Displaying 6 results from an estimated 6 matches for "pfam".
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pam
2015 Jan 26
2
Inspect a "delayed" assigned whose value throws an error?
...this I use is.function() and inherits() to inspect each object.
An aroma.affymetrix user reported on a problem that boiled down to the
following:
# source("http://bioconductor.org/biocLite.R"); biocLite("hgu133a.db")
> library("hgu133a.db")
> is.function(hgu133aPFAM)
Error: hgu133aPFAM is defunct. Please use select() if you need access to PFAM
or PROSITE accessions.
> .Internal(inspect(hgu133aPFAM))
> traceback()
3: stop(paste(msg, collapse = ""), call. = FALSE, domain = NA)
2: .Defunct(msg = msg)
1: (function ()
{
if (grepl("...
2008 Dec 11
3
DO NOT REPLY [Bug 5963] New: rsync fails with errors that make no sense...
...ounted on this (Linux)
system. We're transferring from one directory tree to another with a script
that looks like:
for i in /data2/* /data3/*
do
/usr/local/bin/rsync -a --delete ${i}/ /data1/`basename $i`
done
For some files/dirs, rsync is failing:
rsync: rename "/data1/bordner/Pfam/version_22.0/fasta/.PF09720.fa.8z0Imb" ->
"Pfam/version_22.0/fasta/PF09720.fa": File too large (27)
rsync: rename "/data1/bordner/Pfam/version_22.0/fasta/.PF09721.fa.0OoTTG" ->
"Pfam/version_22.0/fasta/PF09721.fa": File too large (27)
rsync: rename "/da...
2015 Jan 26
2
Inspect a "delayed" assigned whose value throws an error?
..., stop("Hey!"), assign.env = e)
> substitute(foo, e)
>
> delayedAssign("foo", stop("Hey!"))
> substitute(foo)
Hmm... interesting and odd.
Unfortunately, this doesn't seem to help for reaching into the
namespace of hgu133a.db and inspecting 'hgu133aPFAM', e.g.
> library("hgu133a.db")
> substitute(hgu133aPFAM, env=ns)
Error: hgu133aPFAM is defunct. Please use select() if you need access to PFAM
or PROSITE accessions.
> evalq(substitute(hgu133aPFAM), envir=ns)
Error: hgu133aPFAM is defunct. Please use select() if you need...
2015 Jan 26
0
Inspect a "delayed" assigned whose value throws an error?
...nd inherits() to inspect each object.
> An aroma.affymetrix user reported on a problem that boiled down to the
> following:
>
> # source("http://bioconductor.org/biocLite.R"); biocLite("hgu133a.db")
>> library("hgu133a.db")
>> is.function(hgu133aPFAM)
> Error: hgu133aPFAM is defunct. Please use select() if you need access to PFAM
> or PROSITE accessions.
>> .Internal(inspect(hgu133aPFAM))
>
>> traceback()
> 3: stop(paste(msg, collapse = ""), call. = FALSE, domain = NA)
> 2: .Defunct(msg = msg)
> 1: (fun...
2015 Jan 27
0
Inspect a "delayed" assigned whose value throws an error?
...itute(foo, e)
>>
>> delayedAssign("foo", stop("Hey!"))
>> substitute(foo)
> Hmm... interesting and odd.
> Unfortunately, this doesn't seem to help for reaching into the
> namespace of hgu133a.db and inspecting 'hgu133aPFAM', e.g.
>> library("hgu133a.db")
>> substitute(hgu133aPFAM, env=ns)
> Error: hgu133aPFAM is defunct. Please use select() if you need access to PFAM
> or PROSITE accessions.
>> evalq(substitute(hgu133aPFAM), envir=ns)
> Error: hgu133...
2011 Mar 30
2
R CMD build now removes empty dirs
...t/AnnDbPkg-templates/
AFFYHUEX.DB CHIMP.DB MALARIA.DB WORM.DB
ANOPHELES.DB COELICOLOR.DB MOUSECHIP.DB XENOPUSCHIP.DB
ARABIDOPSISCHIP.DB ECOLICHIP.DB MOUSE.DB XENOPUS.DB
ARABIDOPSIS.DB ECOLI.DB ORGANISM.DB YEASTCHIP.DB
BASEPKG.DB FLYCHIP.DB PFAM.DB YEAST.DB
BOVINECHIP.DB FLY.DB PIGCHIP.DB YEASTNCBI.DB
BOVINE.DB GO.DB PIG.DB ZEBRAFISHCHIP.DB
CANINECHIP.DB HUMANCHIP.DB RATCHIP.DB ZEBRAFISH.DB
CANINE.DB HUMAN.DB RAT.DB
CHICKENCHIP.DB INPARANOID.DB RHESUS.DB
CHIC...