The new report is
available:https://bioconductor.org/checkResults/3.19/bioc-LATEST/MSA2dist/.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of Herv� Pag�s
Sent: Wednesday, April 24, 2024 12:27 PM
a day (starting at 3:00pm ET) to go through a complete cycle and
then a few additional hours for content to propagate to the landing pages.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of erhanozer19
via
<https://contributions.bioconductor.org/git-version-control.html?q=cherry%20pick#bug-fix-in-release-and-devel>.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of Michael
Shapiro
Sent: Wednesday, Ma
builder to catch ordered comparisons on language objects:
_R_COMPARE_LANG_OBJECTS=eqonly
For more information, see
https://stat.ethz.ch/pipermail/r-devel/2024-March/083254.html.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
[[alternative HTML version deleted
, and Windows
platforms at https://bioconductor.org/checkResults/3.19/bioc-LATEST/. Thanks
for your understanding.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
[[alternative HTML version deleted]]
___
Bioc-devel@r
Maintenance will be performed on Nebbiolo1 and Nebbiolo2 on Wednesday 2/14, so
Bioconductor build reports may not start again until Friday 2/16. Thanks for
your patience.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
[[alternative HTML version deleted
on the 2024/01/08, it's
possible that it failed due to an issue with another package at that time which
has since been resolved.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of Johannes Griss
Sent: Thursday
Hi Leo,
spatialLIBD is missing DropletUtils in Suggests in the DESCRIPTION. If you add
it there and bump the version, it will pass check.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of Leonardo
Collado
so the errors may be
more consistent in the report in the next day or so.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of Aditya Bhagwat
via Bioc-devel
Sent: Tuesday, November 14, 2023 4:23 AM
To: bioc
might need to update your data object in ReactomeGSA.data.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of Johannes Griss
Sent: Friday, November 3, 2023 4:52 PM
To: bioc-devel@r-project.org
Subject: [Bioc
workaround is found.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of Oleksii
Nikolaienko
Sent: Saturday, October 28, 2023 1:08 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] No cairo device on merida1
Hi Carlotta,
The branch is named devel on git.bioconductor.org. If you want to push from
your local main branch to your repo on git.bioconductor.org, you should do
git push upstream main:devel
See https://contributions.bioconductor.org/git-version-control.html for more
details.
Jennifer
the cache again and troubleshoot more.
Martin,
Regarding your question about updating tensorflow that is made available on the
build machines for CRAN package
tensorflow<https://cran.r-project.org/web/packages/tensorflow/index.html>, it
should be fine to update tensorflow on kunpeng2.
Je
should see this
reflected in the report for next Thursday since the Mac ARM64 devel builds have
already started. Thanks everyone for your help and this discussion.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf
We removed resource EH1524 from the cache so it could be redownloaded. scry's
report does not show errors today:
https://bioconductor.org/checkResults/devel/bioc-LATEST/scry/.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc
Hi Michael,
Java is installed on the devel windows builder Palomino4 in the same way it is
installed on the release 3.17 Windows builder. I think
https://code.bioconductor.org/browse/rRDP/blob/devel/R/RDP.R#L63 assumes that
JAVA_HOME is set, but it is not set on these builders.
Jennifer
e Call for Participation page on the Outreachy website:
https://www.outreachy.org/communities/cfp/.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailin
Both release and devel show the same error. I'm able to reproduce the error
when attempting R CMD INSTALL YAPSA in the Bioconductor docker container
(https://www.bioconductor.org/help/docker/). I recommend using it to
troubleshoot this error.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY
Hi Anatoly,
I see we got a few of these on the most recent build. No action is needed as
the Bioconductor build system will remove the lock files on the next run next
Wednesday.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From
org/mentor/mentor-faq/>
Full details about the Outreachy program and the internship timeline can be
found on the Call for Participation page on the Outreachy website:
https://www.outreachy.org/communities/cfp/
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Cor
.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of Selles Vidal,
Lara
Sent: Monday, June 19, 2023 9:37 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] rfaRm package
* This email originates from a sender
Hi,
The build machines used for single package submissions will be updated today so
they will be temporarily unavailable until 1pm. Thanks for your understanding.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
[[alternative HTML version deleted
will include the mac builder.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of Nils Eling
Sent: Monday, June 5, 2023 5:28 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Adding package to long tests
Hi Meriem,
We had .NET 5.0 on those machines, which I've updated to 6.0. You should see
the errors clear up tomorrow or Thursday.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of Meriem Bahda
Sent
of the builds going forward.
