Re: [Bioc-devel] BiocCheck error

[Pages, Herve]

Or: you could just rename your NPS repo -> BioTIP and recreate a very 
simple NPS repo that contains only a README.md file that says:

   This repository has been moved to 
https://github.com/xyang2uchicago/BioTIP

That kind of redirect should be OK from the grant submission perspective.

H.


On 8/22/19 04:51, Zhezhen Wang wrote:
> I see, thanks Herve and Martin!
> Zhezhen
> 
>> On Aug 22, 2019, at 6:00 AM, Martin Morgan  wrote:
>>
>> The requirement that the repository and package name be the same is 
>> something imposed by Biocondcutor during the submission process (it's 
>> probably best practice, but that isn't why the requirement is there); once 
>> the package is accepted it gets cloned into Bioconductor (as BioTIP) the 
>> github repository used for submission could be deleted -- we will never look 
>> at the github repository again, the maintainer is responsible for pushing 
>> changes to the Bioconductor git repository.
>>
>> So one could create a temporary repository BioTIP and manage the complexity 
>> of two repositories during submission (basically two remotes 'origin' 
>> (github/user/NPS) and 'upstream' (github/user/BioTIP) on the local BioTIP 
>> repository, with any changes pushed to both. Once the package is accepted, 
>> change 'upstream' to g...@git.bioconductor.org:pacakges/BioTIP and delete 
>> github/user/BioTIP. Continue to push to upstream and remote, to keep the 
>> public github and canonical bioconductor repositories in sync. These steps 
>> are described at 
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_developers_how-2Dto_git_=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=dujEzslWeMIvlTaSOpEXKPSBhHSgfjJdT-5vXztzjNc=o36ekG8m2LTVHqFWfa1uu-vxfFxjblw1UE8I7Nm5fpc=
>>
>> Obviously not ideal, and really a workaround for limitations on the 
>> Bioconductor side of the fence, but it would not result in two permanent 
>> github repositories with the same content.
>>
>> Martin
>>
>> On 8/22/19, 12:27 AM, "Pages, Herve"  wrote:
>>
>>> On 8/21/19 18:51, Zhezhen Wang wrote:
>>> Thank you so much for that remainder. The thing is the NPS linkage is
>>> already included in our grant submission, but then we found that there
>>> already is a package called NPS so we decided to change it BioTIP. Is
>>> making another copy and rename that to BioTIP the best way to solve my
>>> situation?
>>
>> But then isn't it going to be somewhat painful to keep the 2 repos in
>> sync? Sounds like using some kind of alias or redirect mechanism would
>> be better but you would need to ask the Git or GitHub experts on how to
>> do this.
>>
>> H.
>>
>>>
>>> Zhezhen
>>> 
>>> *From:* Pages, Herve 
>>> *Sent:* Wednesday, August 21, 2019 7:47 PM
>>> *To:* Zhezhen Wang ; Martin Morgan
>>> ; Vincent Carey 
>>> *Cc:* bioc-devel@r-project.org 
>>> *Subject:* Re: [Bioc-devel] BiocCheck error
>>> Note that the name of the package (BioTIP) differs from the name of the
>>> GitHub repo (NPS). They will need to match if you intend to submit to
>>> Bioconductor. Thanks!
>>>
>>> H.
>>>
>>>
 On 8/20/19 09:20, Zhezhen Wang wrote:
 I see, thank you Martin!
 Zhezhen
 
 From: Martin Morgan 
 Sent: Tuesday, August 20, 2019 11:15 AM
 To: Zhezhen Wang ; Vincent Carey 
 
 Cc: bioc-devel@r-project.org 
 Subject: Re: [Bioc-devel] BiocCheck error

 I think this is from BiocCheck, needing access to CRAN / Bioconductor to 
 look at package status. Likely there are issues accessing these sites 
 (BiocManager::repositories()) from your computer. It seems not to be an 
 issue that you as developer need to worry  about, provided you are 
 confident that you are using current packages.

 Martin

 On 8/20/19, 12:04 PM, "Bioc-devel on behalf of Zhezhen Wang" 
  wrote:

  The github repo is 
 https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_xyang2uchicago_NPS=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw=XROazf2UylAST2t8NvzZfcr0Sv-Y4RL6G3WloKc-yVo=


  
  From: Vincent Carey 
  Sent: Tuesday, August 20, 2019 10:52 AM
  To: Zhezhen Wang 
  Cc: bioc-devel@r-project.org 
  Subject: Re: [Bioc-devel] BiocCheck error

  If your package that generates the error is in a github repo, please 
 give the details.
  If it is already in Bioconductor please give the name of the package 
 and ensure we can
  get access to the code that is generating the error.  In general it 
 is very hard to help unless
  we can reproduce the error you report.

