date:20190821

Re: [Bioc-devel] BiocCheck error

2019-08-21 Thread Pages, Herve

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 list
>>  
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw=rUkBAd61x2nqJmy-a6Ntp-k3RP-XDMucc6r3jZipRFY=
>> 
>>  The information in this e-mail is intended only for the 
>>...{{dropped:14}}
>> 
>>  ___
>>  Bioc-devel@r-project.org mailing list
>>  
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw=rUkBAd61x2nqJmy-a6Ntp-k3RP-XDMucc6r3jZipRFY=
>> 
>> 
>>    [[alternative HTML version deleted]]
>> 
>> ___
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>> 
> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research

Re: [Bioc-devel] BiocCheck error

2019-08-21 Thread Zhezhen Wang

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?

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 list
>  
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw=rUkBAd61x2nqJmy-a6Ntp-k3RP-XDMucc6r3jZipRFY=
>
>  The information in this e-mail is intended only for the ...{{dropped:14}}
>
>  ___
>  Bioc-devel@r-project.org mailing list
>  
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw=rUkBAd61x2nqJmy-a6Ntp-k3RP-XDMucc6r3jZipRFY=
>
>
>[[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
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>

--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

[[alternative HTML version deleted]]

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Re: [Bioc-devel] BiocCheck error

2019-08-21 Thread Pages, Herve

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 list
>  
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw=rUkBAd61x2nqJmy-a6Ntp-k3RP-XDMucc6r3jZipRFY=
> 
>  The information in this e-mail is intended only for the ...{{dropped:14}}
> 
>  ___
>  Bioc-devel@r-project.org mailing list
>  
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw=rUkBAd61x2nqJmy-a6Ntp-k3RP-XDMucc6r3jZipRFY=
> 
> 
>   [[alternative HTML version deleted]]
> 
> ___
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> 

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319
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[Bioc-devel] DMRcate_2.0.0 and updated DMRcatedata

2019-08-21 Thread Tim Peters


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

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Re: [Bioc-devel] rtracklayer::import.bw error situation when there's repeated input ranges in the "selection", leads to S4Vectors

2019-08-21 Thread Michael Lawrence via Bioc-devel

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] Bioconductor
> #  GenomeInfoDbData   1.2.1 2019-07-27 [1] Bioconductor
> #  GenomicAlignments  1.21.42019-06-28 [1] Bioconductor
> #  GenomicRanges  1.37.14   2019-06-24 [1] Bioconductor
> #  glue   1.3.1 2019-03-12 [1] CRAN (R 3.6.0)
> #  IRanges2.19.10   2019-06-11 [1] Bioconductor
> #  lattice0.20-38   2018-11-04 [1] CRAN (R 3.6.1)
> #  magrittr   1.5   2014-11-22 [1] CRAN (R 3.6.0)
> #  Matrix 1.2-172019-03-22 [1] CRAN (R 3.6.1)
> #  matrixStats0.54.02018-07-23 [1] CRAN (R 3.6.0)
> #  memoise1.1.0 2017-04-21 [1] CRAN (R 3.6.0)
> #  pkgbuild   1.0.4 2019-08-05 [1] CRAN (R 3.6.0)
> #  pkgload1.0.2 2018-10-29 [1] CRAN (R 3.6.0)
> #  prettyunits1.0.2 2015-07-13 [1] CRAN (R 3.6.0)
> #  processx   3.4.1

[Bioc-devel] rtracklayer::import.bw error situation when there's repeated input ranges in the "selection", leads to S4Vectors

2019-08-21 Thread Leonardo Collado Torres

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] Bioconductor
#  GenomeInfoDbData   1.2.1 2019-07-27 [1] Bioconductor
#  GenomicAlignments  1.21.42019-06-28 [1] Bioconductor
#  GenomicRanges  1.37.14   2019-06-24 [1] Bioconductor
#  glue   1.3.1 2019-03-12 [1] CRAN (R 3.6.0)
#  IRanges2.19.10   2019-06-11 [1] Bioconductor
#  lattice0.20-38   2018-11-04 [1] CRAN (R 3.6.1)
#  magrittr   1.5   2014-11-22 [1] CRAN (R 3.6.0)
#  Matrix 1.2-172019-03-22 [1] CRAN (R 3.6.1)
#  matrixStats0.54.02018-07-23 [1] CRAN (R 3.6.0)
#  memoise1.1.0 2017-04-21 [1] CRAN (R 3.6.0)
#  pkgbuild   1.0.4 2019-08-05 [1] CRAN (R 3.6.0)
#  pkgload1.0.2 2018-10-29 [1] CRAN (R 3.6.0)
#  prettyunits1.0.2 2015-07-13 [1] CRAN (R 3.6.0)
#  processx   3.4.1 2019-07-18 [1] CRAN (R 3.6.0)
#  ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.0)
#  R6 2.4.0 2019-02-14 [1] CRAN (R 3.6.0)
#  Rcpp   1.0.2 2019-07-25 [1] CRAN (R 3.6.0)
#  RCurl  1.95-4.12 2019-03-04 [1] CRAN (R 3.6.0)
#  remotes2.1.0 2019-06-24 [1] CRAN (R

Re: [Bioc-devel] BiocCheck error

Re: [Bioc-devel] BiocCheck error

Re: [Bioc-devel] BiocCheck error

[Bioc-devel] DMRcate_2.0.0 and updated DMRcatedata

Re: [Bioc-devel] rtracklayer::import.bw error situation when there's repeated input ranges in the "selection", leads to S4Vectors

[Bioc-devel] rtracklayer::import.bw error situation when there's repeated input ranges in the "selection", leads to S4Vectors

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