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FlowSorted.Blood.EPIC #710

Closed lucassalas closed 6 years ago

lucassalas commented 6 years ago

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bioc-issue-bot commented 6 years ago

Hi @lucassalas

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: FlowSorted.Blood.EPIC
Type: Package
Title: Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells
Version: 0.9.0
Date: 2018-02-23
Authors@R: c( person(c("Lucas", "A."),
        "Salas", role = c("cre", "aut"),
        email = "lucas.a.salas.diaz@dartmouth.edu"),
        person(c("Devin", "C."), "Koestler", role = c("aut"),
        email = "dkoestler@kumc.edu"))
Description: Raw data objects to be used for blood cell proportion
        estimation in minfi and similar packages.
License: GPL-3
Depends: R (>= 3.4.0), minfi (>= 1.21.2), SummarizedExperiment, genefilter, 
         quadprog, nlme, S4Vectors,  graphics, stats, utils
LazyData: yes
biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData,
        TissueMicroarrayData, MethylationArrayData, DNASeqData, SequencingData
NeedsCompilation: no
Packaged: 2017-10-31 16:43:10 UTC; biocbuild
Suggests: knitr,
    rmarkdown, EpiDISH, FlowSorted.Blood.450k,FlowSorted.CordBlood.450k,
    FlowSorted.CordBloodNorway.450k,
    testthat
VignetteBuilder: knitr
RoxygenNote: 6.0.1
URL: https://github.com/immunomethylomics/FlowSorted.Blood.EPIC
BugReports: https://github.com/immunomethylomics/FlowSorted.Blood.EPIC/issues

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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.

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.

bioc-issue-bot commented 6 years ago

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

2c733be version bump required

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.

bioc-issue-bot commented 6 years ago

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

fdbc8fa Changes required during package check

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.

lucassalas commented 6 years ago

Dear Marcel, Thanks for reviewing this package. This is my first time using Bioconductor on this end, so I apologize if something might be unclear to me. I have already built the package and passed both Linux and OS except for the an ERROR and one WARNING:

My understanding is that I should keep the 0.9.x while we are in this phase so I am not sure if I should update anything else. I have tested the package using 3.4.4 not 3.5 as some of the dependencies use source and the Rtools is not working with the 3.5 alpha version.

On the other hand I have problems with Windows:

checkRdaFiles("D:/GitHub/FlowSorted.Blood.EPIC/data") size ASCII compress version D:/GitHub/FlowSorted.Blood.EPIC/data/FlowSorted.Blood.EPIC.rda 374760444 FALSE xz 2 D:/GitHub/FlowSorted.Blood.EPIC/data/IDOLOptimizedCpGs.rda 1949 FALSE bzip2 2 D:/GitHub/FlowSorted.Blood.EPIC/data/IDOLOptimizedCpGs450klegacy.rda 1573 FALSE bzip2 2

Thank you for any help or guidance.

Best, Lucas

bioc-issue-bot commented 6 years ago

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

eee32de Error in version

lshep commented 6 years ago

Hey there - You might get a screwy build report - you happen to push changes right when I was pushing some changes to the SinglePackageBuilders - I'm monitoring and once the (buggy) report is done - I will rerun to get a more accurate - Sorry about that -

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.

lshep commented 6 years ago

another report will be generated shortly

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.

lucassalas commented 6 years ago

Hi Marcel @LiNk-NY , I solved the error with the versions and the package was build in Linux and OS. However, it seems that the Windows build is not working the report says: PackageFileSize: -1.00 KiB in the tokay compared to PackageFileSize: 479366.83 KiB in merida 2 or PackageFileSize: 366058.68 KiB in malbec. This is a lfs storage. Could this be a problem on your end? I found that something similar occurred a couple months ago with another package using this system.

Please let me know and thank you.

Lucas

bioc-issue-bot commented 6 years ago

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

21dea49 Correcting indent notes. Travis

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.

LiNk-NY commented 6 years ago

Hi Lucas, @lucassalas

Thanks for your submission. These different sizes may be due to OS-specific calculations although the tokay2 number is invalid. Don't worry about it for now.

The error on tokay2 stems from using the older save function in your version of R. I suggest your resave the datasets using R devel 3.5.0. We would prefer that the package depends on R (>= 3.5.0) because it will be deployed with this version of R (if it gets accepted before the deadline).

Regards, Marcel

bioc-issue-bot commented 6 years ago

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

aac2801 rda files were resaved using R 3.5.0 alpha version

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: "ABNORMAL". 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.

lshep commented 6 years ago

sorry - my fault - rerunning now

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.

lucassalas commented 6 years ago

Hi @lshep and @LiNk-NY , Well, I resaved the rda with the alpha 3.5.0 version and the problem with tokay2 persists.

I believe the tokay2 problem is related to the git clone from the lfs system. It still reports -1.0 KiB instead of the actual size of the package. I checked other build reports and, it seems that this problem is not isolated but it is happening for several tokay2 builds for other contributors.

@lshep Thanks for rerunning the build.

Lucas

lshep commented 6 years ago

I actaully have it running one more time - the ERROR in that last report was an unrelated issue that should be corrected now - you should have a new report shortly

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.

