Re: [Bioc-devel] Accessing updated package through Devel and priming package for next release

[Martin Morgan]

Have you pushed your changes to git.bioconductor.org? I see

HPAStainR master$ git remote -v
origin  g...@git.bioconductor.org:packages/HPAStainR (fetch)
origin  g...@git.bioconductor.org:packages/HPAStainR (push)
HPAStainR master$ git pull
Already up to date.
HPAStainR master$ grep Version DESCRIPTION
Version: 1.1.3



On 3/2/21, 4:50 PM, "Bioc-devel on behalf of Tim Nieuwenhuis" 
 wrote:

Hello,

I am the maintainer of the package HPAStainR. We are about to respond to 
reviewer comments on the package's associated paper, and I am trying to have an 
updated accessible version of the package for the reviewers to use. I currently 
have the updated version of the package as version 1.1.4 on the master branch, 
however when I try to download the developer version of my package with

install.packages("BiocManager")
BiocManager::install(version='devel')
BiocManager::install("HPAStainR")

I end up downloading the previous devel version of HPAStainR which is 
version 1.1.3. I am unsure if I did something wrong in either my versioning, 
git pushes, or in my downloading of the developer version. I know I can just 
have the reviewers acquire the package through github, but I also want to make 
sure that these changes are primed to be entered into the next Bioconductor 
release. Any assistance would be greatly appreciated, and pardon my naivet� on 
the subject.

Github repository:
https://github.com/tnieuwe/HPAStainR

Many thanks,

Tim Nieuwenhuis
4th Year Graduate Student
Human Genetics
Halushka Laboratory
Johns Hopkins University SOM


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[Bioc-devel] Accessing updated package through Devel and priming package for next release

[Tim Nieuwenhuis]

Hello,

I am the maintainer of the package HPAStainR. We are about to respond to 
reviewer comments on the package's associated paper, and I am trying to have an 
updated accessible version of the package for the reviewers to use. I currently 
have the updated version of the package as version 1.1.4 on the master branch, 
however when I try to download the developer version of my package with

install.packages("BiocManager")
BiocManager::install(version='devel')
BiocManager::install("HPAStainR")

I end up downloading the previous devel version of HPAStainR which is version 
1.1.3. I am unsure if I did something wrong in either my versioning, git 
pushes, or in my downloading of the developer version. I know I can just have 
the reviewers acquire the package through github, but I also want to make sure 
that these changes are primed to be entered into the next Bioconductor release. 
Any assistance would be greatly appreciated, and pardon my naivet� on the 
subject.

Github repository:
https://github.com/tnieuwe/HPAStainR

Many thanks,

Tim Nieuwenhuis
4th Year Graduate Student
Human Genetics
Halushka Laboratory
Johns Hopkins University SOM


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[Bioc-devel] Semi-transparency warning in package submitted to Bioconductor

[P. Palenikova]

Dear all,

I have recently submitted a package to Bioconductor and during the 
review some issues with semi-transparency in output plots from two 
functions have been identified. The warning message was:


In grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once 
per page

(https://github.com/Bioconductor/Contributions/issues/1828#issuecomment-763069622).

This warning appears on R Under development (unstable) (2021-02-20 
r80030), Platform: x86_64-pc-linux-gnu (64-bit), Running under: Ubuntu 
20.04.1 LTS, but everything seem to work fine on Windows and Linux with 
R version 4.0.3 as well as Windows with R devel version (2021-02-27 
r80043). I could find other examples of functions producing same 
semi-transparency warning (e.g. 
https://tinyheero.github.io/2015/09/15/semi-transparency-r.html), where 
solutions are for user to change their ~/.Rprofile file. Is there 
anything that can be done with this issue in the code of the package 
functions or in the vignette?


Thank you for any suggestions!

Petra

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Re: [Bioc-devel] ExperimentHub package development - Windows OS specific error

[Murphy, Alan E]

Hey Gavin,

This worked perfectly, thanks!

However, this did lead to another error where one of the datasets from the 
metadata file wasn't found in the ExperimentHub dataset. Again this is Windows 
specific and the dataset in question (alzh_gwas_top100) does exist:


> ### ** Examples
>
>   alzh_gwas_top100()
using temporary cache D:\temp\RtmpCEujsj/working_dir\RtmpY9HMAa/BiocFileCache
snapshotDate(): 2020-04-27
Error in alzh_gwas_top100() :
  resource alzh_gwas_top100 not found in ExperimentHub

This error is thrown in zzz.R here:

objs <- read.csv(system.file("extdata", "metadata.csv",
   package="ewceData"),
   stringsAsFactors=FALSE,fileEncoding = "UTF-8-BOM")$Title
  if (!length(objs))
stop("no objects found")

  ## Functions to load objects by name:
  ns <- asNamespace(pkgname)
  sapply(objs,
 function(xx) {
   func = function(metadata = FALSE) {
 if (!isNamespaceLoaded("ExperimentHub"))
   attachNamespace("ExperimentHub")
 eh <- query(ExperimentHub(), "ewceData")
 ehid <- names(query(eh, xx))
 if (!length(ehid))
   stop(paste0("resource ", xx,
   " not found in ExperimentHub"))
 if (metadata)
   eh[ehid]
 else eh[[ehid]]
   }
   assign(xx, func, envir=ns)
   namespaceExport(ns, xx)
 })

I checked and objs does contain the correct list of titles so the issue isn't 
there. Sorry about the continuation in the question but does anyone know why 
this could be happening?