  On Tue, Aug 20, 2019 at 11:38 AM Zhezhen Wang 
 mailto:zhez...@uchicago.edu>> wrote:
  Hi I am 

Re: [Bioc-devel] DMRcate_2.0.0 and updated DMRcatedata

[Turaga, Nitesh]

Hi Tim,

Based on what your have mentioned, it seems that DMRcatedata should become an 
experiment hub package. 

https://bioconductor.org/packages/devel/bioc/vignettes/ExperimentHub/inst/doc/CreateAnExperimentHubPackage.html

Please take a look that vignette.

Let me know if you have any questions.

Nitesh 

> On Aug 21, 2019, at 7:49 PM, Tim Peters  wrote:
> 
>Hello,
> 
>I have a major update of DMRcate and its associated data package,
>DMRcatedata. They both pass R CMD check and BiocCheck for R 3.6.1.
>Because the new version of DMRcate depends on the updated DMRcatedata 
> package,
>can I host DMRcatedata (it's ~28MB) somewhere for you to download and 
> update Bioconductor, and
>then I can sync the new version of DMRcate please?
> 
>Best,
> 
>Tim
> 
> --
> 
> ===
> 
> Tim Peters, PhD
> 
> Bioinformatics Research Officer | Immunogenomics Laboratory | Immunology 
> Division
> 
> Garvan Institute of Medical Research
> 
> 384 Victoria St., Darlinghurst, NSW, Australia 2010
> 
> E: t.pet...@garvan.org.au | W: http://www.garvan.org.au | P: +612 9295 8325
> 
> NOTICE
> Please consider the environment before printing this email. This message and 
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Re: [Bioc-devel] rtracklayer::import.bw error situation when there's repeated input ranges in the "selection", leads to S4Vectors

[Leonardo Collado Torres]

Hi Michael,

That was using rtracklayer 1.45.3. However I see at
https://github.com/lawremi/rtracklayer/commit/90d4209eae05ae2a4af550072c35cada662b4c89
that you made a recent change. If I use the GitHub version, it all
works =)

> result <- rtracklayer::import(sampleFile,
+ selection = regs,
+ as = 'RleList'
+ )
> result2 <- rtracklayer::import(sampleFile,
+ selection = GenomicRanges::reduce(regs),
+ as = 'RleList'
+ )
> identical(result, result2)
[1] TRUE

library('sessioninfo')
options(width = 120)
session_info()

