Admin: Martin Morgan

gravatar for Martin Morgan
Martin Morgan ♦♦ 24k
Reputation:
23,580
Status:
Trusted
Location:
United States
Website:
http://bioconductor.org/
Last seen:
10 hours ago
Joined:
14 years ago
Email:
m************@gmail.com

Posts by Martin Morgan

<prev • 3,282 results • page 1 of 329 • next >
0
votes
0
answers
25
views
0
answers
Comment: C: AnnotationHub timeout for Ensembl Mouse GTF
... Do you have success downloading the file, e.g., via your browser, from https://annotationhub.bioconductor.org/fetch/70545 ? If that 'works', can you try to download this resource the way AnnotationHub does, via ``` url = "https://annotationhub.bioconductor.org/fetch/70545" response = httr::GET(url, ...
written 11 hours ago by Martin Morgan ♦♦ 24k
1
vote
1
answer
60
views
1
answers
Answer: A: Biostrings dependency cause new warnings on CRAN packages (base function rgb not
... This is an error in Biostrings that has since been addressed https://github.com/Bioconductor/Biostrings/commit/8d5a240c03cce6d0503956d6d99cae4d255c796f and is available now via `BiocManager::install("Biostrings")` when using `BiocManager::version('3.11")`. ...
written 9 days ago by Martin Morgan ♦♦ 24k
0
votes
2
answers
137
views
2
answers
Answer: A: DO.db is missing after repeated installations-ReactomePA-ClusterProfiler-DOSE
... Focus on installing DO.db; I suspect that `BiocManager::install("DO.db")` fails, and that RStudio is not displaying the full reason for failure. I suspect you are on Windows and using a network share `//some-share/...` and that you either need to google for `windows map network drive` and fix that, ...
written 11 days ago by Martin Morgan ♦♦ 24k
0
votes
1
answer
100
views
1
answers
Answer: A: PhyloProfile is not available for R version 3.6.1?
... ``BiocManager` indicates that you are using Bioconductor 3.9. Update to 3.10 ``` BiocManager::install(version = "3.10") ``` and try again. ...
written 13 days ago by Martin Morgan ♦♦ 24k
0
votes
1
answer
77
views
1
answers
Answer: A: SummarizedExperiment no function found corresponding to methods exports from XVe
... These errors (unknown functions) often occur when your installation includes packages from different versions of Bioconductor. Make sure ``` BiocManager::version() ``` returns the version that you want to use. Then that ``` BiocManager::valid() ``` reports no problems. ...
written 15 days ago by Martin Morgan ♦♦ 24k
0
votes
1
answer
42
views
1
answers
Answer: A: Package not found bioconductor gCMAP
... Make sure that you are using the current (3.10) version of Biocoonductor ``` BiocManager::version() # version of Bioconductor, not version of BiocManager BiocManager::install(version="3.10") ``` ...
written 17 days ago by Martin Morgan ♦♦ 24k
2
votes
1
answer
113
views
1
answers
Answer: A: Updating package CATALYST
... Update the version of Bioconductor you're using ``` BiocManager::install(version="3.10") ``` and try again. Note that this will ask to update (and you should) all Bioconductor packages. If it's important to retain your current installation, e.g., for reproducibility, then consider following the di ...
written 21 days ago by Martin Morgan ♦♦ 24k
0
votes
1
answer
653
views
1
answers
Comment: C: samtools loading in R
... The original answer still applies. If the package you are trying to use -- which package? -- requires the samtools application to be installed (and discoverable, so somewhere in specified by the PATH environment variable) then you'll need to install samtools independently of R. If you need help doin ...
written 24 days ago by Martin Morgan ♦♦ 24k
0
votes
1
answer
118
views
1
answers
Comment: C: BiocManager::install() gives ERROR
... My own setup is similar to yours, with different versions of R installed and with only base & recommended packages in the default library, and with different paths for each version of R + Bioconductor I use. I launch different versions of R / Bioconductor with shell aliases ``` $ bioc-3.9 -e ".l ...
written 29 days ago by Martin Morgan ♦♦ 24k
0
votes
0
answers
85
views
0
answers
Comment: C: Question on bgzf_read error
... My guess would be an integer overflow on Windows, the critical size is 'around' 2Gb, specifically ``` > .Machine$integer.max [1] 2147483647 ``` would you be willing to share the problem file? ...
written 4 weeks ago by Martin Morgan ♦♦ 24k

Latest awards to Martin Morgan

Scholar 4 months ago, created an answer that has been accepted. For A: GSEABase: how to extract shortDescription from GeneSetCollection object
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: how does coverage() works
Scholar 4 months ago, created an answer that has been accepted. For A: GSEABase: how to extract shortDescription from GeneSetCollection object
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: how does coverage() works
Popular Question 11 months ago, created a question with more than 1,000 views. For BioC 2017: Where Software and Biology Connect, 26 / 27 - 28 July, Boston, MA
Scholar 11 months ago, created an answer that has been accepted. For A: bplapply with ShortRead functions
Appreciated 11 months ago, created a post with more than 5 votes. For Bioconductor Technical Advisory Board
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: RSVSim insertions from chr1 to chr2
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Rsamtools use for R version 3.4.1
Scholar 11 months ago, created an answer that has been accepted. For A: error with many packages: "Error : .onLoad failed in loadNamespace() for 'org.Hs
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Best alternative annotation package to BiomaRt
Popular Question 11 months ago, created a question with more than 1,000 views. For Bioconductor Senior Programmer / Analyst
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: error with many packages: "Error : .onLoad failed in loadNamespace() for 'org.Hs
Scholar 11 months ago, created an answer that has been accepted. For A: how does coverage() works
Scholar 11 months ago, created an answer that has been accepted. For A: How to get chip information from annotation databases
Scholar 11 months ago, created an answer that has been accepted. For A: Ranges from a fasta file
Scholar 11 months ago, created an answer that has been accepted. For A: DataFrame after splitting and back
Scholar 11 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Appreciated 11 months ago, created a post with more than 5 votes. For Statistics and Computing in Genome Science (CSAMA) Course Material
Scholar 11 months ago, created an answer that has been accepted. For A: GSEABase: how to extract shortDescription from GeneSetCollection object
Scholar 11 months ago, created an answer that has been accepted. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Scholar 11 months ago, created an answer that has been accepted. For A: Is BiocInstaller::biocLite incompatible with withr::with_makevars?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 153 users visited in the last hour