[Bioc-devel] merge the release and the dev version to eliminate errors
Obenchain, Valerie
V@lerie@Obench@in @ending from Ro@wellP@rk@org
Sun Nov 25 16:36:07 CET 2018
Hi Irene,
I'll look into it.
Valerie
On 11/23/18 6:06 PM, Irene Zeng wrote:
> Hi,
> I am trying to fix the package on new dev 3.9. The errors appears to be different from what it is in the release version 3.8.
> The errors in 3.9 is in window system, while the errors in 3.8 are in the other two systems. Is there a way I can merge these two?
>
> https://master.bioconductor.org/checkResults/3.8/bioc-LATEST/mlm4omics/malbec1-install.html
> http://bioconductor.org/checkResults/devel/bioc-LATEST/mlm4omics/
>
>
> I saw the report in 3.9 were all okay once, after I pushed the changes. Now , the vignette seems to have errors. Please advise,
>
>
> Irene SL Zeng
>
>
> ________________________________________
> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of bioc-devel-request using r-project.org <bioc-devel-request using r-project.org>
> Sent: Friday, 23 November 2018 12:05 a.m.
> To: bioc-devel using r-project.org
> Subject: Bioc-devel Digest, Vol 176, Issue 22
>
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> Today's Topics:
>
> 1. Cannot access remote upstream after changing the laptop
> (Tang, Wenhao)
> 2. Re: Cannot access remote upstream after changing the laptop
> (Shepherd, Lori)
> 3. Re: Cannot access remote upstream after changing the laptop
> (Turaga, Nitesh)
> 4. =?gb2312?b?tPC4tDogIENhbm5vdCBhY2Nlc3MgcmVtb3RlIHVw?=
> =?gb2312?b?c3RyZWFtIGFmdGVyIGNoYW5naW5nIHRoZSBsYXB0b3A=?=
> (Tang, Wenhao)
> 5. R 3.6 Compiling issues, are there any binaries available?
> (Casper Peters)
> 6. Re: 80% of man pages must have runnable examples (package
> with numerous Shiny apps) (L Rutter)
> 7. Re: 80% of man pages must have runnable examples (package
> with numerous Shiny apps) (Kevin RUE)
> 8. Re: Cannot access remote upstream after changing the laptop
> (Dario Strbenac)
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 21 Nov 2018 13:27:47 +0000
> From: "Tang, Wenhao" <wenhao.tang15 using imperial.ac.uk>
> To: "bioc-devel using r-project.org" <bioc-devel using r-project.org>
> Subject: [Bioc-devel] Cannot access remote upstream after changing the
> laptop
> Message-ID:
> <AM0PR06MB506060B872E33D788CD521CECDDA0 using AM0PR06MB5060.eurprd06.prod.outlook.com>
>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
>
>
> I am using a new laptop right now, and would like to update package using it. However I can no longer access the upstream when I "git fetch --all":
>
>
> wt215 using DESKTOP-JB3QDC1 MINGW64 /d/RNAseqProject/bayNorm_dev/bayNorm (master)
> $ git remote -v
> origin https://github.com/WT215/bayNorm.git (fetch)
> origin https://github.com/WT215/bayNorm.git (push)
> upstream git using git.bioconductor.org:packages/bayNorm.git (fetch)
> upstream git using git.bioconductor.org:packages/bayNorm.git (push)
>
> wt215 using DESKTOP-JB3QDC1 MINGW64 /d/RNAseqProject/bayNorm_dev/bayNorm (master)
> $ git fetch --all
> Fetching origin
> Fetching upstream
> git using git.bioconductor.org: Permission denied (publickey).
> fatal: Could not read from remote repository.
>
> Please make sure you have the correct access rights
> and the repository exists.
> error: Could not fetch upstream
>
> Because I am using a new machine, the local SSH information may lost, which is highly likely the cause. May I ask what should I do? Thanks a lot!
