BioC 3.4: CHECK report for ChemmineR on zin1
This page was generated on 2016-09-21 03:36:40 -0700 (Wed, 21 Sep 2016).
ChemmineR 2.25.5
Thomas Girke
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR | | Last Changed Rev: 119808 / Revision: 121152 | | Last Changed Date: 2016-08-01 09:07:37 -0700 (Mon, 01 Aug 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | ERROR | skipped | skipped | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
Summary
| Package: ChemmineR |
| Version: 2.25.5 |
| Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ChemmineR_2.25.5.tar.gz |
| StartedAt: 2016-09-20 04:17:25 -0700 (Tue, 20 Sep 2016) |
| EndedAt: 2016-09-20 04:19:08 -0700 (Tue, 20 Sep 2016) |
| EllapsedTime: 102.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ChemmineR.Rcheck |
| Warnings: 0 |
Command output
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###
### Running command:
###
### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ChemmineR_2.25.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/ChemmineR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChemmineR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChemmineR’ version ‘2.25.5’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ChemmineR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘ChemmineOB’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘ChemmineDrugs’ ‘ChemmineOB’ ‘RPostgreSQL’ ‘RSQLite’ ‘fmcsR’ ‘grid’
‘png’ ‘snow’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘BiocGenerics’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File ‘ChemmineR/R/sim.R’:
unlockBinding(".progress_bar_int_cnt", environment(.progress_bar))
.data.frame.to.str: no visible global function definition for
‘write.table’
.data.frame.to.str: no visible binding for global variable ‘string’
.parseV3000: no visible binding for global variable ‘AW’
.rings: no visible global function definition for ‘combn’
applyOptions: no visible global function definition for ‘convertFormat’
browseJob: no visible global function definition for ‘browseURL’
canonicalNumbering: no visible global function definition for
‘canonicalNumbering_OB’
canonicalNumberingOB: no visible global function definition for
‘canonicalNumbering_OB’
cluster.visualize: no visible global function definition for ‘rainbow’
cluster.visualize: no visible global function definition for ‘pdf’
cluster.visualize: no visible global function definition for
‘postscript’
cluster.visualize: no visible global function definition for ‘dev.off’
concatenate_plots: no visible binding for global variable ‘arrangeGrob’
desc2fp: no visible global function definition for ‘data’
draw_sdf: no visible global function definition for ‘rgb’
draw_sdf: no visible global function definition for ‘fmcs’
exactMassOB: no visible global function definition for ‘exactMass_OB’
fingerprintOB: no visible global function definition for
‘fingerprint_OB’
getCompoundFeatures : <anonymous>: no visible global function
definition for ‘write.table’
getCompounds: no visible global function definition for ‘str’
getDbConn: no visible global function definition for ‘error’
handle_raster: no visible global function definition for ‘readPNG’
handle_raster: no visible global function definition for ‘rasterGrob’
handle_segs: no visible binding for global variable ‘C1’
handle_segs: no visible binding for global variable ‘C2’
handle_segs: no visible binding for global variable ‘C1.1’
handle_segs: no visible binding for global variable ‘C2.1’
handle_text: no visible binding for global variable ‘C1’
handle_text: no visible binding for global variable ‘C2’
insertDef: no visible global function definition for
‘dbGetPreparedQuery’
insertDescriptor: no visible global function definition for
‘dbGetPreparedQuery’
insertDescriptorType: no visible global function definition for
‘dbGetPreparedQuery’
