external code is possible. In this case the code is raw C++ compiled at install with zero additional dependencies. I also agree to assume “…responsibility for maintenance of that code. Part of the maintenance responsibility includes keeping the code up to date as bug fixes and updates are released for the mainline third-party project.“ Anyway hopefully this is more of a recommendation than a firm barrier. Let me know otherwise.

tests

  • We strongly recommend that you add unit tests to your functions to make them more robust and reliable.

FIXED

Added a couple tests.

Thanks again for your time. Looking forward to your reply. -Ben

LiNk-NY commented 3 years ago

Hi Ben, @benstory

Thank you for your response. You are right, external C code is allowed in packages and perhaps the GPL-3 license should be respected. We suggest that you add the authors of the SCITE software to your packages DESCRIPTION file. Usually packages containing external C code are kept separate e.g., Rhtslib so that they are more modular and other packages can make use of that library without having to import mitoClone2 for example. Hervé pointed out that it is strange that you provide a standalone executable in ${R_PACKAGE_DIR}/libs/ and perhaps the ~source~ executable should be moved to a more appropriate location, perhaps mitoClone2/inst/exec or mitoClone2/inst/bin but more investigation is needed.

Not sure how to wrap the lines for the manual pages, maybe I need to do that manually?

We don't encourage this if you are using roxygen2 because those changes will be overwritten AFAIK when you "roxygenize"

This parameter is not necessarily supposed to be reused across functions (e.g. user wants to investigate a subset of their data). Also, it is now clarified that the parameter can take both a character or GRanges object as input.

I meant this within the function (see line 21). It looks like you ran it but didn't assign the output to a variable.

I added a knitr option to force wrapping at 70-characters. Hopefully this solves the issue.

I meant this for the source document and not the output.

I tried to cut down the size of everything in the vignette. The recreation of the Ludwig data is just an ideal dataset used to showcase the package. The type of data analysis done in this example is exactly what the package was designed to do. Anyway I removed all the repetitive exact figure creation at the end. I trimmed the vignette down to be shorter, faster, and more for focused on demonstrating functional aspects of the package.

Yes, this is an excellent use case but it is best reserved for a workflow type of package.

Best regards, Marcel

hpages commented 3 years ago

Hi @LiNk-NY @benstory, Just to clarify, I was suggesting ${R_PACKAGE_DIR}/exec/ or ${R_PACKAGE_DIR}/bin/ for the SCITE executable, not for the source code. But now that I think more about it, maybe everything could go in mitoClone2/inst/SCITE, source and executable (this means the executable gets installed in ${R_PACKAGE_DIR}/SCITE/). Would be cleaner than the current layout. Hopefully the changes to the current Makevars are relatively straightforward. Best, H.

benstory commented 3 years ago

Hi @LiNk-NY @hpages ,

Thank you guys for the suggestions I'm perfectly OK with putting the files anywhere. Also, I originally changed the /src folder name from SCITE to SCITEpkg because I was getting a warning at a some point about having a file named 'scite' and a directory named 'SCITE'. I will try to fiddle around with it tomorrow morning (late in Germany). I'm fine with whatever route you think is ideal for including the software.

-

@LiNk-NY

those changes will be overwritten AFAIK when you "roxygenize" source document

Sorry I was referring to the manually changing the #'@examples/#'@name etc... lines in the .R src files, for some reason those lines didn't wrap automatically using formatR I think everything else wrapped successfully. If those #'@ lines need to be wrapped I will try to make some Emacs macros for it.

see line 21

Oops embarrassing - fixed it - will be changed in next push ...

best reserved for a workflow type of package.

I shrunk that whole Overview vignette section drastically and removed all major mentions of the Ludwig source data... should I shrink it even more? I could make the heatmaps very small maybe even 20x20 if needed. It now highlights the two different options for (step 2/4 of the 4 steps). The Clustering vignette now runs in half the time but still runs one instance of SCITE (step 3/4 - two min process) and then step 4/4. If vignette build time is an issue I can just completely remove the Clustering vignette and add an extra to panel to the end of Overview with pre-computed data showcasing the functionality of step 3 and step 4.

Thanks again for helping me with this process! Very excited that we are making good progress.

Best, Ben

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: f943709da5ff9f82a08351f0775373afe4c15824

bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/mitoClone2 to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

benstory commented 3 years ago

@LiNk-NY

Everything should be fixed now. The SCITE source code is present in the 'mitoClone2/inst/SCITEpkg' and when compiled on install, the executable ends up in ${R_PACKAGE_DIR}/SCITE/. The vast majority of the code sits at less than 80 chars per line... some very deep loops seem to still add to the 80 char and 4 space tabs warnings but overall the total percentages are drastically reduced.

I cut the vignettes down a lot although they still aren't crazy fast.

One warning is related to some .RData files I moved out of the data folder to inst/extdata after setting LazyLoading to false. And they are documented in /inst/script/README... but the warning persists.

Let me know if you think anything else needs to be changed.

Best, Ben

LiNk-NY commented 3 years ago

Hi Ben, @benstory

Thanks for making those changes.

I currently only see two warnings:

* checking whether package 'mitoClone2' can be installed ... WARNING
Found the following significant warnings:
  ../inst/SCITEpkg/mcmcBinTreeMove.cpp:75:1: warning: control reaches end of non-void function [-Wreturn-type]
  bam2R_10x.cpp:145:9: warning: ISO C++ forbids variable length array ‘counts’ [-Wvla]
See '/home/mr148/bioc/mitoClone2.Rcheck/00install.out' for details.

* checking R code for possible problems ... NOTE
mitoPlot: no visible binding for global variable ‘type’
mitoPlot: no visible binding for global variable ‘gene’
Undefined global functions or variables:
  gene type

* checking for missing documentation entries ... WARNING
Undocumented data sets:
  ‘M_P1’ ‘M_P2’ ‘N_P1’ ‘N_P2’

It seems like those datasets should be documented. Perhaps you can put them in a list so that you only have to document a single object.

Can you also address the NOTE?

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 2a7697e6bbbb48aa7759d138135c812a50979704

bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/mitoClone2 to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: a8cadbae7a75478948573eca53bd16ca5bcffcc5

bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/mitoClone2 to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 10f38ed556e4bbdd5402665c8a1dcf35daffc03b

bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/mitoClone2 to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

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bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/mitoClone2 to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

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bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/mitoClone2 to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: a23e075484a9319d296c6c2783b47c0f639eae53

bioc-issue-bot commented 3 years ago

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bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 5de67ffaad0ddc4945aa9e5b8d4be8477fd90d14

bioc-issue-bot commented 3 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, 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/mitoClone2 to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 6c079ce2aaec0a8a3dcb63b7ff4f402f87d3b360

bioc-issue-bot commented 3 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/mitoClone2 to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

benstory commented 3 years ago

@LiNk-NY

Hi Marcel,

After much trial and tribulation all of those issues have been solved phew. The 'type' and 'gene' error were related to plotting with ggplot2. Hope everything is good.

Thanks again for your time, Ben