The error can be resolved by adding the missing dependency to Suggests in the
DESCRIPTION file.
You can read the original announcement at
https://stat.ethz.ch/pipermail/bioc-devel/2023-March/019555.html.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core
preprocessCore
qpgraph
sSNAPPY
scGPS
scde
scmap
scran
scuttle
signeR
3.18
BPRMeth
CGEN
CNAnorm
COMPASS
DNAcopy
GGPA
GRENITS
GeneSelectMMD
GeneticsPed
GeoDiff
HDTD
LEA
Linnorm
MSstats
NuPoP
SAIGEgds
SIMLR
SNPRelate
affyPLM
densvis
edgeR
genefilter
graper
iClusterPlus
impute
preprocessCore
Jennifer
Hi,
cfTools will be still be included in 3.17. I don't see the error relating to
conda on today's build report. We don't directly manage conda on the builders
and allow basilisk to handle it. I can try clearing the cache on the 3.17
Windows builder this week to see if that helps.
Jennifer
Hi,
I am updating the Linux builder with a newer version of R. I'll try to provide
a notice for future updates to avoid confusion. I should be finished about 1 PM
ET. Thanks for your patience.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
Hi Jose,
Thanks for your message. I just noticed this issue. I'm working on a fix now
that I hope will resolve the issue later this week.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of Jos� Luiz
everal...
contributions.bioconductor.org
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of matine rb
Sent: Monday, March 27, 2023 4:09 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Push changes to release branch
***ATT
the missing dependency and add it to
Suggests in the DESCRIPTION file.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch
Hi Sarvesh,
Thanks for reporting the issue. I had to reinstall ragg on merida1. The errors
should clear up on tomorrow's build report.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of Sarvesh
Nikumbh
Johannes,
Thanks for reporting this. It should improve in the next build report.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of Rainer
Johannes
Sent: Monday, March 20, 2023 6:44 AM
To: bioc-devel@r
reports, it will be resolved on
Wednesday's report.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of Y-h. Taguchi
Sent: Tuesday, March 7, 2023 8:10 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Fwd
Hi Sarvesh,
The error should go away on tomorrow's build report.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of Sarvesh
Nikumbh
Sent: Monday, March 6, 2023 6:15 AM
To: bioc-devel@r-project.org
Subject
.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of Ahmed Mohamed
Sent: Monday, February 27, 2023 6:11 PM
To: bioc-devel
Subject: [Bioc-devel] libsbml and libxml2 on palomino3 BBS
***ATTENTION: This email came
/Cellar/openssl@3/3.0.5/lib/libssl.a
/opt/homebrew/Cellar/openssl@3/3.0.5/lib/libcrypto.a
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
We have not made any recent changes to these binaries but these are the first
ones we made available for M1 Macs.