Kind regards,
Alan.


From: Gavin Lloyd 
Sent: 02 March 2021 18:10
To: Murphy, Alan E ; bioc-devel@r-project.org 

Subject: Re: ExperimentHub package development - Windows OS specific error


This email from g.r.ll...@bham.ac.uk originates from outside Imperial. Do not 
click on links and attachments unless you recognise the sender. If you trust 
the sender, add them to your safe senders 
list to disable email stamping 
for this address.



Your file seems to be encoded as UTF-8-BOM.


When I read it in on my Windows 10 machine the Title column has extra 
characters at the front ("�..Title"), which is why your function returns "no 
object found" when checking for the Title column.


If I resave your file with UTF-8 format your function works as expected and I 
am able to install your package.


Gavin



From: Bioc-devel  on behalf of Murphy, Alan E 

Sent: 02 March 2021 17:00
To: bioc-devel@r-project.org
Subject: [Bioc-devel] ExperimentHub package development - Windows OS specific 
error

Hi all,

My apologies, I have emailed before on a related issue but now think I have 
found a potential cause of the issue I am having but can't seem to find a fix.

I am working on an ExperimentHub data package; 
ewceData, which fails checks on 
Windows OS but passes on Linux and Mac. On Windows, the package fails to 
install with the following output:


Error: package or namespace load failed for 'ewceData':
 .onLoad failed in loadNamespace() for 'ewceData', details:
  call: fun(libname, pkgname)
  error: no objects found
Error: loading failed
Execution halted

It seems like this error is caused by my onload function. The onload function I 
use (zzz.R) should allow easy access to the stored datasets, allowing a user to 
call the dataset like dataset1(). The error note printed appears because the 
metadata.csv file did not read properly

.onLoad <- function(libname, pkgname) {
  objs <- read.csv(system.file("extdata", "metadata.csv",
   package="ewceData"),
   stringsAsFactors=FALSE)$Title
  if (!length(objs))
stop("no objects found")

It would seem the issue is with either read.csv or system.file and is specific 
to Windows OS. Just to note I also do import read.csv from utils.

If anyone has come across an issue like this before or have good guesses for a 
possible fix it would be greatly appreciated?

Kind regards,
Alan,

Alan Murphy
Bioinformatician
Neurogenomics lab
UK Dementia Research Institute
Imperial College London

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Re: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC?

[Vincent Carey]

My understanding is that we will not permit dependencies outside of Bioc or
CRAN.  If a repository
is created that is at least as rigorous in package admission as CRAN,
perhaps it needs to be
considered.  If there are details known about alternate repositories that
we should learn about, please supply.

On Tue, Mar 2, 2021 at 1:20 PM Henrik Bengtsson 
wrote:

> Related: Does Bioconductor support 'Additional_repositories'? From RWE:
>
> The ‘Additional_repositories’ field is a comma-separated list of
> repository URLs where the packages named in the other fields may be
> found. It is currently used by R CMD check to check that the packages
> can be found, at least as source packages (which can be installed on
> any platform).
>
> FWIW, CRAN allows/supports them (I've only used them for packages
> under 'Suggests:').
>
> /Henrik
>
> On Tue, Mar 2, 2021 at 4:02 AM Rainer Johannes
>  wrote:
> >
> > thanks for the quick reply Lori!
> >
> > OK, so we will have to submit the package to Bioc ASAP.
> >
> > cheers, jo
> >
> > > On 2 Mar 2021, at 12:51, Kern, Lori 
> wrote:
> > >
> > > Currently the builders do not allow the user of remotes and you would
> have to wait for it to be submitted to CRAN or Bioconductor.  All
> Bioconductor dependencies must be on CRAN or Bioconductor.
> > >
> > > Get Outlook for iOS
> > > From: Bioc-devel  on behalf of
> Rainer Johannes 
> > > Sent: Tuesday, March 2, 2021 4:36:05 AM
> > > To: bioc-devel 
> > > Subject: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC?
> > >
> > > Dear All!
> > >
> > > in one of the xcms vignettes we are using a R package which is not yet
> in Bioconductor and I added
> > >
> > > Remotes:
> > > RforMassSpectrometry/MsBackendMgf
> > >
> > > to the DESCRIPTION thinking that on the BioC build machines the
> package might get installed (from github). It does apparently not as we get
> ERROR for this vignette. Is there any way I can use a non-Bioconductor and
> non-CRAN package or do I have to wait until the package is included in
> Bioconductor?
> > >
> > > thanks for any feedback!
> > >
> > > cheers, jo
> > > ___
> > > Bioc-devel@r-project.org mailing list
> > >
> https://secure-web.cisco.com/1H1jWIWyghkLhLM5RAXwwfoWK4PlOlae4Pc1-a_NRbOIOuLSLHtGAyInV-z8t0fCgCfVH0nxURKnBN77cdDWaaKfCoZMnqX4XshZNWoi44Ko2dWmnDvV5BjARxeduRCCmoKigDovJkvgYgbecL-t9v9m2HGULeKeb9va8J3NlYFXnVkCDGyzsNgbeZSN2VlWCKhLL1vQqlJEiglEPQraiCYfRjZdnxkQsRcLPnIkfvjbIHJWHFz0LYJRGav4iCiARcWCn0Uo0qe8ieknAiGloqMR2HJHD6oUNCdG8v7oYy73oVejgIqxYBbvJsrztDawr/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-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.
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

