Admin: shepherl

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shepherl ♦♦ 1.4k
Reputation:
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United States
Last seen:
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3 years, 1 month ago
Email:
l************@roswellpark.org

Bioconductor Core Team Member.

I work as a Bioconductor Core Team Member out of Roswell Park Comprehensive Cancer Center in Buffalo, NY.  I'm active in many areas of the project but notably maintain the Single Package Builder for new submissions, AWS resources, Bioconductor core docker images, the main Bioconductor website, and this support site.  While all members of the team offer support and maintenance of core package and core structures, I'm particularly more responsible for BiocCheck, BiocFileCache, and the Hubs (AnnotationHub, AnnotationHubData, ExperimentHub, ExperimentHubData). 

Posts by shepherl

<prev • 285 results • page 1 of 29 • next >
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Comment: C: no vignettes directory error during BiocCheck checking [SOLVED]
... Just glad you could figure it out and get it running. Let us know if you have any other issues. ...
written 4 days ago by shepherl ♦♦ 1.4k
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Comment: C: no vignettes directory error during BiocCheck checking
... Also I know `create_package` and `use_vignettes` functions can change the R working directory from the original starting location. Are you sure you entered the correct path into the BiocCheck function. Could you also please run and show the output of running the following in R: ``` dir( ) wd ...
written 5 days ago by shepherl ♦♦ 1.4k
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Comment: C: no vignettes directory error during BiocCheck checking
... In R could you do the following and show the results here ``` library(BiocCheck) sessionInfo() ``` ...
written 5 days ago by shepherl ♦♦ 1.4k
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Comment: C: no vignettes directory error during BiocCheck checking
... Can you please show the directory structure of your package. In the directory of your package you can type `tree` . You should get output something like the following: ``` lori@lori-HP-ZBook-15-G2:~/b/Rpacks/BiocFileCache(master)$ tree . ├── DESCRIPTION ├── inst │   └── schema │   └── BiocFil ...
written 5 days ago by shepherl ♦♦ 1.4k
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Comment: C: no vignettes directory error during BiocCheck checking
... I'm currently unable to reproduce this. Could you provide the current directory structure of your package with `system("tree ")` or whatever call you prefer to list the directory structure as well as your `systemInfo()` so we know what OS you are using. ...
written 5 days ago by shepherl ♦♦ 1.4k
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Comment: C: List of Deprecated Packages Bioc 3.10
... GSEAlm has been fixed and will be un-deprecated. ...
written 7 days ago by shepherl ♦♦ 1.4k
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News: List of Deprecated Packages Bioc 3.10
... The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. The list will be updated monthly. The packages condcomp, PathNet and allenpvc have been added to the list. The current list of depreca ...
annotation experimentdata news software release deprecation written 10 days ago by shepherl ♦♦ 1.4k
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Answer: A: Initial List of Deprecated Packages Bioc 3.10
... Two **Annotation Packages** have been user requested deprecated: MafDb.gnomADex.r2.0.1.GRCh38 MafDb.gnomAD.r2.0.1.GRCh38 They are replaced with MafDb.gnomADex.r2.1.GRCh38 MafDb.gnomAD.r2.1.GRCh38 Unmentioned previously the following **Annotation Packages** have also ...
written 24 days ago by shepherl ♦♦ 1.4k
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Comment: C: AH134 and other AnnotationHub objects unavailable as "defunct"
... As mentioned above we started providing 2bit files instead of bgzip resources. It is recommended to update to using the 2bits as this is what Bioconductor will provide by default. See the above post for the mouse and zebrafish options... It seems like the following could be used for Homo sapie ...
written 4 weeks ago by shepherl ♦♦ 1.4k
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Comment: C: biocLite() wants to update current packages
... Firstly For `R 3.6.0` The current Bioconductor release is `Bioc 3.9`. `BiocInstaller` has been removed from Bioconductor. To update and install Bioconductor package please use the functions in `BiocManager`. ``` install.packages("BiocManager") library(BiocManager) BiocManager::valid() ``` ...
written 4 weeks ago by shepherl ♦♦ 1.4k

Latest awards to shepherl

Supporter 5 months ago, voted at least 25 times.
Appreciated 5 months ago, created a post with more than 5 votes. For Updated Support Site Editor
Scholar 5 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Autobiographer 5 months ago, has more than 80 characters in the information field of the user's profile.
Guru 6 months ago, received more than 100 upvotes.
Scholar 7 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Scholar 8 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Scholar 9 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Is there any annotation package for MSEA?
Scholar 10 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Scholar 12 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Centurion 2.0 years ago, created 100 posts.
Scholar 2.0 years ago, created an answer that has been accepted. For A: survcomp package - censor missing
Scholar 2.0 years ago, created an answer that has been accepted. For A: MSstats package update
Appreciated 2.0 years ago, created a post with more than 5 votes. For DOI for packages
Commentator 2.0 years ago, created a comment with at least 3 up-votes. For C: Bioconductor packages now each have a DOI.
Scholar 3.1 years ago, created an answer that has been accepted. For A: survcomp package - censor missing
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: survcomp package - censor missing

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