BgeeCall package #1002

jwollbrett · 2019-02-08T18:48:03Z

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Repository: https://github.com/BgeeDB/BgeeCall

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bioc-issue-bot · 2019-02-08T18:48:05Z

Hi @jwollbrett

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: BgeeCall
Type: Package
Title: BgeeCall, a R package for automatic gene expression calls generation
Version: 0.9.9
Date: 2019-02
Author: Julien Wollbrett [aut, cre], Julien Roux [aut, cre], Sara Fonseca Costa[ctb], Frederic Bastien [aut]
Maintainer: Julien Wollbrett <bgee@sib.swiss>
Description: A package using expertise of Bgee to generate present/absent RNA-Seq expression calls from your own RNA-Seq libraries as long as the species is present in Bgee.
Depends: R (>= 3.5.0)
Imports: GenomicFeatures, rhdf5, tximport, Biostrings, rtracklayer, BgeeDB, biomaRt
License: GPL-3
URL: https://github.com/BgeeDB/BgeeCall
BugReports: https://github.com/BgeeDB/BgeeCall/issues
VignetteBuilder: knitr
biocViews: Workflow, GeneExpressionWorkflow
Suggests: knitr, testthat, rmarkdown, AnnotationHub
LazyLoad: yes
RoxygenNote: 6.1.1
NeedsCompilation: no

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bioc-issue-bot · 2019-02-08T22:33:35Z

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bioc-issue-bot · 2019-02-08T22:38:58Z

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.

nturaga · 2019-02-11T14:55:47Z

Hi @jwollbrett ,

Before we do a package review it's important that your package build status is clean on the Single Package builder i.e no WARNINGS, NOTE, ERROR messages.

Please fix them before we are able to continue with a review.

 ## Installation
 In R:
 ``` {r, message = FALSE, warning = FALSE}
 if (!requireNamespace("BiocManager", quietly = TRUE))
-    install.packages("BiocManager")
-BiocManager::install("BgeeCall", version = "3.8")
+       install.packages("BiocManager")
+BiocManager::install("BgeeCall")

Best,

Nitesh

nturaga · 2019-02-21T16:30:50Z

Hi @jwollbrett

You have 2 weeks from today to get back to me regarding improving and getting your package to a reviewable state (i.e no BUILD , CHECK, INSTALL) errors on the build machine. After going through your package briefly, it has multiple issues in the vignette, please fix them all.

The package needs to build on R > 3.6 and BiocManager - version 3.9.

ubuntu:~/github/package_reviews/BgeeCall$ git diff
diff --git a/DESCRIPTION b/DESCRIPTION
index 249bbc1..3994fa2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -6,7 +6,7 @@ Date: 2019-02
 Author: Julien Wollbrett [aut, cre], Julien Roux [aut, cre], Sara Fonseca Costa[ctb], Frederic Bastien [aut]
 Maintainer: Julien Wollbrett <bgee@sib.swiss>
 Description: A package using expertise of Bgee to generate present/absent RNA-Seq expression calls from your own RNA-Seq libraries as long as the species is present in Bgee.
-Depends: R (>= 3.5.0)
+Depends: R (>= 3.6.0)
 Imports: GenomicFeatures, rhdf5, tximport, Biostrings, rtracklayer, BgeeDB, biomaRt
 License: GPL-3
 URL: https://github.com/BgeeDB/BgeeCall
diff --git a/vignettes/bgeecall-manual.Rmd b/vignettes/bgeecall-manual.Rmd
index 479ecc4..93b80a6 100644
--- a/vignettes/bgeecall-manual.Rmd
+++ b/vignettes/bgeecall-manual.Rmd
@@ -49,7 +49,7 @@ In R:
 ``` {r, message = FALSE, warning = FALSE}
 if (!requireNamespace("BiocManager", quietly = TRUE))
     install.packages("BiocManager")
-BiocManager::install("BgeeCall", version = "3.8")
+BiocManager::install("BgeeCall", version = "3.9")

Even after i've updated the versions as needed the vignette still errors out,

> build("BgeeCall/")
✔  checking for file ‘/home/ubuntu/github/package_reviews/BgeeCall/DESCRIPTION’ ...
─  preparing ‘BgeeCall’:
✔  checking DESCRIPTION meta-information ...
─  installing the package to build vignettes
E  creating vignettes (50.8s)
   Bioconductor version 3.9 (BiocManager 1.30.4), R Under development
     (unstable) (2018-11-05 r75543)
   Installing package(s) 'BgeeCall'
   Warning: package 'BgeeCall' is not available (for R Under development)
   Loading required package: BiocGenerics
   Loading required package: parallel
   
