brainflowprobes package submission

aprice26 commented 5 years ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Repository: https://github.com/LieberInstitute/brainflowprobes

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:

[x] The 'devel' branch for new packages and features.
[x] The stable 'release' branch, made available every six months, for bug fixes.
[x] Bioconductor version control using Git (optionally via GitHub).

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

(next line added by mtmorgan during package acceptance)

AdditionalPackage: https://github.com/LieberInstitute/GenomicState

bioc-issue-bot commented 5 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 5 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 5 years ago

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

bbb1ef0 v0.99.7 -- import methods::is

bioc-issue-bot commented 5 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 5 years ago

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

8f91142 add data to the package, remove load() from functi... c61af71 add exporting of functions 223db24 update data files 9375319 update NAMESPACE to be written by roxygen d917376 remove superfluous files d4d0f56 remove s from https b07547b Add RcolorBrewer 18746fe add vignette 2f48e57 add package 8a572ba brainflowprobes version 0.99.0 Missing: * Vignet... 3e9fc91 change title and description 3e5e22b remove column 686d59a add package data info 6d6e414 first draft of first half of vignette aa1ff42 add column information for pd tables 228c422 update data info 95b1406 finish vignette first pass 158a63b Resolves a NOTE in R CMD check 8e80b0d Make citation title match the DESCRIPTION 46e9eba Put some text in bold. Adjust the height of the pd... 60af159 Save exploration code for how to re-make the gs/ge... 6f539b2 Re-make the genes and gs objects using Gencode v31... ffddc30 Add the CODING_ONLY argument to the functions `... f71b8c5 Add examples with CODING_ONLY = TRUE in all functi... 46900dd update plots for new annotation 3248b4a Update README.md a32411e Update README.md 7c2c40c v0.99.1 -- Clean up a bit the git repo according t... f7e2734 v0.99.2 -- testing the BioC SBP webhook that I jus... 68876d1 v0.99.3 -- address @Liubuntu's requests from https... 6fb2eeb 0.99.4 -- fix the speed gains for plot_coverage() ... b6dee48 v0.99.5 -- add the OUTDIR argument to check_pdf() ... 5825ac8 v0.99.6 -- fix a link to the doc file for GRanges 442db36 Remove GenomicState data from the package ad9f9f2 Removed data/genes.rda 8e32450 v0.99.7 -- use data from GenomicState::GenomicStat... aa3d24a v0.99.8 -- hm.... had to merge

bioc-issue-bot commented 5 years ago

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

bc2f65d v0.99.9 -- update to match BioC installation instr...

lcolladotor commented 5 years ago

Thanks for the AnnotationHub update @lshep!! =D

@Liubuntu I updated both GenomicState and brainflowprobes. If the last commit from brainflowprobes runs the checks successfully, then both packages should be good to go. Well, at least to keep advancing the review of them.

Briefly, GenomicState::GenomicStateHub() returns the output of AnnotationHub::query() (after constructing them so they are unique). brainflowprobes then uses two such queries and accesses the data using the [[1]] syntax from AnnotationHub. GenomicState depends on AnnotationHub due to this, and brainflowprobes only imports GenomicState since a brainflowprobes user won't be expected to use other AnnotationHub resources.

Let me know if you have any questions.

Best, Leo

PS At https://github.com/Bioconductor/Contributions/issues/1191#issuecomment-545101814 lots of changes were detected since I had to use git push --force after removing the data files from the git history using BFG https://rtyley.github.io/bfg-repo-cleaner/.

lshep commented 5 years ago

Hang tight - we are experiencing some delay with the builder. We are in the process of fixing it.

bioc-issue-bot commented 5 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.

Liubuntu commented 5 years ago

Hi @lcolladotor ,

Just looked through your updates in GenomicStates. One (potential) issue in the vignette:

the example of plotRegionCoverage() was generating the first image of a big capital 1. Was it intended? or is there anything else need to be fixed? since it feels to confuse users.

Also please remember to bump version in DESCRIPTION file, so that we can get a build report.

Best, Qian

bioc-issue-bot commented 5 years ago

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

9d21241 v0.99.8 -- hide the page holder from plotRegionCov...

bioc-issue-bot commented 5 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 5 years ago

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

9198f36 v0.99.10 -- looks like the web connection failed i...

bioc-issue-bot commented 5 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.

lcolladotor commented 5 years ago

Hi,

In https://github.com/LieberInstitute/GenomicState/commit/9d2124117c84a9224562ab443b2892a581b37b5e I removed the 1 plot from the vignette in GenomicState.