>
> Best wishes,
> Wenhao
>
>
>
>
>
> [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 21 Nov 2018 13:31:32 +0000
> From: "Shepherd, Lori" <Lori.Shepherd using RoswellPark.org>
> To: "Tang, Wenhao" <wenhao.tang15 using imperial.ac.uk>,
> "bioc-devel using r-project.org" <bioc-devel using r-project.org>
> Subject: Re: [Bioc-devel] Cannot access remote upstream after changing
> the laptop
> Message-ID:
> <MW2PR12MB2364E51ED9736E0DAAE352BFF9DA0 using MW2PR12MB2364.namprd12.prod.outlook.com>
>
> Content-Type: text/plain; charset="utf-8"
>
> You can log onto the Git Credentials App at any time and add new/additional ssh-keys
>
>
> https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> ________________________________
> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Tang, Wenhao <wenhao.tang15 using imperial.ac.uk>
> Sent: Wednesday, November 21, 2018 8:27:47 AM
> To: bioc-devel using r-project.org
> Subject: [Bioc-devel] Cannot access remote upstream after changing the laptop
>
> Hi,
>
>
> I am using a new laptop right now, and would like to update package using it. However I can no longer access the upstream when I "git fetch --all":
>
>
> wt215 using DESKTOP-JB3QDC1 MINGW64 /d/RNAseqProject/bayNorm_dev/bayNorm (master)
> $ git remote -v
> origin https://github.com/WT215/bayNorm.git (fetch)
> origin https://github.com/WT215/bayNorm.git (push)
> upstream git using git.bioconductor.org:packages/bayNorm.git (fetch)
> upstream git using git.bioconductor.org:packages/bayNorm.git (push)
>
> wt215 using DESKTOP-JB3QDC1 MINGW64 /d/RNAseqProject/bayNorm_dev/bayNorm (master)
> $ git fetch --all
> Fetching origin
> Fetching upstream
> git using git.bioconductor.org: Permission denied (publickey).
> fatal: Could not read from remote repository.
>
> Please make sure you have the correct access rights
> and the repository exists.
> error: Could not fetch upstream
>
> Because I am using a new machine, the local SSH information may lost, which is highly likely the cause. May I ask what should I do? Thanks a lot!
>
> Best wishes,
> Wenhao
>
>
>
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
> [[alternative HTML version deleted]]
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 21 Nov 2018 13:34:26 +0000
> From: "Turaga, Nitesh" <Nitesh.Turaga using RoswellPark.org>
> To: "Tang, Wenhao" <wenhao.tang15 using imperial.ac.uk>
> Cc: "bioc-devel using r-project.org" <bioc-devel using r-project.org>
> Subject: Re: [Bioc-devel] Cannot access remote upstream after changing
> the laptop
> Message-ID: <5F58A9D5-36A6-46C6-8B81-74CB4ADB91E0 using roswellpark.org>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> You should log in to the BiocCredentials app with the correct email registered on your package. You should then generate new keys on your laptop, and upload them on the BiocCredentials app.
>
> This will allow you to access your package again.
>
> http://bioconductor.org/developers/how-to/git/
>
> Best,
>
> Nitesh
>
>
>
>> On Nov 21, 2018, at 8:27 AM, Tang, Wenhao <wenhao.tang15 using imperial.ac.uk> wrote:
>>
>> Hi,
>>
>>
>> I am using a new laptop right now, and would like to update package using it. However I can no longer access the upstream when I "git fetch --all":
>>
>>
>> wt215 using DESKTOP-JB3QDC1 MINGW64 /d/RNAseqProject/bayNorm_dev/bayNorm (master)
>> $ git remote -v
>> origin https://github.com/WT215/bayNorm.git (fetch)
>> origin https://github.com/WT215/bayNorm.git (push)
>> upstream git using git.bioconductor.org:packages/bayNorm.git (fetch)
>> upstream git using git.bioconductor.org:packages/bayNorm.git (push)
>>
>> wt215 using DESKTOP-JB3QDC1 MINGW64 /d/RNAseqProject/bayNorm_dev/bayNorm (master)
>> $ git fetch --all
>> Fetching origin
>> Fetching upstream
>> git using git.bioconductor.org: Permission denied (publickey).
>> fatal: Could not read from remote repository.
>>
>> Please make sure you have the correct access rights
>> and the repository exists.
>> error: Could not fetch upstream
>>
>> Because I am using a new machine, the local SSH information may lost, which is highly likely the cause. May I ask what should I do? Thanks a lot!
