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R install failure #7

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justincbagley opened this issue Aug 19, 2016 · 13 comments
Closed

R install failure #7

justincbagley opened this issue Aug 19, 2016 · 13 comments

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@justincbagley
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justincbagley commented Aug 19, 2016 •
edited
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Hi Brian,

I'm using OSX 10.11.16, R v3.2.1, and I am having an issue with the PHRAPL install. When I follow your instructions, I get an error apparently due to failure to unpack a file with a name ending in "-1":

> devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/bomeara/phrapl/zipball/master
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes (323 KB)
==================================================
downloaded 323 KB

Error: Don't know how to decompress files with extension 1-1
> 
>

In response, I downloaded the master dir and tried to use devtools to install locally, but this also failed:

> install("/Users/justinbagley/Downloads/bomeara-phrapl-688acb1")
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes (323 KB)
==================================================
downloaded 323 KB

Error: Don't know how to decompress files with extension 1-1
> 
>

Please help me find a solution to this so I can start working with PHRAPL.
Thanks.

Best,

Justin
@ndjaxon
Copy link
Collaborator

ndjaxon commented Aug 19, 2016

Hi Justin,

It looks like devtools is having a hard time installing the package
'binom', which is a dependency of phrapl. Specifically, it looks like the
tarball suffix has been truncated from the URL (i.e., it should be"'
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.2/binom_1.1-1.tgz").
I'm not sure why that is happening and I can't duplicate it on the machine
I'm using.

Before you install phrapl, perhaps try installing binom alone first by
doing:

install.packages("binom",repos="http://cran.rstudio.com")

Then install phrapl using the devtools command. Let me know if this doesn't
work.

Thanks,

Nathan

On Fri, Aug 19, 2016 at 10:24 AM, Justin C. Bagley <notifications@github.com

wrote:

Hi Brian,

I'm using OSX 10.11.16, R v3.2.1, and I am having an issue with the PHRAPL
install. When I follow your instructions, I get an error apparently due to
failure to unpack a file with a name ending in "-1":

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/bomeara/phrapl/zipball/master
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

Error: Don't know how to decompress files with extension 1-1

In response, I downloaded the master dir and tried to use devtools to
install locally, but this also failed:

install("/Users/justinbagley/Downloads/bomeara-phrapl-688acb1")
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

Error: Don't know how to decompress files with extension 1-1

Please help me find a solution to this so I can start working with PHRAPL.
Thanks.

Best,

Justin

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@justincbagley
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Dear Nathan,

Thanks very much for the quick response. I tried your suggestion and it
looked like it almost worked, at least it passed the previous sticking
point. However, I'm still having an issue, only now the error says "Don't
know how to decompress files with extension 6.3":

install.packages("binom",repos="http://cran.rstudio.com")
Installing package into ‘/Users/justinbagley/Library/R/3.2/library’
(as ‘lib’ is unspecified)
trying URL '
http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/binom_1.1-1.tgz'

Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

The downloaded binary packages are in
/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn/T//RtmpFxXFYU/downloaded_packages

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/bomeara/phrapl/zipball/master
Installing phrapl
trying URL '
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.2/diagram_1.6.3'

Content type 'application/x-gzip' length 560715 bytes (547 KB)

downloaded 547 KB

Error: Don't know how to decompress files with extension 6.3

Can you think of anything else to try? Thanks for your help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Fri, Aug 19, 2016 at 2:06 PM, Nathan D Jackson notifications@github.com
wrote:

Hi Justin,

It looks like devtools is having a hard time installing the package
'binom', which is a dependency of phrapl. Specifically, it looks like the
tarball suffix has been truncated from the URL (i.e., it should be"'
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.2/binom_1.1-1.tgz").
I'm not sure why that is happening and I can't duplicate it on the machine
I'm using.

Before you install phrapl, perhaps try installing binom alone first by
doing:

install.packages("binom",repos="http://cran.rstudio.com")

Then install phrapl using the devtools command. Let me know if this doesn't
work.

Thanks,

Nathan

On Fri, Aug 19, 2016 at 10:24 AM, Justin C. Bagley <
notifications@github.com

wrote:

Hi Brian,

I'm using OSX 10.11.16, R v3.2.1, and I am having an issue with the
PHRAPL
install. When I follow your instructions, I get an error apparently due
to
failure to unpack a file with a name ending in "-1":

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/bomeara/phrapl/zipball/master
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

Error: Don't know how to decompress files with extension 1-1

In response, I downloaded the master dir and tried to use devtools to
install locally, but this also failed:

install("/Users/justinbagley/Downloads/bomeara-phrapl-688acb1")
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

Error: Don't know how to decompress files with extension 1-1

Please help me find a solution to this so I can start working with
PHRAPL.
Thanks.

Best,

Justin

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@ndjaxon
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ndjaxon commented Aug 19, 2016

Hi Justin,

It looks like the same thing is happening, but with another phrapl
dependency ('diagram'). The installation URL is being truncated. To prevent
this from happening, maybe just try pre-installing all of the phrapl
dependencies beforehand by running the following:

if(!require("ape")){install.packages("ape",repos="http://cran.rstudio.com")}
if(!require("partitions")){install.packages("partitions",repos="
http://cran.rstudio.com")}
if(!require("lattice")){install.packages("lattice",repos="
http://cran.rstudio.com")}
if(!require("polynom")){install.packages("polynom",repos="
http://cran.rstudio.com")}
if(!require("gmp")){install.packages("gmp",repos="http://cran.rstudio.com")}
if(!require("rgenoud")){install.packages("rgenoud",repos="
http://cran.rstudio.com")}
if(!require("parallel")){install.packages("parallel",repos="
http://cran.rstudio.com")}
if(!require("optimx")){install.packages("optimx",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="
http://cran.rstudio.com")}
if(!require("numDeriv")){install.packages("numDeriv",repos="
http://cran.rstudio.com")}
if(!require("nloptr")){install.packages("nloptr",repos="
http://cran.rstudio.com")}
if(!require("Matrix")){install.packages("Matrix",repos="
http://cran.rstudio.com")}
if(!require("rgl")){install.packages("rgl",repos="http://cran.rstudio.com")}
if(!require("RColorBrewer")){install.packages("RColorBrewer",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("RColorBrewer",repos="
http://cran.rstudio.com")}
if(!require("diagram")){install.packages("RColorBrewer",repos="
http://cran.rstudio.com")}
if(!require("binom")){install.packages("RColorBrewer",repos="
http://cran.rstudio.com")}

Then install phrapl. I'm not sure if this is just a local problem or a more
general one. If anybody else experiences this issue, I will delve into
fixing it.

Let me know if you have any other issues. Thanks for trying out phrapl!

Nathan

On Fri, Aug 19, 2016 at 11:21 AM, Justin C. Bagley <notifications@github.com

wrote:

Dear Nathan,

Thanks very much for the quick response. I tried your suggestion and it
looked like it almost worked, at least it passed the previous sticking
point. However, I'm still having an issue, only now the error says "Don't
know how to decompress files with extension 6.3":

install.packages("binom",repos="http://cran.rstudio.com")
Installing package into ‘/Users/justinbagley/Library/R/3.2/library’
(as ‘lib’ is unspecified)
trying URL '
http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/binom_1.1-1.tgz'

Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

The downloaded binary packages are in
/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn/T//RtmpFxXFYU/downloaded_
packages

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/bomeara/phrapl/zipball/master
Installing phrapl
trying URL '
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.2/diagram_1.6.3'

Content type 'application/x-gzip' length 560715 bytes (547 KB)

downloaded 547 KB

Error: Don't know how to decompress files with extension 6.3

Can you think of anything else to try? Thanks for your help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Fri, Aug 19, 2016 at 2:06 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Hi Justin,

It looks like devtools is having a hard time installing the package
'binom', which is a dependency of phrapl. Specifically, it looks like the
tarball suffix has been truncated from the URL (i.e., it should be"'
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.2/binom_1.1-1.tgz").
I'm not sure why that is happening and I can't duplicate it on the
machine
I'm using.

Before you install phrapl, perhaps try installing binom alone first by
doing:

install.packages("binom",repos="http://cran.rstudio.com")

Then install phrapl using the devtools command. Let me know if this
doesn't
work.

Thanks,

Nathan

On Fri, Aug 19, 2016 at 10:24 AM, Justin C. Bagley <
notifications@github.com

wrote:

Hi Brian,

I'm using OSX 10.11.16, R v3.2.1, and I am having an issue with the
PHRAPL
install. When I follow your instructions, I get an error apparently due
to
failure to unpack a file with a name ending in "-1":

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/bomeara/phrapl/zipball/master
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

Error: Don't know how to decompress files with extension 1-1

In response, I downloaded the master dir and tried to use devtools to
install locally, but this also failed:

install("/Users/justinbagley/Downloads/bomeara-phrapl-688acb1")
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

Error: Don't know how to decompress files with extension 1-1

Please help me find a solution to this so I can start working with
PHRAPL.
Thanks.

Best,

Justin

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@ndjaxon
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ndjaxon commented Aug 19, 2016

Sorry, I made a mistake with the last three installation calls. Here's the
correct code:

if(!require("ape")){install.packages("ape",repos="http://cran.rstudio.com")}
if(!require("partitions")){install.packages("partitions",repos="
http://cran.rstudio.com")}
if(!require("lattice")){install.packages("lattice",repos="
http://cran.rstudio.com")}
if(!require("polynom")){install.packages("polynom",repos="
http://cran.rstudio.com")}
if(!require("gmp")){install.packages("gmp",repos="http://cran.rstudio.com")}
if(!require("rgenoud")){install.packages("rgenoud",repos="
http://cran.rstudio.com")}
if(!require("parallel")){install.packages("parallel",repos="
http://cran.rstudio.com")}
if(!require("optimx")){install.packages("optimx",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="
http://cran.rstudio.com")}
if(!require("numDeriv")){install.packages("numDeriv",repos="
http://cran.rstudio.com")}
if(!require("nloptr")){install.packages("nloptr",repos="
http://cran.rstudio.com")}
if(!require("Matrix")){install.packages("Matrix",repos="
http://cran.rstudio.com")}
if(!require("rgl")){install.packages("rgl",repos="http://cran.rstudio.com")}
if(!require("RColorBrewer")){install.packages("RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="http://
cran.rstudio.com")}
if(!require("diagram")){install.packages("diagram",repos="http://
cran.rstudio.com")}
if(!require("binom")){install.packages("binom",repos="
http://cran.rstudio.com")}

On Fri, Aug 19, 2016 at 11:35 AM, Nathan Jackson ndjaxon@gmail.com wrote:

Hi Justin,

It looks like the same thing is happening, but with another phrapl
dependency ('diagram'). The installation URL is being truncated. To prevent
this from happening, maybe just try pre-installing all of the phrapl
dependencies beforehand by running the following:

if(!require("ape")){install.packages("ape",repos="http://cran.rstudio.com
")}
if(!require("partitions")){install.packages("partitions",repos="
http://cran.rstudio.com")}
if(!require("lattice")){install.packages("lattice",repos="
http://cran.rstudio.com")}
if(!require("polynom")){install.packages("polynom",repos="
http://cran.rstudio.com")}
if(!require("gmp")){install.packages("gmp",repos="http://cran.rstudio.com
")}
if(!require("rgenoud")){install.packages("rgenoud",repos="
http://cran.rstudio.com")}
if(!require("parallel")){install.packages("parallel",repos="
http://cran.rstudio.com")}
if(!require("optimx")){install.packages("optimx",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="
http://cran.rstudio.com")}
if(!require("numDeriv")){install.packages("numDeriv",repos="
http://cran.rstudio.com")}
if(!require("nloptr")){install.packages("nloptr",repos="
http://cran.rstudio.com")}
if(!require("Matrix")){install.packages("Matrix",repos="
http://cran.rstudio.com")}
if(!require("rgl")){install.packages("rgl",repos="http://cran.rstudio.com
")}
if(!require("RColorBrewer")){install.packages("RColorBrewer",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("diagram")){install.packages("RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("binom")){install.packages("RColorBrewer",repos="
http://cran.rstudio.com")}

Then install phrapl. I'm not sure if this is just a local problem or a
more general one. If anybody else experiences this issue, I will delve into
fixing it.

Let me know if you have any other issues. Thanks for trying out phrapl!

Nathan

On Fri, Aug 19, 2016 at 11:21 AM, Justin C. Bagley <
notifications@github.com> wrote:

Dear Nathan,

Thanks very much for the quick response. I tried your suggestion and it
looked like it almost worked, at least it passed the previous sticking
point. However, I'm still having an issue, only now the error says "Don't
know how to decompress files with extension 6.3":

install.packages("binom",repos="http://cran.rstudio.com")
Installing package into ‘/Users/justinbagley/Library/R/3.2/library’
(as ‘lib’ is unspecified)
trying URL '
http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/binom_1.1-1.tgz'

Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

The downloaded binary packages are in
/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn/T//
RtmpFxXFYU/downloaded_packages

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/bomeara/phrapl/zipball/master
Installing phrapl
trying URL '
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.
2/diagram_1.6.3'

Content type 'application/x-gzip' length 560715 bytes (547 KB)

downloaded 547 KB

Error: Don't know how to decompress files with extension 6.3

Can you think of anything else to try? Thanks for your help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Fri, Aug 19, 2016 at 2:06 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Hi Justin,

It looks like devtools is having a hard time installing the package
'binom', which is a dependency of phrapl. Specifically, it looks like
the
tarball suffix has been truncated from the URL (i.e., it should be"'
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.2/binom_1.1-1.tgz").
I'm not sure why that is happening and I can't duplicate it on the
machine
I'm using.

Before you install phrapl, perhaps try installing binom alone first by
doing:

install.packages("binom",repos="http://cran.rstudio.com")

Then install phrapl using the devtools command. Let me know if this
doesn't
work.

Thanks,

Nathan

On Fri, Aug 19, 2016 at 10:24 AM, Justin C. Bagley <
notifications@github.com

wrote:

Hi Brian,

I'm using OSX 10.11.16, R v3.2.1, and I am having an issue with the
PHRAPL
install. When I follow your instructions, I get an error apparently
due
to
failure to unpack a file with a name ending in "-1":

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/bomeara/phrapl/zipball/master
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

Error: Don't know how to decompress files with extension 1-1

In response, I downloaded the master dir and tried to use devtools to
install locally, but this also failed:

install("/Users/justinbagley/Downloads/bomeara-phrapl-688acb1")
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

Error: Don't know how to decompress files with extension 1-1

Please help me find a solution to this so I can start working with
PHRAPL.
Thanks.