As you can see at http://bioconductor.org/spb_reports/brainflowprobes_buildreport_20191023112906.html and http://bioconductor.org/spb_reports/brainflowprobes_buildreport_20191022163651.html, the build report found an error for brainflowprobes on the MacOS build machine. It looks like rtracklayer is having some issues accessing a BigWig file (see just after 2019-10-23 11:19:04 loadCoverage: loading BigWig file http://brain-flow-rna.s3.us-east-2.amazonaws.com/Sep/Br2074C_RiboZero.bw in the last build report) despite derfinder::loadCoverage() re-trying a couple of times.

Besides that, it all looks good to me.

Best, Leo

Liubuntu commented 5 years ago

Hi @lcolladotor ,

The GenomicState package is ready to go. Also the brainflowprobes looks good except that you need to make sure to report this issue to rtracklayer, maybe here? https://github.com/lawremi/rtracklayer/issues or anywhere else you thought appropriate. Follow up with it for a clear build of your own package.

I'll accept both packages now!

Best, Qian

bioc-issue-bot commented 5 years ago

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.

Thank you for contributing to Bioconductor!

lcolladotor commented 5 years ago

Awesome, thanks Qian @Liubuntu for your thorough review and guidance! And thanks again Lori @lshep for your help too! I know that Amanda @aprice26 is trilled with the news =)

Regarding the MacOS rtracklayer error, I can't reproduce it on my MacOS laptop, so I think that it's an internet connection issue. If it happens again on the Bioconductor nightly builds, I'll report it and/or change derfinder::loadCoverage() (the function that uses rtracklayer::import.bw()) so it'll wait longer between re-tries.

Best, Leo

local macOS check

build

$ R CMD build --keep-empty-dirs --no-resave-data brainflowprobes
Loading required package: colorout
* checking for file ‘brainflowprobes/DESCRIPTION’ ... OK
* preparing ‘brainflowprobes’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘brainflowprobes_0.99.10.tar.gz’

check

$ R CMD check --no-vignettes --timings brainflowprobes_0.99.10.tar.gz
Loading required package: colorout
* using log directory ‘/Users/lcollado/Dropbox/Code/brainflowprobes.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘brainflowprobes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘brainflowprobes’ version ‘0.99.10’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘brainflowprobes’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
plot_coverage          43.048  2.282  72.251
region_info            26.861  0.863  29.491
get_nearest_annotation 10.762  0.502  12.974
four_panels             7.800  0.514  11.942
brainflowprobes_cov     2.047  0.295  11.655
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

session info

> library(brainflowprobes)
> options(width = 120)
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 3.6.1 (2019-07-05)
 os       macOS Mojave 10.14.6
 system   x86_64, darwin15.6.0
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/New_York
 date     2019-10-23

