matR install

[ewilbanks]

Hi folks,

I'm getting an error trying to install matR - any ideas what could be going wrong here?

library(devtools) install_github("MG-RAST/matR") Loading required package: RCurl Loading required package: bitops Installing MG-RAST/matR from hadley Error in file(con, "wb") : cannot open the connection In addition: Warning message: In file(con, "wb") : cannot open file '/var/folders/wr/wrn6m46YGIqIPvJJXoCGME+++TM/-Tmp-//Rtmp9yBKvp/hadley-MG-RAST/matR.zip': No such file or directory

Thanks, Lizzy

[DrOppenheimer]

Hi Lizzy,

Sorry for the trouble.

Are you running on mac / PC / or other?

Try this and let me know what happens

install.packages("devtools", dependencies = TRUE) library(devtools) install_github("MG-RAST/matR") library(matR) dependencies()

If it doesn't work - can you send me the error that R returns then exit R and then run these commands from a terminal

echo "$0" >> R_check.log my_sys=echo 'Sys.info()'|R --slave my_r=which R r_version=echo 'R.Version()'|R --slave installed_packages=echo 'installed.packages()' | R --slave r_version=echo 'R.Version()'|R --slave echo "my_sys: $my_sys" >> R_check.log echo "------------------------------------------------------------------------" >> R_check.log echo "my_r: $my_r" >> R_check.log echo "------------------------------------------------------------------------" >> R_check.log echo "r_version: $r_version" >> R_check.log echo "------------------------------------------------------------------------" >> R_check.log echo "installed_r_packages: " >> R_check.log echo "------------------------------------------------------------------------" >> R_check.log echo "$installed_packages" >> R_check.log echo "------------------------------------------------------------------------" >> R_check.log

This will create a file called "R_check.log", it will contain information about your operating system, the version of R you are running, and all of the installed packages. Cut and paste it's content into your message

Thanks

[DrOppenheimer]

Hi Lizzy,

Sorry for the trouble.

Are you running on mac / PC / or other?

Try this and let me know what happens

install.packages("devtools", dependencies = TRUE) library(devtools) install_github("MG-RAST/matR") library(matR) dependencies()

If it doesn't work - can you send me the error that R returns then exit R and then run these commands from a terminal

(Note - this will work on Mac or any linux/unix, but not on PC)

echo "$0" >> R_check.log my_sys=echo 'Sys.info()'|R --slave my_r=which R r_version=echo 'R.Version()'|R --slave installed_packages=echo 'installed.packages()' | R --slave r_version=echo 'R.Version()'|R --slave echo "my_sys: $my_sys" >> R_check.log echo "------------------------------------------------------------------------"

R_check.log echo "my_r: $my_r" >> R_check.log echo "------------------------------------------------------------------------" R_check.log echo "r_version: $r_version" >> R_check.log echo "------------------------------------------------------------------------" R_check.log echo "installed_r_packages: " >> R_check.log echo "------------------------------------------------------------------------" R_check.log echo "$installed_packages" >> R_check.log echo "------------------------------------------------------------------------" R_check.log

This will create a file called "R_check.log", it will contain information about your operating system, the version of R you are running, and all of the installed packages. Cut and paste it's content into your message

Thanks

Kevin

On Wed, Apr 30, 2014 at 12:57 PM, Lizzy Wilbanks notifications@github.comwrote:

Hi folks,

I'm getting an error trying to install matR - any ideas what could be going wrong here?

library(devtools) install_github("MG-RAST/matR") Loading required package: RCurl Loading required package: bitops Installing MG-RAST/matR from hadley Error in file(con, "wb") : cannot open the connection In addition: Warning message: In file(con, "wb") : cannot open file '/var/folders/wr/wrn6m46YGIqIPvJJXoCGME+++TM/-Tmp-//Rtmp9yBKvp/hadley-MG-RAST/matR.zip': No such file or directory

Thanks, Lizzy

— Reply to this email directly or view it on GitHubhttps://github.com/MG-RAST/matR/issues/59 .

Kevin

---

Kevin P. Keegan, PhD

Argonne National Laboratory (work) 9700 South Cass Avenue Bldg. 240, Rm. 4.G.14 Argonne, IL 60439 (630)252-3703 kkeegan@anl.gov

kevin.p.keegan@gmail.com (home) (847)733-1079

[ewilbanks]

Hi Kevin, thanks for the help! When I run what you said I get the following error:

install.packages("devtools", dependencies = TRUE) library(devtools) install_github("MG-RAST/matR") library(matR) dependencies() Installing package(s) into ‘/Library/Frameworks/R.framework/Resources/library’ (as ‘lib’ is unspecified) trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/leopard/contrib/2.12/devtools_0.2.tgz' Content type 'application/x-gzip' length 53563 bytes (52 Kb)

opened URL

downloaded 52 Kb

The downloaded packages are in /var/folders/wr/wrn6m46YGIqIPvJJXoCGME+++TM/-Tmp-//Rtmp7aBqv7/downloaded_packages Loading required package: RCurl Loading required package: bitops Installing MG-RAST/matR from hadley Error in file(con, "wb") : cannot open the connection In addition: Warning message: In file(con, "wb") : cannot open file '/var/folders/wr/wrn6m46YGIqIPvJJXoCGME+++TM/-Tmp-//Rtmp7aBqv7/hadley-MG-RAST/matR.zip': No such file or directory Error in library(matR) : there is no package called 'matR' Error: could not find function "dependencies"

---

Below is the output of the R_check.log

-bash my_sys: sysname "Darwin" release "10.8.0" version "Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386" nodename "ruby.genomecenter.ucdavis.edu" machine "i386" login "ewilbanks" user

"ewilbanks"

my_R: /usr/bin/R

r_version: $platform [1] "x86_64-apple-darwin9.8.0"

$arch [1] "x86_64"

$os [1] "darwin9.8.0"

$system [1] "x86_64, darwin9.8.0"

$status [1] ""

$major [1] "2"

$minor [1] "12.2"

$year [1] "2011"

$month [1] "02"

$day [1] "25"

$svn rev [1] "54585"

$language [1] "R"

$version.string [1] "R version 2.12.2 (2011-02-25)"

---

installed_r_packages:

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affy "affy"
affydata "affydata"
affyio "affyio"
affyPLM "affyPLM"
affyQCReport "affyQCReport"
alphahull "alphahull"
annaffy "annaffy"
annotate "annotate"
AnnotationDbi "AnnotationDbi" ape "ape"
base "base"
Biobase "Biobase"
biomaRt "biomaRt"
Biostrings "Biostrings"
bitops "bitops"
boot "boot"
BSgenome "BSgenome"
caTools "caTools"
cluster "cluster"
codetools "codetools"
colorspace "colorspace"
corpcor "corpcor"
datasets "datasets"
DBI "DBI"
devtools "devtools"
digest "digest"
DynDoc "DynDoc"
evaluate "evaluate"
gaggle "gaggle"
gcrma "gcrma"
gdata "gdata"
gee "gee"
geneplotter "geneplotter"
GenomicRanges "GenomicRanges" getopt "getopt"
ggplot2 "ggplot2"
GO.db "GO.db"
gplots "gplots"
graph "graph"
graphics "graphics"
grDevices "grDevices"
grid "grid"
gtools "gtools"
hgu95av2.db "hgu95av2.db"
Hmisc "Hmisc"
hwriter "hwriter"
IRanges "IRanges"
iterators "iterators"
itertools "itertools"
KEGG.db "KEGG.db"
klaR "klaR"
lars "lars"
lattice "lattice"
limma "limma"
marray "marray"
MASS "MASS"
Matrix "Matrix"
MeDiChI "MeDiChI"
methods "methods"
multtest "multtest"
mutatr "mutatr"
nlme "nlme"
nws "nws"
optparse "optparse"
org.Hs.eg.db "org.Hs.eg.db"
permute "permute"
plotrix "plotrix"
plyr "plyr"
preprocessCore "preprocessCore" profr "profr"
proto "proto"
quadprog "quadprog"
randomForest "randomForest"
RBGL "RBGL"
RColorBrewer "RColorBrewer"
RCurl "RCurl"
reshape "reshape"
Rgraphviz "Rgraphviz"
rJava "rJava"
rlecuyer "rlecuyer"
Rmpi "Rmpi"
roxygen "roxygen"
Rsamtools "Rsamtools"
RSQLite "RSQLite"
rtracklayer "rtracklayer"
RUnit "RUnit"
scatterplot3d "scatterplot3d" sgeostat "sgeostat"
ShortRead "ShortRead"
simpleaffy "simpleaffy"
sm "sm"
snow "snow"
sp "sp"
SparseM "SparseM"
splancs "splancs"
splines "splines"
spp "spp"
stats "stats"
stats4 "stats4"
stringr "stringr"
survival "survival"
tcltk "tcltk"
TeachingDemos "TeachingDemos" testthat "testthat"
tools "tools"
tripack "tripack"
utils "utils"
vegan "vegan"
violinmplot "violinmplot"
vioplot "vioplot"
vsn "vsn"
xlsx "xlsx"
xlsxjars "xlsxjars"
XML "XML"
xtable "xtable"
LibPath
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ape "2.7-3" NA
base "2.12.2" "base"
Biobase "2.10.0" NA
biomaRt "2.6.0" NA
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bitops "1.0-4.1" NA
boot "1.2-43" "recommended" BSgenome "1.18.3" NA
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cluster "1.13.3" "recommended" codetools "0.2-8" "recommended" colorspace "1.0-1" NA
corpcor "1.5.7" NA
datasets "2.12.2" "base"
DBI "0.2-5" NA
devtools "0.2" NA
digest "0.4.2" NA
DynDoc "1.28.0" NA
evaluate "0.3" NA
gaggle "1.17.0" NA
gcrma "2.22.0" NA
gdata "2.8.0" NA
gee "4.13-17" NA
geneplotter "1.28.0" NA
GenomicRanges "1.2.3" NA
getopt "1.16" NA
ggplot2 "0.8.9" NA
GO.db "2.4.5" NA
gplots "2.8.0" NA
graph "1.28.0" NA
graphics "2.12.2" "base"
grDevices "2.12.2" "base"
grid "2.12.2" "base"
gtools "2.6.2" NA
hgu95av2.db "2.4.5" NA
Hmisc "3.8-3" NA
hwriter "1.3" NA
IRanges "1.8.9" NA
iterators "1.0.3" NA
itertools "0.1-1" NA
KEGG.db "2.4.5" NA
klaR "0.6-5" NA
lars "0.9-7" NA
lattice "0.19-17" "recommended" limma "3.6.9" NA
marray "1.28.0" NA
MASS "7.3-11" "recommended" Matrix "0.999375-47" "recommended" MeDiChI "0.4.0" NA
methods "2.12.2" "base"
multtest "2.6.0" NA
mutatr "0.1.2" NA
nlme "3.1-98" "recommended" nws "1.7.0.1" NA
optparse "0.9.1" NA
org.Hs.eg.db "2.4.6" NA
permute "0.6-1" NA
plotrix "3.1" NA
plyr "1.6" NA
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proto "0.3-9.2" NA
quadprog "1.5-3" NA
randomForest "4.6-2" NA
RBGL "1.26.0" NA
RColorBrewer "1.0-5" NA
RCurl "1.6-10" NA
reshape "0.8.4" NA
Rgraphviz "1.28.0" NA
rJava "0.8-8" NA
rlecuyer "0.3-1" NA
Rmpi "0.5-9" NA
roxygen "0.1-2" NA
Rsamtools "1.2.3" NA
RSQLite "0.9-4" NA
rtracklayer "1.10.6" NA
RUnit "0.4.26" NA
scatterplot3d "0.3-33" NA
sgeostat "1.0-23" NA
ShortRead "1.8.2" NA
simpleaffy "2.26.1" NA
sm "2.2-4.1" NA
snow "0.3-3" NA
sp "0.9-88" NA
SparseM "0.86" NA
splancs "2.01-29" NA
splines "2.12.2" "base"
spp "1.0" NA
stats "2.12.2" "base"
stats4 "2.12.2" "base"
stringr "0.5" NA
survival "2.36-5" "recommended" tcltk "2.12.2" "base"
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testthat "0.5" NA
tools "2.12.2" "base"
tripack "1.3-4" NA
utils "2.12.2" "base"
vegan "2.0-0" NA
violinmplot "0.2.1" NA
vioplot "0.2" NA
vsn "3.18.0" NA
xlsx "0.2.4" NA
xlsxjars "0.3.0" NA
XML "3.2-0" NA
xtable "1.5-6" NA
Depends
affy "R (>= 2.8.0), Biobase (>= 2.5.5)"
affydata "R (>= 2.4.0), affy (>= 1.23.4)"
affyio "R (>= 2.6.0), methods"
affyPLM "R (>= 2.6.0), affy (>= 1.11.0), Biobase, methods, gcrma,\nstats, preprocessCore (>= 1.5.1)"
affyQCReport "Biobase (>= 1.13.16), affy, lattice"
alphahull "tripack, sgeostat, splancs"
annaffy "R (>= 2.5.0), methods, Biobase, GO.db, KEGG.db"
annotate "R (>= 2.4.0), AnnotationDbi (>= 0.1.15)"
AnnotationDbi "R (>= 2.7.0), methods, utils, Biobase (>= 1.17.0)"
ape "R (>= 2.6.0)"
base NA
Biobase "R (>= 2.7.0), methods, utils"
biomaRt "methods"
Biostrings "R (>= 2.8.0), methods, IRanges (>= 1.7.23)"
bitops NA
boot "R (>= 2.9.0), graphics, stats"
BSgenome "R (>= 2.8.0), methods, IRanges (>= 1.7.7), GenomicRanges (>=\n0.0.9), Biostrings (>= 2.17.5)"
caTools "R (>= 2.2.0), bitops"
cluster "R (>= 2.9.0), stats, graphics, utils"
codetools "R (>= 2.1)"
colorspace "R (>= 2.0.0), methods"
corpcor "R (>= 2.7.0)"
datasets NA
DBI "R (>= 2.3.0), methods"
devtools NA
digest "R (>= 2.4.1)"
DynDoc "methods, utils"
evaluate NA
gaggle "R (>= 2.3.0), rJava (>= 0.4), graph (>= 1.10.2), RUnit (>=\n0.4.17)"
gcrma "R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats,\nutils"
gdata "R (>= 2.6.0)"
gee "stats"
geneplotter "Biobase (>= 2.5.5), annotate, lattice"
GenomicRanges "R (>= 2.8.0), methods, IRanges (>= 1.7.31)"
getopt NA
ggplot2 "reshape (>= 0.8.0), grid, proto"
GO.db "R (>= 2.7.0), methods, AnnotationDbi (>= 1.11.8)"
gplots "gtools, gdata, stats, caTools, grid"
graph "R (>= 2.6.0), methods"
graphics NA
grDevices NA
grid NA
gtools NA
hgu95av2.db "R (>= 2.7.0), methods, AnnotationDbi (>= 1.11.8), org.Hs.eg.db\n(>= 2.4.5)"
Hmisc "R (>= 2.4.0), methods, survival"
hwriter "R (>= 2.6.0)"
IRanges "R (>= 2.8.0), methods, utils, stats"
iterators "R (>= 2.5.0), utils"
itertools "R (>= 2.5.0), iterators(>= 1.0.0)"
KEGG.db "R (>= 2.7.0), methods, AnnotationDbi (>= 1.11.8)"
klaR "R (>= 2.0.0), MASS"
lars NA
lattice "R (>= 2.11.0)"
limma "R (>= 2.3.0), methods"
marray "R (>= 1.9.0), limma, methods"
MASS "R (>= 2.12.0), grDevices, graphics, stats, utils"
Matrix "R (>= 2.10.0), stats, methods, utils, lattice"
MeDiChI "R (>= 2.5.0), lars (>= 0.9-5), quadprog (>= 1.4-10), corpcor\n(>= 1.4.5), Matrix (>= 0.99875-0)" methods NA
multtest "R (>= 2.9.0), methods, Biobase"
mutatr NA
nlme "graphics, stats, R (>= 2.10.0)"
nws "R (>= 2.1), methods"
optparse "R (>= 2.9.0), methods, getopt (>= 1.15)"
org.Hs.eg.db "R (>= 2.7.0), methods, AnnotationDbi (>= 1.11.8)"
permute NA
plotrix NA
plyr "R (>= 2.11.0)"
preprocessCore "methods"
profr NA
proto NA
quadprog "R (>= 2.7.0)"
randomForest "R (>= 2.5.0), stats"
RBGL "graph, methods"
RColorBrewer "R (>= 2.0.0)"
RCurl "R (>= 2.7.0), methods, bitops"
reshape "R (>= 2.6.1), plyr"
Rgraphviz "R (>= 2.6.0), methods, utils, graph, grid"
rJava "R (>= 2.5.0), methods"
rlecuyer NA
Rmpi "R (>= 2.2.0)"
roxygen "digest"
Rsamtools "methods, IRanges (>= 1.7.23), GenomicRanges (>= 0.1.0),\nBiostrings (>= 2.15.0)"
RSQLite "R (>= 2.10.0), methods, DBI (>= 0.2-5)"
rtracklayer "R (>= 2.7.0), methods, RCurl (>= 1.4-2)"
RUnit "R (>= 2.5.0), utils (>= 2.5.0), methods (>= 2.5.0)"
scatterplot3d "R (>= 2.7.0)"
sgeostat "stats, grDevices, graphics"
ShortRead "methods, IRanges (>= 1.7.23), GenomicRanges, Biostrings (>=\n2.13.52), lattice, Rsamtools"
simpleaffy "R (>= 2.0.0), affy, genefilter, Biobase, methods, utils, gcrma"
sm "R (>= 2.7.0)"
snow "R (>= 2.3), utils"
sp "R (>= 2.10.0), methods"
SparseM "R (>= 2.4.1), methods, stats, utils"
splancs "R (>= 2.10.0), sp (>= 0.9)"
splines NA
spp "caTools"
stats NA
stats4 "methods, graphics, stats"
stringr "R (>= 2.11.0)"
survival "stats, utils, graphics, splines, R (>= 2.10.0)"
tcltk NA
TeachingDemos NA
testthat "R (>= 2.8)"
tools NA
tripack NA
utils NA
vegan "permute"
violinmplot "lattice"
vioplot "sm"
vsn "Biobase (>= 2.5.5)"
xlsx "xlsxjars, rJava"
xlsxjars "rJava"
XML "R (>= 1.2.0), methods, utils"
xtable "R (>= 2.6.0)"
Imports
affy "affyio (>= 1.13.3), Biobase (>= 2.5.5), graphics, grDevices,\nmethods, preprocessCore, stats, utils"
affydata NA
affyio NA
affyPLM NA
affyQCReport "affy, affyPLM, Biobase, genefilter, graphics, grDevices,\nlattice, RColorBrewer, simpleaffy, stats, utils, xtable" alphahull NA
annaffy "AnnotationDbi (>= 0.1.15)"
annotate "Biobase, AnnotationDbi, DBI, xtable, graphics, utils, stats,\nmethods"
AnnotationDbi "methods, utils, Biobase, DBI, RSQLite"
ape "gee, nlme, lattice"
base NA
Biobase NA
biomaRt "XML, RCurl"
Biostrings "graphics, methods, stats, utils, IRanges, Biobase"
bitops NA
boot NA
BSgenome NA
caTools NA
cluster NA
codetools NA
colorspace NA
corpcor NA
datasets NA
DBI "methods"
devtools NA
digest NA
DynDoc "methods"
evaluate "stringr (>= 0.4)"
gaggle NA
gcrma "Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), Biostrings (>=\n2.11.32), splines"
gdata "gtools"
gee NA
geneplotter "annotate, AnnotationDbi, Biobase (>= 2.5.5), graphics,\ngrDevices, grid, methods, RColorBrewer, stats, utils"
GenomicRanges "methods, IRanges"
getopt NA
ggplot2 "plyr (>= 1.0), splines, MASS, RColorBrewer, digest, colorspace"
GO.db "methods, AnnotationDbi"
gplots NA
graph "methods, stats, tools, utils"
graphics "grDevices"
grDevices NA
grid "grDevices"
gtools NA
hgu95av2.db "methods, AnnotationDbi"
Hmisc "lattice, cluster, survival"
hwriter NA
IRanges "methods, utils, stats"
iterators NA
itertools NA
KEGG.db "methods, AnnotationDbi"
klaR NA
lars NA
lattice "grid, grDevices, graphics, stats, utils"
limma NA
marray NA
MASS NA
Matrix "graphics, grid"
MeDiChI NA
methods "utils"
multtest "survival, MASS"
mutatr "digest"
nlme "lattice"
nws NA
optparse NA
org.Hs.eg.db "methods, AnnotationDbi"
permute NA
plotrix NA
plyr "itertools, iterators"
preprocessCore "stats"
profr "digest"
proto NA
quadprog NA
randomForest NA
RBGL "methods"
RColorBrewer NA
RCurl NA
reshape NA
Rgraphviz "graph, graphics, grDevices, grid, methods, utils"
rJava NA
rlecuyer NA
Rmpi NA
roxygen NA
Rsamtools "methods, utils, IRanges, GenomicRanges, Biostrings"
RSQLite "methods, DBI (>= 0.2-3)"
rtracklayer "XML (>= 1.98-0), IRanges (>= 1.8.7), GenomicRanges (>=\n1.1.34), Biostrings (>= 2.15.22), BSgenome (>= 1.15.17)"
RUnit NA
scatterplot3d NA
sgeostat NA
