Last data update: 2014.03.03
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ChemmineR
Package: ChemmineR
Type: Package
Title: Cheminformatics Toolkit for R
Version: 2.24.2
Date: 2016-01-04
Author: Y. Eddie Cao, Kevin Horan, Tyler Backman, Thomas Girke
Maintainer: Thomas Girke <thomas.girke@ucr.edu>
Description: ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.
License: Artistic-2.0
Depends: R (>= 2.10.0), methods
biocViews: Cheminformatics, BiomedicalInformatics, Pharmacogenetics,
Pharmacogenomics, MicrotitrePlateAssay, CellBasedAssays,
Visualization, Infrastructure, DataImport, Clustering,
Proteomics
Imports: rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp
(>= 0.11.0), ggplot2
Suggests: RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL,
BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineOB (>=
1.3.8), ChemmineDrugs, grid, gridExtra, png
Enhances: ChemmineOB
URL: https://github.com/girke-lab/ChemmineR
VignetteBuilder: knitr
LinkingTo: Rcpp, BH
SystemRequirements: GNU make
NeedsCompilation: yes
Packaged: 2016-05-16 01:59:58 UTC; biocbuild
● BiocViews: BiomedicalInformatics, CellBasedAssays, Cheminformatics, Clustering, DataImport, Infrastructure, MicrotitrePlateAssay, Pharmacogenetics, Pharmacogenomics, Proteomics, Visualization
●
17 images,
115 functions,
6 datasets
●
Reverse Depends: 5
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'ChemmineR' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -c DisjointSets.cpp -o DisjointSets.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -c cluster.cc -o cluster.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -c cstrsplit.cc -o cstrsplit.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -c desc.cc -o desc.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -c fingerprints.cc -o fingerprints.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -c formats.cc -o formats.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -c molecule.cc -o molecule.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -c r_wrap.cc -o r_wrap.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -c script.cc -o script.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -c similarity.cc -o similarity.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o ChemmineR.so DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/ChemmineR/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'as.matrix' from package 'base' in package 'ChemmineR'
Creating a generic function for 'plot' from package 'graphics' in package 'ChemmineR'
Creating a generic function for 'print' from package 'base' in package 'ChemmineR'
** help
*** installing help indices
converting help for package 'ChemmineR'
finding HTML links ... done
AP-class html
APset-class html
ExtSDF-class html
FP-class html
FPset-class html
SDF-class html
SDF2apcmp html
SDFset-class html
SDFset2SDF html
SDFset2list html
SDFstr-class html
SMI-class html
SMIset-class html
addDescriptorType html
addNewFeatures html
ap html
apfp html
apset html
apset2descdb html
atomblock html
atomcount html
atomprop html
atomsubset html
batchByIndex html
bondblock html
bonds html
browseJob html
bufferLines html
bufferResultSet html
byCluster html
canonicalNumbering html
canonicalize html
cid html
cluster.sizestat html
cluster.visualize html
cmp.cluster html
cmp.duplicated html
cmp.parse html
cmp.parse1 html
cmp.search html
cmp.similarity html
conMA html
connections html
datablock html
datablock2ma html
db.explain html
db.subset html
dbTransaction html
desc2fp html
draw_sdf html
exactMassOB html
findCompounds html
findCompoundsByName html
fingerprintOB html
fold html
foldCount html
fp2bit html
fpSim html
fptype html
fromNNMatrix html
genAPDescriptors html
genParameters html
generate3DCoords html
getAllCompoundIds html
getCompoundFeatures html
getCompoundNames html
getCompounds html
getIds html
grepSDFset html
groups html
header html
initDb html
jarvisPatrick html
jarvisPatrick_c html
jobToken-class html
launchCMTool html
listCMTools html
listFeatures html
loadSdf html
makeUnique html
maximallyDissimilar html
nearestNeighbors html
numBits html
obmol html
parBatchByIndex html
plotStruc html
propOB html
pubchemFPencoding html
read.AP html
read.SDFindex html
read.SDFset html
read.SDFstr html
read.SMIset html
regenerateCoords html
result html
rings html
sdf.subset html
sdf.visualize html
sdf2ap html
sdf2list html
sdf2smiles html
sdf2str html
sdfStream html
sdfid html
sdfsample html
sdfstr2list html
searchSim html
searchString html
selectInBatches html
setPriorities html
smartsSearchOB html
smiles2sdf html
smisample html
status html
toolDetails html
trimNeighbors html
validSDF html
view html
write.SDF html
write.SDFsplit html
write.SMI html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ChemmineR)
Making 'packages.html' ... done
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