Re: [Bioc-devel] phloseq error: invalid class “sample_data” object: superclass "vectorORfactor" not defined in the environment of the object's class

2017-02-21 Thread Martin Morgan 

On 02/21/2017 03:24 PM, Levi Waldron wrote:

On Tue, Feb 21, 2017 at 2:02 PM, Hervé Pagès mailto:hpa...@fredhutch.org>> wrote:

Hi Levi,

Were you able to sort this out? I think we should emphasize the
importance of re-installing packages *from source* (i.e. with
biocLite(..., type="source")). This is because some of the package
binaries we distribute seem to be affected by this problem too.
We're planning to fix these binaries over the next couple of days.


Thank you, Hervé. I hadn't re-installed from source, and haven't gotten
around to doing a complete re-install, so I tried again with
`biocLite(..., type="source")`. But it still didn't fix the problem
re-installing `mydep$phyloseq` above with type="source". It isn't a
great rush, so perhaps I'll just wait until you've updated the binaries.


Here's an attempt to fail when the vectorORfactor class is contained in 
'list', which I think is where the problem comes from


trace(
loadNamespace,
quote(print(package)),
exit=quote({
contains <- names(getClass("list")@contains)
if (any(grepl("vectorORfactor", contains)))
stop("found after: ", package)
})
)
library(phyloseq)





Sorry for the inconvenience,


No worries!

-Levi




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Re: [Bioc-devel] phloseq error: invalid class “sample_data” object: superclass "vectorORfactor" not defined in the environment of the object's class

2017-02-21 Thread Levi Waldron 
On Tue, Feb 21, 2017 at 2:02 PM, Hervé Pagès  wrote:

> Hi Levi,
>
> Were you able to sort this out? I think we should emphasize the
> importance of re-installing packages *from source* (i.e. with
> biocLite(..., type="source")). This is because some of the package
> binaries we distribute seem to be affected by this problem too.
> We're planning to fix these binaries over the next couple of days.
>

Thank you, Hervé. I hadn't re-installed from source, and haven't gotten
around to doing a complete re-install, so I tried again with `biocLite(...,
type="source")`. But it still didn't fix the problem re-installing
`mydep$phyloseq` above with type="source". It isn't a great rush, so
perhaps I'll just wait until you've updated the binaries.


> Sorry for the inconvenience,
>

No worries!

-Levi

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Re: [Bioc-devel] phloseq error: invalid class “sample_data” object: superclass "vectorORfactor" not defined in the environment of the object's class

2017-02-21 Thread Hervé Pagès 

Hi Levi,

Were you able to sort this out? I think we should emphasize the
importance of re-installing packages *from source* (i.e. with
biocLite(..., type="source")). This is because some of the package
binaries we distribute seem to be affected by this problem too.
We're planning to fix these binaries over the next couple of days.

Sorry for the inconvenience,

H.

On 02/19/2017 07:58 AM, Levi Waldron wrote:

On Sun, Feb 19, 2017 at 2:54 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:


It is a variant of


https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2017-2DFebruary_010463.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=k6jN8WWwQDF4CDePzuCCjMH2qw1xQUbfc9cy6-FO48g&s=wuuIMKp7aAeTktf4VoEuYw4D22AFWWGGov1aDCNPloQ&e=

and requires re-installation of one or more of your Bioconductor
packages that depend directly or indirectly on S4Vectors; it's easy to



should have been 'not easy'



Thanks, Martin. I reinstalled both the "installme" and "mydep" packages
below using biocLite(installme), then when that didn't work, I also tried
biocLite(mydep$phyloseq). I guess a full Bioconductor reinstall would be a
heavy-handed but effective fix?


db = available.packages(repos=BiocInstaller::biocinstallRepos()[1])

   revdeps = tools::package_dependencies("S4Vectors", db, recursive=TRUE,
   reverse=TRUE)

mydep = tools::package_dependencies("phyloseq", db, recursive=TRUE)
installme = mydep$phyloseq[mydep$phyloseq %in% revdeps$S4Vectors]
mydep

$phyloseq
 [1] "BiocGenerics" "ade4" "ape"  "biomformat"
"Biostrings"
 [6] "cluster"  "data.table"   "foreach"  "ggplot2"  "igraph"

[11] "methods"  "multtest" "plyr" "reshape2" "scales"

[16] "vegan""Biobase"  "utils""graphics" "stats"

[21] "parallel" "jsonlite" "Matrix"   "rhdf5"
 "S4Vectors"
[26] "IRanges"  "XVector"  "survival" "MASS" "stats4"

[31] "zlibbioc"

installme

[1] "Biostrings" "IRanges""XVector"




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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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