ShortRead "IRanges, GenomicRanges, Biostrings, Biobase, hwriter,\nRsamtools"
simpleaffy "affy, Biobase, gcrma, genefilter, graphics, grDevices,\nmethods, stats, utils"
sm NA
snow NA
sp "utils, lattice, grid"
SparseM NA
splancs NA
splines "graphics, stats"
spp NA
stats NA
stats4 NA
stringr "plyr"
survival NA
tcltk NA
TeachingDemos NA
testthat "digest, stringr (>= 0.4), mutatr, evaluate (>= 0.3)"
tools NA
tripack NA
utils NA
vegan "lattice"
violinmplot NA
vioplot NA
vsn "methods, affy (>= 1.23.4), limma, lattice"
xlsx "xlsxjars, rJava"
xlsxjars "rJava"
XML NA
xtable NA
LinkingTo
affy "preprocessCore"
affydata NA
affyio NA
affyPLM "preprocessCore"
affyQCReport NA
alphahull NA
annaffy NA
annotate NA
AnnotationDbi NA
ape NA
base NA
Biobase NA
biomaRt NA
Biostrings "IRanges"
bitops NA
boot NA
BSgenome NA
caTools NA
cluster NA
codetools NA
colorspace NA
corpcor NA
datasets NA
DBI NA
devtools NA
digest NA
DynDoc NA
evaluate NA
gaggle NA
gcrma NA
gdata NA
gee NA
geneplotter NA
GenomicRanges "IRanges"
getopt NA
ggplot2 NA
GO.db NA
gplots NA
graph NA
graphics NA
grDevices NA
grid NA
gtools NA
hgu95av2.db NA
Hmisc NA
hwriter NA
IRanges NA
iterators NA
itertools NA
KEGG.db NA
klaR NA
lars NA
lattice NA
limma NA
marray NA
MASS NA
Matrix NA
MeDiChI NA
methods NA
multtest NA
mutatr NA
nlme NA
nws NA
optparse NA
org.Hs.eg.db NA
permute NA
plotrix NA
plyr NA
preprocessCore NA
profr NA
proto NA
quadprog NA
randomForest NA
RBGL NA
RColorBrewer NA
RCurl NA
reshape NA
Rgraphviz NA
rJava NA
rlecuyer NA
Rmpi NA
roxygen NA
Rsamtools "Biostrings, IRanges" RSQLite NA
rtracklayer "IRanges"
RUnit NA
scatterplot3d NA
sgeostat NA
ShortRead "IRanges, Biostrings" simpleaffy NA
sm NA
snow NA
sp NA
SparseM NA
splancs NA
splines NA
spp NA
stats NA
stats4 NA
stringr NA
survival NA
tcltk NA
TeachingDemos NA
testthat NA
tools NA
tripack NA
utils NA
vegan NA
violinmplot NA
vioplot NA
vsn NA
xlsx NA
xlsxjars NA
XML NA
xtable NA
Suggests
affy "tkWidgets (>= 1.19.0), affydata"
affydata "hgu95av2cdf, hgu133acdf"
affyio NA
affyPLM "affydata"
affyQCReport "tkWidgets (>= 1.5.23), affydata (>= 1.4.1)"
alphahull NA
annaffy "hgu95av2.db, multtest, tcltk"
annotate "Biobase, hgu95av2.db, genefilter, Biostrings (>= 2.4.4),\nrae230a.db, rae230aprobe, tkWidgets, XML (>= 0.92-2), GO.db,\norg.Hs.eg.db, org.Mm.eg.db, hom.Hs.inp.db"
AnnotationDbi "DBI (>= 0.2-4), RSQLite (>= 0.6-4), hgu95av2.db, GO.db,\nhuman.db0, hgu95av2cdf, affy, KEGG.db"
ape "gee"
base NA
Biobase "tools, tkWidgets, ALL"
biomaRt "annotate"
Biostrings "BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>=\n1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11),\ndrosophila2probe, hgu95av2probe, GenomicFeatures (>= 0.1.3),\nhgu95av2cdf, affy, affydata (>= 1.11.5), RUnit" bitops NA
boot "survival"
BSgenome "RUnit, BSgenome.Celegans.UCSC.ce2 (>= 1.3.11),\nBSgenome.Hsapiens.UCSC.hg19 (>= 1.3.11),\nSNPlocs.Hsapiens.dbSNP.20100427, hgu95av2probe, Biobase"
caTools "MASS, rpart"
cluster NA
codetools NA
colorspace "KernSmooth, MASS, kernlab, mvtnorm, vcd"
corpcor ""
datasets NA
DBI NA
devtools "testthat, roxygen, RCurl, profr"
digest NA
DynDoc NA
evaluate NA
gaggle NA
gcrma "affydata, tools, splines, hgu95av2cdf, hgu95av2probe"
gdata NA
gee "MASS"
geneplotter "Biobase (>= 2.5.5), Rgraphviz, annotate, fibroEset,\nhgu95av2.db, hu6800.db, hgu133a.db"
GenomicRanges "RUnit, BSgenome, GenomicFeatures, Rsamtools,\nEatonEtAlChIPseq, leeBamViews, org.Sc.sgd.db,\nBSgenome.Scerevisiae.UCSC.sacCer2"
getopt "testthat"
ggplot2 "quantreg, Hmisc, mapproj, maps, hexbin, gpclib, maptools"
GO.db NA
gplots "gtools"
graph "SparseM (>= 0.36), XML, RBGL, RUnit"
graphics NA
grDevices NA
grid "lattice"
gtools NA
hgu95av2.db "annotate"
Hmisc "lattice, grid, nnet, foreign, chron, acepack, TeachingDemos,\nDesign, cluster, mice, subselect"
hwriter NA
IRanges "RUnit"
iterators "foreach"
itertools "foreach"
KEGG.db NA
klaR "scatterplot3d (>= 0.3-22), som, mlbench, rpart, e1071,\ncombinat"
lars NA
lattice "grid, KernSmooth, MASS"
limma "affy, MASS, org.Hs.eg.db, splines, statmod (>= 1.2.2), vsn"
marray "tkWidgets"
MASS "lattice, nlme, nnet, survival"
Matrix NA
MeDiChI "zoo (>= 1.3-1), lattice, multicore (>= 0.1-3), doMC (>=\n1.2.0)"
methods NA
multtest "snow"
mutatr NA
nlme "Hmisc"
nws NA
optparse NA
org.Hs.eg.db "annotate"
permute "vegan, testthat (>= 0.5)"
plotrix NA
plyr "abind, testthat (>= 0.2), tcltk, foreach"
preprocessCore NA
profr "ggplot2"
proto "graph, Rgraphviz"
quadprog NA
randomForest "RColorBrewer"
RBGL "Rgraphviz"
RColorBrewer NA
RCurl "Rcompression, XML"
reshape NA
Rgraphviz NA
rJava NA
rlecuyer NA
Rmpi "rsprng, rlecuyer"
roxygen "Rgraphviz (>= 1.19.2), tools (>= 2.9.1)"
Rsamtools "ShortRead, GenomicFeatures, RUnit, KEGG.db"
RSQLite "RUnit (>= 0.4.22)"
rtracklayer "humanStemCell, microRNA (>= 1.1.1), genefilter, limma,\norg.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg19"
RUnit NA
scatterplot3d NA
sgeostat NA
ShortRead "biomaRt, RUnit"
simpleaffy NA
sm "rpanel, tkrplot, rgl, misc3d, akima, gam"
snow "Rmpi,rpvm,rlecuyer,rsprng,nws"
sp "lattice, RColorBrewer, rgdal, rgeos (>= 0.1-8)"
SparseM NA
splancs NA
splines NA
spp NA
stats NA
stats4 NA
stringr "testthat (>= 0.3)"
survival NA
tcltk NA
TeachingDemos "tkrplot, lattice, MASS, rgl, sgeostat, mapproj, tcltk,\ntcltk2, R2wd, EBImage, png"
testthat NA
tools NA
tripack NA
utils NA
vegan "MASS, mgcv, lattice, cluster, scatterplot3d, rgl, tcltk"
violinmplot NA
vioplot NA
vsn "affydata, hgu95av2cdf"
xlsx NA
xlsxjars NA
XML "bitops"
xtable NA
Enhances OS_type affy NA NA
affydata NA NA
affyio NA NA
affyPLM NA NA
affyQCReport NA NA
alphahull NA NA
annaffy NA NA
annotate NA NA
AnnotationDbi NA NA
ape NA NA
base NA NA
Biobase NA NA
biomaRt NA NA
Biostrings "Rmpi" NA
bitops NA NA
boot NA NA
BSgenome NA NA
caTools NA NA
cluster "MASS" NA
codetools NA NA
colorspace NA NA
corpcor NA NA
datasets NA NA
DBI NA NA
devtools NA NA
digest NA NA
DynDoc NA NA
evaluate NA NA
gaggle NA NA
gcrma NA NA
gdata NA NA
gee NA NA
geneplotter NA NA
GenomicRanges NA NA
getopt NA NA
ggplot2 NA NA
GO.db NA NA
gplots NA NA
graph NA NA
graphics NA NA
grDevices NA NA
grid NA NA
gtools NA NA
hgu95av2.db NA NA
Hmisc NA NA
hwriter NA NA
IRanges NA NA
iterators NA NA
itertools "foreach, iterators" NA
KEGG.db NA NA
klaR NA NA
lars NA NA
lattice "chron" NA
limma NA NA
marray NA NA
MASS "AER, FrF2, GPArotation" NA
Matrix "MatrixModels, graph, SparseM, sfsmisc" NA
MeDiChI NA NA
methods NA NA
multtest NA NA
mutatr NA NA
nlme NA NA
nws NA NA
optparse NA NA
org.Hs.eg.db NA NA
permute NA NA
plotrix NA NA
plyr NA NA
preprocessCore NA NA
profr NA NA
proto NA NA
quadprog NA NA
randomForest NA NA
RBGL NA NA
RColorBrewer NA NA
RCurl NA NA
reshape NA NA
Rgraphviz NA NA
rJava NA NA
rlecuyer NA NA
Rmpi NA NA
roxygen NA NA
Rsamtools NA NA
RSQLite NA NA
rtracklayer NA NA
RUnit NA NA
scatterplot3d NA NA
sgeostat NA NA
ShortRead "Rmpi, multicore" NA
simpleaffy NA NA
sm NA NA
snow NA NA
sp NA NA
SparseM NA NA
splancs NA NA
splines NA NA
spp NA NA
stats NA NA
stats4 NA NA
stringr NA NA
survival NA NA
tcltk NA NA
TeachingDemos "maptools, qcc" NA
testthat NA NA
tools NA NA
tripack NA NA
utils NA NA
vegan NA NA
violinmplot NA NA
vioplot NA NA
vsn NA NA
xlsx NA NA
xlsxjars NA NA
XML NA NA
xtable NA NA
License Built
affy "LGPL (>= 2.0)" "2.12.0" affydata "GPL (>= 2)" "2.12.1" affyio "LGPL (>= 2)" "2.12.0" affyPLM "GPL (>= 2)" "2.12.2" affyQCReport "LGPL (>= 2)" "2.12.0" alphahull "file LICENSE" "2.12.0" annaffy "LGPL" "2.12.0" annotate "Artistic-2.0" "2.12.2" AnnotationDbi "Artistic-2.0" "2.12.0" ape "GPL (>= 2)" "2.12.2" base "Part of R 2.12.2" "2.12.2" Biobase "Artistic-2.0" "2.12.0" biomaRt "Artistic-2.0" "2.12.0" Biostrings "Artistic-2.0" "2.12.2" bitops "GPL version 2 or later" "2.12.0" boot "Unlimited" "2.12.2" BSgenome "Artistic-2.0" "2.12.1" caTools "GPL-3" "2.12.1" cluster "GPL (>= 2)" "2.12.2" codetools "GPL" "2.12.2" colorspace "BSD" "2.12.0" corpcor "GPL (>= 3)" "2.12.0" datasets "Part of R 2.12.2" "2.12.2" DBI "LGPL (>= 2)" "2.12.0" devtools "MIT" "2.12.2" digest "GPL-2" "2.12.0" DynDoc "Artistic-2.0" "2.12.0" evaluate "GPL" "2.12.0" gaggle "GPL version 2 or newer" "2.12.2" gcrma "LGPL" "2.12.0" gdata "GPL-2" "2.12.0" gee "GPL-2" "2.12.2" geneplotter "Artistic-2.0" "2.12.0" GenomicRanges "Artistic-2.0" "2.12.1" getopt "GPL (>= 2)" "2.12.2" ggplot2 "GPL-2" "2.12.1" GO.db "Artistic-2.0" "2.12.1" gplots "GPL-2" "2.12.0" graph "Artistic-2.0" "2.12.0" graphics "Part of R 2.12.2" "2.12.2" grDevices "Part of R 2.12.2" "2.12.2" grid "Part of R 2.12.2" "2.12.2" gtools "LGPL-2.1" "2.12.0" hgu95av2.db "Artistic-2.0" "2.12.1" Hmisc "GPL (>= 2)" "2.12.0" hwriter "LGPL-2.1" "2.12.0" IRanges "Artistic-2.0" "2.12.1" iterators "Apache License (== 2.0)" "2.12.0" itertools "GPL-2" "2.12.0" KEGG.db "file LICENSE" "2.12.1" klaR "GPL-2" "2.12.2" lars "GPL version 2 or newer" "2.12.0" lattice "GPL (>= 2)" "2.12.1" limma "LGPL" "2.12.0" marray "LGPL" "2.12.0" MASS "GPL-2 | GPL-3" "2.12.2" Matrix "GPL (>= 2)" "2.12.2" MeDiChI "GPL-2" "2.12.0" methods "Part of R 2.12.2" "2.12.2" multtest "LGPL" "2.12.0" mutatr "GPL" "2.12.0" nlme "GPL (>= 2)" "2.12.2" nws "GPL (>= 2)" "2.12.0" optparse "GPL (>= 2)" "2.12.0" org.Hs.eg.db "Artistic-2.0" "2.12.1" permute "GPL-2" "2.12.2" plotrix "GPL (>= 2)" "2.12.2" plyr "MIT" "2.12.2" preprocessCore "LGPL (>= 2)" "2.12.0" profr "MIT" "2.12.1" proto "GPL-2" "2.12.2" quadprog "GPL (>= 2)" "2.12.0" randomForest "GPL (>= 2)" "2.12.1" RBGL "Artistic-2.0" "2.12.0" RColorBrewer "Apache License 2.0" "2.12.2" RCurl "BSD" "2.12.2" reshape "MIT" "2.12.1" Rgraphviz "Artistic-2.0" "2.12.0" rJava "GPL-2" "2.12.1" rlecuyer "GPL (>= 2)" "2.12.0" Rmpi "GPL (>= 2)" "2.12.0" roxygen "GPL (>= 2)" "2.12.0" Rsamtools "Artistic-2.0" "2.12.1" RSQLite "LGPL (>= 2)" "2.12.0" rtracklayer "Artistic-2.0" "2.12.0" RUnit "GPL-2" "2.12.0" scatterplot3d "GPL-2" "2.12.2" sgeostat "file LICENSE" "2.12.0" ShortRead "Artistic-2.0" "2.12.0" simpleaffy "GPL (>= 2)" "2.12.0" sm "GPL-2" "2.12.0" snow "GPL" "2.12.0" sp "GPL (>= 2)" "2.12.2" SparseM "file LICENSE" "2.12.0" splancs "GPL (>= 2)" "2.12.2" splines "Part of R 2.12.2" "2.12.2" spp "GPL-2" "2.12.2" stats "Part of R 2.12.2" "2.12.2" stats4 "Part of R 2.12.2" "2.12.2" stringr "GPL-2" "2.12.2" survival "GPL (>= 2)" "2.12.2" tcltk "Part of R 2.12.2" "2.12.2" TeachingDemos "Artistic-2.0" "2.12.0" testthat "GPL" "2.12.2" tools "Part of R 2.12.2" "2.12.2" tripack "file LICENSE" "2.12.0" utils "Part of R 2.12.2" "2.12.2" vegan "GPL-2" "2.12.2" violinmplot "GPL-2" "2.12.0" vioplot "BSD" "2.12.0" vsn "Artistic-2.0" "2.12.0" xlsx "GPL-3" "2.12.0" xlsxjars "GPL-3" "2.12.2" XML "BSD" "2.12.0"