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
 package                     * version   date       lib source
 acepack                       1.4.1     2016-10-29 [1] CRAN (R 3.6.0)
 AnnotationDbi                 1.47.1    2019-08-20 [1] Bioconductor
 AnnotationFilter              1.9.0     2019-05-02 [1] Bioconductor
 AnnotationHub                 2.17.10   2019-10-01 [1] Bioconductor
 askpass                       1.1       2019-01-13 [1] CRAN (R 3.6.0)
 assertthat                    0.2.1     2019-03-21 [1] CRAN (R 3.6.0)
 backports                     1.1.5     2019-10-02 [1] CRAN (R 3.6.0)
 base64enc                     0.1-3     2015-07-28 [1] CRAN (R 3.6.0)
 bibtex                        0.4.2     2017-06-30 [1] CRAN (R 3.6.0)
 Biobase                       2.45.1    2019-09-04 [1] Bioconductor
 BiocFileCache                 1.9.1     2019-06-03 [1] Bioconductor
 BiocGenerics                  0.31.6    2019-09-19 [1] Bioconductor
 BiocManager                   1.30.9    2019-10-23 [1] CRAN (R 3.6.1)
 BiocParallel                  1.19.5    2019-10-20 [1] Bioconductor
 biomaRt                       2.41.9    2019-10-01 [1] Bioconductor
 Biostrings                    2.53.2    2019-07-09 [1] Bioconductor
 biovizBase                    1.33.1    2019-08-23 [1] Bioconductor
 bit                           1.1-14    2018-05-29 [1] CRAN (R 3.6.0)
 bit64                         0.9-7     2017-05-08 [1] CRAN (R 3.6.0)
 bitops                        1.0-6     2013-08-17 [1] CRAN (R 3.6.0)
 blob                          1.2.0     2019-07-09 [1] CRAN (R 3.6.0)
 brainflowprobes             * 0.99.10   2019-10-23 [1] Github (LieberInstitute/brainflowprobes@9198f36)
 BSgenome                      1.53.2    2019-08-28 [1] Bioconductor
 BSgenome.Hsapiens.UCSC.hg19   1.4.0     2019-07-27 [1] Bioconductor
 bumphunter                    1.27.0    2019-05-02 [1] Bioconductor
 checkmate                     1.9.4     2019-07-04 [1] CRAN (R 3.6.0)
 cli                           1.1.0     2019-03-19 [1] CRAN (R 3.6.0)
 cluster                       2.1.0     2019-06-19 [1] CRAN (R 3.6.1)
 codetools                     0.2-16    2018-12-24 [1] CRAN (R 3.6.1)
 colorspace                    1.4-1     2019-03-18 [1] CRAN (R 3.6.0)
 cowplot                       1.0.0     2019-07-11 [1] CRAN (R 3.6.0)
 crayon                        1.3.4     2017-09-16 [1] CRAN (R 3.6.0)
 curl                          4.2       2019-09-24 [1] CRAN (R 3.6.1)
 data.table                    1.12.6    2019-10-18 [1] CRAN (R 3.6.0)
 DBI                           1.0.0     2018-05-02 [1] CRAN (R 3.6.0)
 dbplyr                        1.4.2     2019-06-17 [1] CRAN (R 3.6.0)
 DelayedArray                  0.11.8    2019-10-08 [1] Bioconductor
 derfinder                     1.19.9    2019-09-21 [1] Bioconductor
 derfinderHelper               1.19.3    2019-09-17 [1] Bioconductor
 derfinderPlot                 1.19.3    2019-09-17 [1] Bioconductor
 dichromat                     2.0-0     2013-01-24 [1] CRAN (R 3.6.0)
 digest                        0.6.22    2019-10-21 [1] CRAN (R 3.6.1)
 doRNG                         1.7.1     2018-06-22 [1] CRAN (R 3.6.0)
 dplyr                         0.8.3     2019-07-04 [1] CRAN (R 3.6.0)
 ensembldb                     2.9.6     2019-09-10 [1] Bioconductor
 fastmap                       1.0.1     2019-10-08 [1] CRAN (R 3.6.0)
 foreach                       1.4.7     2019-07-27 [1] CRAN (R 3.6.0)
 foreign                       0.8-72    2019-08-02 [1] CRAN (R 3.6.0)
 Formula                       1.2-3     2018-05-03 [1] CRAN (R 3.6.0)
 GenomeInfoDb                  1.21.2    2019-09-27 [1] Bioconductor
 GenomeInfoDbData              1.2.1     2019-07-27 [1] Bioconductor
 GenomicAlignments             1.21.7    2019-09-11 [1] Bioconductor
 GenomicFeatures               1.37.4    2019-07-09 [1] Bioconductor
 GenomicFiles                  1.21.0    2019-05-02 [1] Bioconductor
 GenomicRanges                 1.37.17   2019-10-11 [1] Bioconductor
 GenomicState                  0.99.8    2019-10-23 [1] Github (LieberInstitute/GenomicState@9d21241)
 GGally                        1.4.0     2018-05-17 [1] CRAN (R 3.6.0)
 ggbio                         1.33.2    2019-08-24 [1] Bioconductor
 ggplot2                       3.2.1     2019-08-10 [1] CRAN (R 3.6.0)
 glue                          1.3.1     2019-03-12 [1] CRAN (R 3.6.0)
 graph                         1.63.0    2019-05-02 [1] Bioconductor
 gridExtra                     2.3       2017-09-09 [1] CRAN (R 3.6.0)
 gtable                        0.3.0     2019-03-25 [1] CRAN (R 3.6.0)
 Hmisc                         4.2-0     2019-01-26 [1] CRAN (R 3.6.0)
 hms                           0.5.1     2019-08-23 [1] CRAN (R 3.6.0)
 htmlTable                     1.13.2    2019-09-22 [1] CRAN (R 3.6.1)
