From 7a1e59eb1fc5900a8be04b2d375cb355d074772f Mon Sep 17 00:00:00 2001 From: zach charlop-powers Date: Fri, 6 Mar 2020 20:41:59 -0500 Subject: [PATCH 1/9] Update stale URLs --- rcdk/R/formula.R | 2 +- rcdk/R/rcdk.R | 2 +- rcdk/R/smiles.R | 4 ++-- rcdk/man/compare.isotope.pattern.Rd | 2 +- rcdk/man/get.chem.object.builder.Rd | 2 +- rcdk/man/smiles.flavors.Rd | 4 ++-- 6 files changed, 8 insertions(+), 8 deletions(-) diff --git a/rcdk/R/formula.R b/rcdk/R/formula.R index 7eb0e93e24..7f96c3a14f 100644 --- a/rcdk/R/formula.R +++ b/rcdk/R/formula.R @@ -560,7 +560,7 @@ get.isotope.pattern.generator <- function(minAbundance = NULL) { #' @return A numeric value between 0 and 1 indicating the similarity between the two patterns #' @seealso \code{\link{get.isotope.pattern.similarity}} #' @export -#' @references \url{http://cdk.github.io/cdk/2.0/docs/api/org/openscience/cdk/formula/IsotopePatternSimilarity.html} +#' @references \url{http://cdk.github.io/cdk/2.3/docs/api/org/openscience/cdk/formula/IsotopePatternSimilarity.html} #' @author Miguel Rojas Cherto compare.isotope.pattern <- function(iso1, iso2, ips = NULL) { cls <- unique(c(class(iso1), class(iso2))) diff --git a/rcdk/R/rcdk.R b/rcdk/R/rcdk.R index aefe4f142d..2f076d9a3f 100644 --- a/rcdk/R/rcdk.R +++ b/rcdk/R/rcdk.R @@ -14,7 +14,7 @@ #' Note that this is a static object that is created at package load time, #' and the same instance is returned whenever this function is called. #' -#' @return An instance of \href{http://cdk.github.io/cdk/2.2/docs/api/org/openscience/cdk/silent/SilentChemObjectBuilder.html}{SilentChemObjectBuilder} +#' @return An instance of \href{http://cdk.github.io/cdk/2.3/docs/api/org/openscience/cdk/silent/SilentChemObjectBuilder.html}{SilentChemObjectBuilder} #' @export #' @author Rajarshi Guha (\email{rajarshi.guha@@gmail.com}) get.chem.object.builder <- function() { diff --git a/rcdk/R/smiles.R b/rcdk/R/smiles.R index b52b91520a..7d0bd4a2cc 100644 --- a/rcdk/R/smiles.R +++ b/rcdk/R/smiles.R @@ -6,7 +6,7 @@ #' format. Each 'flavor' is represented by an integer and multiple #' customizations are bitwise OR'ed. This method accepts the names of one or #' more customizations and returns the bitwise OR of them. -#' See \href{https://cdk.github.io/cdk/2.0/docs/api/index.html?org/openscience/cdk/smiles/SmiFlavor.html}{CDK documentation} +#' See \href{https://cdk.github.io/cdk/2.3/docs/api/index.html?org/openscience/cdk/smiles/SmiFlavor.html}{CDK documentation} #' for the list of flavors and what they mean. #' #' @param flavors A character vector of flavors. The default is \code{Generic} @@ -42,7 +42,7 @@ #' @md #' @return A numeric representing the bitwise `OR`` of the specified flavors #' @seealso \code{\link{get.smiles}} -#' @references \href{https://cdk.github.io/cdk/2.0/docs/api/index.html?org/openscience/cdk/smiles/SmiFlavor.html}{CDK documentation} +#' @references \href{https://cdk.github.io/cdk/2.3/docs/api/index.html?org/openscience/cdk/smiles/SmiFlavor.html}{CDK documentation} #' @examples #' m <- parse.smiles('C1C=CCC1N(C)c1ccccc1')[[1]] #' get.smiles(m) diff --git a/rcdk/man/compare.isotope.pattern.Rd b/rcdk/man/compare.isotope.pattern.Rd index