xtable "GPL (>= 2)" "2.12.0"

[DrOppenheimer]

Hi Lizzy,

Try upgrading to R 2.15 or later.

Most of the packages that matR relies on require 2.15 or later (on mac I think a default installation will give you version 3.0.1) - it looks as though one or more of those dependencies are failing to load due to your R version (2.12.2)

If you need help upgrading your R version -- especially if you are running anything that requires 2.12 -- let me know and I can help

Cheers Kevin

On Wed, Apr 30, 2014 at 2:04 PM, Lizzy Wilbanks notifications@github.comwrote:

Hi Kevin, thanks for the help! When I run what you said I get the following error:

install.packages("devtools", dependencies = TRUE) library(devtools) install_github("MG-RAST/matR") library(matR) dependencies() Installing package(s) into ‘/Library/Frameworks/R.framework/Resources/library’ (as ‘lib’ is unspecified) trying URL ' http://cran.cnr.Berkeley.edu/bin/macosx/leopard/contrib/2.12/devtools_0.2.tgz ' Content type 'application/x-gzip' length 53563 bytes (52 Kb)

opened URL

downloaded 52 Kb

The downloaded packages are in

/var/folders/wr/wrn6m46YGIqIPvJJXoCGME+++TM/-Tmp-//Rtmp7aBqv7/downloaded_packages

Loading required package: RCurl Loading required package: bitops Installing MG-RAST/matR from hadley Error in file(con, "wb") : cannot open the connection In addition: Warning message: In file(con, "wb") : cannot open file '/var/folders/wr/wrn6m46YGIqIPvJJXoCGME+++TM/-Tmp-//Rtmp7aBqv7/hadley-MG-RAST/matR.zip': No such file or directory Error in library(matR) : there is no package called 'matR' Error: could not find function "dependencies"

---

Below is the output of the R_check.log

-bash my_sys: sysname "Darwin" release "10.8.0" version "Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386" nodename "ruby.genomecenter.ucdavis.edu" machine "i386" login "ewilbanks" user "ewilbanks" my_R: /usr/bin/R

r_version: $platform [1] "x86_64-apple-darwin9.8.0"

$arch [1] "x86_64"

$os [1] "darwin9.8.0"

$system [1] "x86_64, darwin9.8.0"

$status [1] ""

$major [1] "2"

$minor [1] "12.2"

$year [1] "2011"

$month [1] "02"

$day [1] "25"

$svn rev [1] "54585"