Best,

Justin

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@justincbagley
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Dear Nathan,

I gave this another go today. Following your suggestion to pre-install
dependencies didn't work on R 3.2.1, so I updated to the latest
distribution on cran, 3.3.1, called the pre-install code you supplied, then
used devtools to successfully install PHRAPL. Here is the final install:

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/bomeara/phrapl/zipball/master
Installing phrapl
trying URL '
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.3/rgenoud_5.7-12.4.tgz
'

Content type 'application/x-gzip' length 709466 bytes (692 KB)

downloaded 692 KB

Installing rgenoud
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file
--no-environ --no-save --no-restore
--quiet CMD INSTALL \

'/private/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn/T/RtmpkZhAtz/devtoolsa4d82124d81c/rgenoud'
\

--library='/Library/Frameworks/R.framework/Versions/3.3/Resources/library'
--install-tests

  • installing binary package ‘rgenoud’ ...
  • DONE (rgenoud)
    '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file
    --no-environ --no-save --no-restore
    --quiet CMD INSTALL \

'/private/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn/T/RtmpkZhAtz/devtoolsa4d865971217/bomeara-phrapl-688acb1'
\

--library='/Library/Frameworks/R.framework/Versions/3.3/Resources/library'
--install-tests

  • installing source package ‘phrapl’ ...
    ** R
    ** data
    ** inst
    ** preparing package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded
  • DONE (phrapl)

Despite the install success, I am now stuck in the initial stages of a
preliminary analysis. Following through your tutorial I have made it to the
point where I define observed trees to work with, but I can't get past this
point because I get an error stating that keepTaxa matrix is of the wrong
length: "number of items to replace is not a multiple of replacement
length"...

library(phrapl)

setwd("~/Documents/2 - by Project/bin")

Hyptrees <- read.tree("Hyp_besttrees.tre")

assignFile<-read.table("Hyp_fastSTRUCTURE_pop_delim_file_wOut_for_PHRAPL.txt",header=TRUE,stringsAsFactors=FALSE)
popAssignments <- list(c(3,3,3,3,3,3))

assignmentsGlobal <- assignFile
observedTrees <- Hyptrees
subsamplesPerGene <- 10
outgroup = TRUE
outgroupPrune = TRUE

observedTrees <- PrepSubsampling(assignmentsGlobal = assignmentsGlobal,
observedTrees = observedTrees, popAssignments = popAssignments,
subsamplesPerGene = subsamplesPerGene, outgroup = outgroup, outgroupPrune =
outgroupPrune)
Error in retainedTaxaMatrix[rep, ] <- keepTaxa :
number of items to replace is not a multiple of replacement length

My input data are separate gene trees for each of 227 SNP loci from a
RAD-seq experiment... with I think 43 individuals assigned to five ingroup
clades and one outgroup (2 individuals). I tried this again with a
five-length popVector, and with and without pruning the outgroup. However,
I continue getting the same error. Is this a bug in the code that needs to
be ironed out or is there a way I can check or correct this?

Thanks for your help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Fri, Aug 19, 2016 at 2:41 PM, Nathan D Jackson notifications@github.com
wrote:

Sorry, I made a mistake with the last three installation calls. Here's the
correct code:

if(!require("ape")){install.packages("ape",repos="http://cran.rstudio.com
")}
if(!require("partitions")){install.packages("partitions",repos="
http://cran.rstudio.com")}
if(!require("lattice")){install.packages("lattice",repos="
http://cran.rstudio.com")}
if(!require("polynom")){install.packages("polynom",repos="
http://cran.rstudio.com")}
if(!require("gmp")){install.packages("gmp",repos="http://cran.rstudio.com
")}
if(!require("rgenoud")){install.packages("rgenoud",repos="
http://cran.rstudio.com")}
if(!require("parallel")){install.packages("parallel",repos="
http://cran.rstudio.com")}
if(!require("optimx")){install.packages("optimx",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="
http://cran.rstudio.com")}
if(!require("numDeriv")){install.packages("numDeriv",repos="
http://cran.rstudio.com")}
if(!require("nloptr")){install.packages("nloptr",repos="
http://cran.rstudio.com")}
if(!require("Matrix")){install.packages("Matrix",repos="
http://cran.rstudio.com")}
if(!require("rgl")){install.packages("rgl",repos="http://cran.rstudio.com
")}
if(!require("RColorBrewer")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="http://
cran.rstudio.com")}
if(!require("diagram")){install.packages("diagram",repos="http://
cran.rstudio.com")}
if(!require("binom")){install.packages("binom",repos="
http://cran.rstudio.com")}

On Fri, Aug 19, 2016 at 11:35 AM, Nathan Jackson ndjaxon@gmail.com
wrote:

Hi Justin,

It looks like the same thing is happening, but with another phrapl
dependency ('diagram'). The installation URL is being truncated. To
prevent
this from happening, maybe just try pre-installing all of the phrapl
dependencies beforehand by running the following:

if(!require("ape")){install.packages("ape",repos="http://
cran.rstudio.com
")}
if(!require("partitions")){install.packages("partitions",repos="
http://cran.rstudio.com")}
if(!require("lattice")){install.packages("lattice",repos="
http://cran.rstudio.com")}
if(!require("polynom")){install.packages("polynom",repos="
http://cran.rstudio.com")}
if(!require("gmp")){install.packages("gmp",repos="http://
cran.rstudio.com
")}
if(!require("rgenoud")){install.packages("rgenoud",repos="
http://cran.rstudio.com")}
if(!require("parallel")){install.packages("parallel",repos="
http://cran.rstudio.com")}
if(!require("optimx")){install.packages("optimx",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="
http://cran.rstudio.com")}
if(!require("numDeriv")){install.packages("numDeriv",repos="
http://cran.rstudio.com")}
if(!require("nloptr")){install.packages("nloptr",repos="
http://cran.rstudio.com")}
if(!require("Matrix")){install.packages("Matrix",repos="
http://cran.rstudio.com")}
if(!require("rgl")){install.packages("rgl",repos="http://
cran.rstudio.com
")}
if(!require("RColorBrewer")){install.packages("RColorBrewer",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("diagram")){install.packages("RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("binom")){install.packages("RColorBrewer",repos="
http://cran.rstudio.com")}

Then install phrapl. I'm not sure if this is just a local problem or a
more general one. If anybody else experiences this issue, I will delve
into
fixing it.

Let me know if you have any other issues. Thanks for trying out phrapl!

Nathan

On Fri, Aug 19, 2016 at 11:21 AM, Justin C. Bagley <
notifications@github.com> wrote:

Dear Nathan,

Thanks very much for the quick response. I tried your suggestion and it
looked like it almost worked, at least it passed the previous sticking
point. However, I'm still having an issue, only now the error says
"Don't
know how to decompress files with extension 6.3":

install.packages("binom",repos="http://cran.rstudio.com")
Installing package into ‘/Users/justinbagley/Library/R/3.2/library’
(as ‘lib’ is unspecified)
trying URL '
http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/
binom_1.1-1.tgz'

Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

The downloaded binary packages are in
/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn/T//
RtmpFxXFYU/downloaded_packages

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/bomeara/phrapl/zipball/master
Installing phrapl
trying URL '
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.
2/diagram_1.6.3'

Content type 'application/x-gzip' length 560715 bytes (547 KB)

downloaded 547 KB

Error: Don't know how to decompress files with extension 6.3

Can you think of anything else to try? Thanks for your help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Fri, Aug 19, 2016 at 2:06 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Hi Justin,

It looks like devtools is having a hard time installing the package
'binom', which is a dependency of phrapl. Specifically, it looks like
the
tarball suffix has been truncated from the URL (i.e., it should be"'
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.2/binom_1.1-1.tgz").
I'm not sure why that is happening and I can't duplicate it on the
machine
I'm using.

Before you install phrapl, perhaps try installing binom alone first by
doing:

install.packages("binom",repos="http://cran.rstudio.com")

Then install phrapl using the devtools command. Let me know if this
doesn't
work.

Thanks,

Nathan

On Fri, Aug 19, 2016 at 10:24 AM, Justin C. Bagley <
notifications@github.com

wrote:

Hi Brian,

I'm using OSX 10.11.16, R v3.2.1, and I am having an issue with the
PHRAPL
install. When I follow your instructions, I get an error apparently
due
to
failure to unpack a file with a name ending in "-1":

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/bomeara/phrapl/zipball/master
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

Error: Don't know how to decompress files with extension 1-1

In response, I downloaded the master dir and tried to use devtools
to
install locally, but this also failed:

install("/Users/justinbagley/Downloads/bomeara-phrapl-688acb1")
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

Error: Don't know how to decompress files with extension 1-1

Please help me find a solution to this so I can start working with
PHRAPL.
Thanks.

Best,

Justin

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@ndjaxon
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ndjaxon commented Aug 22, 2016

Hi Justin,

I'm not certain what the problem is. Can you send me your tree file and
your assignment file? I'll take a look.

Nathan

On Sun, Aug 21, 2016 at 9:37 PM, Justin C. Bagley notifications@github.com
wrote:

Dear Nathan,

I gave this another go today. Following your suggestion to pre-install
dependencies didn't work on R 3.2.1, so I updated to the latest
distribution on cran, 3.3.1, called the pre-install code you supplied, then
used devtools to successfully install PHRAPL. Here is the final install:

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/bomeara/phrapl/zipball/master
Installing phrapl
trying URL '
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.3/rgenoud_5.7-12.4.tgz
'

Content type 'application/x-gzip' length 709466 bytes (692 KB)

downloaded 692 KB

Installing rgenoud
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file
--no-environ --no-save --no-restore
--quiet CMD INSTALL \

'/private/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn/T/RtmpkZhAtz/
devtoolsa4d82124d81c/rgenoud'
\

--library='/Library/Frameworks/R.framework/Versions/3.3/Resources/library'
--install-tests

  • installing binary package ‘rgenoud’ ...
  • DONE (rgenoud)
    '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file
    --no-environ --no-save --no-restore
    --quiet CMD INSTALL \

'/private/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn/T/RtmpkZhAtz/
devtoolsa4d865971217/bomeara-phrapl-688acb1'
\

--library='/Library/Frameworks/R.framework/Versions/3.3/Resources/library'
--install-tests

  • installing source package ‘phrapl’ ...
    ** R
    ** data
    ** inst
    ** preparing package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded
  • DONE (phrapl)

Despite the install success, I am now stuck in the initial stages of a
preliminary analysis. Following through your tutorial I have made it to the
point where I define observed trees to work with, but I can't get past this
point because I get an error stating that keepTaxa matrix is of the wrong
length: "number of items to replace is not a multiple of replacement
length"...

library(phrapl)

setwd("~/Documents/2 - by Project/bin")

Hyptrees <- read.tree("Hyp_besttrees.tre")

assignFile<-read.table("Hyp_fastSTRUCTURE_pop_delim_file_
wOut_for_PHRAPL.txt",header=TRUE,stringsAsFactors=FALSE)
popAssignments <- list(c(3,3,3,3,3,3))

assignmentsGlobal <- assignFile
observedTrees <- Hyptrees
subsamplesPerGene <- 10
outgroup = TRUE
outgroupPrune = TRUE

observedTrees <- PrepSubsampling(assignmentsGlobal = assignmentsGlobal,
observedTrees = observedTrees, popAssignments = popAssignments,
subsamplesPerGene = subsamplesPerGene, outgroup = outgroup, outgroupPrune =
outgroupPrune)
Error in retainedTaxaMatrix[rep, ] <- keepTaxa :
number of items to replace is not a multiple of replacement length

My input data are separate gene trees for each of 227 SNP loci from a
RAD-seq experiment... with I think 43 individuals assigned to five ingroup
clades and one outgroup (2 individuals). I tried this again with a
five-length popVector, and with and without pruning the outgroup. However,
I continue getting the same error. Is this a bug in the code that needs to
be ironed out or is there a way I can check or correct this?

Thanks for your help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Fri, Aug 19, 2016 at 2:41 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Sorry, I made a mistake with the last three installation calls. Here's
the
correct code:

if(!require("ape")){install.packages("ape",repos="http://
cran.rstudio.com
")}
if(!require("partitions")){install.packages("partitions",repos="
http://cran.rstudio.com")}
if(!require("lattice")){install.packages("lattice",repos="
http://cran.rstudio.com")}
if(!require("polynom")){install.packages("polynom",repos="
http://cran.rstudio.com")}
if(!require("gmp")){install.packages("gmp",repos="http://
cran.rstudio.com
")}
if(!require("rgenoud")){install.packages("rgenoud",repos="
http://cran.rstudio.com")}
if(!require("parallel")){install.packages("parallel",repos="
http://cran.rstudio.com")}
if(!require("optimx")){install.packages("optimx",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="
http://cran.rstudio.com")}
if(!require("numDeriv")){install.packages("numDeriv",repos="
http://cran.rstudio.com")}
if(!require("nloptr")){install.packages("nloptr",repos="
http://cran.rstudio.com")}
if(!require("Matrix")){install.packages("Matrix",repos="
http://cran.rstudio.com")}
if(!require("rgl")){install.packages("rgl",repos="http://
cran.rstudio.com
")}
if(!require("RColorBrewer")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="http://
cran.rstudio.com")}
if(!require("diagram")){install.packages("diagram",repos="http://
cran.rstudio.com")}
if(!require("binom")){install.packages("binom",repos="
http://cran.rstudio.com")}

On Fri, Aug 19, 2016 at 11:35 AM, Nathan Jackson ndjaxon@gmail.com
wrote:

Hi Justin,

It looks like the same thing is happening, but with another phrapl
dependency ('diagram'). The installation URL is being truncated. To
prevent
this from happening, maybe just try pre-installing all of the phrapl
dependencies beforehand by running the following:

if(!require("ape")){install.packages("ape",repos="http://
cran.rstudio.com
")}
if(!require("partitions")){install.packages("partitions",repos="
http://cran.rstudio.com")}
if(!require("lattice")){install.packages("lattice",repos="
http://cran.rstudio.com")}
if(!require("polynom")){install.packages("polynom",repos="
http://cran.rstudio.com")}
if(!require("gmp")){install.packages("gmp",repos="http://
cran.rstudio.com
")}
if(!require("rgenoud")){install.packages("rgenoud",repos="
http://cran.rstudio.com")}
if(!require("parallel")){install.packages("parallel",repos="
http://cran.rstudio.com")}
if(!require("optimx")){install.packages("optimx",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="
http://cran.rstudio.com")}
if(!require("numDeriv")){install.packages("numDeriv",repos="
http://cran.rstudio.com")}
if(!require("nloptr")){install.packages("nloptr",repos="
http://cran.rstudio.com")}
if(!require("Matrix")){install.packages("Matrix",repos="
http://cran.rstudio.com")}
if(!require("rgl")){install.packages("rgl",repos="http://
cran.rstudio.com
")}
if(!require("RColorBrewer")){install.packages("RColorBrewer",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("diagram")){install.packages("RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("binom")){install.packages("RColorBrewer",repos="
http://cran.rstudio.com")}

Then install phrapl. I'm not sure if this is just a local problem or a
more general one. If anybody else experiences this issue, I will delve
into
fixing it.

