NanoStringNCTools #1815

rvitancol · 2020-12-16T02:24:03Z

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bioc-issue-bot · 2020-12-16T02:24:05Z

Hi @rvitancol

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: NanoStringNCTools
Title: NanoString nCounter Tools
Description: Tools for NanoString Technologies nCounter Technology.
Version: 0.99.0
Encoding: UTF-8
Author: Patrick Aboyoun
Maintainer: Nicole Ortogero <nortogero@nanostring.com>, Zhi Yang <zyang@nanostring.com>
Depends: R (>= 3.6), Biobase, S4Vectors, ggplot2
Imports: BiocGenerics, Biostrings, ggbeeswarm, ggiraph, grDevices, IRanges,
         methods, pheatmap, RColorBrewer, stats, utils
Suggests: biovizBase, ggbio, RUnit, rmarkdown, knitr
License: Artistic-2.0
Collate: SignatureSet-class.R
         RccMetadata.R
         NanoStringRccSet-class.R
         NanoStringRccSet-validity.R
         NanoStringRccSet-accessors.R
         NanoStringRccSet-signatures.R
         NanoStringRccSet-subset.R
         NanoStringRccSet-utils.R
         NanoStringRccSet-summary.R
         NanoStringRccSet-qc.R
         NanoStringRccSet-normalize.R
         NanoStringRccSet-munge.R
         NanoStringRccSet-ggplot.R
         NanoStringRccSet-autoplot.R
         readRccFile.R
         readRlfFile.R
         readNanoStringRccSet.R
         writeNanoStringRccSet.R
         utils.R
         zzz.R
biocViews: GeneExpression, Transcription, CellBasedAssays, DataImport, 
 Transcriptomics, Proteomics, mRNAMicroarray, 
 ProprietaryPlatforms, RNASeq
VignetteEngine: knitr
VignetteBuilder: knitr

bioc-issue-bot · 2020-12-16T22:33:10Z

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bioc-issue-bot · 2020-12-16T22:58:49Z

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rvitancol · 2020-12-18T01:50:57Z

AdditionalPackage: https://github.com/Nanostring-Biostats/GeomxTools

bioc-issue-bot · 2020-12-18T01:50:59Z

Hi @rvitancol,
Thanks for submitting your additional package: https://github.com/Nanostring-Biostats/GeomxTools.
We are taking a quick look at it and you will hear back from us soon.

bioc-issue-bot · 2020-12-18T06:56:07Z

Additional Package has been approved for building.

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bioc-issue-bot · 2020-12-18T07:08:46Z

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bioc-issue-bot · 2020-12-18T20:21:28Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 7e152ffe7afda60d1f72a202391225266a8f724f

bioc-issue-bot · 2020-12-18T20:34:22Z

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bioc-issue-bot · 2020-12-18T21:27:13Z

Received a valid push on git.bioconductor.org; starting a build for commit id: ff1d1eb312c96d092154f4d3a713a86c4e5de7b6

bioc-issue-bot · 2020-12-18T21:35:36Z

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bioc-issue-bot · 2020-12-18T23:05:02Z

Received a valid push on git.bioconductor.org; starting a build for commit id: f4d30c6cb8fb1539635bd12e417837d4b7fa6706

bioc-issue-bot · 2020-12-18T23:15:35Z

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bioc-issue-bot · 2020-12-18T23:39:42Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 982d3bc731fbefd4ccd559af0a71a8322404d2da

bioc-issue-bot · 2020-12-18T23:43:35Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 7d83cdedda9150ecaedc746042082b552aac7566

bioc-issue-bot · 2020-12-18T23:48:28Z

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

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bioc-issue-bot · 2020-12-18T23:55:06Z

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

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rvitancol · 2020-12-21T18:37:34Z

Hi @nturaga, can we ask for the check.log from the R CMD check for the Windows build for GeomxTools? The error in the build report does not give us a clue where the error happens and this does not appear in our local R CMD CHECK.
This is the build error report excerpt:
< * checking whether package 'GeomxTools' can be installed ... ERROR>
<Installation failed.>
<See> <'C:/Users/pkgbuild/packagebuilder/workers/jobs/1815/982d3bc731fbefd4ccd559af0a71a8322404d2da/GeomxTools.Rcheck/00install.out' for details.>
<* DONE>