$language [1] "R"

$version.string

[1] "R version 2.12.2 (2011-02-25)"

installed_r_packages:

       Package

affy "affy"

affydata "affydata"

affyio "affyio"

affyPLM "affyPLM"

affyQCReport "affyQCReport"

alphahull "alphahull"

annaffy "annaffy"

annotate "annotate"

AnnotationDbi "AnnotationDbi" ape "ape"

base "base"

Biobase "Biobase"

biomaRt "biomaRt"

Biostrings "Biostrings"

bitops "bitops"

boot "boot"

BSgenome "BSgenome"

caTools "caTools"

cluster "cluster"

codetools "codetools"

colorspace "colorspace"

corpcor "corpcor"

datasets "datasets"

DBI "DBI"

devtools "devtools"

digest "digest"

DynDoc "DynDoc"

evaluate "evaluate"

gaggle "gaggle"

gcrma "gcrma"

gdata "gdata"

gee "gee"

geneplotter "geneplotter"

GenomicRanges "GenomicRanges" getopt "getopt"

ggplot2 "ggplot2"

GO.db "GO.db"

gplots "gplots"

graph "graph"

graphics "graphics"

grDevices "grDevices"

grid "grid"

gtools "gtools"

hgu95av2.db "hgu95av2.db"

Hmisc "Hmisc"

hwriter "hwriter"

IRanges "IRanges"

iterators "iterators"

itertools "itertools"

KEGG.db "KEGG.db"

klaR "klaR"

lars "lars"

lattice "lattice"

limma "limma"

marray "marray"

MASS "MASS"

Matrix "Matrix"

MeDiChI "MeDiChI"

methods "methods"

multtest "multtest"

mutatr "mutatr"

nlme "nlme"

nws "nws"

optparse "optparse"

org.Hs.eg.db "org.Hs.eg.db"

permute "permute"

plotrix "plotrix"

plyr "plyr"

preprocessCore "preprocessCore" profr "profr"

proto "proto"

quadprog "quadprog"

randomForest "randomForest"

RBGL "RBGL"

RColorBrewer "RColorBrewer"

RCurl "RCurl"

reshape "reshape"

Rgraphviz "Rgraphviz"

rJava "rJava"

rlecuyer "rlecuyer"

Rmpi "Rmpi"

roxygen "roxygen"

Rsamtools "Rsamtools"

RSQLite "RSQLite"

rtracklayer "rtracklayer"

RUnit "RUnit"

scatterplot3d "scatterplot3d" sgeostat "sgeostat"

ShortRead "ShortRead"

simpleaffy "simpleaffy"

sm "sm"

snow "snow"

sp "sp"

SparseM "SparseM"

splancs "splancs"

splines "splines"

spp "spp"

stats "stats"

stats4 "stats4"

stringr "stringr"

survival "survival"

tcltk "tcltk"

TeachingDemos "TeachingDemos" testthat "testthat"

tools "tools"

tripack "tripack"

utils "utils"

vegan "vegan"

violinmplot "violinmplot"

vioplot "vioplot"

vsn "vsn"

xlsx "xlsx"

xlsxjars "xlsxjars"

XML "XML"

xtable "xtable"

LibPath

affy "/Library/Frameworks/R.framework/Resources/library" affydata "/Library/Frameworks/R.framework/Resources/library" affyio "/Library/Frameworks/R.framework/Resources/library" affyPLM "/Library/Frameworks/R.framework/Resources/library" affyQCReport "/Library/Frameworks/R.framework/Resources/library" alphahull "/Library/Frameworks/R.framework/Resources/library" annaffy "/Library/Frameworks/R.framework/Resources/library" annotate "/Library/Frameworks/R.framework/Resources/library" AnnotationDbi "/Library/Frameworks/R.framework/Resources/library" ape "/Library/Frameworks/R.framework/Resources/library" base "/Library/Frameworks/R.framework/Resources/library" Biobase "/Library/Frameworks/R.framework/Resources/library" biomaRt "/Library/Frameworks/R.framework/Resources/library" Biostrings "/Library/Frameworks/R.framework/Resources/library" bitops "/Library/Frameworks/R.framework/Resources/library" boot "/Library/Frameworks/R.framework/Resources/library" BSgenome "/Library/Frameworks/R.framework/Resources/library" caTools "/Library/Frameworks/R.framework/Resources/library" cluster "/Library/Frameworks/R.framework/Resources/library" codetools "/Library/Frameworks/R.framework/Resources/library" colorspace "/Library/Frameworks/R.framework/Resources/library" corpcor "/Library/Frameworks/R.framework/Resources/library" datasets "/Library/Frameworks/R.framework/Resources/library" DBI "/Library/Frameworks/R.framework/Resources/library" devtools "/Library/Frameworks/R.framework/Resources/library" digest "/Library/Frameworks/R.framework/Resources/library" DynDoc "/Library/Frameworks/R.framework/Resources/library" evaluate "/Library/Frameworks/R.framework/Resources/library" gaggle "/Library/Frameworks/R.framework/Resources/library" gcrma "/Library/Frameworks/R.framework/Resources/library" gdata "/Library/Frameworks/R.framework/Resources/library" gee "/Library/Frameworks/R.framework/Resources/library" geneplotter "/Library/Frameworks/R.framework/Resources/library" GenomicRanges "/Library/Frameworks/R.framework/Resources/library" getopt "/Library/Frameworks/R.framework/Resources/library" ggplot2 "/Library/Frameworks/R.framework/Resources/library" GO.db "/Library/Frameworks/R.framework/Resources/library" gplots "/Library/Frameworks/R.framework/Resources/library" graph "/Library/Frameworks/R.framework/Resources/library" graphics "/Library/Frameworks/R.framework/Resources/library" grDevices "/Library/Frameworks/R.framework/Resources/library" grid "/Library/Frameworks/R.framework/Resources/library" gtools "/Library/Frameworks/R.framework/Resources/library" hgu95av2.db "/Library/Frameworks/R.framework/Resources/library" Hmisc "/Library/Frameworks/R.framework/Resources/library" hwriter "/Library/Frameworks/R.framework/Resources/library" IRanges "/Library/Frameworks/R.framework/Resources/library" iterators "/Library/Frameworks/R.framework/Resources/library" itertools "/Library/Frameworks/R.framework/Resources/library" KEGG.db "/Library/Frameworks/R.framework/Resources/library" klaR "/Library/Frameworks/R.framework/Resources/library" lars "/Library/Frameworks/R.framework/Resources/library" lattice "/Library/Frameworks/R.framework/Resources/library" limma "/Library/Frameworks/R.framework/Resources/library" marray "/Library/Frameworks/R.framework/Resources/library" MASS "/Library/Frameworks/R.framework/Resources/library" Matrix "/Library/Frameworks/R.framework/Resources/library" MeDiChI "/Library/Frameworks/R.framework/Resources/library" methods "/Library/Frameworks/R.framework/Resources/library" multtest "/Library/Frameworks/R.framework/Resources/library" mutatr "/Library/Frameworks/R.framework/Resources/library" nlme "/Library/Frameworks/R.framework/Resources/library" nws "/Library/Frameworks/R.framework/Resources/library" optparse "/Library/Frameworks/R.framework/Resources/library" org.Hs.eg.db "/Library/Frameworks/R.framework/Resources/library" permute "/Library/Frameworks/R.framework/Resources/library" plotrix "/Library/Frameworks/R.framework/Resources/library" plyr "/Library/Frameworks/R.framework/Resources/library" preprocessCore "/Library/Frameworks/R.framework/Resources/library" profr "/Library/Frameworks/R.framework/Resources/library" proto "/Library/Frameworks/R.framework/Resources/library" quadprog "/Library/Frameworks/R.framework/Resources/library" randomForest "/Library/Frameworks/R.framework/Resources/library" RBGL "/Library/Frameworks/R.framework/Resources/library" RColorBrewer "/Library/Frameworks/R.framework/Resources/library" RCurl "/Library/Frameworks/R.framework/Resources/library" reshape "/Library/Frameworks/R.framework/Resources/library" Rgraphviz "/Library/Frameworks/R.framework/Resources/library" rJava "/Library/Frameworks/R.framework/Resources/library" rlecuyer "/Library/Frameworks/R.framework/Resources/library" Rmpi "/Library/Frameworks/R.framework/Resources/library" roxygen "/Library/Frameworks/R.framework/Resources/library" Rsamtools "/Library/Frameworks/R.framework/Resources/library" RSQLite "/Library/Frameworks/R.framework/Resources/library" rtracklayer "/Library/Frameworks/R.framework/Resources/library" RUnit "/Library/Frameworks/R.framework/Resources/library" scatterplot3d "/Library/Frameworks/R.framework/Resources/library" sgeostat "/Library/Frameworks/R.framework/Resources/library" ShortRead "/Library/Frameworks/R.framework/Resources/library" simpleaffy "/Library/Frameworks/R.framework/Resources/library" sm "/Library/Frameworks/R.framework/Resources/library" snow "/Library/Frameworks/R.framework/Resources/library" sp "/Library/Frameworks/R.framework/Resources/library" SparseM "/Library/Frameworks/R.framework/Resources/library" splancs "/Library/Frameworks/R.framework/Resources/library" splines "/Library/Frameworks/R.framework/Resources/library" spp "/Library/Frameworks/R.framework/Resources/library" stats "/Library/Frameworks/R.framework/Resources/library" stats4 "/Library/Frameworks/R.framework/Resources/library" stringr "/Library/Frameworks/R.framework/Resources/library" survival "/Library/Frameworks/R.framework/Resources/library" tcltk "/Library/Frameworks/R.framework/Resources/library" TeachingDemos "/Library/Frameworks/R.framework/Resources/library" testthat "/Library/Frameworks/R.framework/Resources/library" tools "/Library/Frameworks/R.framework/Resources/library" tripack "/Library/Frameworks/R.framework/Resources/library" utils "/Library/Frameworks/R.framework/Resources/library" vegan "/Library/Frameworks/R.framework/Resources/library" violinmplot "/Library/Frameworks/R.framework/Resources/library" vioplot "/Library/Frameworks/R.framework/Resources/library" vsn "/Library/Frameworks/R.framework/Resources/library" xlsx "/Library/Frameworks/R.framework/Resources/library" xlsxjars "/Library/Frameworks/R.framework/Resources/library" XML "/Library/Frameworks/R.framework/Resources/library" xtable "/Library/Frameworks/R.framework/Resources/library" Version Priority

affy "1.28.0" NA

affydata "1.11.11" NA

affyio "1.18.0" NA

affyPLM "1.26.1" NA

affyQCReport "1.28.1" NA

alphahull "0.2-0" NA

annaffy "1.22.0" NA

annotate "1.28.1" NA

AnnotationDbi "1.12.0" NA

ape "2.7-3" NA

base "2.12.2" "base"