 htmltools                     0.4.0     2019-10-04 [1] CRAN (R 3.6.0)
 htmlwidgets                   1.5.1     2019-10-08 [1] CRAN (R 3.6.0)
 httpuv                        1.5.2     2019-09-11 [1] CRAN (R 3.6.0)
 httr                          1.4.1     2019-08-05 [1] CRAN (R 3.6.0)
 interactiveDisplayBase        1.23.0    2019-05-02 [1] Bioconductor
 IRanges                       2.19.17   2019-10-11 [1] Bioconductor
 iterators                     1.0.12    2019-07-26 [1] CRAN (R 3.6.1)
 knitr                         1.25      2019-09-18 [1] CRAN (R 3.6.1)
 later                         1.0.0     2019-10-04 [1] CRAN (R 3.6.0)
 lattice                       0.20-38   2018-11-04 [1] CRAN (R 3.6.1)
 latticeExtra                  0.6-28    2016-02-09 [1] CRAN (R 3.6.0)
 lazyeval                      0.2.2     2019-03-15 [1] CRAN (R 3.6.0)
 limma                         3.41.18   2019-10-13 [1] Bioconductor
 locfit                        1.5-9.1   2013-04-20 [1] CRAN (R 3.6.0)
 magrittr                      1.5       2014-11-22 [1] CRAN (R 3.6.0)
 Matrix                        1.2-17    2019-03-22 [1] CRAN (R 3.6.1)
 matrixStats                   0.55.0    2019-09-07 [1] CRAN (R 3.6.0)
 memoise                       1.1.0     2017-04-21 [1] CRAN (R 3.6.0)
 mime                          0.7       2019-06-11 [1] CRAN (R 3.6.0)
 munsell                       0.5.0     2018-06-12 [1] CRAN (R 3.6.0)
 nnet                          7.3-12    2016-02-02 [1] CRAN (R 3.6.1)
 openssl                       1.4.1     2019-07-18 [1] CRAN (R 3.6.0)
 OrganismDbi                   1.27.1    2019-08-17 [1] Bioconductor
 pillar                        1.4.2     2019-06-29 [1] CRAN (R 3.6.0)
 pkgconfig                     2.0.3     2019-09-22 [1] CRAN (R 3.6.1)
 pkgmaker                      0.27      2018-05-25 [1] CRAN (R 3.6.0)
 plyr                          1.8.4     2016-06-08 [1] CRAN (R 3.6.0)
 prettyunits                   1.0.2     2015-07-13 [1] CRAN (R 3.6.0)
 progress                      1.2.2     2019-05-16 [1] CRAN (R 3.6.0)
 promises                      1.1.0     2019-10-04 [1] CRAN (R 3.6.0)
 ProtGenerics                  1.17.4    2019-08-20 [1] Bioconductor
 purrr                         0.3.3     2019-10-18 [1] CRAN (R 3.6.0)
 qvalue                        2.17.0    2019-05-02 [1] Bioconductor
 R6                            2.4.0     2019-02-14 [1] CRAN (R 3.6.0)
 rappdirs                      0.3.1     2016-03-28 [1] CRAN (R 3.6.0)
 RBGL                          1.61.0    2019-05-02 [1] Bioconductor
 RColorBrewer                  1.1-2     2014-12-07 [1] CRAN (R 3.6.0)
 Rcpp                          1.0.2     2019-07-25 [1] CRAN (R 3.6.0)
 RCurl                         1.95-4.12 2019-03-04 [1] CRAN (R 3.6.0)
 registry                      0.5-1     2019-03-05 [1] CRAN (R 3.6.0)
 reshape                       0.8.8     2018-10-23 [1] CRAN (R 3.6.0)
 reshape2                      1.4.3     2017-12-11 [1] CRAN (R 3.6.0)
 rlang                         0.4.0     2019-06-25 [1] CRAN (R 3.6.0)
 rngtools                      1.4       2019-07-01 [1] CRAN (R 3.6.0)
 rpart                         4.1-15    2019-04-12 [1] CRAN (R 3.6.1)
 Rsamtools                     2.1.7     2019-10-09 [1] Bioconductor
 RSQLite                       2.1.2     2019-07-24 [1] CRAN (R 3.6.0)
 rstudioapi                    0.10      2019-03-19 [1] CRAN (R 3.6.0)
 rtracklayer                   1.45.6    2019-09-17 [1] Bioconductor
 S4Vectors                     0.23.25   2019-10-02 [1] Bioconductor
 scales                        1.0.0     2018-08-09 [1] CRAN (R 3.6.0)
 sessioninfo                   1.1.1     2018-11-05 [1] CRAN (R 3.6.0)
 shiny                         1.4.0     2019-10-10 [1] CRAN (R 3.6.0)
 stringi                       1.4.3     2019-03-12 [1] CRAN (R 3.6.0)
 stringr                       1.4.0     2019-02-10 [1] CRAN (R 3.6.0)
 SummarizedExperiment          1.15.9    2019-09-11 [1] Bioconductor
 survival                      2.44-1.1  2019-04-01 [1] CRAN (R 3.6.1)
 tibble                        2.1.3     2019-06-06 [1] CRAN (R 3.6.0)
 tidyselect                    0.2.5     2018-10-11 [1] CRAN (R 3.6.0)
 VariantAnnotation             1.31.6    2019-10-11 [1] Bioconductor
 vctrs                         0.2.0     2019-07-05 [1] CRAN (R 3.6.0)
 withr                         2.1.2     2018-03-15 [1] CRAN (R 3.6.0)
 xfun                          0.10      2019-10-01 [1] CRAN (R 3.6.0)
 XML                           3.98-1.20 2019-06-06 [1] CRAN (R 3.6.0)
 xtable                        1.8-4     2019-04-21 [1] CRAN (R 3.6.0)
 XVector                       0.25.0    2019-05-02 [1] Bioconductor
 yaml                          2.2.0     2018-07-25 [1] CRAN (R 3.6.0)
 zeallot                       0.1.0     2018-01-28 [1] CRAN (R 3.6.0)
 zlibbioc                      1.31.0    2019-05-02 [1] Bioconductor