LiNk-NY commented 6 years ago

Hi Lucas, @lucassalas

Please resave the dataset(s) in version 3 and make sure that you are using the argument explicitly as the default in R 3.5 is to save in version 2.

save(..., version = 3)

See https://cran.r-project.org/bin/windows/base/NEWS.R-3.5.0beta.html for details.

Regards, Marcel

bioc-issue-bot commented 6 years ago

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

878adb7 rda saved on R3.5.0 version 3

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, 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.

bioc-issue-bot commented 6 years ago

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

45886bf Solving warning compression saving version 3 resav...

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.

lucassalas commented 6 years ago

Hi @LiNk-NY , I resaved and compressed the rda files using 3.5.0 alpha to version 3. However, the error in tokay2 persists.

PackageFile: -- PackageFileSize: -1.00 KiB BuildID:: FlowSorted.Blood.EPIC_20180413022657 PreProcessing: Accessing git_info. Starting Git clone. Installing dependencies. Installing package: FlowSorted.Blood.EPIC. Starting Build package. PostProcessing: Accessing git_info complete. Finished Git clone. Installing dependency status: 0. Installing package status: 1. Build Package status: 1.

The system did not generate the expected zip file and the process was stopped. Very strange.

Thanks,

Lucas

LiNk-NY commented 6 years ago

Hi Lucas, @lucassalas

It seems like it is trying to run load on a zip file but I'm not sure why. I will have another team member have a look at it.

Regards, Marcel

LiNk-NY commented 6 years ago

Hi Lucas, @lucassalas

Martin @mtmorgan noticed that you are using git LFS. Currently our build system does not support LFS. Please convert the repository to a regular git repository if possible or consider using ExperimentHub to distribute the data in your package.

See: ExperimentHub vignette

Best regards, Marcel

bioc-issue-bot commented 6 years ago

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

722f8d9 Cleaning lfs push build

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.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

bioc-issue-bot commented 6 years ago

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

ea9433f added ExperimentHub to the Namespace

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.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

lucassalas commented 6 years ago

Hi @lshep and @LiNk-NY,

I am sorry, but I will require some additional help here. I am not sure how can I test locally my files and I believe the build report is wrong (all the files are now of size -1.0.) even after updating the Namespace.

Let me try to summarize what I have done so far: These steps I believe are OK:

  1. I have uploaded the FlowSorted.Blood.EPIC.rda to ExperimentHub yesterday using aws.
  2. I have made a make-data.R and make-metadata.R, I generated a metadata.csv and I tested locally using readMetadataFromCsv("D:/GitHub/FlowSorted.Blood.EPIC") and all the results were OK.
  3. I deleted my git lfs files and the .gitatrributes I checked git lfs ls-files and it is empty. All the small rda files are now on git ls-files.

Here the problems

  1. I tried to run to devtools::document() and I got an error as the ExperimentHub snapshotDate is 2017-10-30
  2. The object FlowSorted.Blood.EPIC cannot be onloaded using the zzz.R as it is not present on ExperimentHub

Maybe I am missing something, should I submit my metadata first @lshep ?

I am scratching my head with this, not sure how to proceed on my end.

Thanks for your help.

Lucas

lshep commented 6 years ago

I'm sorry I should have been more clear in the email - after you uploaded your data I still need to add it to the location and into ExperimentHub - that was a temporary location - I will do that now

lshep commented 6 years ago

The data is now on experimentHub in the devel version of Bioconductor 3.7

> hub = ExperimentHub()
updating metadata: retrieving 1 resource
  |======================================================================| 100%
snapshotDate(): 2018-04-20
> query(hub, "FlowSorted")
ExperimentHub with 1 record
# snapshotDate(): 2018-04-20 
# names(): EH1136
# package(): FlowSorted.Blood.EPIC
# $dataprovider: GEO
# $species: Homo sapiens
# $rdataclass: RGChannelSet
# $rdatadateadded: 2018-04-20
# $title: FlowSorted.Blood.EPIC: Illumina Human Methylation data from EPIC o...
# $description: The FlowSorted.Blood.EPIC package contains Illumina HumanMet...
# $taxonomyid: 9606
# $genome: hg19
# $sourcetype: tar.gz
# $sourceurl: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110554
# $sourcesize: NA
# $tags: c("ExperimentData", "Homo_sapiens_Data", "Tissue",
#   "MicroarrayData", "Genome", "TissueMicroarrayData",
#   "MethylationArrayData") 
# retrieve record with 'object[["EH1136"]]' 

Side note: The FlowSorted.Blood.EPIC.Rproj should not be git tracked - please use git rm - if you would like to keep this type of file in the future it should be added to the .gitignore file.

bioc-issue-bot commented 6 years ago

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

a2c997e .gitignore ExperimentHub call devel 3.7

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: "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.

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bioc-issue-bot commented 6 years ago

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

a0aaf5a version bump plus utils

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: "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.

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bioc-issue-bot commented 6 years ago

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

8552cb0 several warnings corrections

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: "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.

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bioc-issue-bot commented 6 years ago

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

3760651 solving error not calling the object from the pack...

bioc-issue-bot commented 6 years ago

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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.

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bioc-issue-bot commented 6 years ago

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

a766584 Error when calling the ExperimentHub 3a54f9e testthat

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: "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.

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bioc-issue-bot commented 6 years ago

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

14493a3 Solving internal code issues when calling the Expe...