-- 
The information in this e-mail is intended only for the ...{{dropped:18}}

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Re: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC?

[Henrik Bengtsson]

Related: Does Bioconductor support 'Additional_repositories'? From RWE:

The ‘Additional_repositories’ field is a comma-separated list of
repository URLs where the packages named in the other fields may be
found. It is currently used by R CMD check to check that the packages
can be found, at least as source packages (which can be installed on
any platform).

FWIW, CRAN allows/supports them (I've only used them for packages
under 'Suggests:').

/Henrik

On Tue, Mar 2, 2021 at 4:02 AM Rainer Johannes
 wrote:
>
> thanks for the quick reply Lori!
>
> OK, so we will have to submit the package to Bioc ASAP.
>
> cheers, jo
>
> > On 2 Mar 2021, at 12:51, Kern, Lori  wrote:
> >
> > Currently the builders do not allow the user of remotes and you would have 
> > to wait for it to be submitted to CRAN or Bioconductor.  All Bioconductor 
> > dependencies must be on CRAN or Bioconductor.
> >
> > Get Outlook for iOS
> > From: Bioc-devel  on behalf of Rainer 
> > Johannes 
> > Sent: Tuesday, March 2, 2021 4:36:05 AM
> > To: bioc-devel 
> > Subject: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC?
> >
> > Dear All!
> >
> > in one of the xcms vignettes we are using a R package which is not yet in 
> > Bioconductor and I added
> >
> > Remotes:
> > RforMassSpectrometry/MsBackendMgf
> >
> > to the DESCRIPTION thinking that on the BioC build machines the package 
> > might get installed (from github). It does apparently not as we get ERROR 
> > for this vignette. Is there any way I can use a non-Bioconductor and 
> > non-CRAN package or do I have to wait until the package is included in 
> > Bioconductor?
> >
> > thanks for any feedback!
> >
> > cheers, jo
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://secure-web.cisco.com/1H1jWIWyghkLhLM5RAXwwfoWK4PlOlae4Pc1-a_NRbOIOuLSLHtGAyInV-z8t0fCgCfVH0nxURKnBN77cdDWaaKfCoZMnqX4XshZNWoi44Ko2dWmnDvV5BjARxeduRCCmoKigDovJkvgYgbecL-t9v9m2HGULeKeb9va8J3NlYFXnVkCDGyzsNgbeZSN2VlWCKhLL1vQqlJEiglEPQraiCYfRjZdnxkQsRcLPnIkfvjbIHJWHFz0LYJRGav4iCiARcWCn0Uo0qe8ieknAiGloqMR2HJHD6oUNCdG8v7oYy73oVejgIqxYBbvJsrztDawr/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-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.
>
> ___
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Re: [Bioc-devel] ExperimentHub package development - Windows OS specific error

[Gavin Lloyd]

Your file seems to be encoded as UTF-8-BOM.


When I read it in on my Windows 10 machine the Title column has extra 
characters at the front ("�..Title"), which is why your function returns "no 
object found" when checking for the Title column.


If I resave your file with UTF-8 format your function works as expected and I 
am able to install your package.


Gavin



From: Bioc-devel  on behalf of Murphy, Alan E 

Sent: 02 March 2021 17:00
To: bioc-devel@r-project.org
Subject: [Bioc-devel] ExperimentHub package development - Windows OS specific 
error

Hi all,

My apologies, I have emailed before on a related issue but now think I have 
found a potential cause of the issue I am having but can't seem to find a fix.

I am working on an ExperimentHub data package; 
ewceData, which fails checks on 
Windows OS but passes on Linux and Mac. On Windows, the package fails to 
install with the following output:


Error: package or namespace load failed for 'ewceData':
 .onLoad failed in loadNamespace() for 'ewceData', details:
  call: fun(libname, pkgname)
  error: no objects found
Error: loading failed
Execution halted

It seems like this error is caused by my onload function. The onload function I 
use (zzz.R) should allow easy access to the stored datasets, allowing a user to 
call the dataset like dataset1(). The error note printed appears because the 
metadata.csv file did not read properly

.onLoad <- function(libname, pkgname) {
  objs <- read.csv(system.file("extdata", "metadata.csv",
   package="ewceData"),
   stringsAsFactors=FALSE)$Title
  if (!length(objs))
stop("no objects found")

It would seem the issue is with either read.csv or system.file and is specific 
to Windows OS. Just to note I also do import read.csv from utils.