[1] /Library/Frameworks/R.framework/Versions/3.6devel/Resources/library

mtmorgan commented 5 years ago

The master branch of your GitHub repository has been added to Bioconductor's git repository.

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See further instructions at

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to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

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(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("brainflowprobes"). The package 'landing page' will be created at

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mtmorgan commented 5 years ago

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/aprice26.keys is not empty), then no further steps are required. Otherwise, do the following:

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("GenomicState"). The package 'landing page' will be created at

https://bioconductor.org/packages/GenomicState

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.

lcolladotor commented 5 years ago

Hi @lshep (or @nturaga),

Can you give me access to both packages too please? I tried bumping the version for brainflowprobes but ran into:

## brainflowprobes
$ git ci -am "v0.99.11 -- test BioC git"
[master 142e749] v0.99.11 -- test BioC git
 1 file changed, 2 insertions(+), 2 deletions(-)
$ git push; git push upstream
Counting objects: 3, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 331 bytes | 331.00 KiB/s, done.
Total 3 (delta 2), reused 0 (delta 0)
remote: Resolving deltas: 100% (2/2), completed with 2 local objects.
To github.com:LieberInstitute/brainflowprobes.git
   9198f36..142e749  master -> master
FATAL: W any packages/brainflowprobes l.collado-torres DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

## GenomicState
$ git ci -am "v0.99.9 -- test BioC git"
[master 54bf472] v0.99.9 -- test BioC git
 1 file changed, 2 insertions(+), 2 deletions(-)
$ git push; git push upstream
Counting objects: 3, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 328 bytes | 164.00 KiB/s, done.
Total 3 (delta 2), reused 0 (delta 0)
remote: Resolving deltas: 100% (2/2), completed with 2 local objects.
To github.com:LieberInstitute/GenomicState.git
   9d21241..54bf472  master -> master
FATAL: W any packages/GenomicState l.collado-torres DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

My username is l.collado-torres

Thanks, Leo

lshep commented 5 years ago

Done.

lcolladotor commented 5 years ago

Awesome, thanks Lori! It all works now =)

lcolladotor commented 5 years ago

Hi @lshep,

I know that there are a lot of things going on with the BioC v3.10 release, but I just wanted to check with you regarding the release of GenomicState. I didn't see it at https://www.bioconductor.org/news/bioc_3_10_release/ and well, that's why the brainflowprobes builds have been failing. I thought that it was related to the frequency on which annotation packages are built, but maybe there's a simple toggle "on" missing for GenomicState.

Thanks, Leo

lshep commented 5 years ago

I'm sorry this slipped through my radar. Annotation Packages like these can be managed in git but still need to be added to the daily builder manually (we are hoping to have Annotation packages behave more like the other types of packages this release cycle.) @Kayla-Morrell Can you please add this annotation package to the builder ( https://github.com/LieberInstitute/GenomicState.git )

lcolladotor commented 5 years ago

Hehe, no worries Lori and thanks again =)

lcolladotor commented 5 years ago

Thanks @Kayla-Morrell and @lshep! I see that both packages have successfully built on the latest build report ^^.

aprice26 commented 5 years ago

Thanks @Kayla-Morrell, @lshep, @lcolladotor and everyone involved! :D

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