<Status: 1 ERROR>
<See>
<'C:/Users/pkgbuild/packagebuilder/workers/jobs/1815/982d3bc731fbefd4ccd559af0a71a8322404d2da/GeomxTools.Rcheck/00check.log'>
<for details.>

bioc-issue-bot · 2020-12-21T20:09:48Z

Received a valid push on git.bioconductor.org; starting a build for commit id: d914164ce3c745bf8a58d20e686b04d2dd0da0f7

bioc-issue-bot · 2020-12-21T20:23:20Z

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

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rvitancol · 2020-12-21T21:31:11Z

Notes on warnings and error related to R version: Tested these packages on the latest version of R, but we also require that they work on an older version (Depends: R (>= 3.6) for a report tool we use internally. The packages have undergone internal V&V as part of the report that we use internally.
Notes on warnings related to using "<-" in documentation: Replacement methods with "<-" causes an error in html since these are illegal symbols in file names on windows. Can we set the check to ignore these?

bioc-issue-bot · 2020-12-21T21:49:15Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 3512b5565d3aaa97cfc8566b96c444dd92ee7d8b

bioc-issue-bot · 2020-12-21T21:53:40Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 82d41fd6e8405c92fac6d1c52e10e86437f88c16

bioc-issue-bot · 2020-12-21T21:57:19Z

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Your package has been built on Linux, Mac, and Windows.

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bioc-issue-bot · 2020-12-21T22:11:27Z

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

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nturaga · 2020-12-23T08:10:48Z

Notes on warnings and error related to R version: Tested these packages on the latest version of R, but we also require that they work on an older version (Depends: R (>= 3.6) for a report tool we use internally. The packages have undergone internal V&V as part of the report that we use internally.
Notes on warnings related to using "<-" in documentation: Replacement methods with "<-" causes an error in html since these are illegal symbols in file names on windows. Can we set the check to ignore these?

Yes, you can ignore these.

nturaga · 2020-12-23T14:18:19Z

NanoStringNCTools review

R CMD build

ok

R CMD check

ok

DESCRIPTION

ok

NAMESPACE

being done manually, instead of by roxygen2. Please make sure
functions/clases exported are all needed.

Build report warnings

WARNING: It seems you want to keep using R 3.6, and it's generating
a warning. So ignore this one.
NOTE: These are the NOTES i'm particular about, please address
these. The rest of them are also solvable for the most part (at
least the ones you see on the linux builder)
```
* NOTE: Avoid sapply(); use vapply()
```

* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
geom_beeswarm_interactive.Rd, SignatureSet.Rd

* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.

The windows build machine issue can be addressed by @hpages better.

R

There is a NOTE about indentation too(2 spaces vs 4 spaces), please
check http://bioconductor.org/developers/how-to/coding-style/ .
Remove commented out lines of code.
I'm not sure why your zzz.R has the 'testPackage' function called
inside of it. This usually isn't the way zzz.R is used.

tests
- ok
man
ok

vignette

ok

hpages · 2020-12-30T22:32:36Z

Hi @nturaga , @rvitancol ,

The error on Windows seems to have occurred during R CMD INSTALL. Unfortunately the SBP doesn't show the output of this command so we don't have any details about this error. FWIW I can run R CMD INSTALL on NanoStringNCTools without any problem on riesling1 (another Windows builder, similar to tokay2). So I'd say let's just ignore the error reported by the SPB. We'll see how it goes the next time the SPB tries to build/check the package which should happen the next time its version gets bumped.