If anyone has come across an issue like this before or have good guesses for a 
possible fix it would be greatly appreciated?

Kind regards,
Alan,

Alan Murphy
Bioinformatician
Neurogenomics lab
UK Dementia Research Institute
Imperial College London

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[Bioc-devel] ExperimentHub package development - Windows OS specific error

[Murphy, Alan E]

Hi all,

My apologies, I have emailed before on a related issue but now think I have 
found a potential cause of the issue I am having but can't seem to find a fix.

I am working on an ExperimentHub data package; 
ewceData, which fails checks on 
Windows OS but passes on Linux and Mac. On Windows, the package fails to 
install with the following output:


Error: package or namespace load failed for 'ewceData':
 .onLoad failed in loadNamespace() for 'ewceData', details:
  call: fun(libname, pkgname)
  error: no objects found
Error: loading failed
Execution halted

It seems like this error is caused by my onload function. The onload function I 
use (zzz.R) should allow easy access to the stored datasets, allowing a user to 
call the dataset like dataset1()​. The error note printed appears because the 
metadata.csv file did not read properly

.onLoad <- function(libname, pkgname) {
  objs <- read.csv(system.file("extdata", "metadata.csv",
   package="ewceData"),
   stringsAsFactors=FALSE)$Title
  if (!length(objs))
stop("no objects found")

It would seem the issue is with either read.csv​ or system.file​ and is 
specific to Windows OS. Just to note I also do import read.csv from utils.

If anyone has come across an issue like this before or have good guesses for a 
possible fix it would be greatly appreciated?

Kind regards,
Alan,

Alan Murphy
Bioinformatician
Neurogenomics lab
UK Dementia Research Institute
Imperial College London

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Re: [Bioc-devel] Lost Credentials

[Morganella Sandro]

All sorted now!
Thanks a lot Nitesh
Sandro

On Tue, Mar 2, 2021 at 4:54 PM Nitesh Turaga  wrote:

> Hi,
>
> You are not an active user of BiocCredentials. You've never set a password
> to reset it.
>
> You have to first activate your account.
>
> https://git.bioconductor.org/BiocCredentials/account_activation
>
> Best,
>
> Nitesh
>
> On 3/2/21, 11:06 AM, "Bioc-devel on behalf of Morganella Sandro" <
> bioc-devel-boun...@r-project.org on behalf of morganella...@gmail.com>
> wrote:
>
> Hi Dev!
> I have been trying to access my package repository (VegaMC), but I
> cannot
> remember my credentials.
>
> I have tried to reset my password, with no luck - I haven't received
> any
> email (I have checked my spam).
>
> Anyone that can help me with this?
> Thanks,
> Sandro
>
> [[alternative HTML version deleted]]
>
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>


-- 
- Sandro Morganella -

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Re: [Bioc-devel] Lost Credentials

[Nitesh Turaga]

Hi,

You are not an active user of BiocCredentials. You've never set a password to 
reset it. 

You have to first activate your account.

https://git.bioconductor.org/BiocCredentials/account_activation

Best,

Nitesh 

On 3/2/21, 11:06 AM, "Bioc-devel on behalf of Morganella Sandro" 
 wrote:

Hi Dev!
I have been trying to access my package repository (VegaMC), but I cannot
remember my credentials.

I have tried to reset my password, with no luck - I haven't received any
email (I have checked my spam).

Anyone that can help me with this?
Thanks,
Sandro

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[Bioc-devel] Lost Credentials

[Morganella Sandro]

Hi Dev!
I have been trying to access my package repository (VegaMC), but I cannot
remember my credentials.

I have tried to reset my password, with no luck - I haven't received any
email (I have checked my spam).

Anyone that can help me with this?
Thanks,
Sandro

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Re: [Bioc-devel] Error on BiocCheckGitClone and Windows build

[Oluwafemi OLUSOJI]

Ah! I didn't bump up the description file. Thank you once again.

Regards,
Daniel

Op di 2 mrt. 2021 om 13:16 schreef Kern, Lori :