   Attaching package: 'BiocGenerics'
   
   The following objects are masked from 'package:parallel':
   
       clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
       clusterExport, clusterMap, parApply, parCapply, parLapply,
       parLapplyLB, parRapply, parSapply, parSapplyLB
   
   The following objects are masked from 'package:stats':
   
       IQR, mad, sd, var, xtabs
   
   The following objects are masked from 'package:base':
   
       Filter, Find, Map, Position, Reduce, anyDuplicated, append,
       as.data.frame, basename, cbind, colMeans, colSums, colnames,
       dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
       intersect, is.unsorted, lapply, mapply, match, mget, order,
       paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans,
       rowSums, rownames, sapply, setdiff, sort, table, tapply,
       union, unique, unsplit, which, which.max, which.min
   
   snapshotDate(): 2019-02-19
   downloading 0 resources
   loading from cache 
       '/home/ubuntu//.AnnotationHub/57527'
   Importing File into R ..
   require("rtracklayer")
   Quitting from lines 90-96 (bgeecall-manual.Rmd) 
   Error: processing vignette 'bgeecall-manual.Rmd' failed with diagnostics:
   Defunct
   Execution halted
Error in processx::run(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout),  : 
  System command error

Please make sure your package is in a runnable state before you submit it for a review. We can close the issue if it takes longer than 2 weeks, and reopen when you are able to actively develop.

Best,

Nitesh

jwollbrett · 2019-02-21T18:58:24Z

Hello Nitesh, I am currently on holiday and will be back the 11th of march. I will solve this build/check problem before the middle of march. Sorry. Julien Le ven. 22 févr. 2019 à 05:30, Nitesh Turaga <notifications@github.com> a écrit :

…

Hi @jwollbrett <https://github.com/jwollbrett> You have 2 weeks from today to get back to me regarding improving and getting your package to a reviewable state (i.e no BUILD , CHECK, INSTALL) errors on the build machine. We can close the issue if it takes longer, and reopen when you are able to actively develop. Best, Nitesh — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1002 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFlVKlylI2FkCD7OFkX-IN3zENfQ2vCsks5vPsm7gaJpZM4axDQQ> .

nturaga · 2019-02-21T19:03:00Z

Hi @jwollbrett ,

That is fine. I'll close the issue and you can reopen it once you are back.

Have a good holiday.

Nitesh

bioc-issue-bot · 2019-03-12T16:36:24Z

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

ba00774 correct warning and notes
3f4cf00 create extdata directory
1656ae2 edit automaticaly generated documentation
7b39249 last vignette correction

jwollbrett · 2019-03-12T16:40:37Z

Hi @nturaga ,

I made some modifications. The package is now building

bioc-issue-bot · 2019-03-12T16:44:38Z

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 · 2019-03-12T17:26:00Z

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

855507a version bump

bioc-issue-bot · 2019-03-12T17:37:44Z

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 · 2019-03-13T08:02:32Z

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

bbac2a8 modify minimum R version to be compatible with Ann...

bioc-issue-bot · 2019-03-13T08:16:43Z

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".
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bioc-issue-bot · 2019-03-14T14:58:57Z

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

775bab9 rerun roxygen
5de95be update examples, vignette and test to be compatibl...
8521cd0 update version number in order to rebuild in Bioco...

bioc-issue-bot · 2019-03-14T15:06:47Z

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.

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bioc-issue-bot · 2019-03-14T15:33:37Z

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

63051dc do not open pdf file

bioc-issue-bot · 2019-03-14T15:51:02Z

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.

jwollbrett · 2019-03-14T16:29:27Z

Hi @nturaga ,

I have an issue with my package.
The build passed for windows (weird as I work on mac..) but failed on mac and linux.
The error on mac looks like that :

dyld: Library not loaded: @rpath/libz.1.dylib
Referenced from: /private/var/folders/gh/37kcv9bj20v2qnpgxq14hh1c0000gq/T/RtmpdziLp3/Rbuild117e75db4ce63/BgeeCall/kallisto/kallisto
Reason: image not found

I am not able to understand where the problem comes from as I never saw this message on my computer. Could you please have a look and confirm that the problem does not come from your devel server?
Could you please also reopen the issue?

