recount

[lcolladotor]

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Repository: https://github.com/leekgroup/recount

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[bioc-issue-bot]

Hi @lcolladotor

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: recount
Title: Explore and download data from the recount project
Version: 0.99.0
Date: 2016-05-31
Authors@R: c(person("Leonardo", "Collado-Torres", role = c("aut", "cre"),
    email = "lcollado@jhu.edu"), person("Abhinav", "Nellore", role = "ctb",
    email = "anellore@gmail.com"), person(c("Andrew", "E."), "Jaffe",
    role = "ctb", email = "andrew.jaffe@libd.org"), person(c("Margaret", "A."),
    "Taub", role = "ctb", email = "mtaub@jhsph.edu"), person("Kai", "Kammers",
    role = "ctb", email = "kai.kammers@gmail.com"), person(c("Shannon", "E."),
    "Ellis", role = "ctb", email = "sellis18@jhmi.edu"), person(c("Kasper",
    "Daniel"), "Hansen", role = c("ctb"),
    email = "kasperdanielhansen@gmail.com"), person("Ben", "Langmead",
    role = "ctb", email = 'langmea@cs.jhu.edu'), person(c("Jeffrey", "T."),
    "Leek", role = c("aut", "ths"), email = "jtleek@gmail.com"))
Depends:
    R (>= 3.3.0)
Imports:
    methods,
    stats,
    utils
Suggests:
    BiocParallel,
    BiocStyle,
    derfinder,
    DESeq2,
    devtools (>= 1.6),
    GEOquery,
    GenomeInfoDb,
    GenomicFeatures,
    GenomicRanges,
    IRanges,
    knitcitations,
    knitr (>= 1.6),
    RCurl,
    regionReport,
    rmarkdown (>= 0.9.5),
    rtracklayer (>= 1.33.3),
    S4Vectors,
    SummarizedExperiment,
    testthat,
    TxDb.Hsapiens.UCSC.hg38.knownGene,
    XML
VignetteBuilder: knitr
Description: Explore and download data from the recount project available at
    https://lcolladotor.shinyapps.io/recount/. Using the recount package you can
    download RangedSummarizedExperiment objects at the gene or exon level,
    the raw counts, the phenotype metadata used, the urls to the sample coverage
    bigWig files or the mean coverage bigWig file for a particular study. The
    RangedSummarizedExperiment objects can be used by different packages for
    performing differential expression analysis. Using
    http://bioconductor.org/packages/derfinder you can perform
    annotation-agnostic differential expression analyses with the data from the
    recount project.
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
URL: https://github.com/leekgroup/recount
BugReports: https://github.com/leekgroup/recount/issues
biocViews: Coverage, DifferentialExpression, GeneExpression, RNASeq, Sequencing,
    Software
RoxygenNote: 5.0.1

[bioc-issue-bot]

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.

[bioc-issue-bot]

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/recount_buildreport_20160607172303.html

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

[bioc-issue-bot]

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

7a419f7 Bump the version to 0.99.1 to force a new build re...

[bioc-issue-bot]

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/recount_buildreport_20160607175447.html

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

[lcolladotor]

Hi @LiNk-NY,

@LiNk-NY I assume that I should be tagging you. If not, please let me know!

The error in moscato2 is because it doesn't have rtracklayer version 1.33.3 or greater. http://bioconductor.org/spb_reports/recount_buildreport_20160607175447.html#moscato2_check_anchor

* checking package dependencies ... ERROR
Package required and available but unsuitable version: 'rtracklayer'

The build fails on zin2 http://bioconductor.org/spb_reports/recount_buildreport_20160607175447.html#zin2_buildsrc_anchor and oaxaca http://bioconductor.org/spb_reports/recount_buildreport_20160607175447.html#oaxaca_buildsrc_anchor because recount::expressed_regions() (used in lines 377-383 of the vignette) is the one that depends on rtracklayer version 1.33.3 or greater. So from this information, I assume that zin2 and oaxaca are both missing the latest rtracklayer as well.

Best, Leo

[dtenenba]

Yeah. The build machines attached to this tracker are still running the release version of Bioconductor. I guess I will work on that...

[lcolladotor]

Ahh, ok! Thanks Dan!

Sadly R Travis is not working right now either due to https://github.com/craigcitro/r-travis/issues/174#issuecomment-224426094 which would show that recount is working (on Linux).

[bioc-issue-bot]

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

b17683b v0.99.2 -- disable examples and tests for expresse...

[bioc-issue-bot]

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/recount_buildreport_20160607182324.html

[bioc-issue-bot]

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

a95233d v0.99.3 -- make geo_info() a little bit more flexi...

[bioc-issue-bot]

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/recount_buildreport_20160607234232.html

[bioc-issue-bot]

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

f49bf20 v0.99.4 -- fixed two NOTEs

[bioc-issue-bot]

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/recount_buildreport_20160608000626.html

[bioc-issue-bot]

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

fcfe991 v0.99.5 -- add the 'sleep' argument to both find_g...