> Did you follow the instructions for setting up remotes to push to
> git.bioconductor.org?
> https://bioconductor.org/developers/how-to/git/new-package-workflow/
>
> And/or set up your git credentials account?
> https://git.bioconductor.org/BiocCredentials
>
>
> and lastly builds are triggered only by a valid version bump in the
> DESCRIPTION.  Please make sure to bump the DESCRIPTION to at least 0.99.5
>
> we encourage further discussion on the issue itself for more specialized
> assistance.
>
> Cheers,
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Oluwafemi OLUSOJI 
> *Sent:* Tuesday, March 2, 2021 4:47 AM
> *To:* Kern, Lori 
> *Cc:* bioc-devel@r-project.org 
> *Subject:* Re: [Bioc-devel] Error on BiocCheckGitClone and Windows build
>
> Hello Lori,
>
> Thank you for your insight. I figured out it pays to expressly state that
> those files not be tracked and committed.
>
> I have re-submitted for a new build but I am not getting any notification
> on the issues page as written out on the Bioconductor website. Is there a
> reason for this?
>
> Regards,
> Daniel
>
> Op ma 1 mrt. 2021 om 19:51 schreef Kern, Lori <
> lori.sheph...@roswellpark.org>:
>
> Please feel free to also comment directly on your issue for your reviewer
> to assist.
>
> The packages not being available on windows is likely on our end and you
> can ignore for now.
>
> System files should not be git tracked. They should be remove using git
> remove and then committed up.
> git rm 
> git commit -a
>
> Cheers,
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel  on behalf of
> Oluwafemi OLUSOJI 
> *Sent:* Monday, March 1, 2021 12:12 PM
> *To:* bioc-devel@r-project.org 
> *Subject:* [Bioc-devel] Error on BiocCheckGitClone and Windows build
>
> Dear All,
>
> I recently submitted a package to Bioconductor and got this error message
> as part of the reply email. I am not sure what to do about it.
>
> The two files are git tracked,  but they are also named in .Rbuildignore so
> I felt they should have been avoided. This is my first experience with
> Bioconductor so any help would be appreciated.
>
> Furthermore, there are errors related to dependencies on the windows build.
> Should I worry about these?
>
> Regards,
> Olusoji Oluwafemi Daniel
>
> ## Error Related to Windows test build 
>
> ===
>
>  R CMD BUILD
>
> ===
>
> * checking for file 'cyanoFilter/DESCRIPTION' ... OK
> * preparing 'cyanoFilter':
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
>   ---
> ERROR: dependencies 'flowCore', 'flowDensity' are not available for
> package 'cyanoFilter'
> * removing
> 'C:/Users/pkgbuild/AppData/Local/Temp/Rtmp0gaTHW/Rinst8fd05a8549f/cyanoFilter'
>   ---
> ERROR: package installation failed
>
>
> ### Error related to git tracked files #
>
> This is BiocCheckGitClone version 1.27.2. BiocCheckGitClone is a work
> in progress. Output and severity of issues may change.
> * Checking valid files...
> * ERROR: System Files found that should not be git tracked:
> .Renviron
> cyanoFilter.Rproj
> * Checking DESCRIPTION...
> * Checking if DESCRIPTION is well formatted...
> * Checking for valid maintainer...
> * Checking CITATION...
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
>
> https://secure-web.cisco.com/1LkQPtM9Sa__fttKDJlUILOT21ohRFC2hdkBIkJ9PDWzt8AkPi0ku7GyBwX4ptPofJfm1KINoBf81e02U-I-Q5o4xKxog5n7Wr5DFfPpMkn32S7K7ukS-s5WsvWWLENLqexxVoRQ0WwoCGhsdu1lcCMfGr0q3DapJZBTAffl-rmpP0dkVX7yJbv2zO2Hvgr2nIEmKghu2nBekg5_KoH36oiFYspLPGHBlpuXoH1QHCvEI5XFYiqp3NAtNsqswBUQpz75VNeUy4zkWeb9mGtCqgypNfTx90AC6Mfq9ogB_Y-2Nmd5fh57Psufxg7m5bnLi/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-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,
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> received this message in error, please notify the sender immediately by
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Re: [Bioc-devel] [Bioc-deve] Check package status / built report

[Kern, Lori]

Additionally,   Please make sure to do a valid version bump.  I took a peak on 
our git.bioconductor.org server and do see the changes pushed but it does not 
appear that it included a valid version bump from 1.17.0 to 1.17.1 .  Without a 
valid version bump the most recent version will not propagate for availability 
to the end users.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Kern, Lori 
Sent: Tuesday, March 2, 2021 7:19 AM
To: Stadler, Michael ; Ines de Santiago 
; bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] [Bioc-deve] Check package status / built report

Michael is right.  Additionally there is some information on the timing of 
pushing / pulling of the build system on the top of this page:
bioconductor.org/developers/how-to/troubleshoot-build-report/

While its possible you made the changes in time for today's report, Most likely 
the changes will be reflected in tomorrow March 3rd report.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Stadler, 
Michael 
Sent: Tuesday, March 2, 2021 3:38 AM
To: Ines de Santiago ; bioc-devel@r-project.org 

Subject: Re: [Bioc-devel] [Bioc-deve] Check package status / built report

Hello Ines

This is not how the builds of accepted packages work.

The builds run once a day, and depending when the builders pull the contents 
from git.bioconductor.org (see date and time at the top of 
https://secure-web.cisco.com/1LNL1nX-IwKA1-4HlWKL2nfDRf5ts2HAUF_LnBW0kxCt17mKOoi_imtDto4zhj9kdT6eQ2YJ3yWFkxeowb8yQQN15fH4ZQ6SloImjuRZfdUisqoFJ6PYeooOqGW9A4Lp5khGSjfKpt3ZPdQRnXDCoPnG_cPWLxRPSIQksMykiHJrBMbSNpEvo5x0unrc2jL2IlTi1kXMEDUuB8L9KTn6SEwCAw3RtA4vTzaTpTiXnpvt5EZp5e_EJfpa4_hTHCobGnjlUjYvGWLOugml9d_f4vDC7AVIJFtI9P_oAWP-9Fb_uGGazrsuJvHf3gugHUA2X/https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.13%2Fbioc-LATEST%2Findex.html),
 your changes may not be reflected in that build yet.