insertFeature: no visible global function definition for
‘dbGetPreparedQuery’
insertNamedDef: no visible global function definition for
‘dbGetPreparedQuery’
listCMTools: no visible global function definition for ‘read.table’
parBatchByIndex: no visible global function definition for
‘clusterExport’
parBatchByIndex: no visible global function definition for
‘clusterApplyLB’
postgresqlWriteTable: no visible global function definition for
‘postgresqlTableRef’
postgresqlWriteTable: no visible global function definition for
‘postgresqlQuoteId’
postgresqlWriteTable: no visible global function definition for
‘postgresqlpqExec’
postgresqlWriteTable: no visible global function definition for
‘postgresqlCopyInDataframe’
postgresqlWriteTable: no visible global function definition for
‘postgresqlgetResult’
propOB: no visible global function definition for ‘prop_OB’
read.AP: no visible global function definition for ‘read.delim’
sdf2OBMol: no visible global function definition for ‘forEachMol’
sdf2smiles: no visible global function definition for ‘convertFormat’
sdf2smilesOB: no visible global function definition for ‘convertFormat’
sdfStream: no visible global function definition for ‘write.table’
setPriorities: no visible global function definition for
‘clusterExport’
smartsSearchOB: no visible global function definition for
‘smartsSearch_OB’
smile2sdfFile: no visible global function definition for
‘convertFormatFile’
smiles2sdf: no visible global function definition for ‘convertFormat’
smiles2sdfOB: no visible global function definition for ‘convertFormat’
updatePriorities: no visible global function definition for
‘dbGetPreparedQuery’
write.SMI: no visible global function definition for ‘write.table’
Undefined global functions or variables:
AW C1 C1.1 C2 C2.1 arrangeGrob browseURL canonicalNumbering_OB
clusterApplyLB clusterExport combn convertFormat convertFormatFile
data dbGetPreparedQuery dev.off error exactMass_OB fingerprint_OB
fmcs forEachMol pdf postgresqlCopyInDataframe postgresqlQuoteId
postgresqlTableRef postgresqlgetResult postgresqlpqExec postscript
prop_OB rainbow rasterGrob read.delim read.table readPNG rgb
smartsSearch_OB str string write.table
Consider adding
importFrom("grDevices", "dev.off", "pdf", "postscript", "rainbow",
"rgb")
importFrom("utils", "browseURL", "combn", "data", "read.delim",
"read.table", "str", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘ChemmineR/libs/ChemmineR.so’:
Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
Objects: ‘desc.o’, ‘formats.o’, ‘script.o’
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Object: ‘cluster.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.
ChemmineR.Rcheck/00install.out:
* installing *source* package ‘ChemmineR’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -Wall -c DisjointSets.cpp -o DisjointSets.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -Wall -c cluster.cc -o cluster.o
cluster.cc: In function ‘int nbr_intersect(std::vector<int>&, std::vector<int>&)’:
cluster.cc:118:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (i < nbrs1.size() and j < nbrs2.size()) {
^
cluster.cc:118:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (i < nbrs1.size() and j < nbrs2.size()) {
^
cluster.cc: In function ‘int contains(int, std::vector<int>&)’:
cluster.cc:131:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0; i < list.size(); i++)
^
cluster.cc: In function ‘DisjointSets cluster(int, int, int, int)’:
cluster.cc:267:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < nbr_list[i].size(); j ++) {
^
cluster.cc: In function ‘void loadNNMatrix(int, int, int, SEXP)’:
cluster.cc:284:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned i=0; i<N; i++) //rows
^
cluster.cc:298:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(nbrs.size() < minNbrs) // will end up a singleton
