Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-10-14 11:36:50 -0400 (Sat, 14 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 318/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChemmineR 3.52.0  (landing page)
Thomas Girke
Snapshot Date: 2023-10-13 14:00:12 -0400 (Fri, 13 Oct 2023)
git_url: https://git.bioconductor.org/packages/ChemmineR
git_branch: RELEASE_3_17
git_last_commit: 444df16
git_last_commit_date: 2023-04-25 09:47:42 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for ChemmineR on merida1


To the developers/maintainers of the ChemmineR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChemmineR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ChemmineR
Version: 3.52.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChemmineR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChemmineR_3.52.0.tar.gz
StartedAt: 2023-10-13 23:36:50 -0400 (Fri, 13 Oct 2023)
EndedAt: 2023-10-13 23:41:49 -0400 (Fri, 13 Oct 2023)
EllapsedTime: 299.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChemmineR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChemmineR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChemmineR_3.52.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/ChemmineR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChemmineR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChemmineR’ version ‘3.52.0’
* 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
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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:
  ‘png’
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 startup messages can be suppressed ... 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’
DUD: no visible global function definition for ‘download.file’
DUD: no visible global function definition for ‘untar’
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’
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 download.file error exactMass_OB fingerprint_OB fmcs
  forEachMol pdf postgresqlCopyInDataframe postgresqlQuoteId
  postgresqlTableRef postgresqlgetResult postgresqlpqExec postscript
  prop_OB rainbow read.delim read.table rgb smartsSearch_OB str string
  untar write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "postscript", "rainbow",
             "rgb")
  importFrom("utils", "browseURL", "combn", "data", "download.file",
             "read.delim", "read.table", "str", "untar", "write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) cmp.duplicated.Rd:29: Escaped LaTeX specials: \$
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '$' and siglist '_p_Descriptors'
  generic '[' and siglist 'ExternalReferenceSwig'
  generic '[<-' and siglist 'ExternalReferenceSwig'
  generic 'coerce' and siglist 'ExternalReferenceSwig,character'
  generic 'length' and siglist 'SWIGArray'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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 nor [v]sprintf. 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
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
addNewFeatures      6.649  0.383   8.936
loadSdf             6.191  0.070   8.015
findCompounds       5.958  0.056   7.620
getCompoundFeatures 5.626  0.049   7.306
* 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, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.



Installation output

ChemmineR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘ChemmineR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -fPIC  -falign-functions=64 -Wall -g -O2  -c DisjointSets.cpp -o DisjointSets.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -fPIC  -falign-functions=64 -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -fPIC  -falign-functions=64 -Wall -g -O2  -c cstrsplit.cc -o cstrsplit.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -fPIC  -falign-functions=64 -Wall -g -O2  -c desc.cc -o desc.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -fPIC  -falign-functions=64 -Wall -g -O2  -c fingerprints.cc -o fingerprints.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -fPIC  -falign-functions=64 -Wall -g -O2  -c formats.cc -o formats.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -fPIC  -falign-functions=64 -Wall -g -O2  -c molecule.cc -o molecule.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -fPIC  -falign-functions=64 -Wall -g -O2  -c r_wrap.cc -o r_wrap.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -fPIC  -falign-functions=64 -Wall -g -O2  -c script.cc -o script.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -fPIC  -falign-functions=64 -Wall -g -O2  -c similarity.cc -o similarity.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/4.3-x86_64/Resources/library/00LOCK-ChemmineR/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ChemmineR)

Tests output

ChemmineR.Rcheck/tests/runTests.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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")
======= testing fpset ===============================================
======= folding... 
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 0.001
Error in DEACTIVATED("local test") : local test
In addition: There were 15 warnings (use warnings() to see them)
Timing stopped at: 0 0 0.001
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
test.formatConversions
Timing stopped at: 0 0 0
Error in DEACTIVATED("removed old version of function") : 
  removed old version of function
In addition: Warning messages:
1: In for (i in seq_len(n)) { :
  closing unused connection 5 (<-localhost:11943)
2: In for (i in seq_len(n)) { :
  closing unused connection 4 (<-localhost:11943)
3: In for (i in seq_len(n)) { :
  closing unused connection 3 (<-localhost:11943)
Timing stopped at: 0 0 0
Error in DEACTIVATED("just for manual testing") : just for manual testing
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
Timing stopped at: 0 0 0.001
Error in DEACTIVATED("Causes SSL protocol version error on BioC") : 
  Causes SSL protocol version error on BioC
[1] "rotable bonds: "
CMP1 CMP2 CMP3 CMP4 CMP5 
  24   20   14   30   10 
[1] "650001" "650002" "650003" "650004" "650005"
2023-10-13 23:41:20.881 R[99881:963536232] XType: com.apple.fonts is not accessible.
2023-10-13 23:41:20.881 R[99881:963536232] XType: XTFontStaticRegistry is enabled.


