Closed lucassalas closed 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
Consider adding SSH keys to your GitHub account. SSH keys will are used to control access to accepted Bioconductor packages. See these instructions to add SSH keys to your GitHub account.
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.
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.
Received a valid push; starting a build. Commits are:
2c733be version bump required
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.
Received a valid push; starting a build. Commits are:
fdbc8fa Changes required during package check
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.
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:
ERROR: package installation failed I have been trying to solve this problem but the only solution that I have found is generating a sysdata.rda which breaks my test and example scripts. Thus I am not sure how to work this problem around. My package was developed using Windows 10 pro the version of the rda in data is 2 and they are compressed using the tools package. as you can see here:
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
Received a valid push; starting a build. Commits are:
eee32de Error in version
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 -
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.
another report will be generated shortly
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.
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
Received a valid push; starting a build. Commits are:
21dea49 Correcting indent notes. Travis
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.
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
Received a valid push; starting a build. Commits are:
aac2801 rda files were resaved using R 3.5.0 alpha version
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.
sorry - my fault - rerunning now
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.
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
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
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.
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
Received a valid push; starting a build. Commits are:
878adb7 rda saved on R3.5.0 version 3
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.
Received a valid push; starting a build. Commits are:
45886bf Solving warning compression saving version 3 resav...
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.
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
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
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.
Best regards, Marcel
Received a valid push; starting a build. Commits are:
722f8d9 Cleaning lfs push build
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.
Received a valid push; starting a build. Commits are:
ea9433f added ExperimentHub to the Namespace
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.
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:
Here the problems
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
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
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.
Received a valid push; starting a build. Commits are:
a2c997e .gitignore ExperimentHub call devel 3.7
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.
Received a valid push; starting a build. Commits are:
a0aaf5a version bump plus utils
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.
Please see the build report for more details.
Received a valid push; starting a build. Commits are:
8552cb0 several warnings corrections
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.
Received a valid push; starting a build. Commits are:
3760651 solving error not calling the object from the pack...
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.
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.
Received a valid push; starting a build. Commits are:
14493a3 Solving internal code issues when calling the Expe...
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
Confirm the following by editing each check box to '[x]'
[x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
[x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.
I am familiar with the essential aspects of Bioconductor software management, including:
For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.