>>
>> Best wishes,
>> Wenhao
>>
>>
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 21 Nov 2018 13:43:02 +0000
> From: "Tang, Wenhao" <wenhao.tang15 using imperial.ac.uk>
> To: "Turaga, Nitesh" <Nitesh.Turaga using RoswellPark.org>
> Cc: "bioc-devel using r-project.org" <bioc-devel using r-project.org>
> Subject: [Bioc-devel]
> =?gb2312?b?tPC4tDogIENhbm5vdCBhY2Nlc3MgcmVtb3RlIHVw?=
> =?gb2312?b?c3RyZWFtIGFmdGVyIGNoYW5naW5nIHRoZSBsYXB0b3A=?=
> Message-ID:
> <AM0PR06MB5060E18C5870BD19B7940074CDDA0 using AM0PR06MB5060.eurprd06.prod.outlook.com>
>
> Content-Type: text/plain; charset="utf-8"
>
> Thank you Nitesh and Lori, it works!
>
>
> Best wishes,
>
> Wenhao
>
> ________________________________
> ������: Turaga, Nitesh <Nitesh.Turaga using RoswellPark.org>
> ����ʱ��: 2018��11��21�� 21:34:26
> �ռ���: Tang, Wenhao
> ����: bioc-devel using r-project.org
> ����: Re: [Bioc-devel] Cannot access remote upstream after changing the laptop
>
> Hi,
>
> You should log in to the BiocCredentials app with the correct email registered on your package. You should then generate new keys on your laptop, and upload them on the BiocCredentials app.
>
> This will allow you to access your package again.
>
> http://bioconductor.org/developers/how-to/git/
>
> Best,
>
> Nitesh
>
>
>
>> On Nov 21, 2018, at 8:27 AM, Tang, Wenhao <wenhao.tang15 using imperial.ac.uk> wrote:
>>
>> Hi,
>>
>>
>> I am using a new laptop right now, and would like to update package using it. However I can no longer access the upstream when I "git fetch --all":
>>
>>
>> wt215 using DESKTOP-JB3QDC1 MINGW64 /d/RNAseqProject/bayNorm_dev/bayNorm (master)
>> $ git remote -v
>> origin https://github.com/WT215/bayNorm.git (fetch)
>> origin https://github.com/WT215/bayNorm.git (push)
>> upstream git using git.bioconductor.org:packages/bayNorm.git (fetch)
>> upstream git using git.bioconductor.org:packages/bayNorm.git (push)
>>
>> wt215 using DESKTOP-JB3QDC1 MINGW64 /d/RNAseqProject/bayNorm_dev/bayNorm (master)
>> $ git fetch --all
>> Fetching origin
>> Fetching upstream
>> git using git.bioconductor.org: Permission denied (publickey).
>> fatal: Could not read from remote repository.
>>
>> Please make sure you have the correct access rights
>> and the repository exists.
>> error: Could not fetch upstream
>>
>> Because I am using a new machine, the local SSH information may lost, which is highly likely the cause. May I ask what should I do? Thanks a lot!
>>
>> Best wishes,
>> Wenhao
>>
>>
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
>
> [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 21 Nov 2018 15:10:30 +0000
> From: Casper Peters <cp100u using hotmail.com>
> To: "bioc-devel using r-project.org" <bioc-devel using r-project.org>
> Subject: [Bioc-devel] R 3.6 Compiling issues, are there any binaries
> available?
> Message-ID:
> <AM0PR05MB52048CB650E5FB251906A13398DA0 using AM0PR05MB5204.eurprd05.prod.outlook.com>
>
> Content-Type: text/plain; charset="utf-8"
>
> Hello!
>
>
> So I am developing an R package for future Bioconductor use, and saw I needed R3.6.
>
> I am having trouble getting the latest snapshot to compile and was wondering if there are any binaries available.
>
>
> I also posted on the forums; https://support.bioconductor.org/p/115331/
>
> I used the following params to configure the make files;
>
>
> ```
>
> ./configure --with-x=no --enable-R-shlib
>
> ```
>
> configuration ends correctly, but I then proceed to get the following make error;
>
>
> ```
>
> /usr/bin/ld: CommandLineArgs.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC CommandLineArgs.o: error adding symbols: Bad value collect2: error: ld returned 1 exit status
>
> ```
>
> This seems to have to do with improperly defined C libraries for 32/64 bit?
>
>
> I used the tar.gz from the 21st Nov 2018. Downloaded the tar here; https://stat.ethz.ch/R/daily/.
>
>
> Is there any other snapshot that is known for working properly?
>
>
> Thanks in advance for any response.