RUNIT TEST PROTOCOL -- Fri Oct 13 23:41:22 2023 
*********************************************** 
Number of test functions: 23 
Number of deactivated test functions: 8 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ChemmineR RUnit Tests - 23 test functions, 0 errors, 0 failures
Number of test functions: 23 
Number of deactivated test functions: 8 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 26.235   2.276  37.862 

Example timings

ChemmineR.Rcheck/ChemmineR-Ex.timings

nameusersystemelapsed
AP-class0.6310.3501.228
APset-class0.6620.3651.327
ExtSDF-class0.0020.0010.002
FP-class0.1020.0180.148
FPset-class0.4540.0960.707
SDF-class0.0940.0310.155
SDF2apcmp0.0370.0030.050
SDFDataTable0.0000.0010.001
SDFset-class0.6330.1350.975
SDFset2SDF0.1390.0350.223
SDFset2list0.1010.1600.339
SDFstr-class0.4970.0180.661
SMI-class0.0030.0030.007
SMIset-class0.0080.0040.015
addDescriptorType0.0000.0010.004
addNewFeatures6.6490.3838.936
ap0.1260.0650.239
apfp0.0040.0030.009
apset0.0060.0050.013
apset2descdb0.5110.3321.061
atomblock0.1570.0770.299
atomcount0.3250.0160.429
atomprop0.0050.0030.011
atomsubset0.0390.0050.053
batchByIndex0.0010.0000.001
bondblock0.1460.0450.243
bonds0.0500.0110.080
browseJob0.0010.0010.003
bufferLines000
bufferResultSet0.0010.0010.002
byCluster1.1880.0531.561
canonicalNumbering0.0000.0000.001
canonicalize0.0000.0000.001
cid0.0300.0040.041
cluster.sizestat0.7940.0321.031
cluster.visualize1.0230.0281.323
cmp.cluster3.4760.0944.468
cmp.duplicated0.0750.0040.098
cmp.parse0.0350.0040.047
cmp.parse10.0000.0000.001
cmp.search1.0330.0481.430
cmp.similarity0.0270.0050.049
conMA0.0990.0510.205
connections0.3850.0090.481
datablock0.4260.0350.565
datablock2ma0.0610.0080.090
db.explain0.0660.0220.112
db.subset0.0030.0020.006
dbTransaction0.0390.0130.062
desc2fp0.1390.0100.191
draw_sdf1.0650.0451.406
exactMassOB000
findCompounds5.9580.0567.620
findCompoundsByName0.5710.0260.750
fingerprintOB0.0000.0000.001
fold0.0020.0010.002
foldCount0.0020.0010.002
fp2bit0.5410.0500.761
fpSim0.5310.0300.718
fptype0.0020.0010.001
fromNNMatrix1.1540.0101.479
genAPDescriptors0.0260.0030.038
genParameters0.6340.0070.816
generate3DCoords0.0000.0000.001
getAllCompoundIds0.5950.0310.790
getAtomAttr0.0000.0010.001
getBondAttr0.0000.0000.001
getCompoundFeatures5.6260.0497.306
getCompoundNames0.5800.0270.798
getCompounds0.6050.0280.809
getIds0.0000.0010.001
grepSDFset0.0740.0040.114
groups0.2780.0320.402
header0.1550.0180.216
initDb0.0400.0130.063
jarvisPatrick3.0320.0453.760
jobToken-class0.0010.0010.005
largestComponent0.0000.0010.001
launchCMTool0.0000.0010.002
listCMTools0.0010.0010.003
listFeatures0.6310.0260.827
loadSdf6.1910.0708.015
makeUnique0.0270.0030.037
maximallyDissimilar0.3730.0040.465
nearestNeighbors1.4710.0111.868
numBits0.0020.0010.002
obmol0.8710.2082.919
openBabelPlot0.0000.0010.001
parBatchByIndex0.0000.0010.001
plotStruc0.6890.0320.866
propOB0.0000.0000.001
pubchemCidToSDF0.0000.0010.002
pubchemFPencoding0.0040.0030.007
pubchemInchi2cid0.0010.0010.001
pubchemInchikey2sdf0.0010.0010.001
pubchemName2CID0.0000.0000.001
pubchemSDFSearch0.0000.0010.003
pubchemSmilesSearch0.0000.0000.001
read.AP0.0240.0040.037
read.SDFindex0.0260.0040.044
read.SDFset1.0070.0061.260
read.SDFstr1.4870.0151.963
read.SMIset0.0020.0030.005
regenerateCoords0.0010.0010.001
result0.0000.0010.001
rings1.3500.0381.755
sdf.subset0.0000.0010.001
sdf.visualize0.0250.0030.033
sdf2ap0.5120.5081.285
sdf2list0.0420.0690.146
sdf2smiles0.0010.0010.001
sdf2str0.0440.0250.089
sdfStream0.0270.0040.043
sdfid0.0260.0030.035
sdfsample0.0610.0190.099
sdfstr2list1.1631.4753.331
searchSim000
searchString0.0000.0000.001
selectInBatches0.0010.0010.002
setPriorities000
smartsSearchOB000
smiles2sdf0.0000.0000.003
smisample0.0040.0030.008
status0.0010.0010.001
toolDetails0.0000.0010.001
trimNeighbors1.9130.0512.474
validSDF0.0330.0030.041
view0.0730.0160.114
write.SDF0.2880.0130.383
write.SDFsplit0.0250.0030.037
write.SMI0.0020.0020.004