Let me know if you have any other issues. Thanks for trying out phrapl!

Nathan

On Fri, Aug 19, 2016 at 11:21 AM, Justin C. Bagley <
notifications@github.com> wrote:

Dear Nathan,

Thanks very much for the quick response. I tried your suggestion and
it
looked like it almost worked, at least it passed the previous sticking
point. However, I'm still having an issue, only now the error says
"Don't
know how to decompress files with extension 6.3":

install.packages("binom",repos="http://cran.rstudio.com")
Installing package into ‘/Users/justinbagley/Library/R/3.2/library’
(as ‘lib’ is unspecified)
trying URL '
http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/
binom_1.1-1.tgz'

Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

The downloaded binary packages are in
/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn/T//
RtmpFxXFYU/downloaded_packages

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/bomeara/phrapl/zipball/master
Installing phrapl
trying URL '
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.
2/diagram_1.6.3'

Content type 'application/x-gzip' length 560715 bytes (547 KB)

downloaded 547 KB

Error: Don't know how to decompress files with extension 6.3

Can you think of anything else to try? Thanks for your help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Fri, Aug 19, 2016 at 2:06 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Hi Justin,

It looks like devtools is having a hard time installing the package
'binom', which is a dependency of phrapl. Specifically, it looks
like
the
tarball suffix has been truncated from the URL (i.e., it should be"'
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.2/binom_1.1-1.tgz").
I'm not sure why that is happening and I can't duplicate it on the
machine
I'm using.

Before you install phrapl, perhaps try installing binom alone first
by
doing:

install.packages("binom",repos="http://cran.rstudio.com")

Then install phrapl using the devtools command. Let me know if this
doesn't
work.

Thanks,

Nathan

On Fri, Aug 19, 2016 at 10:24 AM, Justin C. Bagley <
notifications@github.com

wrote:

Hi Brian,

I'm using OSX 10.11.16, R v3.2.1, and I am having an issue with
the
PHRAPL
install. When I follow your instructions, I get an error
apparently
due
to
failure to unpack a file with a name ending in "-1":

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/
bomeara/phrapl/zipball/master
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

Error: Don't know how to decompress files with extension 1-1

In response, I downloaded the master dir and tried to use devtools
to
install locally, but this also failed:

install("/Users/justinbagley/Downloads/bomeara-phrapl-688acb1")
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

Error: Don't know how to decompress files with extension 1-1

Please help me find a solution to this so I can start working with
PHRAPL.
Thanks.

Best,

Justin

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You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
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@justincbagley
Copy link
Author

Dear Nathan,

Thanks for agreeing to take a look at this. Here I'm attaching the files I
tried to analyze with the code in my last email. Let me know if you can
figure out what was causing the error.

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Mon, Aug 22, 2016 at 1:12 PM, Nathan D Jackson notifications@github.com
wrote:

Hi Justin,

I'm not certain what the problem is. Can you send me your tree file and
your assignment file? I'll take a look.

Nathan

On Sun, Aug 21, 2016 at 9:37 PM, Justin C. Bagley <
notifications@github.com>
wrote:

Dear Nathan,

I gave this another go today. Following your suggestion to pre-install
dependencies didn't work on R 3.2.1, so I updated to the latest
distribution on cran, 3.3.1, called the pre-install code you supplied,
then
used devtools to successfully install PHRAPL. Here is the final install:

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/bomeara/phrapl/zipball/master
Installing phrapl
trying URL '
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.3/rgenoud_5.7-12.4.tgz
'

Content type 'application/x-gzip' length 709466 bytes (692 KB)

downloaded 692 KB

Installing rgenoud
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file
--no-environ --no-save --no-restore
--quiet CMD INSTALL \

'/private/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn/T/RtmpkZhAtz/
devtoolsa4d82124d81c/rgenoud'
\

--library='/Library/Frameworks/R.framework/Versions/3.3/Resources/
library'
--install-tests

  • installing binary package ‘rgenoud’ ...
  • DONE (rgenoud)
    '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file
    --no-environ --no-save --no-restore
    --quiet CMD INSTALL \

'/private/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn/T/RtmpkZhAtz/
devtoolsa4d865971217/bomeara-phrapl-688acb1'
\

--library='/Library/Frameworks/R.framework/Versions/3.3/Resources/
library'
--install-tests

  • installing source package ‘phrapl’ ...
    ** R
    ** data
    ** inst
    ** preparing package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded
  • DONE (phrapl)

Despite the install success, I am now stuck in the initial stages of a
preliminary analysis. Following through your tutorial I have made it to
the
point where I define observed trees to work with, but I can't get past
this
point because I get an error stating that keepTaxa matrix is of the wrong
length: "number of items to replace is not a multiple of replacement
length"...

library(phrapl)

setwd("~/Documents/2 - by Project/bin")

Hyptrees <- read.tree("Hyp_besttrees.tre")

assignFile<-read.table("Hyp_fastSTRUCTURE_pop_delim_file_
wOut_for_PHRAPL.txt",header=TRUE,stringsAsFactors=FALSE)
popAssignments <- list(c(3,3,3,3,3,3))

assignmentsGlobal <- assignFile
observedTrees <- Hyptrees
subsamplesPerGene <- 10
outgroup = TRUE
outgroupPrune = TRUE

observedTrees <- PrepSubsampling(assignmentsGlobal =
assignmentsGlobal,
observedTrees = observedTrees, popAssignments = popAssignments,
subsamplesPerGene = subsamplesPerGene, outgroup = outgroup,
outgroupPrune =
outgroupPrune)
Error in retainedTaxaMatrix[rep, ] <- keepTaxa :
number of items to replace is not a multiple of replacement length

My input data are separate gene trees for each of 227 SNP loci from a
RAD-seq experiment... with I think 43 individuals assigned to five
ingroup
clades and one outgroup (2 individuals). I tried this again with a
five-length popVector, and with and without pruning the outgroup.
However,
I continue getting the same error. Is this a bug in the code that needs
to
be ironed out or is there a way I can check or correct this?

Thanks for your help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Fri, Aug 19, 2016 at 2:41 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Sorry, I made a mistake with the last three installation calls. Here's
the
correct code:

if(!require("ape")){install.packages("ape",repos="http://
cran.rstudio.com
")}
if(!require("partitions")){install.packages("partitions",repos="
http://cran.rstudio.com")}
if(!require("lattice")){install.packages("lattice",repos="
http://cran.rstudio.com")}
if(!require("polynom")){install.packages("polynom",repos="
http://cran.rstudio.com")}
if(!require("gmp")){install.packages("gmp",repos="http://
cran.rstudio.com
")}
if(!require("rgenoud")){install.packages("rgenoud",repos="
http://cran.rstudio.com")}
if(!require("parallel")){install.packages("parallel",repos="
http://cran.rstudio.com")}
if(!require("optimx")){install.packages("optimx",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="
http://cran.rstudio.com")}
if(!require("numDeriv")){install.packages("numDeriv",repos="
http://cran.rstudio.com")}
if(!require("nloptr")){install.packages("nloptr",repos="
http://cran.rstudio.com")}
if(!require("Matrix")){install.packages("Matrix",repos="
http://cran.rstudio.com")}
if(!require("rgl")){install.packages("rgl",repos="http://
cran.rstudio.com
")}
if(!require("RColorBrewer")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="http://
cran.rstudio.com")}
if(!require("diagram")){install.packages("diagram",repos="http://
cran.rstudio.com")}
if(!require("binom")){install.packages("binom",repos="
http://cran.rstudio.com")}

On Fri, Aug 19, 2016 at 11:35 AM, Nathan Jackson ndjaxon@gmail.com
wrote:

Hi Justin,

It looks like the same thing is happening, but with another phrapl
dependency ('diagram'). The installation URL is being truncated. To
prevent
this from happening, maybe just try pre-installing all of the phrapl
dependencies beforehand by running the following:

if(!require("ape")){install.packages("ape",repos="http://
cran.rstudio.com
")}
if(!require("partitions")){install.packages("partitions",repos="
http://cran.rstudio.com")}
if(!require("lattice")){install.packages("lattice",repos="
http://cran.rstudio.com")}
if(!require("polynom")){install.packages("polynom",repos="
http://cran.rstudio.com")}
if(!require("gmp")){install.packages("gmp",repos="http://
cran.rstudio.com
")}
if(!require("rgenoud")){install.packages("rgenoud",repos="
http://cran.rstudio.com")}
if(!require("parallel")){install.packages("parallel",repos="
http://cran.rstudio.com")}
if(!require("optimx")){install.packages("optimx",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="
http://cran.rstudio.com")}
if(!require("numDeriv")){install.packages("numDeriv",repos="
http://cran.rstudio.com")}
if(!require("nloptr")){install.packages("nloptr",repos="
http://cran.rstudio.com")}
if(!require("Matrix")){install.packages("Matrix",repos="
http://cran.rstudio.com")}
if(!require("rgl")){install.packages("rgl",repos="http://
cran.rstudio.com
")}
if(!require("RColorBrewer")){install.packages("RColorBrewer",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("diagram")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("binom")){install.packages("RColorBrewer",repos="
http://cran.rstudio.com")}

Then install phrapl. I'm not sure if this is just a local problem or
a
more general one. If anybody else experiences this issue, I will
delve
into
fixing it.

Let me know if you have any other issues. Thanks for trying out
phrapl!

Nathan

On Fri, Aug 19, 2016 at 11:21 AM, Justin C. Bagley <
notifications@github.com> wrote:

Dear Nathan,

Thanks very much for the quick response. I tried your suggestion and
it
looked like it almost worked, at least it passed the previous
sticking
point. However, I'm still having an issue, only now the error says
"Don't
know how to decompress files with extension 6.3":

install.packages("binom",repos="http://cran.rstudio.com")
Installing package into ‘/Users/justinbagley/Library/R/3.2/library’
(as ‘lib’ is unspecified)
trying URL '
http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/
binom_1.1-1.tgz'

Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

The downloaded binary packages are in
/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn/T//
RtmpFxXFYU/downloaded_packages

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/bomeara/phrapl/zipball/master
Installing phrapl
trying URL '
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.
2/diagram_1.6.3'

Content type 'application/x-gzip' length 560715 bytes (547 KB)

downloaded 547 KB

Error: Don't know how to decompress files with extension 6.3

Can you think of anything else to try? Thanks for your help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Fri, Aug 19, 2016 at 2:06 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Hi Justin,

It looks like devtools is having a hard time installing the
package
'binom', which is a dependency of phrapl. Specifically, it looks
like
the
tarball suffix has been truncated from the URL (i.e., it should
be"'
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.2/binom_1.1-1.tgz").
I'm not sure why that is happening and I can't duplicate it on the
machine
I'm using.

Before you install phrapl, perhaps try installing binom alone
first
by
doing:

install.packages("binom",repos="http://cran.rstudio.com")

Then install phrapl using the devtools command. Let me know if
this
doesn't
work.

Thanks,

Nathan

On Fri, Aug 19, 2016 at 10:24 AM, Justin C. Bagley <
notifications@github.com

wrote:

Hi Brian,

I'm using OSX 10.11.16, R v3.2.1, and I am having an issue with
the
PHRAPL
install. When I follow your instructions, I get an error
apparently
due
to
failure to unpack a file with a name ending in "-1":

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/
bomeara/phrapl/zipball/master
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

Error: Don't know how to decompress files with extension 1-1

In response, I downloaded the master dir and tried to use
devtools
to
install locally, but this also failed:

install("/Users/justinbagley/Downloads/bomeara-phrapl-688acb1")
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

Error: Don't know how to decompress files with extension 1-1

Please help me find a solution to this so I can start working
with
PHRAPL.
Thanks.

Best,

Justin

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TipSample Assignment
HypJCB100 Clades23
HypJCB11 Clade6
HypJCB123 Clades23
HypJCB124 Clade1
HypJCB13 Clade6
HypJCB134 Clade1
HypJCB148 Clades23
HypJCB149 Clade5
HypJCB15 Clade6
HypJCB150 Clade5
HypJCB152 Clade5
HypJCB156 Clade4
HypJCB161 Clade4
HypJCB163 Clade4
HypJCB167 Clade4
HypJCB168 Clade4
HypJCB17 Clade6
HypJCB18 Clade6
HypJCB20 Clade6
HypJCB201 Clade4
HypJCB22 Clades23
HypJCB226 Clades23
HypJCB253 Clades23
HypJCB254 Clades23
HypJCB265 Clade6
HypJCB42 Clades23
HypJCB44 Clade6
HypJCB46 Clade6
HypJCB47 Clade6
HypJCB49 Clade6
HypJCB50 Clade6
HypJCB51 Clade6
HypJCB62 Clades23
HypJCB63 Clade6
HypJCB64 Clades23
HypJCB65 Clade4
HypJCB66 Clades23
HypJCB97 Clade1
HypJCB98 Clades23
HypJCB99 Clades23
HypJCB309 Outgroup
HypJCB310 Outgroup

@ndjaxon
Copy link
Collaborator

ndjaxon commented Aug 22, 2016

Can you send me your "Hyp_besttrees.tre" file as well?

Nathan

On Mon, Aug 22, 2016 at 10:51 AM, Justin C. Bagley <notifications@github.com

wrote:

Dear Nathan,

Thanks for agreeing to take a look at this. Here I'm attaching the files I
tried to analyze with the code in my last email. Let me know if you can
figure out what was causing the error.

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Mon, Aug 22, 2016 at 1:12 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Hi Justin,

I'm not certain what the problem is. Can you send me your tree file and
your assignment file? I'll take a look.