Thank you

bioc-issue-bot · 2019-04-15T14:54:46Z

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

17f22b0 add toy transcriptome file
66f0e40 dump version

bioc-issue-bot · 2019-04-15T15:14:34Z

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.

jwollbrett · 2019-04-15T15:15:34Z

Hello,

First of all, thank you for your clear answer.

I added @return with a short description to all functions.
I also optimized runtime of all my examples and tests.
The package is now building/checking without error/warning/timeout.

I still have 6 NOTES remaining.

The overall size of the package is 9Mb. The size of the extdata folder is 8.6Mb
I created a toy dataset (5Mb) allowing to run the main function of the package (and then run kallisto). As kallisto is not installed on your server this toy dataset is not used anymore but I
still describe how to use it in the quick start section of the vignette. In order to allow user to reproduce result present in the vignette I choose to keep it.
Is this overall size ok for you?

I will be available the full week and will be reactive to any suggestion of modification (I know you are busy with the new release)

jwollbrett · 2019-04-18T13:10:31Z

Hello @nturaga ,
The package looks ready for a review 😄
Could you please confirm that the package can still be part of Bioconductor 3.9 (if I am able to quickly manage modification you could ask me to do) ?
Thank you

nturaga · 2019-04-19T20:01:52Z

Review

DESCRIPTION

There can be only one maintainer, [cre] can be used with one person only.

“Authors@R or Author/Maintainer:” fields: Use either Authors@R field or Author: and Maintainer: fields, not both. A maintainer designation (cre for Authors@R ) is required with an actively maintained email. This email will be used for contact regarding an issues that arise with your package in the future. We prefer the Authors@R format giving all the authors with appropriate roles. For persons with an ORCID identifier (See ORCiD for more information) provide the identifier via an element named “ORCID” in the comment argument of person(). Example: person("Lori", "Shepherd", email=Lori.Shepherd@roswellpark.org, role=c("cre", aut"), comment = c(ORCID = "0000-0002-5910-4010")).

Only one person should be listed in the Maintainer field to ensure a single point of contact. This person by default will have commit access to the git repository on git.bioconductor.org. Commit access can be given to other developers by request on the bioc-devel mailing list. Another option is to add collaborators to the github repository. This approach enables development by many but restricts push access to git.bioconductor.org.

http://bioconductor.org/developers/package-guidelines/

NAMESPACE

ok

R

AbundanceMetadata.R: ok
BgeMetadata.R :
- Use getters and setters instead of accessors (@) in your methods.
http://bioconductor.org/developers/package-guidelines/ (Avoid use of direct slot access with @ or slot(). Accessor methods should be created and utilized)
- remove commented code.

Maybe come up with a better way than hardcoding these links? What if
they change? I would suggest a "unit test" in your package where
these links are checked for existence. That way you know from the
build report when these links go invalid so you can change them
either manually or write a function to change them in an automated
fashion.

      kallisto_windows_url = 
      "https://github.com/pachterlab/kallisto/releases/download/v0.45.0/kallisto_windows-v0.45.0.zip",
  kallisto_linux_url = 
      "https://github.com/pachterlab/kallisto/releases/download/v0.45.0/kallisto_linux-v0.45.0.tar.gz",
  kallisto_osx_url = 
      "https://github.com/pachterlab/kallisto/releases/download/v0.45.0/kallisto_mac-v0.45.0.tar.gz",

In listIntergenicRelease.R:
- Some cat statments should be replaced by message
  statements. Unless you want "Downloading...." to go to stdout
  
  The traditional output functions are:
  print()
  cat()
  message()
  warning()
  stop()
  
  The first two functions (print() and cat()) send their output to
  stdout or standard output. The last three functions (message(),
  warning(), and stop()) send their output to stderr or the
  standard error.
  
  It's possible that users would want to write a script and pipe
  the output of your package, since it uses Kallisto, which might
  take time. If you think of it in that regard, you might want to
  take a minute to really think about which messages you want
  going to stdout and std err.
  
  eg:
```
  R -f "script.R" 1> log.out 2> log.err
```
You want to use the function isS4 instead of
typeof(userMetadata[[1]]) == "S4"). It's more robust.
Use seq_along(fastq_files) instead of
seq_len(length(fastq_files))). Note the difference between the
two.