>
>
> With kind regards,
>
>
> Casper
>
> [[alternative HTML version deleted]]
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 21 Nov 2018 11:29:17 -0500
> From: L Rutter <lindsayannerutter using gmail.com>
> To: kevinrue67 using gmail.com
> Cc: Lori.Shepherd using roswellpark.org, bioc-devel using r-project.org
> Subject: Re: [Bioc-devel] 80% of man pages must have runnable
> examples (package with numerous Shiny apps)
> Message-ID:
> <CADobdkpFkNxVh2kdc-ZYGqBF8PKr=fQ7Mo8b6s_spO6P8F=VNg using mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Lori and Kevin:
>
> Thank you for your helpful responses! I was able to use "if
> (interactive()) { ... }" format and return the appDir object for the
> user. Thanks again!
>
> Lindsay
> On Mon, Nov 19, 2018 at 3:02 PM Kevin RUE <kevinrue67 using gmail.com> wrote:
>>
>> Hi Lindsay,
>>
>> Check out https://github.com/csoneson/iSEE/blob/master/R/iSEE-main.R function "iSEE" for an example of both the function return value, and the man page.
>>
>> First, I would suggest that your function _returns_ the "appDir" object to the user, and that you leave it to the user to call "shiny::runApp" with options appropriate to their system or preferences (e.g launch.browser=FALSE, port=1234, etc).
>>
>> Second, for the man page, you don't have to put the _entire_ @example block inside \dontrun{}. You can put everything that doesn't launch the Shiny app outside the \dontrun{} block and only put the one "shiny" line inside the \dontrun{}. The one line will represent less than 80% of the man page.
>>
>> However, even better, you can avoid the \dontrun{} option altogether and put the "shiny" statement within a "if (interactive()) { ... }" block.
>>
>> So adapting you existing code, I would have
>> #' @examples
>> #' # Example 1: Create an interactive litre plot for the logged data using
>> #' # default background of hexagons.
>> #'
>> #' data(soybean_ir_sub)
>> #' data(soybean_ir_sub_metrics)
>> #' soybean_ir_sub_log <- soybean_ir_sub
>> #' soybean_ir_sub_log[,-1] <- log(soybean_ir_sub[,-1]+1)
>> #' if (interactive()){
>> #' plotLitreApp(data = soybean_ir_sub_log, dataMetrics = soybean_ir_sub_metrics)
>> #' }
>> #'
>> #' # Example 2: Repeat the same process, only now plot background data as
>> #' # individual points. Note this may be too slow now that all points are drawn
>> #' # in the background.
>> #' if (interactive()){
>> #' plotLitreApp(data = soybean_ir_sub_log, dataMetrics = soybean_ir_sub_metrics,
>> #' option = "allPoints", pointColor = "red")
>> #' }
>>
>> However, once more, I suggest that you return "appDir", and you would then have something like:
>> #' app <- plotLitreApp(data = soybean_ir_sub_log, dataMetrics = soybean_ir_sub_metrics)
>> #' if (interactive()){
>> #' shiny::runApp(app, [options defined by your user])
>> #' }
>>
>> I hope this helps. Otherwise, let me know and I can chime in the review of your package
>>
>> Best wishes
>> Kevin
>>
>> On Mon, Nov 19, 2018 at 7:00 PM Shepherd, Lori <Lori.Shepherd using roswellpark.org> wrote:
>>>
>>> Submit with the dontrun{} and temporarily ignore the ERROR - when submitting please reference the explanation below. Your reviewer could provide more information and will decide how to proceed - generally examples will be run manually to check for accuracy and an exception can be made.