^
cluster.cc: In function ‘void loadNNList(int, int, SEXP)’:
cluster.cc:314:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned i=0; i<N; i++) //rows
^
cluster.cc:332:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(nbrs.size() < minNbrs) // will end up a singleton
^
cluster.cc: In function ‘SEXPREC* jarvis_patrick(SEXP, SEXP, SEXP, SEXP, SEXP)’:
cluster.cc:390:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned i=0; i<N; i++){
^
cluster.cc: At global scope:
cluster.cc:49:13: warning: ‘void prepare_neighbors(const char*, int, int)’ defined but not used [-Wunused-function]
void static prepare_neighbors(const char* nbr_file, int skip, int p)
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -Wall -c cstrsplit.cc -o cstrsplit.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -Wall -c desc.cc -o desc.o
desc.cc: In function ‘SEXPREC* genAPDescriptor(SEXP)’:
desc.cc:249:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0; i < descs.size(); i++)
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -Wall -c fingerprints.cc -o fingerprints.o
fingerprints.cc: In function ‘SEXPREC* uniquifyAtomPairs(SEXP)’:
fingerprints.cc:138:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0; i < aps.size(); i++)
^
fingerprints.cc:145:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0; i < aps.size(); i++){
^
fingerprints.cc:158:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0; i < aps.size(); i++){
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -Wall -c formats.cc -o formats.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -Wall -c molecule.cc -o molecule.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -Wall -c r_wrap.cc -o r_wrap.o
r_wrap.cc: In function ‘SEXPREC* SWIG_MakePtr(void*, const char*, R_SWIG_Owner)’:
r_wrap.cc:949:15: warning: variable ‘p’ set but not used [-Wunused-but-set-variable]
const char *p = typeName;
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -Wall -c script.cc -o script.o
In file included from script.cc:2:0:
desc.h:39:13: warning: ‘elements’ defined but not used [-Wunused-variable]
static char elements[112][3] = {
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include" -DNO_MAIN -DNO_DEBUG -fpic -g -O2 -Wall -c similarity.cc -o similarity.o
In file included from similarity.cc:1:0:
desc.h:39:13: warning: ‘elements’ defined but not used [-Wunused-variable]
static char elements[112][3] = {
^
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -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/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/ChemmineR.Rcheck/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
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ChemmineR)
ChemmineR.Rcheck/ChemmineR-Ex.timings:
| name | user | system | elapsed
|
| AP-class | 0.372 | 0.048 | 0.418 |
|
| APset-class | 0.308 | 0.028 | 0.337 |
|
| ExtSDF-class | 0.000 | 0.000 | 0.001 |
|
| FP-class | 0.088 | 0.000 | 0.088 |
|
| FPset-class | 0.340 | 0.012 | 0.351 |
|
| SDF-class | 0.056 | 0.000 | 0.056 |
|
| SDF2apcmp | 0.028 | 0.000 | 0.027 |
|
| SDFset-class | 0.308 | 0.016 | 0.321 |
|
| SDFset2SDF | 0.092 | 0.004 | 0.095 |
|
| SDFset2list | 0.040 | 0.020 | 0.059 |
|
| SDFstr-class | 0.244 | 0.000 | 0.243 |
|
| SMI-class | 0.000 | 0.004 | 0.002 |
|
| SMIset-class | 0.004 | 0.000 | 0.005 |
|
| addDescriptorType | 0 | 0 | 0 |
|
| addNewFeatures | 2.376 | 0.012 | 2.391 |
|
| ap | 0.084 | 0.004 | 0.089 |
|
| apfp | 0.004 | 0.000 | 0.002 |
|
| apset | 0.004 | 0.000 | 0.005 |
|
| apset2descdb | 0.296 | 0.040 | 0.338 |
|
| atomblock | 0.076 | 0.012 | 0.088 |
|
| atomcount | 0.220 | 0.000 | 0.216 |
|
| atomprop | 0.004 | 0.000 | 0.004 |
|
| atomsubset | 0.024 | 0.000 | 0.024 |
|
| batchByIndex | 0.000 | 0.000 | 0.001 |
|
| bondblock | 0.08 | 0.00 | 0.08 |
|
| bonds | 0.028 | 0.000 | 0.029 |
|