NEWS

Make sure it's parsable by utils::news

vignettes

There is no sessionInfo() call at the end of the vignette. Make sure
you follow the vignette section as closely as possible.

http://bioconductor.org/developers/how-to/buildingPackagesForBioc/#vignettes

http://bioconductor.org/developers/package-guidelines/#vignettes

nturaga · 2019-04-19T20:11:33Z

Hello @nturaga ,
The package looks ready for a review 😄
Could you please confirm that the package can still be part of Bioconductor 3.9 (if I am able to quickly manage modification you could ask me to do) ?
Thank you

Just as additional information, your package is pretty good now, and with a few minor modifications which were suggested in the review you can make it to the next release.

jwollbrett · 2019-04-23T07:25:58Z

Hello @nturaga ,

Thank you for your review.
I saw that submission deadline is Wed 24th (tomorrow).
I will try to fix everything before this evening.

bioc-issue-bot · 2019-04-23T15:32:22Z

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

0b7f19e generate new output file summaryzing S4 slots valu...
b5cf0a6 provide only one maintainer
02b7eb6 test availability of kallisto URLs
8ab29dd remove cat statements
c77fc12 use isS4() function
b652f5e replace seq_len(length(...)) by seq_along(...)
a571c8e solve error
b7fc6ff add sessionInfo to vignette
59a1200 generate useful accessors for BgeeMetadata slots
ceb2060 create accessors for the UserMetadata class
c5efc10 bump version

bioc-issue-bot · 2019-04-23T15:44:59Z

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 build report for more details.

bioc-issue-bot · 2019-04-23T15:50:30Z

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

4c93e78 bump version

jwollbrett · 2019-04-23T15:52:41Z

Hello @nturaga ,

I did some modifications taking into account the comments of your review.

Review

DESCRIPTION

There can be only one maintainer, [cre] can be used with one person only.

“Authors@R or Author/Maintainer:” fields: Use either Authors@R field or Author: and Maintainer: fields, not both. A maintainer designation (cre for Authors@R ) is required with an actively maintained email. This email will be used for contact regarding an issues that arise with your package in the future. We prefer the Authors@R format giving all the authors with appropriate roles. For persons with an ORCID identifier (See ORCiD for more information) provide the identifier via an element named “ORCID” in the comment argument of person(). Example: person("Lori", "Shepherd", email=Lori.Shepherd@roswellpark.org, role=c("cre", aut"), comment = c(ORCID = "0000-0002-5910-4010")).

Only one person should be listed in the Maintainer field to ensure a single point of contact. This person by default will have commit access to the git repository on git.bioconductor.org. Commit access can be given to other developers by request on the bioc-devel mailing list. Another option is to add collaborators to the github repository. This approach enables development by many but restricts push access to git.bioconductor.org.

http://bioconductor.org/developers/package-guidelines/

Done

NAMESPACE

ok

R

AbundanceMetadata.R: ok

BgeMetadata.R :

Use getters and setters instead of accessors (@) in your methods.

http://bioconductor.org/developers/package-guidelines/ (Avoid use of direct slot access with @ or slot(). Accessor methods should be created and utilized)

I created getters/setters for slots of BgeeMetadata and UserMetadata classes that can be used by user.

remove commented code.

Thank you. I totally forgot to reactivate these 3 lines of code.
Done

Maybe come up with a better way than hardcoding these links? What if
they change? I would suggest a "unit test" in your package where
these links are checked for existence. That way you know from the
build report when these links go invalid so you can change them
either manually or write a function to change them in an automated
fashion.
      kallisto_windows_url = 
      "https://github.com/pachterlab/kallisto/releases/download/v0.45.0/kallisto_windows-v0.45.0.zip",
  kallisto_linux_url = 
      "https://github.com/pachterlab/kallisto/releases/download/v0.45.0/kallisto_linux-v0.45.0.tar.gz",
  kallisto_osx_url = 
      "https://github.com/pachterlab/kallisto/releases/download/v0.45.0/kallisto_mac-v0.45.0.tar.gz",

The package already tested that kallisto can be downloaded.
I added a new unit test testing that the URL return a 200 status.

* In listIntergenicRelease.R:

* Some `cat` statments should be replaced by `message`
  statements. Unless you want "Downloading...." to go to stdout
  The traditional output functions are:
  print()
  cat()
  message()
  warning()
  stop()
  The first two functions (print() and cat()) send their output to
  stdout or standard output. The last three functions (message(),
  warning(), and stop()) send their output to stderr or the
  standard error.
  It's possible that users would want to write a script and pipe
  the output of your package, since it uses Kallisto, which might
  take time. If you think of it in that regard, you might want to
  take a minute to really think about which messages you want
  going to stdout and std err.
  eg:
  ```
    R -f "script.R" 1> log.out 2> log.err
  ```

I was not aware of the differences between cat and message. Thank you.
I replaced cat statements by message statements.