Regards,
Michael

-Urspr�ngliche Nachricht-
Von: Bioc-devel  Im Auftrag von Ines de 
Santiago
Gesendet: Dienstag, 2. M�rz 2021 09:33
An: bioc-devel@r-project.org
Betreff: [Bioc-devel] [Bioc-deve] Check package status / built report

Hello. I updated my package and pushed the changes to bioconductor github 
Everything went smoothly with no errors,

git clone g...@git.bioconductor.org:packages/BaalChIP
(changes... add.. rename origin...etc)
git push upstream master

I thought that by pushing to bioconductor github it would trigger the package 
Built process.
however, when I go to the webpage:
https://secure-web.cisco.com/1LNL1nX-IwKA1-4HlWKL2nfDRf5ts2HAUF_LnBW0kxCt17mKOoi_imtDto4zhj9kdT6eQ2YJ3yWFkxeowb8yQQN15fH4ZQ6SloImjuRZfdUisqoFJ6PYeooOqGW9A4Lp5khGSjfKpt3ZPdQRnXDCoPnG_cPWLxRPSIQksMykiHJrBMbSNpEvo5x0unrc2jL2IlTi1kXMEDUuB8L9KTn6SEwCAw3RtA4vTzaTpTiXnpvt5EZp5e_EJfpa4_hTHCobGnjlUjYvGWLOugml9d_f4vDC7AVIJFtI9P_oAWP-9Fb_uGGazrsuJvHf3gugHUA2X/https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.13%2Fbioc-LATEST%2Findex.html
I still see my package with the same "WARNINGS"
Am I checking in the right place?

[[alternative HTML version deleted]]

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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, 
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Re: [Bioc-devel] [Bioc-deve] Check package status / built report

[Kern, Lori]

Michael is right.  Additionally there is some information on the timing of 
pushing / pulling of the build system on the top of this page:
bioconductor.org/developers/how-to/troubleshoot-build-report/

While its possible you made the changes in time for today's report, Most likely 
the changes will be reflected in tomorrow March 3rd report.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Stadler, 
Michael 
Sent: Tuesday, March 2, 2021 3:38 AM
To: Ines de Santiago ; bioc-devel@r-project.org 

Subject: Re: [Bioc-devel] [Bioc-deve] Check package status / built report

Hello Ines

This is not how the builds of accepted packages work.

The builds run once a day, and depending when the builders pull the contents 
from git.bioconductor.org (see date and time at the top of 
https://secure-web.cisco.com/1LNL1nX-IwKA1-4HlWKL2nfDRf5ts2HAUF_LnBW0kxCt17mKOoi_imtDto4zhj9kdT6eQ2YJ3yWFkxeowb8yQQN15fH4ZQ6SloImjuRZfdUisqoFJ6PYeooOqGW9A4Lp5khGSjfKpt3ZPdQRnXDCoPnG_cPWLxRPSIQksMykiHJrBMbSNpEvo5x0unrc2jL2IlTi1kXMEDUuB8L9KTn6SEwCAw3RtA4vTzaTpTiXnpvt5EZp5e_EJfpa4_hTHCobGnjlUjYvGWLOugml9d_f4vDC7AVIJFtI9P_oAWP-9Fb_uGGazrsuJvHf3gugHUA2X/https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.13%2Fbioc-LATEST%2Findex.html),
 your changes may not be reflected in that build yet.

Regards,
Michael

-Urspr�ngliche Nachricht-
Von: Bioc-devel  Im Auftrag von Ines de 
Santiago
Gesendet: Dienstag, 2. M�rz 2021 09:33
An: bioc-devel@r-project.org
Betreff: [Bioc-devel] [Bioc-deve] Check package status / built report

Hello. I updated my package and pushed the changes to bioconductor github 
Everything went smoothly with no errors,

git clone g...@git.bioconductor.org:packages/BaalChIP
(changes... add.. rename origin...etc)
git push upstream master

I thought that by pushing to bioconductor github it would trigger the package 
Built process.
however, when I go to the webpage:
https://secure-web.cisco.com/1LNL1nX-IwKA1-4HlWKL2nfDRf5ts2HAUF_LnBW0kxCt17mKOoi_imtDto4zhj9kdT6eQ2YJ3yWFkxeowb8yQQN15fH4ZQ6SloImjuRZfdUisqoFJ6PYeooOqGW9A4Lp5khGSjfKpt3ZPdQRnXDCoPnG_cPWLxRPSIQksMykiHJrBMbSNpEvo5x0unrc2jL2IlTi1kXMEDUuB8L9KTn6SEwCAw3RtA4vTzaTpTiXnpvt5EZp5e_EJfpa4_hTHCobGnjlUjYvGWLOugml9d_f4vDC7AVIJFtI9P_oAWP-9Fb_uGGazrsuJvHf3gugHUA2X/https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.13%2Fbioc-LATEST%2Findex.html
I still see my package with the same "WARNINGS"
Am I checking in the right place?