| browseJob | 0 | 0 | 0 |
|
| bufferLines | 0.000 | 0.000 | 0.001 |
|
| bufferResultSet | 0.004 | 0.000 | 0.000 |
|
| byCluster | 0.692 | 0.000 | 0.692 |
|
| canonicalNumbering | 0.192 | 0.004 | 0.492 |
|
| canonicalize | 0.036 | 0.000 | 0.034 |
|
| cid | 0.02 | 0.00 | 0.02 |
|
| cluster.sizestat | 0.496 | 0.004 | 0.499 |
|
| cluster.visualize | 0.600 | 0.004 | 0.602 |
|
| cmp.cluster | 1.856 | 0.016 | 1.874 |
|
| cmp.duplicated | 0.064 | 0.000 | 0.062 |
|
| cmp.parse | 0.024 | 0.000 | 0.023 |
|
| cmp.parse1 | 0 | 0 | 0 |
|
| cmp.search | 0.612 | 0.000 | 0.620 |
|
| cmp.similarity | 0.020 | 0.000 | 0.019 |
|
| conMA | 0.048 | 0.004 | 0.054 |
|
| connections | 0.148 | 0.004 | 0.175 |
|
| datablock | 0.208 | 0.000 | 0.211 |
|
| datablock2ma | 0.028 | 0.000 | 0.031 |
|
| db.explain | 0.040 | 0.000 | 0.042 |
|
| db.subset | 0.004 | 0.000 | 0.004 |
|
| dbTransaction | 0.024 | 0.004 | 0.025 |
|
| desc2fp | 0.096 | 0.004 | 0.099 |
|
| draw_sdf | 0.344 | 0.008 | 0.352 |
|
| exactMassOB | 0.536 | 0.004 | 0.547 |
|
| findCompounds | 2.004 | 0.008 | 2.013 |
|
| findCompoundsByName | 0.264 | 0.008 | 0.275 |
|
| fingerprintOB | 0.000 | 0.000 | 0.001 |
|
| fold | 0.000 | 0.000 | 0.001 |
|
| foldCount | 0.000 | 0.000 | 0.001 |
|
| fp2bit | 0.404 | 0.004 | 0.407 |
|
| fpSim | 0.260 | 0.004 | 0.619 |
|
| fptype | 0.000 | 0.000 | 0.001 |
|
| fromNNMatrix | 0.764 | 0.000 | 0.764 |
|
| genAPDescriptors | 0.020 | 0.000 | 0.019 |
|
| genParameters | 0.552 | 0.000 | 0.553 |
|
| generate3DCoords | 0 | 0 | 0 |
|
| getAllCompoundIds | 0.276 | 0.004 | 0.280 |
|
| getCompoundFeatures | 1.972 | 0.000 | 1.969 |
|
| getCompoundNames | 0.292 | 0.004 | 0.297 |
|
| getCompounds | 0.388 | 0.000 | 0.390 |
|
| getIds | 0 | 0 | 0 |
|
| grepSDFset | 0.044 | 0.000 | 0.044 |
|
| groups | 0.108 | 0.000 | 0.109 |
|
| header | 0.076 | 0.000 | 0.079 |
|
| initDb | 0.028 | 0.000 | 0.028 |
|
| jarvisPatrick | 1.796 | 0.000 | 1.794 |
|
| jobToken-class | 0.000 | 0.000 | 0.001 |
|
| launchCMTool | 0.004 | 0.000 | 0.000 |
|
| listCMTools | 0.000 | 0.000 | 0.001 |
|
| listFeatures | 0.320 | 0.000 | 0.319 |
|
| loadSdf | 2.220 | 0.004 | 2.230 |
|
| makeUnique | 0.016 | 0.000 | 0.016 |
|
| maximallyDissimilar | 0.212 | 0.000 | 0.213 |
|
| nearestNeighbors | 1.044 | 0.000 | 1.057 |
|
| numBits | 0.000 | 0.000 | 0.001 |
|
| obmol | 0.028 | 0.000 | 0.027 |
|
| parBatchByIndex | 0 | 0 | 0 |
|
| plotStruc | 0.312 | 0.000 | 0.312 |
|
| propOB | 0.000 | 0.000 | 0.001 |
|
| pubchemFPencoding | 0.004 | 0.000 | 0.003 |
|
| read.AP | 0.016 | 0.000 | 0.015 |
|
| read.SDFindex | 0.016 | 0.000 | 0.016 |
|
| read.SDFset | 0.568 | 0.000 | 0.567 |
|
| read.SDFstr | 0.816 | 0.000 | 0.813 |
|
| read.SMIset | 0.000 | 0.000 | 0.001 |
|
| regenerateCoords | 0.004 | 0.000 | 0.001 |
|
| result | 0.000 | 0.000 | 0.001 |
|
| rings | 0.456 | 0.000 | 0.455 |
|
| sdf.subset | 0.000 | 0.000 | 0.001 |
|
| sdf.visualize | 0.016 | 0.000 | 0.016 |
|
| sdf2ap | 0.308 | 0.052 | 0.360 |
|
| sdf2list | 0.024 | 0.004 | 0.026 |
|
| sdf2smiles | 0.000 | 0.000 | 0.001 |
|
| sdf2str | 0.032 | 0.000 | 0.031 |
|
| sdfStream | 0.016 | 0.000 | 0.017 |
|
| sdfid | 0.016 | 0.000 | 0.017 |
|
| sdfsample | 0.048 | 0.000 | 0.046 |
|
| sdfstr2list | 0.752 | 0.132 | 0.885 |
|
| searchSim | 0.004 | 0.000 | 0.000 |
|
| searchString | 0.000 | 0.000 | 0.001 |
|
| selectInBatches | 0.000 | 0.000 | 0.001 |
|
| setPriorities | 0.004 | 0.000 | 0.001 |
|
| smartsSearchOB | 0.000 | 0.000 | 0.001 |
|
| smiles2sdf | 0 | 0 | 0 |
|
| smisample | 0.004 | 0.000 | 0.003 |
|
| status | 0 | 0 | 0 |
|
| toolDetails | 0.000 | 0.000 | 0.001 |
|
| trimNeighbors | 1.500 | 0.000 | 1.507 |
|
| validSDF | 0.020 | 0.000 | 0.018 |
|
| view | 0.044 | 0.004 | 0.047 |
|
| write.SDF | 0.148 | 0.000 | 0.146 |
|
| write.SDFsplit | 0.016 | 0.000 | 0.016 |
|
| write.SMI | 0.000 | 0.000 | 0.002 |
|