>>>
>>>
>>> Lori Shepherd
>>>
>>> Bioconductor Core Team
>>>
>>> Roswell Park Cancer Institute
>>>
>>> Department of Biostatistics & Bioinformatics
>>>
>>> Elm & Carlton Streets
>>>
>>> Buffalo, New York 14263
>>>
>>> ________________________________
>>> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of L Rutter <lindsayannerutter using gmail.com>
>>> Sent: Monday, November 19, 2018 1:49:50 PM
>>> To: bioc-devel using r-project.org
>>> Subject: [Bioc-devel] 80% of man pages must have runnable examples (package with numerous Shiny apps)
>>>
>>> Hello all:
>>>
>>> I am planning to submit a package to Bioconductor and have one last
>>> item from BiocCheck (error, warning, note) I have been unable to
>>> resolve:
>>>
>>> ERROR: At least 80% of man pages documenting exported objects must
>>> have runnable examples. The following pages do not: plotLitreApp.Rd,
>>> plotPCPApp.Rd, plotSMApp.Rd, plotVolcanoApp.Rd
>>>
>>> I have 18 man pages (9 function-related, 8 data-related, and 1
>>> package-related). Of these, 4 of the function-related man pages (the
>>> ones listed in the ERROR) are Shiny applications of the following
>>> format:
>>>
>>> appDir <- system.file("shiny-examples", "plotLitreApp", package = "bigPint")
>>> shiny::runApp(appDir, display.mode = "normal")
>>>
>>> If I do not have \dontrun{} around these shiny app examples, then R
>>> CMD check permanently halts on the "checking examples..." step. If I
>>> do have \dontrun{} around these shiny app examples, then R CMD
>>> BiocCheck gives me the error above. My question is: What is the
>>> recommended procedure in such a situation where the package is being
>>> prepared for Bioconductor submission?
>>>
>>> An example of one script causing the error can be found at:
>>> https://github.com/lrutter/bigPint/blob/master/R/plotLitreApp.R
>>>
>>> Thank you for any advice!
>>> Lindsay
>>>
>>> _______________________________________________
>>> Bioc-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>> This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Wed, 21 Nov 2018 18:10:36 +0000
> From: Kevin RUE <kevinrue67 using gmail.com>
> To: L Rutter <lindsayannerutter using gmail.com>
> Cc: "Shepherd, Lori" <Lori.Shepherd using roswellpark.org>, bioc-devel
> <bioc-devel using r-project.org>
> Subject: Re: [Bioc-devel] 80% of man pages must have runnable
> examples (package with numerous Shiny apps)
> Message-ID:
> <CAJ3Kd8v=7eePXO5enbKG=A7i1oX9Ch_G0OvDoUf_QL4HAiEQkQ using mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Glad to be of help!
>
> Nice package too! I managed to install it and give it a run!
>
> Best wishes,
> Kevin
>
> On Wed, Nov 21, 2018 at 4:29 PM L Rutter <lindsayannerutter using gmail.com>
> wrote:
>
>> Hi Lori and Kevin:
>>
>> Thank you for your helpful responses! I was able to use "if
>> (interactive()) { ... }" format and return the appDir object for the
>> user. Thanks again!
>>
>> Lindsay
>> On Mon, Nov 19, 2018 at 3:02 PM Kevin RUE <kevinrue67 using gmail.com> wrote:
>>>
>>> Hi Lindsay,
>>>
>>> Check out https://github.com/csoneson/iSEE/blob/master/R/iSEE-main.R
>> function "iSEE" for an example of both the function return value, and the
>> man page.
>>>
>>> First, I would suggest that your function _returns_ the "appDir" object
>> to the user, and that you leave it to the user to call "shiny::runApp" with
>> options appropriate to their system or preferences (e.g
>> launch.browser=FALSE, port=1234, etc).
>>>
>>> Second, for the man page, you don't have to put the _entire_ @example
>> block inside \dontrun{}. You can put everything that doesn't launch the
>> Shiny app outside the \dontrun{} block and only put the one "shiny" line
>> inside the \dontrun{}. The one line will represent less than 80% of the man
>> page.
>>>
>>> However, even better, you can avoid the \dontrun{} option altogether and
>> put the "shiny" statement within a "if (interactive()) { ... }" block.
>>>
>>> So adapting you existing code, I would have
>>> #' @examples
>>> #' # Example 1: Create an interactive litre plot for the logged data
>> using
>>> #' # default background of hexagons.
>>> #'
>>> #' data(soybean_ir_sub)
>>> #' data(soybean_ir_sub_metrics)
>>> #' soybean_ir_sub_log <- soybean_ir_sub
>>> #' soybean_ir_sub_log[,-1] <- log(soybean_ir_sub[,-1]+1)
>>> #' if (interactive()){
>>> #' plotLitreApp(data = soybean_ir_sub_log, dataMetrics =
>> soybean_ir_sub_metrics)
>>> #' }
>>> #'
>>> #' # Example 2: Repeat the same process, only now plot background data as
>>> #' # individual points. Note this may be too slow now that all points
>> are drawn
>>> #' # in the background.