Nathan

On Sun, Aug 21, 2016 at 9:37 PM, Justin C. Bagley <
notifications@github.com>
wrote:

Dear Nathan,

I gave this another go today. Following your suggestion to pre-install
dependencies didn't work on R 3.2.1, so I updated to the latest
distribution on cran, 3.3.1, called the pre-install code you supplied,
then
used devtools to successfully install PHRAPL. Here is the final
install:

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/bomeara/phrapl/zipball/master
Installing phrapl
trying URL '
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.3/rgenoud_5.7-12.4.tgz
'

Content type 'application/x-gzip' length 709466 bytes (692 KB)

downloaded 692 KB

Installing rgenoud
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file
--no-environ --no-save --no-restore
--quiet CMD INSTALL \

'/private/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn/T/RtmpkZhAtz/
devtoolsa4d82124d81c/rgenoud'
\

--library='/Library/Frameworks/R.framework/Versions/3.3/Resources/
library'
--install-tests

  • installing binary package ‘rgenoud’ ...
  • DONE (rgenoud)
    '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file
    --no-environ --no-save --no-restore
    --quiet CMD INSTALL \

'/private/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn/T/RtmpkZhAtz/
devtoolsa4d865971217/bomeara-phrapl-688acb1'
\

--library='/Library/Frameworks/R.framework/Versions/3.3/Resources/
library'
--install-tests

  • installing source package ‘phrapl’ ...
    ** R
    ** data
    ** inst
    ** preparing package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded
  • DONE (phrapl)

Despite the install success, I am now stuck in the initial stages of a
preliminary analysis. Following through your tutorial I have made it to
the
point where I define observed trees to work with, but I can't get past
this
point because I get an error stating that keepTaxa matrix is of the
wrong
length: "number of items to replace is not a multiple of replacement
length"...

library(phrapl)

setwd("~/Documents/2 - by Project/bin")

Hyptrees <- read.tree("Hyp_besttrees.tre")

assignFile<-read.table("Hyp_fastSTRUCTURE_pop_delim_file_
wOut_for_PHRAPL.txt",header=TRUE,stringsAsFactors=FALSE)
popAssignments <- list(c(3,3,3,3,3,3))

assignmentsGlobal <- assignFile
observedTrees <- Hyptrees
subsamplesPerGene <- 10
outgroup = TRUE
outgroupPrune = TRUE

observedTrees <- PrepSubsampling(assignmentsGlobal =
assignmentsGlobal,
observedTrees = observedTrees, popAssignments = popAssignments,
subsamplesPerGene = subsamplesPerGene, outgroup = outgroup,
outgroupPrune =
outgroupPrune)
Error in retainedTaxaMatrix[rep, ] <- keepTaxa :
number of items to replace is not a multiple of replacement length

My input data are separate gene trees for each of 227 SNP loci from a
RAD-seq experiment... with I think 43 individuals assigned to five
ingroup
clades and one outgroup (2 individuals). I tried this again with a
five-length popVector, and with and without pruning the outgroup.
However,
I continue getting the same error. Is this a bug in the code that needs
to
be ironed out or is there a way I can check or correct this?

Thanks for your help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Fri, Aug 19, 2016 at 2:41 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Sorry, I made a mistake with the last three installation calls.
Here's
the
correct code:

if(!require("ape")){install.packages("ape",repos="http://
cran.rstudio.com
")}
if(!require("partitions")){install.packages("partitions",repos="
http://cran.rstudio.com")}
if(!require("lattice")){install.packages("lattice",repos="
http://cran.rstudio.com")}
if(!require("polynom")){install.packages("polynom",repos="
http://cran.rstudio.com")}
if(!require("gmp")){install.packages("gmp",repos="http://
cran.rstudio.com
")}
if(!require("rgenoud")){install.packages("rgenoud",repos="
http://cran.rstudio.com")}
if(!require("parallel")){install.packages("parallel",repos="
http://cran.rstudio.com")}
if(!require("optimx")){install.packages("optimx",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="
http://cran.rstudio.com")}
if(!require("numDeriv")){install.packages("numDeriv",repos="
http://cran.rstudio.com")}
if(!require("nloptr")){install.packages("nloptr",repos="
http://cran.rstudio.com")}
if(!require("Matrix")){install.packages("Matrix",repos="
http://cran.rstudio.com")}
if(!require("rgl")){install.packages("rgl",repos="http://
cran.rstudio.com
")}
if(!require("RColorBrewer")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="http://
cran.rstudio.com")}
if(!require("diagram")){install.packages("diagram",repos="http://
cran.rstudio.com")}
if(!require("binom")){install.packages("binom",repos="
http://cran.rstudio.com")}

On Fri, Aug 19, 2016 at 11:35 AM, Nathan Jackson ndjaxon@gmail.com
wrote:

Hi Justin,

It looks like the same thing is happening, but with another phrapl
dependency ('diagram'). The installation URL is being truncated. To
prevent
this from happening, maybe just try pre-installing all of the
phrapl
dependencies beforehand by running the following:

if(!require("ape")){install.packages("ape",repos="http://
cran.rstudio.com
")}
if(!require("partitions")){install.packages("partitions",repos="
http://cran.rstudio.com")}
if(!require("lattice")){install.packages("lattice",repos="
http://cran.rstudio.com")}
if(!require("polynom")){install.packages("polynom",repos="
http://cran.rstudio.com")}
if(!require("gmp")){install.packages("gmp",repos="http://
cran.rstudio.com
")}
if(!require("rgenoud")){install.packages("rgenoud",repos="
http://cran.rstudio.com")}
if(!require("parallel")){install.packages("parallel",repos="
http://cran.rstudio.com")}
if(!require("optimx")){install.packages("optimx",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="
http://cran.rstudio.com")}
if(!require("numDeriv")){install.packages("numDeriv",repos="
http://cran.rstudio.com")}
if(!require("nloptr")){install.packages("nloptr",repos="
http://cran.rstudio.com")}
if(!require("Matrix")){install.packages("Matrix",repos="
http://cran.rstudio.com")}
if(!require("rgl")){install.packages("rgl",repos="http://
cran.rstudio.com
")}
if(!require("RColorBrewer")){install.packages("
RColorBrewer",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("diagram")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("binom")){install.packages("RColorBrewer",repos="
http://cran.rstudio.com")}

Then install phrapl. I'm not sure if this is just a local problem
or
a
more general one. If anybody else experiences this issue, I will
delve
into
fixing it.

Let me know if you have any other issues. Thanks for trying out
phrapl!

Nathan

On Fri, Aug 19, 2016 at 11:21 AM, Justin C. Bagley <
notifications@github.com> wrote:

Dear Nathan,

Thanks very much for the quick response. I tried your suggestion
and
it
looked like it almost worked, at least it passed the previous
sticking
point. However, I'm still having an issue, only now the error says
"Don't
know how to decompress files with extension 6.3":

install.packages("binom",repos="http://cran.rstudio.com")
Installing package into ‘/Users/justinbagley/Library/
R/3.2/library’
(as ‘lib’ is unspecified)
trying URL '
http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/
binom_1.1-1.tgz'

Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

The downloaded binary packages are in
/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn/T//
RtmpFxXFYU/downloaded_packages

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/
bomeara/phrapl/zipball/master
Installing phrapl
trying URL '
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.
2/diagram_1.6.3'

Content type 'application/x-gzip' length 560715 bytes (547 KB)

downloaded 547 KB

Error: Don't know how to decompress files with extension 6.3

Can you think of anything else to try? Thanks for your help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Fri, Aug 19, 2016 at 2:06 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Hi Justin,

It looks like devtools is having a hard time installing the
package
'binom', which is a dependency of phrapl. Specifically, it looks
like
the
tarball suffix has been truncated from the URL (i.e., it should
be"'
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.2/binom_1.1-1.tgz").
I'm not sure why that is happening and I can't duplicate it on
the
machine
I'm using.

Before you install phrapl, perhaps try installing binom alone
first
by
doing:

install.packages("binom",repos="http://cran.rstudio.com")

Then install phrapl using the devtools command. Let me know if
this
doesn't
work.

Thanks,

Nathan

On Fri, Aug 19, 2016 at 10:24 AM, Justin C. Bagley <
notifications@github.com

wrote:

Hi Brian,

I'm using OSX 10.11.16, R v3.2.1, and I am having an issue
with
the
PHRAPL
install. When I follow your instructions, I get an error
apparently
due
to
failure to unpack a file with a name ending in "-1":

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/
bomeara/phrapl/zipball/master
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

Error: Don't know how to decompress files with extension 1-1

In response, I downloaded the master dir and tried to use
devtools
to
install locally, but this also failed:

install("/Users/justinbagley/Downloads/bomeara-phrapl-
688acb1")
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

Error: Don't know how to decompress files with extension 1-1

Please help me find a solution to this so I can start working
with
PHRAPL.
Thanks.

Best,

Justin

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TipSample Assignment
HypJCB100 Clades23
HypJCB11 Clade6
HypJCB123 Clades23
HypJCB124 Clade1
HypJCB13 Clade6
HypJCB134 Clade1
HypJCB148 Clades23
HypJCB149 Clade5
HypJCB15 Clade6
HypJCB150 Clade5
HypJCB152 Clade5
HypJCB156 Clade4
HypJCB161 Clade4
HypJCB163 Clade4
HypJCB167 Clade4
HypJCB168 Clade4
HypJCB17 Clade6
HypJCB18 Clade6
HypJCB20 Clade6
HypJCB201 Clade4
HypJCB22 Clades23
HypJCB226 Clades23
HypJCB253 Clades23
HypJCB254 Clades23
HypJCB265 Clade6
HypJCB42 Clades23
HypJCB44 Clade6
HypJCB46 Clade6
HypJCB47 Clade6
HypJCB49 Clade6
HypJCB50 Clade6
HypJCB51 Clade6
HypJCB62 Clades23
HypJCB63 Clade6
HypJCB64 Clades23
HypJCB65 Clade4
HypJCB66 Clades23
HypJCB97 Clade1
HypJCB98 Clades23
HypJCB99 Clades23
HypJCB309 Outgroup
HypJCB310 Outgroup

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@justincbagley
Copy link
Author

Hi, it was attached! Here it is again.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Mon, Aug 22, 2016 at 2:37 PM, Nathan D Jackson notifications@github.com
wrote:

Can you send me your "Hyp_besttrees.tre" file as well?

Nathan

On Mon, Aug 22, 2016 at 10:51 AM, Justin C. Bagley <
notifications@github.com

wrote:

Dear Nathan,

Thanks for agreeing to take a look at this. Here I'm attaching the files
I
tried to analyze with the code in my last email. Let me know if you can
figure out what was causing the error.

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Mon, Aug 22, 2016 at 1:12 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Hi Justin,

I'm not certain what the problem is. Can you send me your tree file and
your assignment file? I'll take a look.

Nathan

On Sun, Aug 21, 2016 at 9:37 PM, Justin C. Bagley <
notifications@github.com>
wrote:

Dear Nathan,

I gave this another go today. Following your suggestion to
pre-install
dependencies didn't work on R 3.2.1, so I updated to the latest
distribution on cran, 3.3.1, called the pre-install code you
supplied,
then
used devtools to successfully install PHRAPL. Here is the final
install:

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/bomeara/phrapl/zipball/master
Installing phrapl
trying URL '
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.3/rgenoud_5.7-12.4.tgz
'

Content type 'application/x-gzip' length 709466 bytes (692 KB)

downloaded 692 KB

Installing rgenoud
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file
--no-environ --no-save --no-restore
--quiet CMD INSTALL \

'/private/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn
/T/RtmpkZhAtz/
devtoolsa4d82124d81c/rgenoud'
\

--library='/Library/Frameworks/R.framework/Versions/3.3/Resources/
library'
--install-tests

  • installing binary package ‘rgenoud’ ...
  • DONE (rgenoud)
    '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file
    --no-environ --no-save --no-restore
    --quiet CMD INSTALL \

'/private/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn
/T/RtmpkZhAtz/
devtoolsa4d865971217/bomeara-phrapl-688acb1'
\

--library='/Library/Frameworks/R.framework/Versions/3.3/Resources/
library'
--install-tests

  • installing source package ‘phrapl’ ...
    ** R
    ** data
    ** inst
    ** preparing package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded
  • DONE (phrapl)

Despite the install success, I am now stuck in the initial stages of
a
preliminary analysis. Following through your tutorial I have made it
to
the
point where I define observed trees to work with, but I can't get
past
this
point because I get an error stating that keepTaxa matrix is of the
wrong
length: "number of items to replace is not a multiple of replacement
length"...

library(phrapl)

setwd("~/Documents/2 - by Project/bin")

Hyptrees <- read.tree("Hyp_besttrees.tre")

assignFile<-read.table("Hyp_fastSTRUCTURE_pop_delim_file_
wOut_for_PHRAPL.txt",header=TRUE,stringsAsFactors=FALSE)
popAssignments <- list(c(3,3,3,3,3,3))

assignmentsGlobal <- assignFile
observedTrees <- Hyptrees
subsamplesPerGene <- 10
outgroup = TRUE
outgroupPrune = TRUE

observedTrees <- PrepSubsampling(assignmentsGlobal =
assignmentsGlobal,
observedTrees = observedTrees, popAssignments = popAssignments,
subsamplesPerGene = subsamplesPerGene, outgroup = outgroup,
outgroupPrune =
outgroupPrune)
Error in retainedTaxaMatrix[rep, ] <- keepTaxa :
number of items to replace is not a multiple of replacement length

My input data are separate gene trees for each of 227 SNP loci from a
RAD-seq experiment... with I think 43 individuals assigned to five
ingroup
clades and one outgroup (2 individuals). I tried this again with a
five-length popVector, and with and without pruning the outgroup.
However,
I continue getting the same error. Is this a bug in the code that
needs
to
be ironed out or is there a way I can check or correct this?

