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CHECK report for ChemmineR on merida2

This page was generated on 2018-10-17 08:47:56 -0400 (Wed, 17 Oct 2018).

Package 222/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChemmineR 3.32.1
Thomas Girke
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ChemmineR
Branch: RELEASE_3_7
Last Commit: fd105a4
Last Changed Date: 2018-05-30 12:27:39 -0400 (Wed, 30 May 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ChemmineR
Version: 3.32.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChemmineR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChemmineR_3.32.1.tar.gz
StartedAt: 2018-10-16 20:22:31 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:25:17 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 166.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ChemmineR.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChemmineR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChemmineR_3.32.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ChemmineR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘3.32.1’
* 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 ... WARNING
Found the following significant warnings:
  r_wrap.cc:1689:14: warning: explicitly assigning value of variable of type 'void *' to itself [-Wself-assign]
See ‘/Users/biocbuild/bbs-3.7-bioc/meat/ChemmineR.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘png’ ‘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’ ‘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’
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_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’
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’
sdf2image: no visible global function definition for ‘convertToImage’
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’
searchSim: no visible binding for global variable ‘smiles’
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’
write.SMI: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  AW C1 C1.1 C2 C2.1 browseURL canonicalNumbering_OB clusterApplyLB
  clusterExport combn convertFormat convertFormatFile convertToImage
  data dev.off error exactMass_OB fingerprint_OB fmcs forEachMol pdf
  postgresqlCopyInDataframe postgresqlQuoteId postgresqlTableRef
  postgresqlgetResult postgresqlpqExec postscript prop_OB rainbow
  read.delim read.table rgb smartsSearch_OB smiles 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ChemmineR/libs/ChemmineR.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.



Installation output

ChemmineR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ChemmineR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ChemmineR’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c DisjointSets.cpp -o DisjointSets.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c cluster.cc -o cluster.o
cluster.cc:49:13: warning: unused function 'prepare_neighbors' [-Wunused-function]
void static prepare_neighbors(const char* nbr_file, int skip, int p)
            ^
1 warning generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c cstrsplit.cc -o cstrsplit.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c desc.cc -o desc.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c fingerprints.cc -o fingerprints.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c formats.cc -o formats.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c molecule.cc -o molecule.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c r_wrap.cc -o r_wrap.o
r_wrap.cc:1689:14: warning: explicitly assigning value of variable of type 'void *' to itself [-Wself-assign]
  clientdata = clientdata;
  ˜˜˜˜˜˜˜˜˜˜ ^ ˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c script.cc -o script.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c similarity.cc -o similarity.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ChemmineR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ChemmineR)

Tests output

ChemmineR.Rcheck/tests/runTests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("ChemmineR")
Loading required package: RSQLite
[1] "createing db"
[1] "createing db"
[1] "loading first half, no features"
[1] "createing db"
[1] "loading first half,with features"
adding new features to existing compounds. This could take a while
[1] "loading incomplete features"
[1] "loading second half"
adding new features to existing compounds. This could take a while
[1] "done loading"
[1] "createing db"
adding new features to existing compounds. This could take a while
[1] "found 70  compounds"
[1] "found 20  compounds"
Timing stopped at: 0 0 0
Error in DEACTIVATED("local test") : local test
In addition: There were 14 warnings (use warnings() to see them)
Timing stopped at: 0 0 0
Error in DEACTIVATED("local test only") : local test only
found 100 ids
  [1] 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218
 [19] 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236
 [37] 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254
 [55] 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272
 [73] 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290
 [91] 291 292 293 294 295 296 297 298 299 300
starting parBatchByIndex
Loading required package: snow
 int [1:100] 201 202 203 204 205 206 207 208 209 210 ...
NULL
[1] "results:  parBench-sub-1,parBench-sub-2,parBench-sub-3,parBench-sub-4,parBench-sub-5,parBench-sub-6,parBench-sub-7,parBench-sub-8,parBench-sub-9,parBench-sub-10"
[1] "loading duplications"
loading 1 new compounds, updating 1 compounds
fetching features: 
Timing stopped at: 0 0 0
Error in DEACTIVATED("causing timeout on bioc, disabling for now") : 
  causing timeout on bioc, disabling for now
In addition: Warning messages:
1: In is.factor(x) : closing unused connection 6 (<-localhost:11574)
2: In is.factor(x) : closing unused connection 5 (<-localhost:11574)
3: In is.factor(x) : closing unused connection 4 (<-localhost:11574)
test.formatConversions
Timing stopped at: 0 0 0.001
Error in DEACTIVATED("removed old version of function") : 
  removed old version of function
Timing stopped at: 0 0 0
Error in DEACTIVATED("requires local files") : requires local files
Timing stopped at: 0 0 0
Error in DEACTIVATED("fails on ubuntu 16.04") : fails on ubuntu 16.04
cid to sdf, length: 2
smiles search, length: 11
url: https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastsimilarity_2d/sdf/SDF
sdf search, length: 92
url: https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastsimilarity_2d/sdf/PNG
[1] "rotable bonds: "
CMP1 CMP2 CMP3 CMP4 CMP5 
  24   20   14   30   10 
[1] "650001" "650002" "650003" "650004" "650005"