## Same as yesterday except:
 rtracklayer1.45.32019-08-22 [1] Github
(lawremi/rtracklayer@2dac472)

Best,
Leo

On Wed, Aug 21, 2019 at 3:33 PM Michael Lawrence
 wrote:
>
> Sorry, please try 1.45.3. If that works then I'll push it over to release.
>
> On Wed, Aug 21, 2019 at 11:48 AM Leonardo Collado Torres
>  wrote:
> >
> > Dear Bioc-devel,
> >
> > In BioC 3.9 and 3.10 I've noticed some errors on recount which today I
> > finally traced. It looks like the internals of
> > rtracklayer::import.bw() changed (or mabye S4Vectors:::normarg_names)
> > in such a way that if you specify as input to rtracklayer::import()
> > the "selection" argument with a named GRanges object that has repeated
> > ranges, the function call fails. This can be avoided from a user's
> > perspective by using GenomicRanges::reduce() on the input to
> > "selection", which I guess is ultimately the best option. I now use
> > GenomicRanges::reduce() on derfinder version 1.18.4 (BioC 3.9) and
> > 1.19.4 (BioC 3.10) to solve this issue for recount. But well, I
> > thought that it would be best to share this with all of you.
> >
> > Best,
> > Leo
> >
> > Here's the actual R code for reproducing this situation:
> >
> >
> >
> > sampleFile <- c(
> > 'SRR38' = 'http://duffel.rail.bio/recount/SRP009615/bw/SRR38.bw'
> > )
> > regs <- GenomicRanges::GRanges(
> > 'chrY',
> > IRanges::IRanges(start = c(1, 1), width = 10),
> > strand = '-'
> > )
> > names(regs) <- c(1:2)
> > result <- rtracklayer::import(sampleFile,
> > selection = regs,
> > as = 'RleList'
> > )
> > # Error in S4Vectors:::normarg_names(value, class(x), length(x)) :
> > #   attempt to set too many names (2) on IRanges object of length 1
> >
> > # 12: stop(wmsg("attempt to set too many names (", names_len, ") ",
> > # "on ", x_class, " object of length ", x_len))
> > # 11: S4Vectors:::normarg_names(value, class(x), length(x))
> > # 10: `names<-`(`*tmp*`, value = nm)
> > # 9: `names<-`(`*tmp*`, value = nm)
> > # 8: setNames(ranges(x), value)
> > # 7: `names<-`(`*tmp*`, value = names(flatWhich))
> > # 6: `names<-`(`*tmp*`, value = names(flatWhich))
> > # 5: .local(con, format, text, ...)
> > # 4: import(FileForFormat(con), ...)
> > # 3: import(FileForFormat(con), ...)
> > # 2: rtracklayer::import(sampleFile, selection = regs, as = "RleList")
> > # 1: rtracklayer::import(sampleFile, selection = regs, as = "RleList")
> >
> > result <- rtracklayer::import(sampleFile,
> > selection = GenomicRanges::reduce(regs),
> > as = 'RleList'
> > )
> >
> > library('sessioninfo')
> > options(width = 120)
> > session_info()
> >
> > # ─ Session info
> > ───
> > #  setting  value
> > #  version  R version 3.6.1 (2019-07-05)
> > #  os   macOS Mojave 10.14.6
> > #  system   x86_64, darwin15.6.0
> > #  ui   X11
> > #  language (EN)
> > #  collate  en_US.UTF-8
> > #  ctypeen_US.UTF-8
> > #  tz   America/New_York
> > #  date 2019-08-21
> > #
> > # ─ Packages 
> > ───
> > #  package  * version   date   lib source
> > #  assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0)
> > #  backports  1.1.4 2019-04-10 [1] CRAN (R 3.6.0)
> > #  Biobase2.45.02019-05-02 [1] Bioconductor
> > #  BiocGenerics   0.31.52019-07-03 [1] Bioconductor
> > #  BiocParallel   1.19.22019-08-07 [1] Bioconductor
> > #  Biostrings 2.53.22019-07-09 [1] Bioconductor
> > #  bitops 1.0-6 2013-08-17 [1] CRAN (R 3.6.0)
> > #  callr  3.3.1 2019-07-18 [1] CRAN (R 3.6.0)
> > #  cli1.1.0 2019-03-19 [1] CRAN (R 3.6.0)
> > #  colorout * 1.2-1 2019-07-27 [1] Github
> > (jalvesaq/colorout@7ea9440)
> > #  crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0)
> > #  DelayedArray   0.11.42019-07-03 [1] Bioconductor
> > #  desc   1.2.0 2018-05-01 [1] CRAN (R 3.6.0)
> > #  devtools * 2.1.0 2019-07-06 [1] CRAN (R 3.6.0)
> > #  digest 0.6.202019-07-04 [1] CRAN (R 3.6.0)
> > #  fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.0)
> > #  GenomeInfoDb   1.21.12019-05-16 [1] 

Re: [Bioc-devel] BiocCheck error

[Zhezhen Wang]