Thanks for your help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Fri, Aug 19, 2016 at 2:41 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Sorry, I made a mistake with the last three installation calls.
Here's
the
correct code:

if(!require("ape")){install.packages("ape",repos="http://
cran.rstudio.com
")}
if(!require("partitions")){install.packages("partitions",repos="
http://cran.rstudio.com")}
if(!require("lattice")){install.packages("lattice",repos="
http://cran.rstudio.com")}
if(!require("polynom")){install.packages("polynom",repos="
http://cran.rstudio.com")}
if(!require("gmp")){install.packages("gmp",repos="http://
cran.rstudio.com
")}
if(!require("rgenoud")){install.packages("rgenoud",repos="
http://cran.rstudio.com")}
if(!require("parallel")){install.packages("parallel",repos="
http://cran.rstudio.com")}
if(!require("optimx")){install.packages("optimx",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="
http://cran.rstudio.com")}
if(!require("numDeriv")){install.packages("numDeriv",repos="
http://cran.rstudio.com")}
if(!require("nloptr")){install.packages("nloptr",repos="
http://cran.rstudio.com")}
if(!require("Matrix")){install.packages("Matrix",repos="
http://cran.rstudio.com")}
if(!require("rgl")){install.packages("rgl",repos="http://
cran.rstudio.com
")}
if(!require("RColorBrewer")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="http://
cran.rstudio.com")}
if(!require("diagram")){install.packages("diagram",repos="http://
cran.rstudio.com")}
if(!require("binom")){install.packages("binom",repos="
http://cran.rstudio.com")}

On Fri, Aug 19, 2016 at 11:35 AM, Nathan Jackson <
ndjaxon@gmail.com>
wrote:

Hi Justin,

It looks like the same thing is happening, but with another
phrapl
dependency ('diagram'). The installation URL is being truncated.
To
prevent
this from happening, maybe just try pre-installing all of the
phrapl
dependencies beforehand by running the following:

if(!require("ape")){install.packages("ape",repos="http://
cran.rstudio.com
")}
if(!require("partitions")){install.packages("partitions",repos="
http://cran.rstudio.com")}
if(!require("lattice")){install.packages("lattice",repos="
http://cran.rstudio.com")}
if(!require("polynom")){install.packages("polynom",repos="
http://cran.rstudio.com")}
if(!require("gmp")){install.packages("gmp",repos="http://
cran.rstudio.com
")}
if(!require("rgenoud")){install.packages("rgenoud",repos="
http://cran.rstudio.com")}
if(!require("parallel")){install.packages("parallel",repos="
http://cran.rstudio.com")}
if(!require("optimx")){install.packages("optimx",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="
http://cran.rstudio.com")}
if(!require("numDeriv")){install.packages("numDeriv",repos="
http://cran.rstudio.com")}
if(!require("nloptr")){install.packages("nloptr",repos="
http://cran.rstudio.com")}
if(!require("Matrix")){install.packages("Matrix",repos="
http://cran.rstudio.com")}
if(!require("rgl")){install.packages("rgl",repos="http://
cran.rstudio.com
")}
if(!require("RColorBrewer")){install.packages("
RColorBrewer",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("diagram")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("binom")){install.packages("RColorBrewer",repos="
http://cran.rstudio.com")}

Then install phrapl. I'm not sure if this is just a local problem
or
a
more general one. If anybody else experiences this issue, I will
delve
into
fixing it.

Let me know if you have any other issues. Thanks for trying out
phrapl!

Nathan

On Fri, Aug 19, 2016 at 11:21 AM, Justin C. Bagley <
notifications@github.com> wrote:

Dear Nathan,

Thanks very much for the quick response. I tried your suggestion
and
it
looked like it almost worked, at least it passed the previous
sticking
point. However, I'm still having an issue, only now the error
says
"Don't
know how to decompress files with extension 6.3":

install.packages("binom",repos="http://cran.rstudio.com")
Installing package into ‘/Users/justinbagley/Library/
R/3.2/library’
(as ‘lib’ is unspecified)
trying URL '
http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/
binom_1.1-1.tgz'

Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

The downloaded binary packages are in
/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn/T//
RtmpFxXFYU/downloaded_packages

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/
bomeara/phrapl/zipball/master
Installing phrapl
trying URL '
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.
2/diagram_1.6.3'

Content type 'application/x-gzip' length 560715 bytes (547 KB)

downloaded 547 KB

Error: Don't know how to decompress files with extension 6.3

Can you think of anything else to try? Thanks for your help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Fri, Aug 19, 2016 at 2:06 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Hi Justin,

It looks like devtools is having a hard time installing the
package
'binom', which is a dependency of phrapl. Specifically, it
looks
like
the
tarball suffix has been truncated from the URL (i.e., it
should
be"'
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.2/binom_1.1-1.tgz").
I'm not sure why that is happening and I can't duplicate it on
the
machine
I'm using.

Before you install phrapl, perhaps try installing binom alone
first
by
doing:

install.packages("binom",repos="http://cran.rstudio.com")

Then install phrapl using the devtools command. Let me know if
this
doesn't
work.

Thanks,

Nathan

On Fri, Aug 19, 2016 at 10:24 AM, Justin C. Bagley <
notifications@github.com

wrote:

Hi Brian,

I'm using OSX 10.11.16, R v3.2.1, and I am having an issue
with
the
PHRAPL
install. When I follow your instructions, I get an error
apparently
due
to
failure to unpack a file with a name ending in "-1":

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/
bomeara/phrapl/zipball/master
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes (323
KB)

downloaded 323 KB

Error: Don't know how to decompress files with extension 1-1

In response, I downloaded the master dir and tried to use
devtools
to
install locally, but this also failed:

install("/Users/justinbagley/Downloads/bomeara-phrapl-
688acb1")
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes (323
KB)

downloaded 323 KB

Error: Don't know how to decompress files with extension 1-1

Please help me find a solution to this so I can start
working
with
PHRAPL.
Thanks.

Best,

Justin

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TipSample Assignment
HypJCB100 Clades23
HypJCB11 Clade6
HypJCB123 Clades23
HypJCB124 Clade1
HypJCB13 Clade6
HypJCB134 Clade1
HypJCB148 Clades23
HypJCB149 Clade5
HypJCB15 Clade6
HypJCB150 Clade5
HypJCB152 Clade5
HypJCB156 Clade4
HypJCB161 Clade4
HypJCB163 Clade4
HypJCB167 Clade4
HypJCB168 Clade4
HypJCB17 Clade6
HypJCB18 Clade6
HypJCB20 Clade6
HypJCB201 Clade4
HypJCB22 Clades23
HypJCB226 Clades23
HypJCB253 Clades23
HypJCB254 Clades23
HypJCB265 Clade6
HypJCB42 Clades23
HypJCB44 Clade6
HypJCB46 Clade6
HypJCB47 Clade6
HypJCB49 Clade6
HypJCB50 Clade6
HypJCB51 Clade6
HypJCB62 Clades23
HypJCB63 Clade6
HypJCB64 Clades23
HypJCB65 Clade4
HypJCB66 Clades23
HypJCB97 Clade1
HypJCB98 Clades23
HypJCB99 Clades23
HypJCB309 Outgroup
HypJCB310 Outgroup

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@ndjaxon
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ndjaxon commented Aug 22, 2016

Hmm, for some reason the attachments aren't coming through. Could you
attach them to a direct email to ndjaxon@gmail.com (or put them on dropbox)?

Thanks!

Nathan

On Mon, Aug 22, 2016 at 11:45 AM, Justin C. Bagley <notifications@github.com

wrote:

Hi, it was attached! Here it is again.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Mon, Aug 22, 2016 at 2:37 PM, Nathan D Jackson <
notifications@github.com>

wrote:

Can you send me your "Hyp_besttrees.tre" file as well?

Nathan

On Mon, Aug 22, 2016 at 10:51 AM, Justin C. Bagley <
notifications@github.com

wrote:

Dear Nathan,

Thanks for agreeing to take a look at this. Here I'm attaching the
files
I
tried to analyze with the code in my last email. Let me know if you can
figure out what was causing the error.

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Mon, Aug 22, 2016 at 1:12 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Hi Justin,

I'm not certain what the problem is. Can you send me your tree file
and
your assignment file? I'll take a look.

Nathan

On Sun, Aug 21, 2016 at 9:37 PM, Justin C. Bagley <
notifications@github.com>
wrote:

Dear Nathan,

I gave this another go today. Following your suggestion to
pre-install
dependencies didn't work on R 3.2.1, so I updated to the latest
distribution on cran, 3.3.1, called the pre-install code you
supplied,
then
used devtools to successfully install PHRAPL. Here is the final
install:

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/
bomeara/phrapl/zipball/master
Installing phrapl
trying URL '
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.3/rgenoud_5.7-12.4.tgz
'

Content type 'application/x-gzip' length 709466 bytes (692 KB)

downloaded 692 KB

Installing rgenoud
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file
--no-environ --no-save --no-restore
--quiet CMD INSTALL \

'/private/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn
/T/RtmpkZhAtz/
devtoolsa4d82124d81c/rgenoud'
\

--library='/Library/Frameworks/R.framework/Versions/3.3/Resources/
library'
--install-tests

  • installing binary package ‘rgenoud’ ...
  • DONE (rgenoud)
    '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file
    --no-environ --no-save --no-restore
    --quiet CMD INSTALL \

'/private/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn
/T/RtmpkZhAtz/
devtoolsa4d865971217/bomeara-phrapl-688acb1'
\

--library='/Library/Frameworks/R.framework/Versions/3.3/Resources/
library'
--install-tests

  • installing source package ‘phrapl’ ...
    ** R
    ** data
    ** inst
    ** preparing package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded
  • DONE (phrapl)

Despite the install success, I am now stuck in the initial stages
of
a
preliminary analysis. Following through your tutorial I have made
it
to
the
point where I define observed trees to work with, but I can't get
past
this
point because I get an error stating that keepTaxa matrix is of the
wrong
length: "number of items to replace is not a multiple of
replacement
length"...

library(phrapl)

setwd("~/Documents/2 - by Project/bin")

Hyptrees <- read.tree("Hyp_besttrees.tre")

assignFile<-read.table("Hyp_fastSTRUCTURE_pop_delim_file_
wOut_for_PHRAPL.txt",header=TRUE,stringsAsFactors=FALSE)
popAssignments <- list(c(3,3,3,3,3,3))

assignmentsGlobal <- assignFile
observedTrees <- Hyptrees
subsamplesPerGene <- 10
outgroup = TRUE
outgroupPrune = TRUE

observedTrees <- PrepSubsampling(assignmentsGlobal =
assignmentsGlobal,
observedTrees = observedTrees, popAssignments = popAssignments,
subsamplesPerGene = subsamplesPerGene, outgroup = outgroup,
outgroupPrune =
outgroupPrune)
Error in retainedTaxaMatrix[rep, ] <- keepTaxa :
number of items to replace is not a multiple of replacement length

My input data are separate gene trees for each of 227 SNP loci
from a
RAD-seq experiment... with I think 43 individuals assigned to five
ingroup
clades and one outgroup (2 individuals). I tried this again with a
five-length popVector, and with and without pruning the outgroup.
However,
I continue getting the same error. Is this a bug in the code that
needs
to
be ironed out or is there a way I can check or correct this?

Thanks for your help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Fri, Aug 19, 2016 at 2:41 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Sorry, I made a mistake with the last three installation calls.
Here's
the
correct code:

if(!require("ape")){install.packages("ape",repos="http://
cran.rstudio.com
")}
if(!require("partitions")){install.packages("partitions",repos="
http://cran.rstudio.com")}
if(!require("lattice")){install.packages("lattice",repos="
http://cran.rstudio.com")}
if(!require("polynom")){install.packages("polynom",repos="
http://cran.rstudio.com")}
if(!require("gmp")){install.packages("gmp",repos="http://
cran.rstudio.com
")}
if(!require("rgenoud")){install.packages("rgenoud",repos="
http://cran.rstudio.com")}
if(!require("parallel")){install.packages("parallel",repos="
http://cran.rstudio.com")}
if(!require("optimx")){install.packages("optimx",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="
http://cran.rstudio.com")}
if(!require("numDeriv")){install.packages("numDeriv",repos="
http://cran.rstudio.com")}
if(!require("nloptr")){install.packages("nloptr",repos="
http://cran.rstudio.com")}
if(!require("Matrix")){install.packages("Matrix",repos="
http://cran.rstudio.com")}
if(!require("rgl")){install.packages("rgl",repos="http://
cran.rstudio.com
")}
if(!require("RColorBrewer")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="http://
cran.rstudio.com")}
if(!require("diagram")){install.packages("diagram",
repos="http://
cran.rstudio.com")}
if(!require("binom")){install.packages("binom",repos="
http://cran.rstudio.com")}

On Fri, Aug 19, 2016 at 11:35 AM, Nathan Jackson <
ndjaxon@gmail.com>
wrote:

Hi Justin,

It looks like the same thing is happening, but with another
phrapl
dependency ('diagram'). The installation URL is being
truncated.
To
prevent
this from happening, maybe just try pre-installing all of the
phrapl
dependencies beforehand by running the following:

if(!require("ape")){install.packages("ape",repos="http://
cran.rstudio.com
")}
if(!require("partitions")){install.packages("partitions",
repos="
http://cran.rstudio.com")}
if(!require("lattice")){install.packages("lattice",repos="
http://cran.rstudio.com")}
if(!require("polynom")){install.packages("polynom",repos="
http://cran.rstudio.com")}
if(!require("gmp")){install.packages("gmp",repos="http://
cran.rstudio.com
")}
if(!require("rgenoud")){install.packages("rgenoud",repos="
http://cran.rstudio.com")}
if(!require("parallel")){install.packages("parallel",repos="
http://cran.rstudio.com")}
if(!require("optimx")){install.packages("optimx",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="
http://cran.rstudio.com")}
if(!require("numDeriv")){install.packages("numDeriv",repos="
http://cran.rstudio.com")}
if(!require("nloptr")){install.packages("nloptr",repos="
http://cran.rstudio.com")}
if(!require("Matrix")){install.packages("Matrix",repos="
http://cran.rstudio.com")}
if(!require("rgl")){install.packages("rgl",repos="http://
cran.rstudio.com
")}
if(!require("RColorBrewer")){install.packages("
RColorBrewer",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("diagram")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("binom")){install.packages("RColorBrewer",repos="
http://cran.rstudio.com")}

Then install phrapl. I'm not sure if this is just a local
problem
or
a
more general one. If anybody else experiences this issue, I
will
delve
into
fixing it.

Let me know if you have any other issues. Thanks for trying out
phrapl!