[bioc-issue-bot]

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/recount_buildreport_20160608004312.html

[lcolladotor]

Hi,

R Travis works again so you can see the result of the build for https://github.com/leekgroup/recount/commit/fcfe991b5983e773026b831c4ee382342f9dfb8e at https://travis-ci.org/leekgroup/recount/builds/136046285 Best, Leo

[bioc-issue-bot]

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

829f56c v0.99.6 -- show in the vignette how to get gene in...

[bioc-issue-bot]

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/recount_buildreport_20160608154525.html

[bioc-issue-bot]

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

3848e64 v0.99.7 -- update the genes info with the gene sym...

[bioc-issue-bot]

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/recount_buildreport_20160608174450.html

[bioc-issue-bot]

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

36dcdae v0.99.8 -- fix 2 NOTEs and a WARNING

[bioc-issue-bot]

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/recount_buildreport_20160608180650.html

[bioc-issue-bot]

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

a908a40 v0.99.9 -- made changes to reduce the size of the ...

[bioc-issue-bot]

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/recount_buildreport_20160608183738.html

[LiNk-NY]

Hi @lcolladotor, I'm sure you're aware but you're getting an error message from building of the recount-quickstart vignette.

Quitting from lines 268-297 (recount-quickstart.Rmd) 
Error: processing vignette 'recount-quickstart.Rmd' failed with diagnostics:
"characteristics" %in% colnames(pheno) is not TRUE
Execution halted

It seems that the error originates in line 34 of the geo_characteristics.R file.

    stopifnot('characteristics' %in% colnames(pheno))

We will do a more complete review once we get a clean build. Please let us know if you have any questions.

Regards, Marcel

[lcolladotor]

Hi @LiNk-NY,

I'm not seeing that error at https://travis-ci.org/leekgroup/recount/builds/136288390 nor http://bioconductor.org/spb_reports/recount_buildreport_20160608183738.html

Can you tell me where you are seeing it? Thanks!

Best, Leo

[LiNk-NY]

Hi @lcolladotor, @vobencha and I were able to reproduce this error by building the package using R CMD build recount at the command line on our linux machines.

If you look at the second link you provided, the build is failing for both zin2 and oaxaca build servers (but not for moscato).

Regards, Marcel

[bioc-issue-bot]

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

7a7ea73 v0.99.10 -- No longer depends on find_geo() for th...

[lcolladotor]

Hi @LiNk-NY,

I was able to reproduce

Quitting from lines 268-298 (recount-quickstart.Rmd)
Error: processing vignette 'recount-quickstart.Rmd' failed with diagnostics:
"characteristics" %in% colnames(pheno) is not TRUE

when using R CMD build --no-manual --no-resave-data recount with the latest packages from Bioc. As you can see in the commit message for https://github.com/leekgroup/recount/commit/7a7ea7330f045abe4559f4121259bbb0ebe71266, this error did not occur before and I cannot trace it. However, I made a change to the vignette which removes this error when building (on my computer).

Now, about zin2 and oaxaca, the errors you mention from http://bioconductor.org/spb_reports/recount_buildreport_20160608183738.html are the same ones that I explained at https://github.com/Bioconductor/Contributions/issues/9#issuecomment-224428904 which are due to the fact that the build system is using Bioc-release and not Bioc-devel as Dan mentioned earlier https://github.com/Bioconductor/Contributions/issues/9#issuecomment-224429467. These errors are not shown for moscato because it's R code that depends on import.bw() which is not supported on Windows machines.

Best, Leo

[bioc-issue-bot]

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/recount_buildreport_20160612122609.html

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

[bioc-issue-bot]

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

c84e417 v0.99.11 -- added some details info to coverage_ma...

[bioc-issue-bot]

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

889a9b2 v0.99.12 -- Fix reading of the pheno table from th...

[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/recount_buildreport_20160615124209.html

[bioc-issue-bot]

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

c8d8367 v0.99.13 -- change find_geo() to use rentrez

[bioc-issue-bot]

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

87f5e31 v0.99.14 -- fix a test for find_geo()

[bioc-issue-bot]

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.

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[bioc-issue-bot]

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

57cca66 v0.99.15 -- made geo_info() more flexible, as in s...

[bioc-issue-bot]

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.

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[bioc-issue-bot]

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

ef868d0 v0.99.17 -- Address some of the issues at http://b...

[bioc-issue-bot]

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

816c349 v0.99.17 -- use Sys.sleep() at geo_info() only if ...

[bioc-issue-bot]

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 following build report for more details:

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[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/recount_buildreport_20160617112321.html

[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/recount_buildreport_20160617113302.html

[bioc-issue-bot]

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

616957b v0.99.18 -- switch from utils::download.file() to ...

[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/recount_buildreport_20160617164209.html

[bioc-issue-bot]

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

ce229c6 v0.99.19 -- Make changes to address https://github...