You want to use the function isS4 instead of
typeof(userMetadata[[1]]) == "S4"). It's more robust.

Done

Use seq_along(fastq_files) instead of
seq_len(length(fastq_files))). Note the difference between the
two.

Done

NEWS

Make sure it's parsable by utils::news

vignettes

There is no sessionInfo() call at the end of the vignette. Make sure
you follow the vignette section as closely as possible.
http://bioconductor.org/developers/how-to/buildingPackagesForBioc/#vignettes
http://bioconductor.org/developers/package-guidelines/#vignettes

Done

bioc-issue-bot · 2019-04-23T16:04:13Z

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 build report for more details.

nturaga · 2019-04-23T16:09:45Z

Hi @jwollbrett

You are really close to getting your package accepted. Thank you for the helpful commit messages so I can easily review your package.

I need you to fix the WARNING messages though,

* WARNING: Use TRUE/FALSE instead of T/F
      Found in R/ directory functions:
        generate_presence_absence()

Best,

Nitesh

bioc-issue-bot · 2019-04-24T08:26:21Z

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

38ba880 replace T/F by TRUE/FALSE

bioc-issue-bot · 2019-04-24T08:43:58Z

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.

jwollbrett · 2019-04-24T09:11:33Z

Hello @nturaga ,

Sorry for this warning message. Everything build/check well now.
Hope the package can still be part of Bioconductor 3.9 😃

bioc-issue-bot · 2019-04-24T13:46:23Z

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!

mtmorgan · 2019-04-24T21:28:08Z

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/jwollbrett.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("BgeeCall"). The package 'landing page' will be created at

https://bioconductor.org/packages/BgeeCall

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.

bioc-issue-bot added the 1. awaiting moderation label Feb 8, 2019

bioc-issue-bot added 2. review in progress assign a reviewer and a more thorough review of package code and documentation taking place and removed 1. awaiting moderation labels Feb 8, 2019

bioc-issue-bot assigned nturaga Feb 8, 2019

bioc-issue-bot added the ERROR label Feb 8, 2019

nturaga closed this as completed Feb 21, 2019

bioc-issue-bot added VERSION BUMP REQUIRED and removed VERSION BUMP REQUIRED labels Mar 11, 2019

bioc-issue-bot added the VERSION BUMP REQUIRED label Mar 12, 2019

bioc-issue-bot removed the VERSION BUMP REQUIRED label Mar 12, 2019

lshep reopened this Mar 15, 2019

bioc-issue-bot added the ERROR label Apr 15, 2019

bioc-issue-bot added OK and removed ERROR labels Apr 15, 2019

bioc-issue-bot added WARNINGS VERSION BUMP REQUIRED and removed OK VERSION BUMP REQUIRED labels Apr 23, 2019

bioc-issue-bot added OK and removed WARNINGS labels Apr 24, 2019

nturaga added 3a. accepted will be ingested into Bioconductor daily builder for distribution and removed 2. review in progress assign a reviewer and a more thorough review of package code and documentation taking place labels Apr 24, 2019

mtmorgan closed this as completed Apr 24, 2019

BgeeCall package #1002

BgeeCall package #1002

Comments

jwollbrett commented Feb 8, 2019

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nturaga commented Feb 11, 2019 • edited

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nturaga commented Feb 21, 2019

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jwollbrett commented Mar 14, 2019 • edited

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jwollbrett commented Apr 18, 2019

nturaga commented Apr 19, 2019

Review

DESCRIPTION

NAMESPACE

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vignettes

nturaga commented Apr 19, 2019

jwollbrett commented Apr 23, 2019

bioc-issue-bot commented Apr 23, 2019

bioc-issue-bot commented Apr 23, 2019

bioc-issue-bot commented Apr 23, 2019

jwollbrett commented Apr 23, 2019

Review

DESCRIPTION

NAMESPACE

R

NEWS

vignettes

bioc-issue-bot commented Apr 23, 2019

nturaga commented Apr 23, 2019

bioc-issue-bot commented Apr 24, 2019

bioc-issue-bot commented Apr 24, 2019

jwollbrett commented Apr 24, 2019

bioc-issue-bot commented Apr 24, 2019

mtmorgan commented Apr 24, 2019

nturaga commented Feb 11, 2019 •

edited

nturaga commented Feb 21, 2019 •

edited

jwollbrett commented Mar 14, 2019 •

edited