[[alternative HTML version deleted]]

___
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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 
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Re: [Bioc-devel] Error on BiocCheckGitClone and Windows build

[Kern, Lori]

Did you follow the instructions for setting up remotes to push to 
git.bioconductor.org?
https://bioconductor.org/developers/how-to/git/new-package-workflow/

And/or set up your git credentials account?
https://git.bioconductor.org/BiocCredentials


and lastly builds are triggered only by a valid version bump in the 
DESCRIPTION.  Please make sure to bump the DESCRIPTION to at least 0.99.5

we encourage further discussion on the issue itself for more specialized 
assistance.

Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Oluwafemi OLUSOJI 
Sent: Tuesday, March 2, 2021 4:47 AM
To: Kern, Lori 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] Error on BiocCheckGitClone and Windows build

Hello Lori,

Thank you for your insight. I figured out it pays to expressly state that those 
files not be tracked and committed.

I have re-submitted for a new build but I am not getting any notification on 
the issues page as written out on the Bioconductor website. Is there a reason 
for this?

Regards,
Daniel

Op ma 1 mrt. 2021 om 19:51 schreef Kern, Lori 
mailto:lori.sheph...@roswellpark.org>>:
Please feel free to also comment directly on your issue for your reviewer to 
assist.

The packages not being available on windows is likely on our end and you can 
ignore for now.

System files should not be git tracked. They should be remove using git remove 
and then committed up.
git rm 
git commit -a

Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Oluwafemi OLUSOJI 
mailto:oluwafemi.olus...@uhasselt.be>>
Sent: Monday, March 1, 2021 12:12 PM
To: bioc-devel@r-project.org 
mailto:bioc-devel@r-project.org>>
Subject: [Bioc-devel] Error on BiocCheckGitClone and Windows build

Dear All,

I recently submitted a package to Bioconductor and got this error message
as part of the reply email. I am not sure what to do about it.

The two files are git tracked,  but they are also named in .Rbuildignore so
I felt they should have been avoided. This is my first experience with
Bioconductor so any help would be appreciated.

Furthermore, there are errors related to dependencies on the windows build.
Should I worry about these?

Regards,
Olusoji Oluwafemi Daniel

## Error Related to Windows test build 

===

 R CMD BUILD

===

* checking for file 'cyanoFilter/DESCRIPTION' ... OK
* preparing 'cyanoFilter':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
  ---
ERROR: dependencies 'flowCore', 'flowDensity' are not available for
package 'cyanoFilter'
* removing 
'C:/Users/pkgbuild/AppData/Local/Temp/Rtmp0gaTHW/Rinst8fd05a8549f/cyanoFilter'
  ---
ERROR: package installation failed


### Error related to git tracked files #

This is BiocCheckGitClone version 1.27.2. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
.Renviron
cyanoFilter.Rproj
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...

[[alternative HTML version deleted]]

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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.


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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recipient(s), you are hereby 

Re: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC?

[Rainer Johannes]

thanks for the quick reply Lori!

OK, so we will have to submit the package to Bioc ASAP.

cheers, jo

> On 2 Mar 2021, at 12:51, Kern, Lori  wrote:
> 
> Currently the builders do not allow the user of remotes and you would have to 
> wait for it to be submitted to CRAN or Bioconductor.  All Bioconductor 
> dependencies must be on CRAN or Bioconductor. 
> 
> Get Outlook for iOS
> From: Bioc-devel  on behalf of Rainer 
> Johannes 
> Sent: Tuesday, March 2, 2021 4:36:05 AM
> To: bioc-devel 
> Subject: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC?
>  
> Dear All!
> 
> in one of the xcms vignettes we are using a R package which is not yet in 
> Bioconductor and I added
> 
> Remotes:
> RforMassSpectrometry/MsBackendMgf
> 
> to the DESCRIPTION thinking that on the BioC build machines the package might 
> get installed (from github). It does apparently not as we get ERROR for this 
> vignette. Is there any way I can use a non-Bioconductor and non-CRAN package 
> or do I have to wait until the package is included in Bioconductor?
> 
> thanks for any feedback!
> 
> cheers, jo
> ___
> Bioc-devel@r-project.org mailing list
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> 
> 
> 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.

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Re: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC?

[Kern, Lori]

Currently the builders do not allow the user of remotes and you would have to 
wait for it to be submitted to CRAN or Bioconductor.  All Bioconductor 
dependencies must be on CRAN or Bioconductor.

Get Outlook for iOS

From: Bioc-devel  on behalf of Rainer 
Johannes 
Sent: Tuesday, March 2, 2021 4:36:05 AM
To: bioc-devel 
Subject: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC?

Dear All!

in one of the xcms vignettes we are using a R package which is not yet in 
Bioconductor and I added

Remotes:
RforMassSpectrometry/MsBackendMgf

to the DESCRIPTION thinking that on the BioC build machines the package might 
get installed (from github). It does apparently not as we get ERROR for this 
vignette. Is there any way I can use a non-Bioconductor and non-CRAN package or 
do I have to wait until the package is included in Bioconductor?

thanks for any feedback!

cheers, jo
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this message in error, please notify the sender immediately by e-mail and 
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Re: [Bioc-devel] Error on BiocCheckGitClone and Windows build

[Oluwafemi OLUSOJI]

Hello Lori,

Thank you for your insight. I figured out it pays to expressly state that
those files not be tracked and committed.

