Admin: shepherl

gravatar for shepherl
shepherl ♦♦ 830
Reputation:
830
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Trusted
Location:
United States
Last seen:
9 hours ago
Joined:
2 years, 5 months ago
Email:
l************@roswellpark.org

Bioconductor Core Team Member

Posts by shepherl

<prev • 182 results • page 1 of 19 • next >
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News: ensembl 94 gtfs and fasta twobits have been added to AnnotationHub
... Hello all, The ensembl 94 gtf (converted to GRanges on the fly) and fasta (twobit files) been added to AnnotationHub and are currently available in Bioc 3.8 Bioconductor version 3.8 (BiocManager 1.30.3), ?BiocManager::install for help > library(AnnotationHub) > hub = AnnotationHub() |==== ...
annotationdata annotationhub news ensembl gtf 2bit written 9 hours ago by shepherl ♦♦ 830
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Answer: A: Circular dependencies between data and software packages: how best to avoid
... The Single Package Builder  (SPB) automatically installs each package before the build and check stage as part of the process.  Each issue that goes through the SPB for new submits temporarily gets its own directory to use for Rlib, installing itself and referencing any additional dependencies -  Th ...
written 5 days ago by shepherl ♦♦ 830
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Answer: A: Question: Problem fetching resources from AnnotationHub, AH62557,error 403
... We apologize for the inconvenience. We have fixed the bug in the code and you should now be able to download the resource. Please let us know if you have any further issues. ...
written 6 days ago by shepherl ♦♦ 830
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Comment: C: Question: Problem fetching resources from AnnotationHub, AH62557,error 403
... Thank you for reporting this. It appears to be an ERROR in the AnnotationHub with how it handles special characters in the download link (ie. #). I will be investigating immediately and let you know when we have fixed the bug. ...
written 7 days ago by shepherl ♦♦ 830
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Comment: C: MLInterfaces package problem
... It appears that the package later is now required. Try seeing if after installing later it can properly load biocLite("later") If there are any new error messages or it still doesn't load please include those messages. ...
written 9 days ago by shepherl ♦♦ 830
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Answer: A: biocLite doesn't work
... The package has been removed from Bioconductor as documented on the removed packacage page. The link on the removed package page will have the last known working version of the package. ...
written 10 days ago by shepherl ♦♦ 830
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News: Package Submission Deadline is TODAY!!
... The final day to submit new packages to the Bioconductor contributions tracker to have a shot at being included in the upcoming 3.8 release is TODAY! Please note: submission by this date does not guarantee it will be included - the package must undergo an official review and be accepted by Wednesda ...
news release package submission new submission deadline written 11 days ago by shepherl ♦♦ 830
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Comment: C: Can't access devel version of ExperimentHub in Travis CI
... Try also adding ask='FALSE' to the argument remotes::install_github("Bioconductor/BiocManager") BiocManager::install(version='devel', ask=FALSE) And assuming that we can get this devel version issue straightened out for BiocManager. I would still recommend installing BiocManager at the top of th ...
written 13 days ago by shepherl ♦♦ 830
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Comment: C: Can't access devel version of ExperimentHub in Travis CI
... Maybe also try updating to use BiocManager instead of BiocInstaller and install instead of biocLite. install.package("BiocManager") BiocManager::install(version="devel") BiocManager::install(ask=FALSE) When I searched the above log, I could not find where you ran possibleDates() or where Exper ...
written 14 days ago by shepherl ♦♦ 830
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News: Deadline for devel branch 3.8 to pass R CMD build and R CMD check
... The deadline for all packages (software, data experiment, workflows) to pass R CMD build and R CMD check without TIMEOUT, ERROR, or WARNING is Friday October 26th. The devel branch will temporarily be frozen on Monday October 29th to branch for the October 31st release. Any changes after the freeze ...
news release devel freeze deadline written 15 days ago by shepherl ♦♦ 830

Latest awards to shepherl

Scholar 5 weeks ago, created an answer that has been accepted. For A: survcomp package - censor missing
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Is there any annotation package for MSEA?
Scholar 9 weeks ago, created an answer that has been accepted. For A: survcomp package - censor missing
Scholar 4 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Appreciated 16 months ago, created a post with more than 5 votes. For DOI for packages
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: Bioconductor packages now each have a DOI.
Scholar 16 months ago, created an answer that has been accepted. For A: MSstats package update
Scholar 16 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Centurion 16 months ago, created 100 posts.
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: survcomp package - censor missing
Scholar 2.5 years ago, created an answer that has been accepted. For A: survcomp package - censor missing

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