RUNIT TEST PROTOCOL -- Tue Oct 16 20:25:08 2018 
*********************************************** 
Number of test functions: 24 
Number of deactivated test functions: 6 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ChemmineR RUnit Tests - 24 test functions, 0 errors, 0 failures
Number of test functions: 24 
Number of deactivated test functions: 6 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In paste(extradata[(exindex[x, 1] + 1):(exindex[x, 2] - 1)], collapse = " __ ") :
  closing unused connection 5 (https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastsimilarity_2d/smiles/C1CCCCCC1/SDF)
2: In paste(extradata[(exindex[x, 1] + 1):(exindex[x, 2] - 1)], collapse = " __ ") :
  closing unused connection 4 (https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/434,435/SDF)
> 
> proc.time()
   user  system elapsed 
 20.847   1.261  45.016 

Example timings

ChemmineR.Rcheck/ChemmineR-Ex.timings

nameusersystemelapsed
AP-class0.4050.0950.504
APset-class0.4480.1070.561
ExtSDF-class0.0020.0000.002
FP-class0.0810.0050.088
FPset-class0.3570.0330.396
SDF-class0.0910.0100.101
SDF2apcmp0.0220.0010.023
SDFDataTable2.2090.1902.539
SDFset-class0.4680.0450.524
SDFset2SDF0.1370.0100.147
SDFset2list0.0770.0350.111
SDFstr-class0.2970.0070.308
SMI-class0.0050.0010.006
SMIset-class0.0070.0010.009
addDescriptorType0.0010.0000.001
addNewFeatures4.5510.1494.782
ap0.1200.0150.138
apfp0.0030.0010.004
apset0.0050.0010.005
apset2descdb0.3840.1080.496
atomblock0.0940.0160.112
atomcount0.2200.0050.234
atomprop0.0060.0010.007
atomsubset0.0390.0020.041
batchByIndex0.0030.0010.002
bondblock0.1220.0140.136
bonds0.0440.0030.047
browseJob0.0030.0010.003
bufferLines0.0020.0000.002
bufferResultSet0.0030.0000.004
byCluster0.7850.0660.855
canonicalNumbering0.0480.0020.050
canonicalize0.0580.0020.059
cid0.0290.0020.030
cluster.sizestat0.5630.0410.614
cluster.visualize0.6890.0350.732
cmp.cluster2.1780.0842.280
cmp.duplicated0.0600.0060.065
cmp.parse0.0360.0010.038
cmp.parse10.0010.0000.002
cmp.search0.6530.0270.688
cmp.similarity0.0200.0020.022
conMA0.0850.0190.105
connections0.2210.0030.227
datablock0.3060.0090.322
datablock2ma0.0600.0030.063
db.explain0.0580.0070.064
db.subset0.0050.0010.005
dbTransaction0.0350.0040.064
desc2fp0.0870.0040.092
draw_sdf0.5820.0380.637
exactMassOB0.6640.0030.672
findCompounds3.5660.0313.638
findCompoundsByName0.3620.0080.374
fingerprintOB0.0010.0000.001
fold0.0020.0000.002
foldCount0.0030.0000.003
fp2bit0.3140.0450.360
fpSim0.3040.0380.350
fptype0.0020.0000.003
fromNNMatrix0.7430.0400.799
genAPDescriptors0.0200.0010.021
genParameters0.5530.0090.565
generate3DCoords0.0010.0000.001
getAllCompoundIds0.3910.0090.403
getCompoundFeatures3.7580.0243.838
getCompoundNames0.4430.0090.459
getCompounds0.4610.0090.474
getIds0.0010.0000.002
grepSDFset0.0410.0020.043
groups0.2040.0060.212
header0.1090.0040.118
initDb0.0220.0040.026
jarvisPatrick1.8440.0621.934
jobToken-class0.0020.0000.003
launchCMTool0.0030.0010.003
listCMTools0.0030.0000.002
listFeatures0.4270.0090.438
loadSdf3.7370.0313.807
makeUnique0.0250.0010.027
maximallyDissimilar0.2530.0040.261
nearestNeighbors1.0140.0431.062
numBits0.0020.0000.002
obmol0.0430.0020.045
openBabelPlot0.0020.0000.001
parBatchByIndex0.0020.0000.003
plotStruc0.3280.0070.338
propOB0.0010.0000.001
pubchemCidToSDF0.0010.0000.002
pubchemFPencoding0.0050.0010.006
pubchemSDFSearch0.0020.0000.002
pubchemSmilesSearch0.0010.0000.002
read.AP0.0270.0010.029
read.SDFindex0.0240.0020.027
read.SDFset0.7850.0030.792
read.SDFstr1.1570.0041.172
read.SMIset0.0040.0010.005
regenerateCoords0.0010.0000.002
result0.0020.0000.001
rings0.8340.0090.853
sdf.subset0.0010.0000.001
sdf.visualize0.0240.0000.026
sdf2ap0.3910.0940.489
sdf2list0.0580.0150.100
sdf2smiles0.0020.0000.002
sdf2str0.0610.0120.094
sdfStream0.0300.0010.030
sdfid0.0300.0010.031
sdfsample0.0710.0050.075
sdfstr2list1.6650.4552.161
searchSim0.0010.0010.001
searchString0.0010.0000.001
selectInBatches0.0020.0000.002
setPriorities0.0010.0000.001
smartsSearchOB0.0020.0000.002
smiles2sdf0.0010.0000.002
smisample0.0050.0010.007
status0.0020.0010.003
toolDetails0.0020.0000.002
trimNeighbors1.2640.0441.322
validSDF0.0300.0010.032
view0.0770.0050.083
write.SDF0.2310.0050.239
write.SDFsplit0.0260.0020.027
write.SMI0.0030.0010.005