I have re-submitted for a new build but I am not getting any notification
on the issues page as written out on the Bioconductor website. Is there a
reason for this?

Regards,
Daniel

Op ma 1 mrt. 2021 om 19:51 schreef Kern, Lori :

> Please feel free to also comment directly on your issue for your reviewer
> to assist.
>
> The packages not being available on windows is likely on our end and you
> can ignore for now.
>
> System files should not be git tracked. They should be remove using git
> remove and then committed up.
> git rm 
> git commit -a
>
> Cheers,
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel  on behalf of
> Oluwafemi OLUSOJI 
> *Sent:* Monday, March 1, 2021 12:12 PM
> *To:* bioc-devel@r-project.org 
> *Subject:* [Bioc-devel] Error on BiocCheckGitClone and Windows build
>
> Dear All,
>
> I recently submitted a package to Bioconductor and got this error message
> as part of the reply email. I am not sure what to do about it.
>
> The two files are git tracked,  but they are also named in .Rbuildignore so
> I felt they should have been avoided. This is my first experience with
> Bioconductor so any help would be appreciated.
>
> Furthermore, there are errors related to dependencies on the windows build.
> Should I worry about these?
>
> Regards,
> Olusoji Oluwafemi Daniel
>
> ## Error Related to Windows test build 
>
> ===
>
>  R CMD BUILD
>
> ===
>
> * checking for file 'cyanoFilter/DESCRIPTION' ... OK
> * preparing 'cyanoFilter':
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
>   ---
> ERROR: dependencies 'flowCore', 'flowDensity' are not available for
> package 'cyanoFilter'
> * removing
> 'C:/Users/pkgbuild/AppData/Local/Temp/Rtmp0gaTHW/Rinst8fd05a8549f/cyanoFilter'
>   ---
> ERROR: package installation failed
>
>
> ### Error related to git tracked files #
>
> This is BiocCheckGitClone version 1.27.2. BiocCheckGitClone is a work
> in progress. Output and severity of issues may change.
> * Checking valid files...
> * ERROR: System Files found that should not be git tracked:
> .Renviron
> cyanoFilter.Rproj
> * Checking DESCRIPTION...
> * Checking if DESCRIPTION is well formatted...
> * Checking for valid maintainer...
> * Checking CITATION...
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
>
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>
>
> 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,
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> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.

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[Bioc-devel] Remotes in DESCRIPTION not supported for BioC?

[Rainer Johannes]

Dear All!

in one of the xcms vignettes we are using a R package which is not yet in 
Bioconductor and I added

Remotes:
RforMassSpectrometry/MsBackendMgf

to the DESCRIPTION thinking that on the BioC build machines the package might 
get installed (from github). It does apparently not as we get ERROR for this 
vignette. Is there any way I can use a non-Bioconductor and non-CRAN package or 
do I have to wait until the package is included in Bioconductor?

thanks for any feedback!

cheers, jo
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Re: [Bioc-devel] [Bioc-deve] Check package status / built report

[Stadler, Michael]

Hello Ines

This is not how the builds of accepted packages work. 

The builds run once a day, and depending when the builders pull the contents 
from git.bioconductor.org (see date and time at the top of 
https://master.bioconductor.org/checkResults/3.13/bioc-LATEST/index.html), your 
changes may not be reflected in that build yet.

Regards,
Michael

-Ursprüngliche Nachricht-
Von: Bioc-devel  Im Auftrag von Ines de 
Santiago
Gesendet: Dienstag, 2. März 2021 09:33
An: bioc-devel@r-project.org
Betreff: [Bioc-devel] [Bioc-deve] Check package status / built report

Hello. I updated my package and pushed the changes to bioconductor github 
Everything went smoothly with no errors,

git clone g...@git.bioconductor.org:packages/BaalChIP
(changes... add.. rename origin...etc)
git push upstream master

I thought that by pushing to bioconductor github it would trigger the package 
Built process.
however, when I go to the webpage:
https://master.bioconductor.org/checkResults/3.13/bioc-LATEST/index.html
I still see my package with the same "WARNINGS"
Am I checking in the right place?

[[alternative HTML version deleted]]

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[Bioc-devel] [Bioc-deve] Check package status / built report

[Ines de Santiago]

Hello. I updated my package and pushed the changes to bioconductor github
Everything went smoothly with no errors,

git clone g...@git.bioconductor.org:packages/BaalChIP
(changes... add.. rename origin...etc)
git push upstream master

I thought that by pushing to bioconductor github it would trigger the
package Built process.
however, when I go to the webpage:
https://master.bioconductor.org/checkResults/3.13/bioc-LATEST/index.html
I still see my package with the same "WARNINGS"
Am I checking in the right place?

[[alternative HTML version deleted]]

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