Jennifer
Hi Sergi,
I agree these are due to newer pandoc versions on these machines. I'm going
make sure both linux and both macs use the same versions this week so we get
consistent results.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
These are the results for merida1:
merida1$ java --version
openjdk 18.0.1.1 2022-04-22
OpenJDK Runtime Environment (build 18.0.1.1+2-6)
OpenJDK 64-Bit Server VM (build 18.0.1.1+2-6, mixed mode, sharing)
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
Using the mailing list or the #bioc-builds channel on the community slack are
good ways to reach out to the Bioconductor core team. I'll look into the dotnet
issues for rmspc.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc
and
submit.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of Graciela Uria
Regojo
Sent: Tuesday, January 17, 2023 9:14 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Maftools not working on Mac
Hi Anna,
If your package was recently accepted around the holidays, it should be
processed by the end of the week.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
From: Bioc-devel on behalf of Anna Pa��nkov�
Sent: Monday, January 2
Hi Dana,
Hope you had a great holiday. I updated MiKTex and was able to build PloGO2
manually on palomino4. Let's check the build report tomorrow and see if the
error is cleared up.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPS
Bioconductor Core Team
Hi Pedro,
I don't see these issues on today's build report, so they may have been
resolved. If you see the issue again, let us know.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPS
Bioconductor Core Team
From: Bioc-devel on behalf of Pedro Madrigal
Sent
Thanks for your email. I'll look into this.
From: Bioc-devel on behalf of vandenbulcke
stijn
Sent: Friday, October 28, 2022 9:29 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] palomino4 CHECK error "permission denied" msqrob2
***ATTENTION: This email
Hi Sarvesh,
I've installed packaging on our devel Windows builder. We should see the issue
resolved in the next build report.
Jen
From: Bioc-devel on behalf of Sarvesh
Nikumbh
Sent: Thursday, October 20, 2022 12:08 PM
To: bioc-devel@r-project.org
Subject:
package to work with .NET 6.0 in
the future.
Jennifer Wokaty
they/them
Bioconductor Core Team
CUNY SPH
From: Bioc-devel on behalf of Meriem Bahda
Sent: Wednesday, September 28, 2022 11:48:47 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Package
Hi Rocio,
Thanks for bringing this to our attention. I've fixed the DOI for SINGLe.
Jennifer Wokaty
they/them
Bioconductor Core Team
CUNY SPH
From: Bioc-devel on behalf of Rocio Espada
via Bioc-devel
Sent: Wednesday, September 28, 2022 7:51 AM
BiocManager::install() as usual
Note: BiocManager::install() will automatically pick the new arm64 binaries so
you should no longer need Xcode.
Jennifer Wokaty
they/them
Bioconductor Core Team
CUNY SPH
[[alternative HTML version deleted]]
___
Bioc
on Friday so some of them didn't complete
Saturday's run to update the build report, which sometimes happens with a fresh
install of R and may have added some confusion.
Jennifer Wokaty
they/them
Bioconductor Core Team
CUNY SPH
From: Bioc-devel
as we will only be looking for
errors on Palomino3 (as well as Nebbiolo1 and Merida1). This machine has the
new R tool chain for R that we must use going forward for the Windows builds. ?
Jennifer Wokaty
Bioconductor Core Team
From: Oleksii Nikolaienko
Sent
Hi Meriem,
Thanks for reporting this issue. I've installed .NET 5.0 on nebbiolo1 and
confirmed that I can build rmspc; however, the error may still show up on the
build report Friday because we've already started building packages. So it
should pass on the build report after that.
Jennifer
You can follow
https://bioconductor.org/developers/how-to/git/push-to-github-bioc/ to push to
both Github and Bioconductor repositories.
Jennifer Wokaty
Bioconductor Core Team
From: Bioc-devel on behalf of Emanuela
Iovino
Sent: Monday, December 20
Hi Johannes,
We've updated the certificates on the release Mac builder yesterday, so we
should see these issues clear up on the next release build report Friday.
Jennifer Wokaty
Bioconductor Core Team
From: Bioc-devel on behalf of Johannes Griss
l Python, for
example using `.Platform$OS.type`. The reason it isn't also failing on Mac is
that `python` exists, but it's Python 2, which we no longer support and will
likely be removed in the future.
Jennifer Wokaty (they/them)
Bioconductor Core Team
Fr
Zheng,
I talked to Herve about your issue as well as the build machines. You should
use `python` for Windows and `python3` for Linux and Mac.
Jennifer Wokaty
Bioconductor Core Team
Waldron Lab
CUNY Graduate School of Public Health and Health Policy
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