Biobase "2.10.0" NA

biomaRt "2.6.0" NA

Biostrings "2.18.4" NA

bitops "1.0-4.1" NA

boot "1.2-43" "recommended" BSgenome "1.18.3" NA

caTools "1.11" NA

cluster "1.13.3" "recommended" codetools "0.2-8" "recommended" colorspace "1.0-1" NA

corpcor "1.5.7" NA

datasets "2.12.2" "base"

DBI "0.2-5" NA

devtools "0.2" NA

digest "0.4.2" NA

DynDoc "1.28.0" NA

evaluate "0.3" NA

gaggle "1.17.0" NA

gcrma "2.22.0" NA

gdata "2.8.0" NA

gee "4.13-17" NA

geneplotter "1.28.0" NA

GenomicRanges "1.2.3" NA

getopt "1.16" NA

ggplot2 "0.8.9" NA

GO.db "2.4.5" NA

gplots "2.8.0" NA

graph "1.28.0" NA

graphics "2.12.2" "base"

grDevices "2.12.2" "base"

grid "2.12.2" "base"

gtools "2.6.2" NA

hgu95av2.db "2.4.5" NA

Hmisc "3.8-3" NA

hwriter "1.3" NA

IRanges "1.8.9" NA

iterators "1.0.3" NA

itertools "0.1-1" NA

KEGG.db "2.4.5" NA

klaR "0.6-5" NA

lars "0.9-7" NA

lattice "0.19-17" "recommended" limma "3.6.9" NA

marray "1.28.0" NA

MASS "7.3-11" "recommended" Matrix "0.999375-47" "recommended" MeDiChI "0.4.0" NA

methods "2.12.2" "base"

multtest "2.6.0" NA

mutatr "0.1.2" NA

nlme "3.1-98" "recommended" nws "1.7.0.1" NA

optparse "0.9.1" NA

org.Hs.eg.db "2.4.6" NA

permute "0.6-1" NA

plotrix "3.1" NA

plyr "1.6" NA

preprocessCore "1.12.0" NA

profr "0.2" NA

proto "0.3-9.2" NA

quadprog "1.5-3" NA

randomForest "4.6-2" NA

RBGL "1.26.0" NA

RColorBrewer "1.0-5" NA

RCurl "1.6-10" NA

reshape "0.8.4" NA

Rgraphviz "1.28.0" NA

rJava "0.8-8" NA

rlecuyer "0.3-1" NA

Rmpi "0.5-9" NA

roxygen "0.1-2" NA

Rsamtools "1.2.3" NA

RSQLite "0.9-4" NA

rtracklayer "1.10.6" NA

RUnit "0.4.26" NA

scatterplot3d "0.3-33" NA

sgeostat "1.0-23" NA

ShortRead "1.8.2" NA

simpleaffy "2.26.1" NA

sm "2.2-4.1" NA

snow "0.3-3" NA

sp "0.9-88" NA

SparseM "0.86" NA

splancs "2.01-29" NA

splines "2.12.2" "base"

spp "1.0" NA

stats "2.12.2" "base"

stats4 "2.12.2" "base"

stringr "0.5" NA

survival "2.36-5" "recommended" tcltk "2.12.2" "base"

TeachingDemos "2.7" NA

testthat "0.5" NA

tools "2.12.2" "base"

tripack "1.3-4" NA

utils "2.12.2" "base"

vegan "2.0-0" NA

violinmplot "0.2.1" NA

vioplot "0.2" NA

vsn "3.18.0" NA

xlsx "0.2.4" NA

xlsxjars "0.3.0" NA

XML "3.2-0" NA

xtable "1.5-6" NA

Depends

affy "R (>= 2.8.0), Biobase (>= 2.5.5)"

affydata "R (>= 2.4.0), affy (>= 1.23.4)"

affyio "R (>= 2.6.0), methods"

affyPLM "R (>= 2.6.0), affy (>= 1.11.0), Biobase, methods, gcrma,\nstats, preprocessCore (>= 1.5.1)"

affyQCReport "Biobase (>= 1.13.16), affy, lattice"

alphahull "tripack, sgeostat, splancs"

annaffy "R (>= 2.5.0), methods, Biobase, GO.db, KEGG.db"

annotate "R (>= 2.4.0), AnnotationDbi (>= 0.1.15)"

AnnotationDbi "R (>= 2.7.0), methods, utils, Biobase (>= 1.17.0)"

ape "R (>= 2.6.0)"

base NA

Biobase "R (>= 2.7.0), methods, utils"

biomaRt "methods"

Biostrings "R (>= 2.8.0), methods, IRanges (>= 1.7.23)"

bitops NA

boot "R (>= 2.9.0), graphics, stats"

BSgenome "R (>= 2.8.0), methods, IRanges (>= 1.7.7), GenomicRanges (>=\n0.0.9), Biostrings (>= 2.17.5)"

caTools "R (>= 2.2.0), bitops"

cluster "R (>= 2.9.0), stats, graphics, utils"

codetools "R (>= 2.1)"

colorspace "R (>= 2.0.0), methods"

corpcor "R (>= 2.7.0)"

datasets NA

DBI "R (>= 2.3.0), methods"

devtools NA

digest "R (>= 2.4.1)"

DynDoc "methods, utils"

evaluate NA

gaggle "R (>= 2.3.0), rJava (>= 0.4), graph (>= 1.10.2), RUnit (>=\n0.4.17)"

gcrma "R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats,\nutils"

gdata "R (>= 2.6.0)"

gee "stats"

geneplotter "Biobase (>= 2.5.5), annotate, lattice"

GenomicRanges "R (>= 2.8.0), methods, IRanges (>= 1.7.31)"

getopt NA

ggplot2 "reshape (>= 0.8.0), grid, proto"

GO.db "R (>= 2.7.0), methods, AnnotationDbi (>= 1.11.8)"

gplots "gtools, gdata, stats, caTools, grid"

graph "R (>= 2.6.0), methods"

graphics NA

grDevices NA

grid NA

gtools NA

hgu95av2.db "R (>= 2.7.0), methods, AnnotationDbi (>= 1.11.8), org.Hs.eg.db\n(>= 2.4.5)"

Hmisc "R (>= 2.4.0), methods, survival"

hwriter "R (>= 2.6.0)"

IRanges "R (>= 2.8.0), methods, utils, stats"

iterators "R (>= 2.5.0), utils"

itertools "R (>= 2.5.0), iterators(>= 1.0.0)"

KEGG.db "R (>= 2.7.0), methods, AnnotationDbi (>= 1.11.8)"

klaR "R (>= 2.0.0), MASS"

lars NA

lattice "R (>= 2.11.0)"

limma "R (>= 2.3.0), methods"

marray "R (>= 1.9.0), limma, methods"

MASS "R (>= 2.12.0), grDevices, graphics, stats, utils"

Matrix "R (>= 2.10.0), stats, methods, utils, lattice"

MeDiChI "R (>= 2.5.0), lars (>= 0.9-5), quadprog (>= 1.4-10), corpcor\n(>= 1.4.5), Matrix (>= 0.99875-0)" methods NA

multtest "R (>= 2.9.0), methods, Biobase"

mutatr NA

nlme "graphics, stats, R (>= 2.10.0)"

nws "R (>= 2.1), methods"

optparse "R (>= 2.9.0), methods, getopt (>= 1.15)"

org.Hs.eg.db "R (>= 2.7.0), methods, AnnotationDbi (>= 1.11.8)"

permute NA

plotrix NA

plyr "R (>= 2.11.0)"

preprocessCore "methods"

profr NA

proto NA

quadprog "R (>= 2.7.0)"

randomForest "R (>= 2.5.0), stats"

RBGL "graph, methods"

RColorBrewer "R (>= 2.0.0)"

RCurl "R (>= 2.7.0), methods, bitops"

reshape "R (>= 2.6.1), plyr"

Rgraphviz "R (>= 2.6.0), methods, utils, graph, grid"

rJava "R (>= 2.5.0), methods"

rlecuyer NA

Rmpi "R (>= 2.2.0)"

roxygen "digest"

Rsamtools "methods, IRanges (>= 1.7.23), GenomicRanges (>= 0.1.0),\nBiostrings (>= 2.15.0)"

RSQLite "R (>= 2.10.0), methods, DBI (>= 0.2-5)"

rtracklayer "R (>= 2.7.0), methods, RCurl (>= 1.4-2)"

RUnit "R (>= 2.5.0), utils (>= 2.5.0), methods (>= 2.5.0)"

scatterplot3d "R (>= 2.7.0)"

sgeostat "stats, grDevices, graphics"

ShortRead "methods, IRanges (>= 1.7.23), GenomicRanges, Biostrings (>=\n2.13.52), lattice, Rsamtools"

simpleaffy "R (>= 2.0.0), affy, genefilter, Biobase, methods, utils, gcrma"

sm "R (>= 2.7.0)"

snow "R (>= 2.3), utils"

sp "R (>= 2.10.0), methods"

SparseM "R (>= 2.4.1), methods, stats, utils"

splancs "R (>= 2.10.0), sp (>= 0.9)"

splines NA

spp "caTools"

stats NA

stats4 "methods, graphics, stats"

stringr "R (>= 2.11.0)"

survival "stats, utils, graphics, splines, R (>= 2.10.0)"

tcltk NA

TeachingDemos NA

testthat "R (>= 2.8)"

tools NA

tripack NA

utils NA

vegan "permute"

violinmplot "lattice"

vioplot "sm"

vsn "Biobase (>= 2.5.5)"

xlsx "xlsxjars, rJava"

xlsxjars "rJava"