I see, thanks Herve and Martin!
Zhezhen 

> On Aug 22, 2019, at 6:00 AM, Martin Morgan  wrote:
> 
> The requirement that the repository and package name be the same is something 
> imposed by Biocondcutor during the submission process (it's probably best 
> practice, but that isn't why the requirement is there); once the package is 
> accepted it gets cloned into Bioconductor (as BioTIP) the github repository 
> used for submission could be deleted -- we will never look at the github 
> repository again, the maintainer is responsible for pushing changes to the 
> Bioconductor git repository.
> 
> So one could create a temporary repository BioTIP and manage the complexity 
> of two repositories during submission (basically two remotes 'origin' 
> (github/user/NPS) and 'upstream' (github/user/BioTIP) on the local BioTIP 
> repository, with any changes pushed to both. Once the package is accepted, 
> change 'upstream' to g...@git.bioconductor.org:pacakges/BioTIP and delete 
> github/user/BioTIP. Continue to push to upstream and remote, to keep the 
> public github and canonical bioconductor repositories in sync. These steps 
> are described at http://bioconductor.org/developers/how-to/git/
> 
> Obviously not ideal, and really a workaround for limitations on the 
> Bioconductor side of the fence, but it would not result in two permanent 
> github repositories with the same content.
> 
> Martin
> 
> On 8/22/19, 12:27 AM, "Pages, Herve"  wrote:
> 
>>On 8/21/19 18:51, Zhezhen Wang wrote:
>> Thank you so much for that remainder. The thing is the NPS linkage is 
>> already included in our grant submission, but then we found that there 
>> already is a package called NPS so we decided to change it BioTIP. Is 
>> making another copy and rename that to BioTIP the best way to solve my 
>> situation?
> 
>But then isn't it going to be somewhat painful to keep the 2 repos in 
>sync? Sounds like using some kind of alias or redirect mechanism would 
>be better but you would need to ask the Git or GitHub experts on how to 
>do this.
> 
>H.
> 
>> 
>> Zhezhen
>> 
>> *From:* Pages, Herve 
>> *Sent:* Wednesday, August 21, 2019 7:47 PM
>> *To:* Zhezhen Wang ; Martin Morgan 
>> ; Vincent Carey 
>> *Cc:* bioc-devel@r-project.org 
>> *Subject:* Re: [Bioc-devel] BiocCheck error
>> Note that the name of the package (BioTIP) differs from the name of the
>> GitHub repo (NPS). They will need to match if you intend to submit to
>> Bioconductor. Thanks!
>> 
>> H.
>> 
>> 
>>> On 8/20/19 09:20, Zhezhen Wang wrote:
>>> I see, thank you Martin!
>>> Zhezhen
>>> 
>>> From: Martin Morgan 
>>> Sent: Tuesday, August 20, 2019 11:15 AM
>>> To: Zhezhen Wang ; Vincent Carey 
>>> 
>>> Cc: bioc-devel@r-project.org 
>>> Subject: Re: [Bioc-devel] BiocCheck error
>>> 
>>> I think this is from BiocCheck, needing access to CRAN / Bioconductor to 
>>> look at package status. Likely there are issues accessing these sites 
>>> (BiocManager::repositories()) from your computer. It seems not to be an 
>>> issue that you as developer need to worry  about, provided you are 
>>> confident that you are using current packages.
>>> 
>>> Martin
>>> 
>>> On 8/20/19, 12:04 PM, "Bioc-devel on behalf of Zhezhen Wang" 
>>>  wrote:
>>> 
>>> The github repo is 
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_xyang2uchicago_NPS=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw=XROazf2UylAST2t8NvzZfcr0Sv-Y4RL6G3WloKc-yVo=
>>> 
>>> 
>>> 
>>> From: Vincent Carey 
>>> Sent: Tuesday, August 20, 2019 10:52 AM
>>> To: Zhezhen Wang 
>>> Cc: bioc-devel@r-project.org 
>>> Subject: Re: [Bioc-devel] BiocCheck error
>>> 
>>> If your package that generates the error is in a github repo, please 
>>> give the details.
>>> If it is already in Bioconductor please give the name of the package 
>>> and ensure we can
>>> get access to the code that is generating the error.  In general it is 
>>> very hard to help unless
>>> we can reproduce the error you report.
>>> 
>>> On Tue, Aug 20, 2019 at 11:38 AM Zhezhen Wang 
>>> mailto:zhez...@uchicago.edu>> wrote:
>>> Hi I am running BiocCheck on my new package and I get the following 
>>> error message
>>> 
>>>   *   Checking for deprecated package usage... Warning in 
>>> readLines(file, skipNul = TRUE) : InternetOpenUrl failed: 'The server name 
>>> or address could not be resolved' Error in readLines(file, skipNul = TRUE) 
>>> : cannot open the connection
>>> 
>>> May I know what this error message means and how I can correct it?
>>> 
>>> Zhezhen
>>> 
>>> 
>>> [[alternative HTML version deleted]]
>>> 
>>> ___
>>> Bioc-devel@r-project.org mailing 

Re: [Bioc-devel] GLAD quotation

[Pariksheet Nanda]

Hi Patricia,

Whoops, my mistake!  GLAD is indeed a Bioconductor package:

$ R -q
> BiocManager::available("glad")
[1] "GLAD"  "GladiaTOX"
>

You don't need to purchase any software license.
You can install the package freely inside R.
See:
https://bioconductor.org/packages/release/bioc/html/GLAD.html

If you're not familiar with using R, a good place to start is the Software
Carpentry lesson:
https://swcarpentry.github.io/r-novice-gapminder/

Pariksheet

On Thu, Aug 22, 2019 at 6:33 AM P q  wrote:

> Dear Support assistant,
>
> I am a doctoral student of Dr. Nicolas Carrels at FIOCRUZ and I am in
> charge to ask for softwares quotations for the lab. I would like a
> quotation for 4 years GLAD software license and It is for non-profit
> research. The quotation document must contain these informations
> below:
>
> 1)Head Researcher/ Scientist: Nicolas Carrels  CPF 84166770500
> 2)Institution: Fundacao Oswaldo Cruz -FIOCRUZ-Centro de Desenvolv.
> Tecn. em Saude Publica-CDTS
> 3)Address: Av.Brasil, 4036 - predio da expansão - 8˚ andar - sala 814
> cep 21040-361 - Rio de Janeiro-RJ - Brasil
>
>
> If you do have any questions, please, contact me by e-mail or by
> telephone: +55 21 965515609
>
>
> Best Regards,
> Patricia Queiroz Monteiro
>
> [[alternative HTML version deleted]]
>
> ___
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>
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Re: [Bioc-devel] GLAD quotation

[Pariksheet Nanda]

Hi Patricia,

You've got the wrong e-mail address.
Bioconductor doesn't sell proprietary software licenses.
This mailing list is for developers to discuss technical matters with the R
or Bioconductor software packages.

I don't know what the website or e-mail address you need for purchasing the
GLAD software; my NCBI and web searches are failing me.
You might need to ask Prof. Carrels?

Good luck,
Pariksheet

On Thu, Aug 22, 2019 at 6:33 AM P q  wrote:

> Dear Support assistant,
>
> I am a doctoral student of Dr. Nicolas Carrels at FIOCRUZ and I am in
> charge to ask for softwares quotations for the lab. I would like a
> quotation for 4 years GLAD software license and It is for non-profit
> research. The quotation document must contain these informations
> below:
>
> 1)Head Researcher/ Scientist: Nicolas Carrels  CPF 84166770500
> 2)Institution: Fundacao Oswaldo Cruz -FIOCRUZ-Centro de Desenvolv.
> Tecn. em Saude Publica-CDTS
> 3)Address: Av.Brasil, 4036 - predio da expansão - 8˚ andar - sala 814
> cep 21040-361 - Rio de Janeiro-RJ - Brasil
>
>
> If you do have any questions, please, contact me by e-mail or by
> telephone: +55 21 965515609
>
>
> Best Regards,
> Patricia Queiroz Monteiro
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
>
> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-develdata=02%7C01%7Cpariksheet.nanda%40uconn.edu%7C904fbfa340e94e99ccf208d726ec221f%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637020667966450005sdata=FBmicjyZJN2DfCI9%2By%2BVxNxubI9cJGUQVn5enwnNuMs%3Dreserved=0
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Re: [Bioc-devel] BiocCheck error

[Martin Morgan]

The requirement that the repository and package name be the same is something 
imposed by Biocondcutor during the submission process (it's probably best 
practice, but that isn't why the requirement is there); once the package is 
accepted it gets cloned into Bioconductor (as BioTIP) the github repository 
used for submission could be deleted -- we will never look at the github 
repository again, the maintainer is responsible for pushing changes to the 
Bioconductor git repository.

So one could create a temporary repository BioTIP and manage the complexity of 
two repositories during submission (basically two remotes 'origin' 
(github/user/NPS) and 'upstream' (github/user/BioTIP) on the local BioTIP 
repository, with any changes pushed to both. Once the package is accepted, 
change 'upstream' to g...@git.bioconductor.org:pacakges/BioTIP and delete 
github/user/BioTIP. Continue to push to upstream and remote, to keep the public 
github and canonical bioconductor repositories in sync. These steps are 
described at http://bioconductor.org/developers/how-to/git/

Obviously not ideal, and really a workaround for limitations on the 
Bioconductor side of the fence, but it would not result in two permanent github 
repositories with the same content.

