Closed antagomir closed 7 years ago
Hi @antagomir
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: microbiome
Type: Package
Title: Microbiome Analytics
Description: Utilities for microbiome analysis.
Encoding: UTF-8
Version: 0.99.2
Date: 2017-06-04
Authors@R: c(
person("Leo", "Lahti", email = "leo.lahti@iki.fi", role = c("aut", "cre")),
person("Sudarshan", "Shetty", role = "ctb"),
person("Jarkko", "Salojarvi", role = "ctb"))
biocViews: Clustering, Metagenomics, Microbiome, Sequencing, SystemsBiology
License: BSD_2_clause + file LICENSE
Depends:
R (>= 3.4.0),
phyloseq
Imports:
ade4,
dplyr,
ggplot2,
graphics,
grDevices,
MASS,
moments,
plyr,
reshape2,
scales,
stats,
tidyr,
utils,
vegan,
WGCNA
Suggests:
BiocGenerics,
BiocStyle,
Cairo,
devtools,
DESeq2,
diptest,
FD,
GGally,
gcookbook,
ggnet,
gridExtra,
Hmisc,
hrbrthemes,
igraph,
intergraph,
knitcitations,
knitr,
limma,
lme4,
magrittr,
netresponse,
network,
RColorBrewer,
rmarkdown,
sna,
SpiecEasi,
structSSI,
testthat,
tidyverse,
viridis
URL: http://microbiome.github.io/microbiome
MailingList: microbiome <microbiome-devel@googlegroups.com>
BugReports: https://github.com/microbiome/microbiome/issues
VignetteBuilder: knitr
Packaged: 2014-09-14 14:19:39 UTC; lei
RoxygenNote: 6.0.1
Your package has been approved for building. Your package is now submitted to our queue.
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.
I'm surprised that you do not make use of existing microbiome packages and established infrastructure, and that you do not exploit standard ways for representing annotated rectangular data structures (in particular SummarizedExperiment). A great strength of Bioconductor is easy interoperability, e.g., so that users can easily compare your implementation to alternatives without having to spend time on highly error-prone translation between different data representations.
Also the very complex dependencies in your package mean that it will be very fragile and difficult to maintain. I strongly encourage you to evaluate the functionality that you offer and remove marginally useful functionality.
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 following build report for more details:
http://bioconductor.org/spb_reports/microbiome_buildreport_20170604121517.html
Thanks for the feedback.
Dependencies I have now considerably reduced the number of dependencies, and removed some marginal functionality, compared to the first push.
Use of established infrastructure I am already using existing microbiome infrastructure from Bioconductor: the package is based on the phyloseq class structure from Bioconductor. To me this seems to be perhaps the most well-thought class structure in R to represent 16S rRNA profiling data, including phylogenetic tree information that may be relevant in such analyses. Another microbiome data structure in Bioconductor, the PathStat is in fact extension of the phyloseq class. And for the other microbiome packages that I've found from Bioconductor (manta, DirichletMultinomial, eudysbiome, ..), they focus on methods and use standard data formats (such as matrices) and do not provide plausible alternatives for microbiome data structures. The SummarizedExperiment could be a valid alternative but I am not sure how well it could handle the phylogenetic tree information and since we already have a custom class infrastructure in Bioconductor, the phyloseq, I have intentionally chosen to support that.
Thanks, sorry I missed phyloseq in the original DESCRIPTION file; that was really what I was looking for.
I have set up a webhook and it seems to be fine but the updates to my master branch do not seem to trigger updates here. How should I troubleshoot this ?
There needs to be a version bump where the new version is 'larger' than the old version; it looks like you went from .23 to .3, but this is interpreted as sub-minor version '23' and then sub-minor version '3', and '3' is < '23' so not a version bump that triggers a build. Try '.24'
Received a valid push; starting a build. Commits are:
6e91ce0 version bump
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 following build report for more details:
http://bioconductor.org/spb_reports/microbiome_buildreport_20170605184619.html
Received a valid push; starting a build. Commits are:
7552d77 ready for bioc
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 following build report for more details:
http://bioconductor.org/spb_reports/microbiome_buildreport_20170606044625.html
Received a valid push; starting a build. Commits are:
09c0540 vignette update
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 following build report for more details:
http://bioconductor.org/spb_reports/microbiome_buildreport_20170606050648.html
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 following build report for more details:
http://bioconductor.org/spb_reports/microbiome_buildreport_20170606053959.html
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 following build report for more details:
http://bioconductor.org/spb_reports/microbiome_buildreport_20170606074326.html
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the following build report for more details:
http://bioconductor.org/spb_reports/microbiome_buildreport_20170606082557.html
Reassigning this package to @hpages to continue the review from the previous tracker issue.
Received a valid push; starting a build. Commits are:
806b8cc top_taxa fix 27b57f7 ok d1a2f56 top taxa bug fix 4f2dcca ok 3d7beea sync 5381a2b divergence checks e0faf5e ok a87ed56 mods ff9ab93 core plot mod dde80f8 ok cbba763 closes #42 a85b191 ok 691dc75 version requirement loosened d6e0635 Merge branch 'devel' of https://github.com/microbi... adbbddf vreq a708087 docs testing
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 following build report for more details:
http://bioconductor.org/spb_reports/microbiome_buildreport_20170628070348.html
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 following build report for more details:
http://bioconductor.org/spb_reports/microbiome_buildreport_20170704071036.html
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 following build report for more details:
http://bioconductor.org/spb_reports/microbiome_buildreport_20170705053146.html
Hi Leo,
Thanks for re-submitting microbiome.