XML "R (>= 1.2.0), methods, utils"

xtable "R (>= 2.6.0)"

Imports

affy "affyio (>= 1.13.3), Biobase (>= 2.5.5), graphics, grDevices,\nmethods, preprocessCore, stats, utils"

affydata NA

affyio NA

affyPLM NA

affyQCReport "affy, affyPLM, Biobase, genefilter, graphics, grDevices,\nlattice, RColorBrewer, simpleaffy, stats, utils, xtable" alphahull NA

annaffy "AnnotationDbi (>= 0.1.15)"

annotate "Biobase, AnnotationDbi, DBI, xtable, graphics, utils, stats,\nmethods"

AnnotationDbi "methods, utils, Biobase, DBI, RSQLite"

ape "gee, nlme, lattice"

base NA

Biobase NA

biomaRt "XML, RCurl"

Biostrings "graphics, methods, stats, utils, IRanges, Biobase"

bitops NA

boot NA

BSgenome NA

caTools NA

cluster NA

codetools NA

colorspace NA

corpcor NA

datasets NA

DBI "methods"

devtools NA

digest NA

DynDoc "methods"

evaluate "stringr (>= 0.4)"

gaggle NA

gcrma "Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), Biostrings (>=\n2.11.32), splines"

gdata "gtools"

gee NA

geneplotter "annotate, AnnotationDbi, Biobase (>= 2.5.5), graphics,\ngrDevices, grid, methods, RColorBrewer, stats, utils"

GenomicRanges "methods, IRanges"

getopt NA

ggplot2 "plyr (>= 1.0), splines, MASS, RColorBrewer, digest, colorspace"

GO.db "methods, AnnotationDbi"

gplots NA

graph "methods, stats, tools, utils"

graphics "grDevices"

grDevices NA

grid "grDevices"

gtools NA

hgu95av2.db "methods, AnnotationDbi"

Hmisc "lattice, cluster, survival"

hwriter NA

IRanges "methods, utils, stats"

iterators NA

itertools NA

KEGG.db "methods, AnnotationDbi"

klaR NA

lars NA

lattice "grid, grDevices, graphics, stats, utils"

limma NA

marray NA

MASS NA

Matrix "graphics, grid"

MeDiChI NA

methods "utils"

multtest "survival, MASS"

mutatr "digest"

nlme "lattice"

nws NA

optparse NA

org.Hs.eg.db "methods, AnnotationDbi"

permute NA

plotrix NA

plyr "itertools, iterators"

preprocessCore "stats"

profr "digest"

proto NA

quadprog NA

randomForest NA

RBGL "methods"

RColorBrewer NA

RCurl NA

reshape NA

Rgraphviz "graph, graphics, grDevices, grid, methods, utils"

rJava NA

rlecuyer NA

Rmpi NA

roxygen NA

Rsamtools "methods, utils, IRanges, GenomicRanges, Biostrings"

RSQLite "methods, DBI (>= 0.2-3)"

rtracklayer "XML (>= 1.98-0), IRanges (>= 1.8.7), GenomicRanges (>=\n1.1.34), Biostrings (>= 2.15.22), BSgenome (>= 1.15.17)"

RUnit NA

scatterplot3d NA

sgeostat NA

ShortRead "IRanges, GenomicRanges, Biostrings, Biobase, hwriter,\nRsamtools"

simpleaffy "affy, Biobase, gcrma, genefilter, graphics, grDevices,\nmethods, stats, utils"

sm NA

snow NA

sp "utils, lattice, grid"

SparseM NA

splancs NA

splines "graphics, stats"

spp NA

stats NA

stats4 NA

stringr "plyr"

survival NA

tcltk NA

TeachingDemos NA

testthat "digest, stringr (>= 0.4), mutatr, evaluate (>= 0.3)"

tools NA

tripack NA

utils NA

vegan "lattice"

violinmplot NA

vioplot NA

vsn "methods, affy (>= 1.23.4), limma, lattice"

xlsx "xlsxjars, rJava"

xlsxjars "rJava"

XML NA

xtable NA

LinkingTo

affy "preprocessCore"

affydata NA

affyio NA

affyPLM "preprocessCore"

affyQCReport NA

alphahull NA

annaffy NA

annotate NA

AnnotationDbi NA

ape NA

base NA

Biobase NA

biomaRt NA

Biostrings "IRanges"

bitops NA

boot NA

BSgenome NA

caTools NA

cluster NA

codetools NA

colorspace NA

corpcor NA

datasets NA

DBI NA

devtools NA

digest NA

DynDoc NA

evaluate NA

gaggle NA

gcrma NA

gdata NA

gee NA

geneplotter NA

GenomicRanges "IRanges"

getopt NA

ggplot2 NA

GO.db NA

gplots NA

graph NA

graphics NA

grDevices NA

grid NA

gtools NA

hgu95av2.db NA

Hmisc NA

hwriter NA

IRanges NA

iterators NA

itertools NA

KEGG.db NA

klaR NA

lars NA

lattice NA

limma NA

marray NA

MASS NA

Matrix NA

MeDiChI NA

methods NA

multtest NA

mutatr NA

nlme NA

nws NA

optparse NA

org.Hs.eg.db NA

permute NA

plotrix NA

plyr NA

preprocessCore NA

profr NA

proto NA

quadprog NA

randomForest NA

RBGL NA

RColorBrewer NA

RCurl NA

reshape NA

Rgraphviz NA

rJava NA

rlecuyer NA

Rmpi NA

roxygen NA

Rsamtools "Biostrings, IRanges" RSQLite NA

rtracklayer "IRanges"

RUnit NA

scatterplot3d NA

sgeostat NA

ShortRead "IRanges, Biostrings" simpleaffy NA

sm NA

snow NA

sp NA

SparseM NA

splancs NA

splines NA

spp NA

stats NA

stats4 NA

stringr NA

survival NA

tcltk NA

TeachingDemos NA

testthat NA

tools NA

tripack NA

utils NA

vegan NA

violinmplot NA

vioplot NA

vsn NA

xlsx NA

xlsxjars NA

XML NA

xtable NA

Suggests

affy "tkWidgets (>= 1.19.0), affydata"

affydata "hgu95av2cdf, hgu133acdf"

affyio NA

affyPLM "affydata"

affyQCReport "tkWidgets (>= 1.5.23), affydata (>= 1.4.1)"

alphahull NA

annaffy "hgu95av2.db, multtest, tcltk"

annotate "Biobase, hgu95av2.db, genefilter, Biostrings (>= 2.4.4),\nrae230a.db, rae230aprobe, tkWidgets, XML (>= 0.92-2), GO.db,\norg.Hs.eg.db, org.Mm.eg.db, hom.Hs.inp.db"

AnnotationDbi "DBI (>= 0.2-4), RSQLite (>= 0.6-4), hgu95av2.db, GO.db,\nhuman.db0, hgu95av2cdf, affy, KEGG.db"

ape "gee"

base NA

Biobase "tools, tkWidgets, ALL"

biomaRt "annotate"

Biostrings "BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>=\n1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11),\ndrosophila2probe, hgu95av2probe, GenomicFeatures (>= 0.1.3),\nhgu95av2cdf, affy, affydata (>= 1.11.5), RUnit" bitops NA

boot "survival"

BSgenome "RUnit, BSgenome.Celegans.UCSC.ce2 (>= 1.3.11),\nBSgenome.Hsapiens.UCSC.hg19 (>= 1.3.11),\nSNPlocs.Hsapiens.dbSNP.20100427, hgu95av2probe, Biobase"

caTools "MASS, rpart"

cluster NA

codetools NA

colorspace "KernSmooth, MASS, kernlab, mvtnorm, vcd"

corpcor ""

datasets NA

DBI NA

devtools "testthat, roxygen, RCurl, profr"

digest NA

DynDoc NA

evaluate NA

gaggle NA

gcrma "affydata, tools, splines, hgu95av2cdf, hgu95av2probe"

gdata NA

gee "MASS"

geneplotter "Biobase (>= 2.5.5), Rgraphviz, annotate, fibroEset,\nhgu95av2.db, hu6800.db, hgu133a.db"

GenomicRanges "RUnit, BSgenome, GenomicFeatures, Rsamtools,\nEatonEtAlChIPseq, leeBamViews, org.Sc.sgd.db,\nBSgenome.Scerevisiae.UCSC.sacCer2"

getopt "testthat"

ggplot2 "quantreg, Hmisc, mapproj, maps, hexbin, gpclib, maptools"

GO.db NA

gplots "gtools"

graph "SparseM (>= 0.36), XML, RBGL, RUnit"

graphics NA

grDevices NA

grid "lattice"

gtools NA

hgu95av2.db "annotate"

Hmisc "lattice, grid, nnet, foreign, chron, acepack, TeachingDemos,\nDesign, cluster, mice, subselect"

hwriter NA

IRanges "RUnit"

iterators "foreach"

itertools "foreach"

KEGG.db NA

klaR "scatterplot3d (>= 0.3-22), som, mlbench, rpart, e1071,\ncombinat"

lars NA

lattice "grid, KernSmooth, MASS"

limma "affy, MASS, org.Hs.eg.db, splines, statmod (>= 1.2.2), vsn"

marray "tkWidgets"

MASS "lattice, nlme, nnet, survival"

Matrix NA

MeDiChI "zoo (>= 1.3-1), lattice, multicore (>= 0.1-3), doMC (>=\n1.2.0)"

methods NA

multtest "snow"

mutatr NA

nlme "Hmisc"

nws NA

optparse NA

org.Hs.eg.db "annotate"

permute "vegan, testthat (>= 0.5)"

plotrix NA

plyr "abind, testthat (>= 0.2), tcltk, foreach"

preprocessCore NA

profr "ggplot2"

proto "graph, Rgraphviz"

quadprog NA

randomForest "RColorBrewer"

RBGL "Rgraphviz"

RColorBrewer NA

RCurl "Rcompression, XML"

reshape NA

Rgraphviz NA

rJava NA

rlecuyer NA

Rmpi "rsprng, rlecuyer"

roxygen "Rgraphviz (>= 1.19.2), tools (>= 2.9.1)"