Nathan

On Fri, Aug 19, 2016 at 11:21 AM, Justin C. Bagley <
notifications@github.com> wrote:

Dear Nathan,

Thanks very much for the quick response. I tried your
suggestion
and
it
looked like it almost worked, at least it passed the previous
sticking
point. However, I'm still having an issue, only now the error
says
"Don't
know how to decompress files with extension 6.3":

install.packages("binom",repos="http://cran.rstudio.com")
Installing package into ‘/Users/justinbagley/Library/
R/3.2/library’
(as ‘lib’ is unspecified)
trying URL '
http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/
binom_1.1-1.tgz'

Content type 'application/x-gzip' length 331405 bytes (323 KB)

downloaded 323 KB

The downloaded binary packages are in
/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn/T//
RtmpFxXFYU/downloaded_packages

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/
bomeara/phrapl/zipball/master
Installing phrapl
trying URL '
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.
2/diagram_1.6.3'

Content type 'application/x-gzip' length 560715 bytes (547 KB)

downloaded 547 KB

Error: Don't know how to decompress files with extension 6.3

Can you think of anything else to try? Thanks for your help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Fri, Aug 19, 2016 at 2:06 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Hi Justin,

It looks like devtools is having a hard time installing the
package
'binom', which is a dependency of phrapl. Specifically, it
looks
like
the
tarball suffix has been truncated from the URL (i.e., it
should
be"'
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.2/binom_1.1-1.tgz").
I'm not sure why that is happening and I can't duplicate it
on
the
machine
I'm using.

Before you install phrapl, perhaps try installing binom
alone
first
by
doing:

install.packages("binom",repos="http://cran.rstudio.com")

Then install phrapl using the devtools command. Let me know
if
this
doesn't
work.

Thanks,

Nathan

On Fri, Aug 19, 2016 at 10:24 AM, Justin C. Bagley <
notifications@github.com

wrote:

Hi Brian,

I'm using OSX 10.11.16, R v3.2.1, and I am having an issue
with
the
PHRAPL
install. When I follow your instructions, I get an error
apparently
due
to
failure to unpack a file with a name ending in "-1":

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/
bomeara/phrapl/zipball/master
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes (323
KB)

downloaded 323 KB

Error: Don't know how to decompress files with extension
1-1

In response, I downloaded the master dir and tried to use
devtools
to
install locally, but this also failed:

install("/Users/justinbagley/Downloads/bomeara-phrapl-
688acb1")
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes (323
KB)

downloaded 323 KB

Error: Don't know how to decompress files with extension
1-1

Please help me find a solution to this so I can start
working
with
PHRAPL.
Thanks.

Best,

Justin

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TipSample Assignment
HypJCB100 Clades23
HypJCB11 Clade6
HypJCB123 Clades23
HypJCB124 Clade1
HypJCB13 Clade6
HypJCB134 Clade1
HypJCB148 Clades23
HypJCB149 Clade5
HypJCB15 Clade6
HypJCB150 Clade5
HypJCB152 Clade5
HypJCB156 Clade4
HypJCB161 Clade4
HypJCB163 Clade4
HypJCB167 Clade4
HypJCB168 Clade4
HypJCB17 Clade6
HypJCB18 Clade6
HypJCB20 Clade6
HypJCB201 Clade4
HypJCB22 Clades23
HypJCB226 Clades23
HypJCB253 Clades23
HypJCB254 Clades23
HypJCB265 Clade6
HypJCB42 Clades23
HypJCB44 Clade6
HypJCB46 Clade6
HypJCB47 Clade6
HypJCB49 Clade6
HypJCB50 Clade6
HypJCB51 Clade6
HypJCB62 Clades23
HypJCB63 Clade6
HypJCB64 Clades23
HypJCB65 Clade4
HypJCB66 Clades23
HypJCB97 Clade1
HypJCB98 Clades23
HypJCB99 Clades23
HypJCB309 Outgroup
HypJCB310 Outgroup

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@ndjaxon
Copy link
Collaborator

ndjaxon commented Aug 23, 2016

Hi Justin,

Any locus must include at least enough samples per population/species to
subsample the number of individuals specified (by popAssignments). So if
your desired subsampling is popVector = c(3,3,3,3,3), meaning that you want
to subsample 3 individuals for each of 5 populations, then there must be at
least 3 representative individuals for each population/species in the tree.
This is not the case for many of your loci. For example, for the first
locus, there are no samples present from Clade 1.

If you toss all loci that do not meet the minimum sampling requirements of
3 samples per population/species, you are left with 68 out of the original
227 loci. I have attached a .tre file that includes only those loci that
meet the minimum sampling requirements. Running PrepSubsampling on this
file should work successfully. You could increase the number of loci to 94
if you do midpoint rooting (because 26 loci are simply missing an outgroup,
but otherwise meet the sampling requirements).

Let me know if you run across any additional snags.

Nathan

On Mon, Aug 22, 2016 at 11:50 AM, Nathan Jackson ndjaxon@gmail.com wrote:

Hmm, for some reason the attachments aren't coming through. Could you
attach them to a direct email to ndjaxon@gmail.com (or put them on
dropbox)?

Thanks!

Nathan

On Mon, Aug 22, 2016 at 11:45 AM, Justin C. Bagley <
notifications@github.com> wrote:

Hi, it was attached! Here it is again.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Mon, Aug 22, 2016 at 2:37 PM, Nathan D Jackson <
notifications@github.com>

wrote:

Can you send me your "Hyp_besttrees.tre" file as well?

Nathan

On Mon, Aug 22, 2016 at 10:51 AM, Justin C. Bagley <
notifications@github.com

wrote:

Dear Nathan,

Thanks for agreeing to take a look at this. Here I'm attaching the
files
I
tried to analyze with the code in my last email. Let me know if you
can
figure out what was causing the error.

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Mon, Aug 22, 2016 at 1:12 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Hi Justin,

I'm not certain what the problem is. Can you send me your tree file
and
your assignment file? I'll take a look.

Nathan

On Sun, Aug 21, 2016 at 9:37 PM, Justin C. Bagley <
notifications@github.com>
wrote:

Dear Nathan,

I gave this another go today. Following your suggestion to
pre-install
dependencies didn't work on R 3.2.1, so I updated to the latest
distribution on cran, 3.3.1, called the pre-install code you
supplied,
then
used devtools to successfully install PHRAPL. Here is the final
install:

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/b
omeara/phrapl/zipball/master
Installing phrapl
trying URL '
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.3/rgenoud_5.7-12.4.tgz
'

Content type 'application/x-gzip' length 709466 bytes (692 KB)

downloaded 692 KB

Installing rgenoud
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file
--no-environ --no-save --no-restore
--quiet CMD INSTALL \

'/private/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn
/T/RtmpkZhAtz/
devtoolsa4d82124d81c/rgenoud'
\

--library='/Library/Frameworks/R.framework/Versions/3.3/
Resources/
library'
--install-tests

  • installing binary package ‘rgenoud’ ...
  • DONE (rgenoud)
    '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file
    --no-environ --no-save --no-restore
    --quiet CMD INSTALL \

'/private/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn
/T/RtmpkZhAtz/
devtoolsa4d865971217/bomeara-phrapl-688acb1'
\

--library='/Library/Frameworks/R.framework/Versions/3.3/
Resources/
library'
--install-tests

  • installing source package ‘phrapl’ ...
    ** R
    ** data
    ** inst
    ** preparing package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded
  • DONE (phrapl)

Despite the install success, I am now stuck in the initial stages
of
a
preliminary analysis. Following through your tutorial I have made
it
to
the
point where I define observed trees to work with, but I can't get
past
this
point because I get an error stating that keepTaxa matrix is of
the
wrong
length: "number of items to replace is not a multiple of
replacement
length"...

library(phrapl)

setwd("~/Documents/2 - by Project/bin")

Hyptrees <- read.tree("Hyp_besttrees.tre")

assignFile<-read.table("Hyp_fastSTRUCTURE_pop_delim_file_
wOut_for_PHRAPL.txt",header=TRUE,stringsAsFactors=FALSE)
popAssignments <- list(c(3,3,3,3,3,3))

assignmentsGlobal <- assignFile
observedTrees <- Hyptrees
subsamplesPerGene <- 10
outgroup = TRUE
outgroupPrune = TRUE

observedTrees <- PrepSubsampling(assignmentsGlobal =
assignmentsGlobal,
observedTrees = observedTrees, popAssignments = popAssignments,
subsamplesPerGene = subsamplesPerGene, outgroup = outgroup,
outgroupPrune =
outgroupPrune)
Error in retainedTaxaMatrix[rep, ] <- keepTaxa :
number of items to replace is not a multiple of replacement length

My input data are separate gene trees for each of 227 SNP loci
from a
RAD-seq experiment... with I think 43 individuals assigned to five
ingroup
clades and one outgroup (2 individuals). I tried this again with a
five-length popVector, and with and without pruning the outgroup.
However,
I continue getting the same error. Is this a bug in the code that
needs
to
be ironed out or is there a way I can check or correct this?

Thanks for your help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Fri, Aug 19, 2016 at 2:41 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Sorry, I made a mistake with the last three installation calls.
Here's
the
correct code:

if(!require("ape")){install.packages("ape",repos="http://
cran.rstudio.com
")}
if(!require("partitions")){install.packages("partitions",rep
os="
http://cran.rstudio.com")}
if(!require("lattice")){install.packages("lattice",repos="
http://cran.rstudio.com")}
if(!require("polynom")){install.packages("polynom",repos="
http://cran.rstudio.com")}
if(!require("gmp")){install.packages("gmp",repos="http://
cran.rstudio.com
")}
if(!require("rgenoud")){install.packages("rgenoud",repos="
http://cran.rstudio.com")}
if(!require("parallel")){install.packages("parallel",repos="
http://cran.rstudio.com")}
if(!require("optimx")){install.packages("optimx",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="
http://cran.rstudio.com")}
if(!require("numDeriv")){install.packages("numDeriv",repos="
http://cran.rstudio.com")}
if(!require("nloptr")){install.packages("nloptr",repos="
http://cran.rstudio.com")}
if(!require("Matrix")){install.packages("Matrix",repos="
http://cran.rstudio.com")}
if(!require("rgl")){install.packages("rgl",repos="http://
cran.rstudio.com
")}
if(!require("RColorBrewer")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="http://
cran.rstudio.com")}
if(!require("diagram")){install.packages("diagram",repos="
http://
cran.rstudio.com")}
if(!require("binom")){install.packages("binom",repos="
http://cran.rstudio.com")}

On Fri, Aug 19, 2016 at 11:35 AM, Nathan Jackson <
ndjaxon@gmail.com>
wrote:

Hi Justin,

It looks like the same thing is happening, but with another
phrapl
dependency ('diagram'). The installation URL is being
truncated.
To
prevent
this from happening, maybe just try pre-installing all of the
phrapl
dependencies beforehand by running the following:

if(!require("ape")){install.packages("ape",repos="http://
cran.rstudio.com
")}
if(!require("partitions")){install.packages("partitions",rep
os="
http://cran.rstudio.com")}
if(!require("lattice")){install.packages("lattice",repos="
http://cran.rstudio.com")}
if(!require("polynom")){install.packages("polynom",repos="
http://cran.rstudio.com")}
if(!require("gmp")){install.packages("gmp",repos="http://
cran.rstudio.com
")}
if(!require("rgenoud")){install.packages("rgenoud",repos="
http://cran.rstudio.com")}
if(!require("parallel")){install.packages("parallel",repos="
http://cran.rstudio.com")}
if(!require("optimx")){install.packages("optimx",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="
http://cran.rstudio.com")}
if(!require("numDeriv")){install.packages("numDeriv",repos="
http://cran.rstudio.com")}
if(!require("nloptr")){install.packages("nloptr",repos="
http://cran.rstudio.com")}
if(!require("Matrix")){install.packages("Matrix",repos="
http://cran.rstudio.com")}
if(!require("rgl")){install.packages("rgl",repos="http://
cran.rstudio.com
")}
if(!require("RColorBrewer")){install.packages("
RColorBrewer",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("diagram")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("binom")){install.packages("RColorBrewer",repos="
http://cran.rstudio.com")}

Then install phrapl. I'm not sure if this is just a local
problem
or
a
more general one. If anybody else experiences this issue, I
will
delve
into
fixing it.

Let me know if you have any other issues. Thanks for trying
out
phrapl!

Nathan

On Fri, Aug 19, 2016 at 11:21 AM, Justin C. Bagley <
notifications@github.com> wrote:

Dear Nathan,

Thanks very much for the quick response. I tried your
suggestion
and
it
looked like it almost worked, at least it passed the previous
sticking
point. However, I'm still having an issue, only now the error
says
"Don't
know how to decompress files with extension 6.3":

install.packages("binom",repos="http://cran.rstudio.com")
Installing package into ‘/Users/justinbagley/Library/
R/3.2/library’
(as ‘lib’ is unspecified)
trying URL '
http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/
binom_1.1-1.tgz'
Content type 'application/x-gzip' length 331405 bytes (323

KB)

downloaded 323 KB

The downloaded binary packages are in
/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn/T//
RtmpFxXFYU/downloaded_packages

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/
bomeara/phrapl/zipball/master
Installing phrapl
trying URL '
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.
2/diagram_1.6.3'
Content type 'application/x-gzip' length 560715 bytes (547

KB)

downloaded 547 KB

Error: Don't know how to decompress files with extension 6.3

Can you think of anything else to try? Thanks for your help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Fri, Aug 19, 2016 at 2:06 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Hi Justin,

It looks like devtools is having a hard time installing the
package
'binom', which is a dependency of phrapl. Specifically, it
looks
like
the
tarball suffix has been truncated from the URL (i.e., it
should
be"'
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.2/binom_1.1-1.tgz").
I'm not sure why that is happening and I can't duplicate
it on
the
machine
I'm using.

Before you install phrapl, perhaps try installing binom
alone
first
by
doing:

install.packages("binom",repos="http://cran.rstudio.com")

Then install phrapl using the devtools command. Let me
know if
this
doesn't
work.

Thanks,

Nathan

On Fri, Aug 19, 2016 at 10:24 AM, Justin C. Bagley <
notifications@github.com

wrote:

Hi Brian,

I'm using OSX 10.11.16, R v3.2.1, and I am having an
issue
with
the
PHRAPL
install. When I follow your instructions, I get an error
apparently
due
to
failure to unpack a file with a name ending in "-1":

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/
bomeara/phrapl/zipball/master
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes
(323
KB)

downloaded 323 KB

Error: Don't know how to decompress files with extension
1-1

In response, I downloaded the master dir and tried to use
devtools
to
install locally, but this also failed:

install("/Users/justinbagley/Downloads/bomeara-phrapl-
688acb1")
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes
(323
KB)

downloaded 323 KB

Error: Don't know how to decompress files with extension
1-1

Please help me find a solution to this so I can start
working
with
PHRAPL.
Thanks.