The package is in much better shape than when I first looked at it in 2014. Thanks for all these improvements. One little thing that remains though is that the section numbers in the vignette are all prefixed with 0.
. Could these prefixes be removed?
Otherwise, the package will be ready for inclusion to Bioconductor.
Regards, H.
Received a valid push; starting a build. Commits are:
466b9b7 line fixes f27839d Example data for read_phyloseq function For Biom ... bb1c0b3 read_mothur2phyloseq.R Updated example file names ecdfa87 Updated read_csv2phyloseq.R Added example file na... ac63a91 Updated read_biom2phyloseq.R Added example file n... 43f5d0f Update read_csv2phyloseq.R cdcceb2 Update read_mothur2phyloseq.R 8bc2d1a Update read_biom2phyloseq.R a4c21c1 ok 0d639e2 heatmap ordering now possible with labels dec5b00 heat update 7caa4cb ok bcdaccf synced f540b5f added age and bmi grouping ad4472e ok dc3eb29 Shortening the lines to bioc reqs 33d1dee made the read functions executable now - closing #... a7f36e6 vignette update 51a1d1a package build ok - vignette headers also fixed b00647e builds ok
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 following build report for more details:
http://bioconductor.org/spb_reports/microbiome_buildreport_20170714161838.html
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the following build report for more details:
http://bioconductor.org/spb_reports/microbiome_buildreport_20170714170016.html
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the following build report for more details:
http://bioconductor.org/spb_reports/microbiome_buildreport_20170715051505.html
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the following build report for more details:
http://bioconductor.org/spb_reports/microbiome_buildreport_20170715063218.html
Thanks ! I think it should all be fine now.
Received a valid push; starting a build. Commits are:
af5c6a7 vignette updates e02086b homepage update 423596a corrected formatting Build check was okay c9ad178 formatted for line length 1140e9a Update write_phyloseq.R param type 'OTU' or 'TAXA... 4ac5dfc divergence extended 3d13b8d Merge branch 'devel' of https://github.com/microbi... e35a75c Fixed clr bug 1e59d4a read_biom example fix 94c1661 fix man pages e325deb added color in plot_regression c98656a check 3acfc19 homepage update 6beff2f vignette update
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the following build report for more details:
http://bioconductor.org/spb_reports/microbiome_buildreport_20170808131835.html
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the following build report for more details:
http://bioconductor.org/spb_reports/microbiome_buildreport_20170816150956.html
I have completed all the requested changes. Could this now be ready for bioc devel ?
Received a valid push; starting a build. Commits are:
de9f2de sync adfc6fc sync a1ef9e5 sync d4369f2 divergence sample names added 72f397c divergence update 955ffc2 ok 45b9217 minor 522aca8 minor 0619ff9 tabs 76b3002 legend issue in composition plot #14 added code t... 784d156 Merge pull request #56 from microbiome/devel Deve...
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the following build report for more details:
http://bioconductor.org/spb_reports/microbiome_buildreport_20170831121556.html
Hi Leo,
Thanks for making these changes. Everything looks good now. I'm marking the package as accepted.
Thanks a lot for your patience thru this long review process!
Cheers, H.
Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be sent to the maintainer email address in the next several days.
Thank you for contributing to Bioconductor!
Hi Leo -- while adding your repository to Bioconductor's git, I noticed that (and maybe other files) mean that your repository is larger than the Bioconductor guidelines (less than 4MB on disk). Can this be avoided, e.g., by using smaller data in the vignette / examples?
Ok I have now shrank the pkg size by removing some example data sets. The github repository is still larger but we have taken advantage of .Rbuildignore, and the package size is now (after my latest changes) less than 3Mb. It would be handy if we can still store some other files associated with the package in the github repository.
Thanks Leo; since we're tracking only the 'master' branch maybe an appropriate compromise is to make it slim, with the extras on a different branch (even making the git branch the default, via settings in github).
I guess I'm trying to work out policies for Bioc git repositories, and while the differences in your repo size is not dramatic I'm aware that we have 1400 packages that require storage and management (e.g., by the build system, which clones all repos).
Hmm.. ok. The online tutorials and associated figures take quite some space (34Mb) in github. They are in the standard docs/ directory, which allows us to easily use the automated utilities without maintaining the tutorial under a different branch (gh-pages), which turned out to be somewhat tricky. But if it really is not possible to have our docs directory in the bioc master branch, I will have to investigate in more detail what's the best solution. This may take some extra time now.
GitHub repository of the package we wish to submit to Bioconductor
Note: this is a resubmission of the microbiome package in Bioconductor after the package has been completely rewritten following the feedback from H. Pages in 10/2014 (tracker.fhcrc.org/roundup/bioc_submit/issue1031). Therefore the verrsion number is 0.99.2 rather than 0.99.0 but the submission system has changed and as far as I can see, opening a new issue is the cleanest way to get forward.
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