-Wunused-variable]
>39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
> | ^~~
> make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:195:
> hmmMiscFunctions.o] Error 1
> ERROR: compilation failed for package ‘groHMM’
> * removing
Sent: Tuesday, December 3, 2024 3:14 PM
To: Mike Smith
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] groHMM package error
Hi,
I edited the file based on Mike' s suggestion on the git page (image1) but
doesn't seem to reflect when I clone the file using the git clone bioconductor
pack
Nandu
mailto:tulip.na...@utsouthwestern.edu>>; James
W. MacDonald mailto:jmac...@uw.edu>>; Mike Smith
mailto:grimbo...@gmail.com>>
Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
mailto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] groHMM package error
I
ew York 14263
From: Tulip Nandu
Sent: Thursday, December 5, 2024 12:25 PM
To: Kern, Lori ; James W. MacDonald
; Mike Smith
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] groHMM package error
Hi,
I have updated the groHMM developer's version with the edits
-project.org
Subject: Re: [Bioc-devel] groHMM package error
I don't see a valid version bump? If there is no version bump, then it will
not propagate on our system
Lori Shepherd - Kern
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioin
; Mike Smith
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] groHMM package error
Hi,
Thank you for your earlier message.
tulipnandu@tulips-mbp groHMM % git remote -v
origin g...@github.com:Kraus-Lab/groHMM.git (fetch)
origin g...@github.com:Kraus-Lab/groHMM.git (pus
bioc-devel@r-project.org
Subject: Re: [Bioc-devel] groHMM package error
Hi,
I edited the file based on Mike' s suggestion on the git page (image1) but
doesn't seem to reflect when I clone the file using the git clone bioconductor
package yet. Can someone confirm it will be done and nothing els
tml
-Original Message-
From: Bioc-devel On Behalf Of Tulip Nandu
Sent: Tuesday, December 3, 2024 3:14 PM
To: Mike Smith
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] groHMM package error
Hi,
I edited the file based on Mike' s suggestion on the git page (image1) but
doesn&#
rds,
Tulip.
From: Mike Smith
Sent: Tuesday, November 26, 2024 2:50 AM
To: Tulip Nandu
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] groHMM package error
EXTERNAL MAIL
Dear Tulip,
The decideTestsDGE() function was deprecated in edgeR 4.2 and removed in the
new 4
Dear Tulip,
The decideTestsDGE() function was deprecated in edgeR 4.2 and removed in
the new 4.4 release. You can find some notes ion this n the NEWS at
https://bioconductor.org/packages/release/bioc/news/edgeR/NEWS
It looks to me like you should be able to use decideTests() as a drop in
replac
Hi,
This same error has resurfaced. Can someone please look into this for the
groHMM package.
Regards,
Tulip.
From: Herv� Pag�s
Sent: Saturday, October 28, 2023 1:51 PM
To: Tulip Nandu ; Kern, Lori
; bioc-devel@r-project.org
Subject: Re: [Bioc-devel
Package is all green today on the 3.18 report:
https://bioconductor.org/checkResults/3.18/bioc-LATEST/groHMM/
Cheers,
H.
On 10/25/23 16:11, Hervé Pagès wrote:
>
> Addressed in S4Vectors 0.40.1. Today's builds have started already so
> the fix won't be reflected on tomorrow's report (Thursday),
Addressed in S4Vectors 0.40.1. Today's builds have started already so
the fix won't be reflected on tomorrow's report (Thursday), only on Friday.
Sorry again for the inconvenience.
Best,
H.
On 10/25/23 15:34, Hervé Pagès wrote:
>
> Hi Tulip,
>
> I think this is caused by a late change in S4Vec
Hi Lori,
Thank you for your prompt response. I haven't changed anything in the
development package (on git on anywhere else) then why the error message has
suddenly come up. As per the package what exactly they want me to change so it
passes the R CMD Check goes on without errors.
Regards,
Tu
You should make sure you are using the latest version of R and have updated
Bioconductor/CRAN packages by running BiocManager::valid and/or
BiocManager:install . I can reproduce this locally.
Running your vignette it has to do with this line:
> upGenes <- kgChr7[de==1,]
Error: invalid subscrip
There is no RELEASE_3_18 branch until the release next week (created
automatically by the core team on release day) . All updates should be pushed
to the devel branch.
Lori Shepherd - Kern
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinf
Hi,
On Wed, Oct 18, 2023 at 11:31 PM Tulip Nandu
wrote:
> Hi,
>
> I just got an email from the Bioconductor stating,
>
> According to the Multiple platform build/check report for BioC 3.18,
> the groHMM package has the following problem(s):
>
> o ERROR for 'R CMD build' on nebbiolo2. See the de
Is this error to be neglected then?
Package: groHMM
Version: 1.35.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs
--no-resave-data groHMM
StartedAt: 2023-10-17 17:05:26 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 17:07:18 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 112.0
There are .o and .so files in /src in the repo. These should not be
present in any source package. Please
remove them.
On Sat, Sep 24, 2022 at 6:58 AM Tulip Nandu
wrote:
> Hi,
>
> I received the following email,
> "According to the Multiple platform build/check report for BioC 3.16,
> the
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