Best,

Justin

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TipSample Assignment
HypJCB100 Clades23
HypJCB11 Clade6
HypJCB123 Clades23
HypJCB124 Clade1
HypJCB13 Clade6
HypJCB134 Clade1
HypJCB148 Clades23
HypJCB149 Clade5
HypJCB15 Clade6
HypJCB150 Clade5
HypJCB152 Clade5
HypJCB156 Clade4
HypJCB161 Clade4
HypJCB163 Clade4
HypJCB167 Clade4
HypJCB168 Clade4
HypJCB17 Clade6
HypJCB18 Clade6
HypJCB20 Clade6
HypJCB201 Clade4
HypJCB22 Clades23
HypJCB226 Clades23
HypJCB253 Clades23
HypJCB254 Clades23
HypJCB265 Clade6
HypJCB42 Clades23
HypJCB44 Clade6
HypJCB46 Clade6
HypJCB47 Clade6
HypJCB49 Clade6
HypJCB50 Clade6
HypJCB51 Clade6
HypJCB62 Clades23
HypJCB63 Clade6
HypJCB64 Clades23
HypJCB65 Clade4
HypJCB66 Clades23
HypJCB97 Clade1
HypJCB98 Clades23
HypJCB99 Clades23
HypJCB309 Outgroup
HypJCB310 Outgroup

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@justincbagley
Copy link
Author

Dear Nathan,

Thanks very much, but I also am not receiving the attachments, so please
resend to centrarchidae@gmail.com. Also, how did you quickly determine
which loci met the minimum sampling requirements and make a file containing
all of those loci? Could you share that code/tool with me? Thanks for your
help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Tue, Aug 23, 2016 at 3:36 AM, Nathan D Jackson notifications@github.com
wrote:

Hi Justin,

Any locus must include at least enough samples per population/species to
subsample the number of individuals specified (by popAssignments). So if
your desired subsampling is popVector = c(3,3,3,3,3), meaning that you want
to subsample 3 individuals for each of 5 populations, then there must be at
least 3 representative individuals for each population/species in the tree.
This is not the case for many of your loci. For example, for the first
locus, there are no samples present from Clade 1.

If you toss all loci that do not meet the minimum sampling requirements of
3 samples per population/species, you are left with 68 out of the original
227 loci. I have attached a .tre file that includes only those loci that
meet the minimum sampling requirements. Running PrepSubsampling on this
file should work successfully. You could increase the number of loci to 94
if you do midpoint rooting (because 26 loci are simply missing an outgroup,
but otherwise meet the sampling requirements).

Let me know if you run across any additional snags.

Nathan

On Mon, Aug 22, 2016 at 11:50 AM, Nathan Jackson ndjaxon@gmail.com
wrote:

Hmm, for some reason the attachments aren't coming through. Could you
attach them to a direct email to ndjaxon@gmail.com (or put them on
dropbox)?

Thanks!

Nathan

On Mon, Aug 22, 2016 at 11:45 AM, Justin C. Bagley <
notifications@github.com> wrote:

Hi, it was attached! Here it is again.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Mon, Aug 22, 2016 at 2:37 PM, Nathan D Jackson <
notifications@github.com>

wrote:

Can you send me your "Hyp_besttrees.tre" file as well?

Nathan

On Mon, Aug 22, 2016 at 10:51 AM, Justin C. Bagley <
notifications@github.com

wrote:

Dear Nathan,

Thanks for agreeing to take a look at this. Here I'm attaching the
files
I
tried to analyze with the code in my last email. Let me know if you
can
figure out what was causing the error.

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Mon, Aug 22, 2016 at 1:12 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Hi Justin,

I'm not certain what the problem is. Can you send me your tree
file
and
your assignment file? I'll take a look.

Nathan

On Sun, Aug 21, 2016 at 9:37 PM, Justin C. Bagley <
notifications@github.com>
wrote:

Dear Nathan,

I gave this another go today. Following your suggestion to
pre-install
dependencies didn't work on R 3.2.1, so I updated to the latest
distribution on cran, 3.3.1, called the pre-install code you
supplied,
then
used devtools to successfully install PHRAPL. Here is the final
install:

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/b
omeara/phrapl/zipball/master
Installing phrapl
trying URL '
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.3/rgenoud_5.7-12.4.tgz
'

Content type 'application/x-gzip' length 709466 bytes (692 KB)

downloaded 692 KB

Installing rgenoud
'/Library/Frameworks/R.framework/Resources/bin/R'
--no-site-file
--no-environ --no-save --no-restore
--quiet CMD INSTALL \

'/private/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn
/T/RtmpkZhAtz/
devtoolsa4d82124d81c/rgenoud'
\

--library='/Library/Frameworks/R.framework/Versions/3.3/
Resources/
library'
--install-tests

  • installing binary package ‘rgenoud’ ...
  • DONE (rgenoud)
    '/Library/Frameworks/R.framework/Resources/bin/R'
    --no-site-file
    --no-environ --no-save --no-restore
    --quiet CMD INSTALL \

'/private/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn
/T/RtmpkZhAtz/
devtoolsa4d865971217/bomeara-phrapl-688acb1'
\

--library='/Library/Frameworks/R.framework/Versions/3.3/
Resources/
library'
--install-tests

  • installing source package ‘phrapl’ ...
    ** R
    ** data
    ** inst
    ** preparing package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded
  • DONE (phrapl)

Despite the install success, I am now stuck in the initial
stages
of
a
preliminary analysis. Following through your tutorial I have
made
it
to
the
point where I define observed trees to work with, but I can't
get
past
this
point because I get an error stating that keepTaxa matrix is of
the
wrong
length: "number of items to replace is not a multiple of
replacement
length"...

library(phrapl)

setwd("~/Documents/2 - by Project/bin")

Hyptrees <- read.tree("Hyp_besttrees.tre")

assignFile<-read.table("Hyp_fastSTRUCTURE_pop_delim_file_
wOut_for_PHRAPL.txt",header=TRUE,stringsAsFactors=FALSE)
popAssignments <- list(c(3,3,3,3,3,3))

assignmentsGlobal <- assignFile
observedTrees <- Hyptrees
subsamplesPerGene <- 10
outgroup = TRUE
outgroupPrune = TRUE

observedTrees <- PrepSubsampling(assignmentsGlobal =
assignmentsGlobal,
observedTrees = observedTrees, popAssignments = popAssignments,
subsamplesPerGene = subsamplesPerGene, outgroup = outgroup,
outgroupPrune =
outgroupPrune)
Error in retainedTaxaMatrix[rep, ] <- keepTaxa :
number of items to replace is not a multiple of replacement
length

My input data are separate gene trees for each of 227 SNP loci
from a
RAD-seq experiment... with I think 43 individuals assigned to
five
ingroup
clades and one outgroup (2 individuals). I tried this again
with a
five-length popVector, and with and without pruning the
outgroup.
However,
I continue getting the same error. Is this a bug in the code
that
needs
to
be ironed out or is there a way I can check or correct this?

Thanks for your help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Fri, Aug 19, 2016 at 2:41 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Sorry, I made a mistake with the last three installation
calls.
Here's
the
correct code:

if(!require("ape")){install.packages("ape",repos="http://
cran.rstudio.com
")}
if(!require("partitions")){install.packages("partitions",rep
os="
http://cran.rstudio.com")}

if(!require("lattice")){install.packages("lattice",repos="
http://cran.rstudio.com")}
if(!require("polynom")){install.packages("polynom",repos="
http://cran.rstudio.com")}
if(!require("gmp")){install.packages("gmp",repos="http://
cran.rstudio.com
")}
if(!require("rgenoud")){install.packages("rgenoud",repos="
http://cran.rstudio.com")}
if(!require("parallel")){install.packages("parallel",repos="
http://cran.rstudio.com")}
if(!require("optimx")){install.packages("optimx",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="
http://cran.rstudio.com")}
if(!require("numDeriv")){install.packages("numDeriv",repos="
http://cran.rstudio.com")}
if(!require("nloptr")){install.packages("nloptr",repos="
http://cran.rstudio.com")}
if(!require("Matrix")){install.packages("Matrix",repos="
http://cran.rstudio.com")}
if(!require("rgl")){install.packages("rgl",repos="http://
cran.rstudio.com
")}
if(!require("RColorBrewer")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",
repos="http://
cran.rstudio.com")}
if(!require("diagram")){install.packages("diagram",repos="
http://
cran.rstudio.com")}
if(!require("binom")){install.packages("binom",repos="
http://cran.rstudio.com")}

On Fri, Aug 19, 2016 at 11:35 AM, Nathan Jackson <
ndjaxon@gmail.com>
wrote:

Hi Justin,

It looks like the same thing is happening, but with another
phrapl
dependency ('diagram'). The installation URL is being
truncated.
To
prevent
this from happening, maybe just try pre-installing all of
the
phrapl
dependencies beforehand by running the following:

if(!require("ape")){install.packages("ape",repos="http://
cran.rstudio.com
")}
if(!require("partitions")){install.packages("partitions",
rep
os="
http://cran.rstudio.com")}

if(!require("lattice")){install.packages("lattice",repos="
http://cran.rstudio.com")}
if(!require("polynom")){install.packages("polynom",repos="
http://cran.rstudio.com")}
if(!require("gmp")){install.packages("gmp",repos="http://
cran.rstudio.com
")}
if(!require("rgenoud")){install.packages("rgenoud",repos="
http://cran.rstudio.com")}
if(!require("parallel")){install.packages("parallel",
repos="
http://cran.rstudio.com")}
if(!require("optimx")){install.packages("optimx",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="
http://cran.rstudio.com")}
if(!require("numDeriv")){install.packages("numDeriv",
repos="
http://cran.rstudio.com")}
if(!require("nloptr")){install.packages("nloptr",repos="
http://cran.rstudio.com")}
if(!require("Matrix")){install.packages("Matrix",repos="
http://cran.rstudio.com")}
if(!require("rgl")){install.packages("rgl",repos="http://
cran.rstudio.com
")}
if(!require("RColorBrewer")){install.packages("
RColorBrewer",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("diagram")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("binom")){install.
packages("RColorBrewer",repos="
http://cran.rstudio.com")}

Then install phrapl. I'm not sure if this is just a local
problem
or
a
more general one. If anybody else experiences this issue, I
will
delve
into
fixing it.

Let me know if you have any other issues. Thanks for trying
out
phrapl!

Nathan

On Fri, Aug 19, 2016 at 11:21 AM, Justin C. Bagley <
notifications@github.com> wrote:

Dear Nathan,

Thanks very much for the quick response. I tried your
suggestion
and
it
looked like it almost worked, at least it passed the
previous
sticking
point. However, I'm still having an issue, only now the
error
says
"Don't
know how to decompress files with extension 6.3":

install.packages("binom",repos="http://cran.rstudio.com
")
Installing package into ‘/Users/justinbagley/Library/
R/3.2/library’
(as ‘lib’ is unspecified)
trying URL '
http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/
binom_1.1-1.tgz'
Content type 'application/x-gzip' length 331405 bytes (323

KB)

downloaded 323 KB

The downloaded binary packages are in
/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn/T//
RtmpFxXFYU/downloaded_packages

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/
bomeara/phrapl/zipball/master
Installing phrapl
trying URL '
http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/3.
2/diagram_1.6.3'
Content type 'application/x-gzip' length 560715 bytes (547

KB)

downloaded 547 KB

Error: Don't know how to decompress files with extension
6.3

Can you think of anything else to try? Thanks for your
help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Fri, Aug 19, 2016 at 2:06 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Hi Justin,

It looks like devtools is having a hard time installing
the
package
'binom', which is a dependency of phrapl. Specifically,
it
looks
like
the
tarball suffix has been truncated from the URL (i.e., it
should
be"'
http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/
3.2/binom_1.1-1.tgz").
I'm not sure why that is happening and I can't duplicate
it on
the
machine
I'm using.

Before you install phrapl, perhaps try installing binom
alone
first
by
doing:

install.packages("binom",repos="http://cran.rstudio.com
")

Then install phrapl using the devtools command. Let me
know if
this
doesn't
work.

Thanks,

Nathan

On Fri, Aug 19, 2016 at 10:24 AM, Justin C. Bagley <
notifications@github.com

wrote:

Hi Brian,

I'm using OSX 10.11.16, R v3.2.1, and I am having an
issue
with
the
PHRAPL
install. When I follow your instructions, I get an
error
apparently
due
to
failure to unpack a file with a name ending in "-1":

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/
bomeara/phrapl/zipball/master
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes
(323
KB)

downloaded 323 KB

Error: Don't know how to decompress files with
extension
1-1

In response, I downloaded the master dir and tried to
use
devtools
to
install locally, but this also failed:

install("/Users/justinbagley/Downloads/bomeara-phrapl-
688acb1")
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes
(323
KB)

downloaded 323 KB

Error: Don't know how to decompress files with
extension
1-1

Please help me find a solution to this so I can start
working
with
PHRAPL.
Thanks.

Best,

Justin

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TipSample Assignment
HypJCB100 Clades23
HypJCB11 Clade6
HypJCB123 Clades23
HypJCB124 Clade1
HypJCB13 Clade6
HypJCB134 Clade1
HypJCB148 Clades23
HypJCB149 Clade5
HypJCB15 Clade6
HypJCB150 Clade5
HypJCB152 Clade5
HypJCB156 Clade4
HypJCB161 Clade4
HypJCB163 Clade4
HypJCB167 Clade4
HypJCB168 Clade4
HypJCB17 Clade6
HypJCB18 Clade6
HypJCB20 Clade6
HypJCB201 Clade4
HypJCB22 Clades23
HypJCB226 Clades23
HypJCB253 Clades23
HypJCB254 Clades23
HypJCB265 Clade6
HypJCB42 Clades23
HypJCB44 Clade6
HypJCB46 Clade6
HypJCB47 Clade6
HypJCB49 Clade6
HypJCB50 Clade6
HypJCB51 Clade6
HypJCB62 Clades23
HypJCB63 Clade6
HypJCB64 Clades23
HypJCB65 Clade4
HypJCB66 Clades23
HypJCB97 Clade1
HypJCB98 Clades23
HypJCB99 Clades23
HypJCB309 Outgroup
HypJCB310 Outgroup

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@ndjaxon
Copy link
Collaborator

ndjaxon commented Aug 23, 2016

Right, sorry. I'll send those to you directly.