dcc672e73e..a31a2fb8a7 100644 --- a/rcdk/man/compare.isotope.pattern.Rd +++ b/rcdk/man/compare.isotope.pattern.Rd @@ -20,7 +20,7 @@ A numeric value between 0 and 1 indicating the similarity between the two patter Computes a similarity score between two different isotope abundance patterns. } \references{ -\url{http://cdk.github.io/cdk/2.0/docs/api/org/openscience/cdk/formula/IsotopePatternSimilarity.html} +\url{http://cdk.github.io/cdk/2.3/docs/api/org/openscience/cdk/formula/IsotopePatternSimilarity.html} } \seealso{ \code{\link{get.isotope.pattern.similarity}} diff --git a/rcdk/man/get.chem.object.builder.Rd b/rcdk/man/get.chem.object.builder.Rd index 2fa0cd5fa0..72e5a7e089 100644 --- a/rcdk/man/get.chem.object.builder.Rd +++ b/rcdk/man/get.chem.object.builder.Rd @@ -7,7 +7,7 @@ get.chem.object.builder() } \value{ -An instance of \href{http://cdk.github.io/cdk/2.2/docs/api/org/openscience/cdk/silent/SilentChemObjectBuilder.html}{SilentChemObjectBuilder} +An instance of \href{http://cdk.github.io/cdk/2.3/docs/api/org/openscience/cdk/silent/SilentChemObjectBuilder.html}{SilentChemObjectBuilder} } \description{ The CDK employs a builder design pattern to construct diff --git a/rcdk/man/smiles.flavors.Rd b/rcdk/man/smiles.flavors.Rd index b2c8f9390e..9621a33a09 100644 --- a/rcdk/man/smiles.flavors.Rd +++ b/rcdk/man/smiles.flavors.Rd @@ -50,7 +50,7 @@ the use of lower case symbols for aromatic compounds to the use of the ChemAxon format. Each 'flavor' is represented by an integer and multiple customizations are bitwise OR'ed. This method accepts the names of one or more customizations and returns the bitwise OR of them. -See \href{https://cdk.github.io/cdk/2.0/docs/api/index.html?org/openscience/cdk/smiles/SmiFlavor.html}{CDK documentation} +See \href{https://cdk.github.io/cdk/2.3/docs/api/index.html?org/openscience/cdk/smiles/SmiFlavor.html}{CDK documentation} for the list of flavors and what they mean. } \examples{ @@ -64,7 +64,7 @@ get.smiles(m,flavor = smiles.flavors(c("CxSmiles","UseAromaticSymbols"))) } \references{ -\href{https://cdk.github.io/cdk/2.0/docs/api/index.html?org/openscience/cdk/smiles/SmiFlavor.html}{CDK documentation} +\href{https://cdk.github.io/cdk/2.3/docs/api/index.html?org/openscience/cdk/smiles/SmiFlavor.html}{CDK documentation} } \seealso{ \code{\link{get.smiles}} From eb690e95d111515702da88831747d8e7fb1589d8 Mon Sep 17 00:00:00 2001 From: zach charlop-powers Date: Fri, 6 Mar 2020 20:44:03 -0500 Subject: [PATCH 2/9] update date --- rcdk/DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rcdk/DESCRIPTION b/rcdk/DESCRIPTION index 8d3bffacef..d8532736ec 100644 --- a/rcdk/DESCRIPTION +++ b/rcdk/DESCRIPTION @@ -1,6 +1,6 @@ Package: rcdk Version: 3.5.0 -Date: 2019-01-21 +Date: 2019-03-06 Title: Interface to the 'CDK' Libraries Authors@R: c(person('Rajarshi', 'Guha', role=c('aut',"cph"), email='rajarshi.guha@gmail.com'), person('Zachary', 'Charlop-Powers', role=c('cre'), email='zach.charlop.powers@gmail.com'), From 6e489884a60e2b537f5e0fbb21d78b0f5c41927c Mon Sep 17 00:00:00 2001 From: zach charlop-powers Date: Fri, 6 Mar 2020 20:52:37 -0500 Subject: [PATCH 3/9] fix another stale link --- rcdk/R/smiles.R | 2 +- rcdk/man/smiles.flavors.Rd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/rcdk/R/smiles.R b/rcdk/R/smiles.R index 7d0bd4a2cc..40b41f8447 100644 --- a/rcdk/R/smiles.R +++ b/rcdk/R/smiles.R @@ -2,7 +2,7 @@ #' #' The CDK supports a variety of customizations for SMILES generation including #' the use of lower case symbols for aromatic compounds to the use of the ChemAxon -#' \href{https://www.chemaxon.com/marvin-archive/latest/help/formats/cxsmiles-doc.html}{CxSmiles} +#' \href{http://www.chemeddl.org/tools/marvin/help/formats/cxsmiles-doc.html}{CxSmiles} #' format. Each 'flavor' is represented by an integer and multiple #' customizations are bitwise OR'ed. This method accepts the names of one or #' more customizations and returns the bitwise OR of them. diff --git a/rcdk/man/smiles.flavors.Rd b/rcdk/man/smiles.flavors.Rd index 9621a33a09..d45127ebd5 100644 --- a/rcdk/man/smiles.flavors.Rd +++ b/rcdk/man/smiles.flavors.Rd @@ -46,7 +46,7 @@ A numeric representing the bitwise `OR`` of the specified flavors \description{ The CDK supports a variety of customizations for SMILES generation including the use of lower case symbols for aromatic compounds to the use of the ChemAxon -\href{https://www.chemaxon.com/marvin-archive/latest/help/formats/cxsmiles-doc.html}{CxSmiles} +\href{http://www.chemeddl.org/tools/marvin/help/formats/cxsmiles-doc.html}{CxSmiles} format. Each 'flavor' is represented by an integer and multiple customizations are bitwise OR'ed. This method accepts the names of one or more customizations and returns the bitwise OR of them. From 3a9f23803d0f1dadf518a6110d75dce14a07da53 Mon Sep 17 00:00:00 2001 From: zach charlop-powers Date: Sat, 7 Mar 2020 14:19:09 -0500 Subject: [PATCH 4/9] update date --- rcdk/DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rcdk/DESCRIPTION b/rcdk/DESCRIPTION index d8532736ec..64b400cd77 100644 --- a/rcdk/DESCRIPTION +++ b/rcdk/DESCRIPTION @@ -1,6 +1,6 @@ Package: rcdk Version: 3.5.0 -Date: 2019-03-06 +Date: 2020-03-06 Title: Interface to the 'CDK' Libraries Authors@R: c(person('Rajarshi', 'Guha', role=c('aut',"cph"), email='rajarshi.guha@gmail.com'), person('Zachary', 'Charlop-Powers', role=c('cre'), email='zach.charlop.powers@gmail.com'), From e2829a8405d466928df64407ea168c4ea073ff98 Mon Sep 17 00:00:00 2001 From: zach charlop-powers Date: Sat, 7 Mar 2020 14:23:39 -0500 Subject: [PATCH 5/9] fix a few dead links --- rcdk/vignettes/molform.Rmd | 2 +- rcdk/vignettes/using-rcdk.Rmd | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/rcdk/vignettes/molform.Rmd b/rcdk/vignettes/molform.Rmd index 3dc596cecc..9685bc6f13 100644 --- a/rcdk/vignettes/molform.Rmd +++ b/rcdk/vignettes/molform.Rmd @@ -44,7 +44,7 @@ formula <- get.mol2formula(molecule,charge=0) Note that the above formula object is a `CDKFormula-class`. This class contains some attributes that defines a molecular formula. For example, the mass, the charge, the isotopes, the character representation of the -molecular formula and the [IMolecularFormula](https://cdk.github.io/cdk/2.0/docs/api/org/openscience/cdk/interfaces/IMolecularFormula.html) `jobjRef` object. +molecular formula and the [IMolecularFormula](https://cdk.github.io/cdk/2.3/docs/api/org/openscience/cdk/interfaces/IMolecularFormula.html) `jobjRef` object. The molecular mass, charge and string representation for this formula are given by ```{r} diff --git a/rcdk/vignettes/using-rcdk.Rmd b/rcdk/vignettes/using-rcdk.Rmd index 79c8bcee69..c41dac2c69 100644 --- a/rcdk/vignettes/using-rcdk.Rmd +++ b/rcdk/vignettes/using-rcdk.Rmd @@ -26,7 +26,7 @@ chemical information with the R environment. The [CDK](https://cdk.github.io) is a Java library for cheminformatics that supports a wide variety of cheminformatics functionality ranging from reading molecular file formats, performing ring perception and armaticity detection to fingerprint -generation and molecular descriptors. The CDK website provides links to useful documentation as well as complete [Javadocs](https://cdk.github.io/cdk/2.0/docs/api/index.html?overview-summary.html) +generation and molecular descriptors. The CDK website provides links to useful documentation as well as complete [Javadocs](https://cdk.github.io/cdk/2.3/docs/api/index.html?overview-summary.html) ## Getting started @@ -136,7 +136,7 @@ unlist(lapply(mols, get.smiles)) ``` - The [CDK](https://cdk.github.io) supports a number of _flavors_ when generating SMILES. For example, you can generate a SMILES with or without chirality information or generate SMILES in [Kekule form](https://www.chemguide.co.uk/basicorg/bonding/benzene1.html). The `smiles.flavors` generates an object that represents the various flavors desired for SMILES output. See the [SmiFlavor javadocs](https://cdk.github.io/cdk/2.0/docs/api/index.html?org/openscience/cdk/smiles/SmiFlavor.html) for the full list of possible flavors. Example usage is + The [CDK](https://cdk.github.io) supports a number of _flavors_ when generating SMILES. For example, you can generate a SMILES with or without chirality information or generate SMILES in [Kekule form](https://www.chemguide.co.uk/basicorg/bonding/benzene1.html). The `smiles.flavors` generates an object that represents the various flavors desired for SMILES output. See the [SmiFlavor javadocs](https://cdk.github.io/cdk/2.3/docs/api/index.html?org/openscience/cdk/smiles/SmiFlavor.html) for the full list of possible flavors. Example usage is ```{r} smiles <- c('CCC', 'c1ccccc1', 'CCc1ccccc1CC(C)(C)CC(=O)NC') @@ -145,7 +145,7 @@ get.smiles(mols[[3]], smiles.flavors(c('UseAromaticSymbols'))) get.smiles(mols[[3]], smiles.flavors(c('Generic','CxSmiles'))) ``` -Using the [CxSmiles](https://www.chemaxon.com/marvin-archive/latest/help/formats/cxsmiles-doc.html) flavors allows the user to encode a variety of information in the SMILES string, such as 2D or 3D coordinates. +Using the [CxSmiles](http://www.chemeddl.org/tools/marvin/help/formats/cxsmiles-doc.html) flavors allows the user to encode a variety of information in the SMILES string, such as 2D or 3D coordinates. ```{r} m <- parse.smiles('CCC')[[1]] From 9570e76891417229885b1409270cf16ed2742902 Mon Sep 17 00:00:00 2001 From: zach charlop-powers Date: Sat, 7 Mar 2020 15:03:17 -0500 Subject: [PATCH 6/9] require 2.3 libs --- rcdk/DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rcdk/DESCRIPTION b/rcdk/DESCRIPTION