Rsamtools "ShortRead, GenomicFeatures, RUnit, KEGG.db"

RSQLite "RUnit (>= 0.4.22)"

rtracklayer "humanStemCell, microRNA (>= 1.1.1), genefilter, limma,\norg.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg19"

RUnit NA

scatterplot3d NA

sgeostat NA

ShortRead "biomaRt, RUnit"

simpleaffy NA

sm "rpanel, tkrplot, rgl, misc3d, akima, gam"

snow "Rmpi,rpvm,rlecuyer,rsprng,nws"

sp "lattice, RColorBrewer, rgdal, rgeos (>= 0.1-8)"

SparseM NA

splancs NA

splines NA

spp NA

stats NA

stats4 NA

stringr "testthat (>= 0.3)"

survival NA

tcltk NA

TeachingDemos "tkrplot, lattice, MASS, rgl, sgeostat, mapproj, tcltk,\ntcltk2, R2wd, EBImage, png"

testthat NA

tools NA

tripack NA

utils NA

vegan "MASS, mgcv, lattice, cluster, scatterplot3d, rgl, tcltk"

violinmplot NA

vioplot NA

vsn "affydata, hgu95av2cdf"

xlsx NA

xlsxjars NA

XML "bitops"

xtable NA

Enhances OS_type affy NA NA

affydata NA NA

affyio NA NA

affyPLM NA NA

affyQCReport NA NA

alphahull NA NA

annaffy NA NA

annotate NA NA

AnnotationDbi NA NA

ape NA NA

base NA NA

Biobase NA NA

biomaRt NA NA

Biostrings "Rmpi" NA

bitops NA NA

boot NA NA

BSgenome NA NA

caTools NA NA

cluster "MASS" NA

codetools NA NA

colorspace NA NA

corpcor NA NA

datasets NA NA

DBI NA NA

devtools NA NA

digest NA NA

DynDoc NA NA

evaluate NA NA

gaggle NA NA

gcrma NA NA

gdata NA NA

gee NA NA

geneplotter NA NA

GenomicRanges NA NA

getopt NA NA

ggplot2 NA NA

GO.db NA NA

gplots NA NA

graph NA NA

graphics NA NA

grDevices NA NA

grid NA NA

gtools NA NA

hgu95av2.db NA NA

Hmisc NA NA

hwriter NA NA

IRanges NA NA

iterators NA NA

itertools "foreach, iterators" NA

KEGG.db NA NA

klaR NA NA

lars NA NA

lattice "chron" NA

limma NA NA

marray NA NA

MASS "AER, FrF2, GPArotation" NA

Matrix "MatrixModels, graph, SparseM, sfsmisc" NA

MeDiChI NA NA

methods NA NA

multtest NA NA

mutatr NA NA

nlme NA NA

nws NA NA

optparse NA NA

org.Hs.eg.db NA NA

permute NA NA

plotrix NA NA

plyr NA NA

preprocessCore NA NA

profr NA NA

proto NA NA

quadprog NA NA

randomForest NA NA

RBGL NA NA

RColorBrewer NA NA

RCurl NA NA

reshape NA NA

Rgraphviz NA NA

rJava NA NA

rlecuyer NA NA

Rmpi NA NA

roxygen NA NA

Rsamtools NA NA

RSQLite NA NA

rtracklayer NA NA

RUnit NA NA

scatterplot3d NA NA

sgeostat NA NA

ShortRead "Rmpi, multicore" NA

simpleaffy NA NA

sm NA NA

snow NA NA

sp NA NA

SparseM NA NA

splancs NA NA

splines NA NA

spp NA NA

stats NA NA

stats4 NA NA

stringr NA NA

survival NA NA

tcltk NA NA

TeachingDemos "maptools, qcc" NA

testthat NA NA

tools NA NA

tripack NA NA

utils NA NA

vegan NA NA

violinmplot NA NA

vioplot NA NA

vsn NA NA

xlsx NA NA

xlsxjars NA NA

XML NA NA

xtable NA NA

License Built

affy "LGPL (>= 2.0)" "2.12.0" affydata "GPL (>= 2)" "2.12.1" affyio "LGPL (>= 2)" "2.12.0" affyPLM "GPL (>= 2)" "2.12.2" affyQCReport "LGPL (>= 2)" "2.12.0" alphahull "file LICENSE" "2.12.0" annaffy "LGPL" "2.12.0" annotate "Artistic-2.0" "2.12.2" AnnotationDbi "Artistic-2.0" "2.12.0" ape "GPL (>= 2)" "2.12.2" base "Part of R 2.12.2" "2.12.2" Biobase "Artistic-2.0" "2.12.0" biomaRt "Artistic-2.0" "2.12.0" Biostrings "Artistic-2.0" "2.12.2" bitops "GPL version 2 or later" "2.12.0" boot "Unlimited" "2.12.2" BSgenome "Artistic-2.0" "2.12.1" caTools "GPL-3" "2.12.1" cluster "GPL (>= 2)" "2.12.2" codetools "GPL" "2.12.2" colorspace "BSD" "2.12.0" corpcor "GPL (>= 3)" "2.12.0" datasets "Part of R 2.12.2" "2.12.2" DBI "LGPL (>= 2)" "2.12.0" devtools "MIT" "2.12.2" digest "GPL-2" "2.12.0" DynDoc "Artistic-2.0" "2.12.0" evaluate "GPL" "2.12.0" gaggle "GPL version 2 or newer" "2.12.2" gcrma "LGPL" "2.12.0" gdata "GPL-2" "2.12.0" gee "GPL-2" "2.12.2" geneplotter "Artistic-2.0" "2.12.0" GenomicRanges "Artistic-2.0" "2.12.1" getopt "GPL (>= 2)" "2.12.2" ggplot2 "GPL-2" "2.12.1" GO.db "Artistic-2.0" "2.12.1" gplots "GPL-2" "2.12.0" graph "Artistic-2.0" "2.12.0" graphics "Part of R 2.12.2" "2.12.2" grDevices "Part of R 2.12.2" "2.12.2" grid "Part of R 2.12.2" "2.12.2" gtools "LGPL-2.1" "2.12.0" hgu95av2.db "Artistic-2.0" "2.12.1" Hmisc "GPL (>= 2)" "2.12.0" hwriter "LGPL-2.1" "2.12.0" IRanges "Artistic-2.0" "2.12.1" iterators "Apache License (== 2.0)" "2.12.0" itertools "GPL-2" "2.12.0" KEGG.db "file LICENSE" "2.12.1" klaR "GPL-2" "2.12.2" lars "GPL version 2 or newer" "2.12.0" lattice "GPL (>= 2)" "2.12.1" limma "LGPL" "2.12.0" marray "LGPL" "2.12.0" MASS "GPL-2 | GPL-3" "2.12.2" Matrix "GPL (>= 2)" "2.12.2" MeDiChI "GPL-2" "2.12.0" methods "Part of R 2.12.2" "2.12.2" multtest "LGPL" "2.12.0" mutatr "GPL" "2.12.0" nlme "GPL (>= 2)" "2.12.2" nws "GPL (>= 2)" "2.12.0" optparse "GPL (>= 2)" "2.12.0" org.Hs.eg.db "Artistic-2.0" "2.12.1" permute "GPL-2" "2.12.2" plotrix "GPL (>= 2)" "2.12.2" plyr "MIT" "2.12.2" preprocessCore "LGPL (>= 2)" "2.12.0" profr "MIT" "2.12.1" proto "GPL-2" "2.12.2" quadprog "GPL (>= 2)" "2.12.0" randomForest "GPL (>= 2)" "2.12.1" RBGL "Artistic-2.0" "2.12.0" RColorBrewer "Apache License 2.0" "2.12.2" RCurl "BSD" "2.12.2" reshape "MIT" "2.12.1" Rgraphviz "Artistic-2.0" "2.12.0" rJava "GPL-2" "2.12.1" rlecuyer "GPL (>= 2)" "2.12.0" Rmpi "GPL (>= 2)" "2.12.0" roxygen "GPL (>= 2)" "2.12.0" Rsamtools "Artistic-2.0" "2.12.1" RSQLite "LGPL (>= 2)" "2.12.0" rtracklayer "Artistic-2.0" "2.12.0" RUnit "GPL-2" "2.12.0" scatterplot3d "GPL-2" "2.12.2" sgeostat "file LICENSE" "2.12.0" ShortRead "Artistic-2.0" "2.12.0" simpleaffy "GPL (>= 2)" "2.12.0" sm "GPL-2" "2.12.0" snow "GPL" "2.12.0" sp "GPL (>= 2)" "2.12.2" SparseM "file LICENSE" "2.12.0" splancs "GPL (>= 2)" "2.12.2" splines "Part of R 2.12.2" "2.12.2" spp "GPL-2" "2.12.2" stats "Part of R 2.12.2" "2.12.2" stats4 "Part of R 2.12.2" "2.12.2" stringr "GPL-2" "2.12.2" survival "GPL (>= 2)" "2.12.2" tcltk "Part of R 2.12.2" "2.12.2" TeachingDemos "Artistic-2.0" "2.12.0" testthat "GPL" "2.12.2" tools "Part of R 2.12.2" "2.12.2" tripack "file LICENSE" "2.12.0" utils "Part of R 2.12.2" "2.12.2" vegan "GPL-2" "2.12.2" violinmplot "GPL-2" "2.12.0" vioplot "BSD" "2.12.0" vsn "Artistic-2.0" "2.12.0" xlsx "GPL-3" "2.12.0" xlsxjars "GPL-3" "2.12.2" XML "BSD" "2.12.0" xtable "GPL (>= 2)" "2.12.0"

— Reply to this email directly or view it on GitHubhttps://github.com/MG-RAST/matR/issues/59#issuecomment-41836232 .

Kevin

---

Kevin P. Keegan, PhD

Argonne National Laboratory (work) 9700 South Cass Avenue Bldg. 240, Rm. 4.G.14 Argonne, IL 60439 (630)252-3703 kkeegan@anl.gov

kevin.p.keegan@gmail.com (home) (847)733-1079

[wltrimbl]

The dependencies and install procedure have changed since this issue came up; it is unlikely the same problem persists.