>>> #' if (interactive()){
>>> #' plotLitreApp(data = soybean_ir_sub_log, dataMetrics =
>> soybean_ir_sub_metrics,
>>> #' option = "allPoints", pointColor = "red")
>>> #' }
>>>
>>> However, once more, I suggest that you return "appDir", and you would
>> then have something like:
>>> #' app <- plotLitreApp(data = soybean_ir_sub_log, dataMetrics =
>> soybean_ir_sub_metrics)
>>> #' if (interactive()){
>>> #' shiny::runApp(app, [options defined by your user])
>>> #' }
>>>
>>> I hope this helps. Otherwise, let me know and I can chime in the review
>> of your package
>>>
>>> Best wishes
>>> Kevin
>>>
>>> On Mon, Nov 19, 2018 at 7:00 PM Shepherd, Lori <
>> Lori.Shepherd using roswellpark.org> wrote:
>>>>
>>>> Submit with the dontrun{} and temporarily ignore the ERROR - when
>> submitting please reference the explanation below. Your reviewer could
>> provide more information and will decide how to proceed - generally
>> examples will be run manually to check for accuracy and an exception can be
>> made.
>>>>
>>>>
>>>> Lori Shepherd
>>>>
>>>> Bioconductor Core Team
>>>>
>>>> Roswell Park Cancer Institute
>>>>
>>>> Department of Biostatistics & Bioinformatics
>>>>
>>>> Elm & Carlton Streets
>>>>
>>>> Buffalo, New York 14263
>>>>
>>>> ________________________________
>>>> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of L
>> Rutter <lindsayannerutter using gmail.com>
>>>> Sent: Monday, November 19, 2018 1:49:50 PM
>>>> To: bioc-devel using r-project.org
>>>> Subject: [Bioc-devel] 80% of man pages must have runnable examples
>> (package with numerous Shiny apps)
>>>>
>>>> Hello all:
>>>>
>>>> I am planning to submit a package to Bioconductor and have one last
>>>> item from BiocCheck (error, warning, note) I have been unable to
>>>> resolve:
>>>>
>>>> ERROR: At least 80% of man pages documenting exported objects must
>>>> have runnable examples. The following pages do not: plotLitreApp.Rd,
>>>> plotPCPApp.Rd, plotSMApp.Rd, plotVolcanoApp.Rd
>>>>
>>>> I have 18 man pages (9 function-related, 8 data-related, and 1
>>>> package-related). Of these, 4 of the function-related man pages (the
>>>> ones listed in the ERROR) are Shiny applications of the following
>>>> format:
>>>>
>>>> appDir <- system.file("shiny-examples", "plotLitreApp", package =
>> "bigPint")
>>>> shiny::runApp(appDir, display.mode = "normal")
>>>>
>>>> If I do not have \dontrun{} around these shiny app examples, then R
>>>> CMD check permanently halts on the "checking examples..." step. If I
>>>> do have \dontrun{} around these shiny app examples, then R CMD
>>>> BiocCheck gives me the error above. My question is: What is the
>>>> recommended procedure in such a situation where the package is being
>>>> prepared for Bioconductor submission?
>>>>
>>>> An example of one script causing the error can be found at:
>>>> https://github.com/lrutter/bigPint/blob/master/R/plotLitreApp.R
>>>>
>>>> Thank you for any advice!
>>>> Lindsay
>>>>
>>>> _______________________________________________
>>>> Bioc-devel using r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>>
>>>> This email message may contain legally privileged and/or confidential
>> information. If you are not the intended recipient(s), or the employee or
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>> distribution, or use of this email message is prohibited. If you have
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>>>> [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
>>>> Bioc-devel using r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
> [[alternative HTML version deleted]]
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Thu, 22 Nov 2018 01:00:06 +0000
> From: Dario Strbenac <dstr7320 using uni.sydney.edu.au>
> To: "bioc-devel using r-project.org" <bioc-devel using r-project.org>
> Subject: Re: [Bioc-devel] Cannot access remote upstream after changing
> the laptop
> Message-ID:
> <SYCPR01MB4111211FFECF86BBCE26A10ACDDA0 using SYCPR01MB4111.ausprd01.prod.outlook.com>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Good day,
>
> You could also copy the private key from the old computer to the new computer, if you still can use the old computer.
>
> --------------------------------------
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
>
>
>
> ------------------------------
>
> Subject: Digest Footer
>
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> Bioc-devel using r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> ------------------------------
>
> End of Bioc-devel Digest, Vol 176, Issue 22
> *******************************************
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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