On Tue, Aug 23, 2016 at 4:41 AM, Justin C. Bagley notifications@github.com
wrote:

Dear Nathan,

Thanks very much, but I also am not receiving the attachments, so please
resend to centrarchidae@gmail.com. Also, how did you quickly determine
which loci met the minimum sampling requirements and make a file containing
all of those loci? Could you share that code/tool with me? Thanks for your
help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Tue, Aug 23, 2016 at 3:36 AM, Nathan D Jackson <
notifications@github.com>

wrote:

Hi Justin,

Any locus must include at least enough samples per population/species to
subsample the number of individuals specified (by popAssignments). So if
your desired subsampling is popVector = c(3,3,3,3,3), meaning that you
want
to subsample 3 individuals for each of 5 populations, then there must be
at
least 3 representative individuals for each population/species in the
tree.
This is not the case for many of your loci. For example, for the first
locus, there are no samples present from Clade 1.

If you toss all loci that do not meet the minimum sampling requirements
of
3 samples per population/species, you are left with 68 out of the
original
227 loci. I have attached a .tre file that includes only those loci that
meet the minimum sampling requirements. Running PrepSubsampling on this
file should work successfully. You could increase the number of loci to
94
if you do midpoint rooting (because 26 loci are simply missing an
outgroup,
but otherwise meet the sampling requirements).

Let me know if you run across any additional snags.

Nathan

On Mon, Aug 22, 2016 at 11:50 AM, Nathan Jackson ndjaxon@gmail.com
wrote:

Hmm, for some reason the attachments aren't coming through. Could you
attach them to a direct email to ndjaxon@gmail.com (or put them on
dropbox)?

Thanks!

Nathan

On Mon, Aug 22, 2016 at 11:45 AM, Justin C. Bagley <
notifications@github.com> wrote:

Hi, it was attached! Here it is again.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Mon, Aug 22, 2016 at 2:37 PM, Nathan D Jackson <
notifications@github.com>

wrote:

Can you send me your "Hyp_besttrees.tre" file as well?

Nathan

On Mon, Aug 22, 2016 at 10:51 AM, Justin C. Bagley <
notifications@github.com

wrote:

Dear Nathan,

Thanks for agreeing to take a look at this. Here I'm attaching the
files
I
tried to analyze with the code in my last email. Let me know if
you
can
figure out what was causing the error.

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Mon, Aug 22, 2016 at 1:12 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Hi Justin,

I'm not certain what the problem is. Can you send me your tree
file
and
your assignment file? I'll take a look.

Nathan

On Sun, Aug 21, 2016 at 9:37 PM, Justin C. Bagley <
notifications@github.com>
wrote:

Dear Nathan,

I gave this another go today. Following your suggestion to
pre-install
dependencies didn't work on R 3.2.1, so I updated to the
latest
distribution on cran, 3.3.1, called the pre-install code you
supplied,
then
used devtools to successfully install PHRAPL. Here is the
final
install:

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/b
omeara/phrapl/zipball/master
Installing phrapl
trying URL '
http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/
3.3/rgenoud_5.7-12.4.tgz
'

Content type 'application/x-gzip' length 709466 bytes (692 KB)

downloaded 692 KB

Installing rgenoud
'/Library/Frameworks/R.framework/Resources/bin/R'
--no-site-file
--no-environ --no-save --no-restore
--quiet CMD INSTALL \

'/private/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn
/T/RtmpkZhAtz/
devtoolsa4d82124d81c/rgenoud'
\

--library='/Library/Frameworks/R.framework/Versions/3.3/
Resources/
library'
--install-tests

  • installing binary package ‘rgenoud’ ...
  • DONE (rgenoud)
    '/Library/Frameworks/R.framework/Resources/bin/R'
    --no-site-file
    --no-environ --no-save --no-restore
    --quiet CMD INSTALL \

'/private/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn
/T/RtmpkZhAtz/
devtoolsa4d865971217/bomeara-phrapl-688acb1'
\

--library='/Library/Frameworks/R.framework/Versions/3.3/
Resources/
library'
--install-tests

  • installing source package ‘phrapl’ ...
    ** R
    ** data
    ** inst
    ** preparing package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded
  • DONE (phrapl)

Despite the install success, I am now stuck in the initial
stages
of
a
preliminary analysis. Following through your tutorial I have
made
it
to
the
point where I define observed trees to work with, but I can't
get
past
this
point because I get an error stating that keepTaxa matrix is
of
the
wrong
length: "number of items to replace is not a multiple of
replacement
length"...

library(phrapl)

setwd("~/Documents/2 - by Project/bin")

Hyptrees <- read.tree("Hyp_besttrees.tre")

assignFile<-read.table("Hyp_fastSTRUCTURE_pop_delim_file_
wOut_for_PHRAPL.txt",header=TRUE,stringsAsFactors=FALSE)
popAssignments <- list(c(3,3,3,3,3,3))

assignmentsGlobal <- assignFile
observedTrees <- Hyptrees
subsamplesPerGene <- 10
outgroup = TRUE
outgroupPrune = TRUE

observedTrees <- PrepSubsampling(assignmentsGlobal =
assignmentsGlobal,
observedTrees = observedTrees, popAssignments =
popAssignments,
subsamplesPerGene = subsamplesPerGene, outgroup = outgroup,
outgroupPrune =
outgroupPrune)
Error in retainedTaxaMatrix[rep, ] <- keepTaxa :
number of items to replace is not a multiple of replacement
length

My input data are separate gene trees for each of 227 SNP loci
from a
RAD-seq experiment... with I think 43 individuals assigned to
five
ingroup
clades and one outgroup (2 individuals). I tried this again
with a
five-length popVector, and with and without pruning the
outgroup.
However,
I continue getting the same error. Is this a bug in the code
that
needs
to
be ironed out or is there a way I can check or correct this?

Thanks for your help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Fri, Aug 19, 2016 at 2:41 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Sorry, I made a mistake with the last three installation
calls.
Here's
the
correct code:

if(!require("ape")){install.packages("ape",repos="http://
cran.rstudio.com
")}
if(!require("partitions")){install.packages("partitions",
rep
os="
http://cran.rstudio.com")}

if(!require("lattice")){install.packages("lattice",repos="
http://cran.rstudio.com")}
if(!require("polynom")){install.packages("polynom",repos="
http://cran.rstudio.com")}
if(!require("gmp")){install.packages("gmp",repos="http://
cran.rstudio.com
")}
if(!require("rgenoud")){install.packages("rgenoud",repos="
http://cran.rstudio.com")}
if(!require("parallel")){install.packages("parallel",
repos="
http://cran.rstudio.com")}
if(!require("optimx")){install.packages("optimx",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="
http://cran.rstudio.com")}
if(!require("numDeriv")){install.packages("numDeriv",
repos="
http://cran.rstudio.com")}
if(!require("nloptr")){install.packages("nloptr",repos="
http://cran.rstudio.com")}
if(!require("Matrix")){install.packages("Matrix",repos="
http://cran.rstudio.com")}
if(!require("rgl")){install.packages("rgl",repos="http://
cran.rstudio.com
")}
if(!require("RColorBrewer")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",
repos="http://
cran.rstudio.com")}
if(!require("diagram")){install.packages("diagram",repos="
http://
cran.rstudio.com")}
if(!require("binom")){install.packages("binom",repos="
http://cran.rstudio.com")}

On Fri, Aug 19, 2016 at 11:35 AM, Nathan Jackson <
ndjaxon@gmail.com>
wrote:

Hi Justin,

It looks like the same thing is happening, but with
another
phrapl
dependency ('diagram'). The installation URL is being
truncated.
To
prevent
this from happening, maybe just try pre-installing all of
the
phrapl
dependencies beforehand by running the following:

if(!require("ape")){install.packages("ape",repos="http://
cran.rstudio.com
")}
if(!require("partitions")){install.packages("partitions",
rep
os="
http://cran.rstudio.com")}

if(!require("lattice")){install.packages("lattice",
repos="
http://cran.rstudio.com")}
if(!require("polynom")){install.packages("polynom",
repos="
http://cran.rstudio.com")}
if(!require("gmp")){install.packages("gmp",repos="http://
cran.rstudio.com
")}
if(!require("rgenoud")){install.packages("rgenoud",
repos="
http://cran.rstudio.com")}
if(!require("parallel")){install.packages("parallel",
repos="
http://cran.rstudio.com")}
if(!require("optimx")){install.packages("optimx",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("igraph",repos="
http://cran.rstudio.com")}
if(!require("numDeriv")){install.packages("numDeriv",
repos="
http://cran.rstudio.com")}

if(!require("nloptr")){install.packages("nloptr",repos="
http://cran.rstudio.com")}
if(!require("Matrix")){install.packages("Matrix",repos="
http://cran.rstudio.com")}
if(!require("rgl")){install.packages("rgl",repos="http://
cran.rstudio.com
")}
if(!require("RColorBrewer")){install.packages("
RColorBrewer",repos="
http://cran.rstudio.com")}
if(!require("igraph")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("diagram")){install.packages("
RColorBrewer",repos="http://
cran.rstudio.com")}
if(!require("binom")){install.
packages("RColorBrewer",repos="
http://cran.rstudio.com")}

Then install phrapl. I'm not sure if this is just a local
problem
or
a
more general one. If anybody else experiences this issue,
I
will
delve
into
fixing it.

Let me know if you have any other issues. Thanks for
trying
out
phrapl!

Nathan

On Fri, Aug 19, 2016 at 11:21 AM, Justin C. Bagley <
notifications@github.com> wrote:

Dear Nathan,

Thanks very much for the quick response. I tried your
suggestion
and
it
looked like it almost worked, at least it passed the
previous
sticking
point. However, I'm still having an issue, only now the
error
says
"Don't
know how to decompress files with extension 6.3":

install.packages("binom",repos="
http://cran.rstudio.com
")
Installing package into ‘/Users/justinbagley/Library/
R/3.2/library’
(as ‘lib’ is unspecified)
trying URL '
http://cran.rstudio.com/bin/
macosx/mavericks/contrib/3.2/
binom_1.1-1.tgz'
Content type 'application/x-gzip' length 331405 bytes
(323

KB)

downloaded 323 KB

The downloaded binary packages are in
/var/folders/qy/50knq60d42z3gwjxhx0gm8bc0000gn/T//
RtmpFxXFYU/downloaded_packages

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/
bomeara/phrapl/zipball/master
Installing phrapl
trying URL '
http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/3.
2/diagram_1.6.3'
Content type 'application/x-gzip' length 560715 bytes
(547

KB)

downloaded 547 KB

Error: Don't know how to decompress files with extension
6.3

Can you think of anything else to try? Thanks for your
help.

Best,

Justin

Justin C. Bagley, Ph.D.
CNPq Young Talent Fellow (Postdoc)
& Senior Research Associate
Departamento de Zoologia
Universidade de Brasília
70910-900 Brasília, DF, Brasil
jcbagley@unb.br
Website: http://www.justinbagley.org
Lattes CV: http://lattes.cnpq.br/0028570120872581

On Fri, Aug 19, 2016 at 2:06 PM, Nathan D Jackson <
notifications@github.com>
wrote:

Hi Justin,

It looks like devtools is having a hard time installing
the
package
'binom', which is a dependency of phrapl. Specifically,
it
looks
like
the
tarball suffix has been truncated from the URL (i.e.,
it
should
be"'
http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/
3.2/binom_1.1-1.tgz").
I'm not sure why that is happening and I can't
duplicate
it on
the
machine
I'm using.

Before you install phrapl, perhaps try installing binom
alone
first
by
doing:

install.packages("binom",repos="
http://cran.rstudio.com
")

Then install phrapl using the devtools command. Let me
know if
this
doesn't
work.

Thanks,

Nathan

On Fri, Aug 19, 2016 at 10:24 AM, Justin C. Bagley <
notifications@github.com

wrote:

Hi Brian,

I'm using OSX 10.11.16, R v3.2.1, and I am having an
issue
with
the
PHRAPL
install. When I follow your instructions, I get an
error
apparently
due
to
failure to unpack a file with a name ending in "-1":

devtools::install_github("bomeara/phrapl")
Downloading GitHub repo bomeara/phrapl@master
from URL https://api.github.com/repos/
bomeara/phrapl/zipball/master
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes
(323
KB)

downloaded 323 KB

Error: Don't know how to decompress files with
extension
1-1

In response, I downloaded the master dir and tried to
use
devtools
to
install locally, but this also failed:

install("/Users/justinbagley/
Downloads/bomeara-phrapl-
688acb1")
Installing phrapl
trying URL 'http://cran.cnr.Berkeley.edu/
bin/macosx/mavericks/contrib/
3.2/binom_1.1-1'
Content type 'application/x-gzip' length 331405 bytes
(323
KB)

downloaded 323 KB

Error: Don't know how to decompress files with
extension
1-1

Please help me find a solution to this so I can start
working
with
PHRAPL.
Thanks.

Best,

Justin

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TipSample Assignment
HypJCB100 Clades23
HypJCB11 Clade6
HypJCB123 Clades23
HypJCB124 Clade1
HypJCB13 Clade6
HypJCB134 Clade1
HypJCB148 Clades23
HypJCB149 Clade5
HypJCB15 Clade6
HypJCB150 Clade5
HypJCB152 Clade5
HypJCB156 Clade4
HypJCB161 Clade4
HypJCB163 Clade4
HypJCB167 Clade4
HypJCB168 Clade4
HypJCB17 Clade6
HypJCB18 Clade6
HypJCB20 Clade6
HypJCB201 Clade4
HypJCB22 Clades23
HypJCB226 Clades23
HypJCB253 Clades23
HypJCB254 Clades23
HypJCB265 Clade6
HypJCB42 Clades23
HypJCB44 Clade6
HypJCB46 Clade6
HypJCB47 Clade6
HypJCB49 Clade6
HypJCB50 Clade6
HypJCB51 Clade6
HypJCB62 Clades23
HypJCB63 Clade6
HypJCB64 Clades23
HypJCB65 Clade4
HypJCB66 Clades23
HypJCB97 Clade1
HypJCB98 Clades23
HypJCB99 Clades23
HypJCB309 Outgroup
HypJCB310 Outgroup

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@bomeara bomeara closed this as completed Jan 8, 2017
@dashee87 dashee87 mentioned this issue Jan 13, 2017
Open
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@bomeara @ndjaxon @justincbagley