H.

bioc-issue-bot · 2021-01-06T19:41:00Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 9c451811389d10403d86bf1494e4d45a6ee8cdd4

bioc-issue-bot · 2021-01-06T20:10:48Z

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

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bioc-issue-bot · 2021-01-06T21:40:02Z

Received a valid push on git.bioconductor.org; starting a build for commit id: c6bd6f9dc9aa6ed79805e756f30edbcc20b306fa

bioc-issue-bot · 2021-01-06T21:45:39Z

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NicoleEO · 2021-01-06T22:53:47Z

@nturaga I believe our packages are ready to go.
We have addressed the notes you highlighted above with the exception of one sapply that is used in a function that extends sapply to our class for users.
I did receive the below error in the last build, which seems to be an issue unrelated to our package.

In regards to our Additional Package, GeomxTools, it failed the build at the last check only because of R version requirements (3.6) so this one should also be ready.

bioc-issue-bot · 2021-01-12T20:50:05Z

Received a valid push on git.bioconductor.org; starting a build for commit id: d2eb6cc4bba5258a5f8ccd73fb4d025ad7893b9d

bioc-issue-bot · 2021-01-12T21:03:58Z

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

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nturaga · 2021-01-22T05:29:41Z

Hi @NicoleEO ,

There is still one sapply() you have to fix in: NanoStringRccSet-utils.R (line 75, column 5). I'm otherwise ok with the changes you've made.
I'm actually not sure how I can accept this package as there is no build tarball produced on the Linux machine. @lshep or @hpages can answer maybe?

lshep · 2021-01-22T11:55:28Z

@nturaga why do you say there is no build tarball produced for Linux? The package only has a check warning for Linux. The package didn't build for Mac and as we explained multiple times this is likely do to Mac binaries not being produced on CRAN yet for Rdevel and should be ignored. This is confirmed by searching for the package not available https://cran.r-project.org/web/packages/ggiraph/index.html . Please ignore the Mac error and accept based on the other two build reports.

NicoleEO · 2021-01-22T17:27:24Z

@nturaga the last sapply is used to extend sapply to our class for users. Would it be possible to pass this one by as it is purposely kept as sapply to allow the user flexibility with unknown data types they may apply on?

nturaga · 2021-01-22T17:37:42Z

That's fine. We suggest vapply() to specify "return" type rather than input type. Whatever you are writing with sapply, you can write with vapply.

bioc-issue-bot · 2021-01-22T17:37:54Z

Your package has been accepted. It will be added to the
Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

NicoleEO · 2021-01-22T18:22:57Z

@nturaga thanks for accepting. Does this also automatically apply to our additional package as well?

nturaga · 2021-01-22T21:07:38Z

Yes.

…

On Fri, Jan 22, 2021 at 8:23 AM Nicole Ortogero ***@***.***> wrote: @nturaga <https://github.com/nturaga> thanks for accepting. Does this also automatically apply to our additional package as well? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1815 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAU6QSYEKXNMIS6L4UV7EI3S3G7BDANCNFSM4U5I3FMQ> .

mtmorgan · 2021-01-23T22:33:46Z

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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("NanoStringNCTools"). The package 'landing page' will be created at

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mtmorgan · 2021-01-23T22:33:53Z

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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("GeomxTools"). The package 'landing page' will be created at

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bioc-issue-bot added the 1. awaiting moderation submitted and waiting clearance to access resources label Dec 16, 2020

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zhiiiyang mentioned this issue Dec 28, 2020

Comments from the Bioconductor reviewer Nanostring-Biostats/NanoStringNCTools#5

Closed

8 tasks

bioc-issue-bot removed the WARNINGS label Jan 6, 2021

bioc-issue-bot added the WARNINGS label Jan 6, 2021

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 Jan 22, 2021

mtmorgan closed this as completed Jan 23, 2021

NanoStringNCTools #1815

NanoStringNCTools #1815

Comments

rvitancol commented Dec 16, 2020

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nturaga commented Dec 23, 2020

nturaga commented Dec 23, 2020

NanoStringNCTools review

R CMD build

R CMD check

DESCRIPTION

NAMESPACE

Build report warnings

R

tests

man

vignette

hpages commented Dec 30, 2020

bioc-issue-bot commented Jan 6, 2021

bioc-issue-bot commented Jan 6, 2021

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