index 64b400cd77..296360f7c8 100644 --- a/rcdk/DESCRIPTION +++ b/rcdk/DESCRIPTION @@ -6,7 +6,7 @@ Authors@R: c(person('Rajarshi', 'Guha', role=c('aut',"cph"), email='rajarshi.guh person('Zachary', 'Charlop-Powers', role=c('cre'), email='zach.charlop.powers@gmail.com'), person('Emma', 'Schymanski', role=c('ctb'), email='schymane@gmail.com')) Depends: - rcdklibs (>= 2.0) + rcdklibs (>= 2.3) Imports: fingerprint, rJava, From fa4f947c5cf111bfb3d32762d27ac6e1daecec62 Mon Sep 17 00:00:00 2001 From: zach charlop-powers Date: Mon, 9 Mar 2020 11:35:04 -0400 Subject: [PATCH 7/9] fix test for matrix which must now use 'inherits' --- rcdk/inst/unitTests/runit.match.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rcdk/inst/unitTests/runit.match.R b/rcdk/inst/unitTests/runit.match.R index 51419f89f8..26fcc47edb 100644 --- a/rcdk/inst/unitTests/runit.match.R +++ b/rcdk/inst/unitTests/runit.match.R @@ -64,7 +64,7 @@ test.mcs2 <- function() { lapply(mols, do.aromaticity) lapply(mols, do.typing) mcs <- get.mcs(mols[[1]], mols[[2]], FALSE) - checkEquals("matrix", class(mcs)) + checkTrue(inherits(mcs, "matrix")) checkEquals(9, nrow(mcs)) checkEquals(2, ncol(mcs)) } From b0c357388ce75424b61466a26106145d1f4d8749 Mon Sep 17 00:00:00 2001 From: zach charlop-powers Date: Mon, 9 Mar 2020 11:40:39 -0400 Subject: [PATCH 8/9] rebuild jarfile --- rcdk/inst/cont/rcdk.jar | Bin 50068 -> 50068 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/rcdk/inst/cont/rcdk.jar b/rcdk/inst/cont/rcdk.jar index bf252f59b95a098f3c5568d44d1faf90fd14c665..edfd90b74b8830dfce0bf568def5770b813acaf3 100644 GIT binary patch delta 851 zcmYk3T}V@57{}jp&OF-@mhEORhHWre*_aZ|Qt%^T;nJ}60bR5VBs6JKU=g8_WnzM^ zk5}lTC1iFXt*{Q;+0MRK5QaBi1`!Hf=uLD}D=(t6|9gba&F}wzp8xwk&pBsqN|>7x z%)uVPP)&%5kaB3~k$Io+OGEPv@X-Nm)m1=ubM;^==LN%D6S&A7043f*%Uq4F8}y8W zuJ=~aKHg%{?g*0q9vgkzWu*^FB8~FZm9)IXw;CZfrI%F@4{P@F5UOR{2BCQFu}u5H zfPl*Mp<5D!bmW2o;pNXRkzJX%Mc5s7w8Nc3;sDzDymu~_+u-SUhh zWSb|Xb0;QyXL4-P_t}MAm`$T55n_H}L&Si)g=yy{?bM)w5ckd(lVeM_*&+?G4Gy_A zqi^fAHo>GV)1v3xa_Ei1CRmr3*@2aJn$UhV9g8`%0S^NBX_ zYvL&ARyx5~ik(g>E?u|l89Oy5_e1-VesDB-9Q>5*13jtJ;GI+eTuq$-_o%195ta2< z)RXYF=@2-UX8pDFIrzp5<7_4fzn(b*9?mjGvKQfhX4$#!+%UYFy8-(0*TGo+8t5v7 j!N&!5?~lS+`0gU(Vv+6hyV#HV`4YSTLumls`+o2r%nN2T delta 851 zcmYk3T}V@57{}jp&fIo{WxE-Su{M~jY)lDfDfp4FaB0~30538F2`!owSVU-KnV6vK z;}yDS37K6;E3C1d?d*FAVtC_a5TVe8-b6QHc@b^@XF})Z_y0f7|9zk5oHIKq%}z=N zf0v}GWK7SPU8#R+I3!t%Xq=WxZp8*{SC_!|3pHS~;06Oi1Gpd@0cFv~cZ904t}SP5 ze51R9_lZVh@eV)x?=kZa9VY&`pyeU4vXqW2ip@HRE%{9a#FMInB7|z(HA5(_hm>ip z_erQs9la|<$j2{fAg*~E(BiKn(e^75&H; z+T#0|mA24~50Ds|5GB0Oi#1a4yyY zev6#|ok~0SR Date: Mon, 9 Mar 2020 12:45:22 -0400 Subject: [PATCH 9/9] change DESCRIPTION --- rcdk/DESCRIPTION | 1 + 1 file changed, 1 insertion(+) diff --git a/rcdk/DESCRIPTION b/rcdk/DESCRIPTION index 296360f7c8..80361ea7ed 100644 --- a/rcdk/DESCRIPTION +++ b/rcdk/DESCRIPTION @@ -22,6 +22,7 @@ Suggests: SystemRequirements: Java JDK 8 or higher License: LGPL LazyLoad: yes +LazyData: true Description: Allows the user to access functionality in the 'CDK', a Java framework for chemoinformatics. This allows the user to load molecules, evaluate fingerprints, calculate molecular descriptors and so on.