Martin

On 8/22/19, 12:27 AM, "Pages, Herve"  wrote:

On 8/21/19 18:51, Zhezhen Wang wrote:
> Thank you so much for that remainder. The thing is the NPS linkage is 
> already included in our grant submission, but then we found that there 
> already is a package called NPS so we decided to change it BioTIP. Is 
> making another copy and rename that to BioTIP the best way to solve my 
> situation?

But then isn't it going to be somewhat painful to keep the 2 repos in 
sync? Sounds like using some kind of alias or redirect mechanism would 
be better but you would need to ask the Git or GitHub experts on how to 
do this.

H.

> 
> Zhezhen
> 
> *From:* Pages, Herve 
> *Sent:* Wednesday, August 21, 2019 7:47 PM
> *To:* Zhezhen Wang ; Martin Morgan 
> ; Vincent Carey 
> *Cc:* bioc-devel@r-project.org 
> *Subject:* Re: [Bioc-devel] BiocCheck error
> Note that the name of the package (BioTIP) differs from the name of the
> GitHub repo (NPS). They will need to match if you intend to submit to
> Bioconductor. Thanks!
> 
> H.
> 
> 
> On 8/20/19 09:20, Zhezhen Wang wrote:
>> I see, thank you Martin!
>> Zhezhen
>> 
>> From: Martin Morgan 
>> Sent: Tuesday, August 20, 2019 11:15 AM
>> To: Zhezhen Wang ; Vincent Carey 

>> Cc: bioc-devel@r-project.org 
>> Subject: Re: [Bioc-devel] BiocCheck error
>> 
>> I think this is from BiocCheck, needing access to CRAN / Bioconductor to 
look at package status. Likely there are issues accessing these sites 
(BiocManager::repositories()) from your computer. It seems not to be an issue 
that you as developer need to worry  about, provided you are confident that you 
are using current packages.
>> 
>> Martin
>> 
>> On 8/20/19, 12:04 PM, "Bioc-devel on behalf of Zhezhen Wang" 
 wrote:
>> 
>>  The github repo is 
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_xyang2uchicago_NPS=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw=XROazf2UylAST2t8NvzZfcr0Sv-Y4RL6G3WloKc-yVo=
>> 
>> 
>>  
>>  From: Vincent Carey 
>>  Sent: Tuesday, August 20, 2019 10:52 AM
>>  To: Zhezhen Wang 
>>  Cc: bioc-devel@r-project.org 
>>  Subject: Re: [Bioc-devel] BiocCheck error
>> 
>>  If your package that generates the error is in a github repo, 
please give the details.
>>  If it is already in Bioconductor please give the name of the 
package and ensure we can
>>  get access to the code that is generating the error.  In general it 
is very hard to help unless
>>  we can reproduce the error you report.
>> 
>>  On Tue, Aug 20, 2019 at 11:38 AM Zhezhen Wang 
mailto:zhez...@uchicago.edu>> wrote:
>>  Hi I am running BiocCheck on my new package and I get the following 
error message
>> 
>>*   Checking for deprecated package usage... Warning in 
readLines(file, skipNul = TRUE) : InternetOpenUrl failed: 'The server name or 
address could not be resolved' Error in readLines(file, skipNul = TRUE) : 
cannot open the connection
>> 
>>  May I know what this error message means and how I can correct it?
>> 
>>  Zhezhen
>> 
>> 
>>  [[alternative HTML version deleted]]
>> 
>>  ___
>>  Bioc-devel@r-project.org 

[Bioc-devel] GLAD quotation

[P q]

Dear Support assistant,

I am a doctoral student of Dr. Nicolas Carrels at FIOCRUZ and I am in
charge to ask for softwares quotations for the lab. I would like a
quotation for 4 years GLAD software license and It is for non-profit
research. The quotation document must contain these informations
below:

1)Head Researcher/ Scientist: Nicolas Carrels  CPF 84166770500
2)Institution: Fundacao Oswaldo Cruz -FIOCRUZ-Centro de Desenvolv.
Tecn. em Saude Publica-CDTS
3)Address: Av.Brasil, 4036 - predio da expansão - 8˚ andar - sala 814
cep 21040-361 - Rio de Janeiro-RJ - Brasil


If you do have any questions, please, contact me by e-mail or by
telephone: +55 21 965515609


Best Regards,
Patricia Queiroz Monteiro

[[alternative HTML version deleted]]

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