Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-01 12:04 -0400 (Wed, 01 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4843
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4631
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4575
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 333/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChemmineR 3.61.2  (landing page)
Thomas Girke
Snapshot Date: 2025-09-30 13:45 -0400 (Tue, 30 Sep 2025)
git_url: https://git.bioconductor.org/packages/ChemmineR
git_branch: devel
git_last_commit: f54ad3e
git_last_commit_date: 2025-09-09 11:35:36 -0400 (Tue, 09 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for ChemmineR on lconway

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: 3.61.2
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_3.61.2.tar.gz
StartedAt: 2025-09-30 20:10:35 -0400 (Tue, 30 Sep 2025)
EndedAt: 2025-09-30 20:13:10 -0400 (Tue, 30 Sep 2025)
EllapsedTime: 154.9 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_3.61.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ChemmineR.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChemmineR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChemmineR’ version ‘3.61.2’
* 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: ‘MacOSX11.3.1.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 code 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 whether 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’
.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’
write.SMI: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  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 code objects:
  ‘sdfid<-’
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'
  generic 'sdfid<-' and siglist 'SDF'
  generic 'sdfid<-' and siglist 'SDFset'
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 ... NOTE
Argument items with no description in Rd file 'cmp.search.Rd':
  ‘visualize’ ‘visualize.browse’ ‘visualize.query’
* 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/4.5-x86_64/Resources/library/ChemmineR/libs/ChemmineR.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
File ‘ChemmineR/libs/ChemmineR.so’:
  Found non-API call to R: ‘SET_S4_OBJECT’

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.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
* 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 ... 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, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-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/4.5-x86_64/Resources/library’
* installing *source* package ‘ChemmineR’ ...
** this is package ‘ChemmineR’ version ‘3.61.2’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -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/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -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/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -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/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -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/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -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/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -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/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -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/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fPIC  -falign-functions=64 -Wall -g -O2   -c r_wrap.cc -o r_wrap.o
r_wrap.cc:758:10: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
# define R_NO_REMAP
         ^
<command line>:5:9: note: previous definition is here
#define R_NO_REMAP 1
        ^
r_wrap.cc:761:10: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined]
# define STRICT_R_HEADERS
         ^
<command line>:4:9: note: previous definition is here
#define STRICT_R_HEADERS 1
        ^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -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/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -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 -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
installing to /Library/Frameworks/R.framework/Versions/4.5-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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 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: closing unused connection 5 (<-localhost:11558) 
2: closing unused connection 4 (<-localhost:11558) 
3: closing unused connection 3 (<-localhost:11558) 
test.formatConversions
Timing stopped at: 0 0 0
Error in DEACTIVATED("removed old version of function") : 
  removed old version of function
==============================
*** Open Babel Warning  in ParseSmiles
  Invalid SMILES string: 1 unmatched ring bonds.

==============================
*** Open Babel Error  in ParseSimple
  SMILES string contains a character 'G' which is invalid
==============================
*** Open Babel Warning  in ParseSmiles
  Invalid SMILES string: 1 unmatched ring bonds.

==============================
*** Open Babel Error  in ParseSimple
  SMILES string contains a character 'G' which is invalid
==============================
*** Open Babel Warning  in ParseSmiles
  Invalid SMILES string: 1 unmatched ring bonds.

==============================
*** Open Babel Error  in ParseSimple
  SMILES string contains a character 'G' which is invalid
==============================
*** Open Babel Warning  in ParseSmiles
  Invalid SMILES string: 1 unmatched ring bonds.

==============================
*** Open Babel Error  in ParseSimple
  SMILES string contains a character 'G' which is invalid
Timing stopped at: 0 0 0.001
Error in DEACTIVATED("just for manual testing") : just for manual testing
In addition: Warning messages:
1: In smiles2sdf(smiles) : Could not convert FailingSmile1'. Skipping.
2: In smiles2sdf(smiles) : Could not convert FailingSmile2'. Skipping.
3: In smiles2sdf(smiles[c(2, 3, 1, 4)]) :
  Could not convert FailingSmile1'. Skipping.
4: In smiles2sdf(smiles[c(2, 3, 1, 4)]) :
  Could not convert FailingSmile2'. Skipping.
5: In smiles2sdf(smiles[c(1, 4, 2, 3)]) :
  Could not convert FailingSmile1'. Skipping.
6: In smiles2sdf(smiles[c(1, 4, 2, 3)]) :
  Could not convert FailingSmile2'. Skipping.
7: In smiles2sdf(smiles[c(2, 3)]) :
  Could not convert FailingSmile1'. Skipping.
8: In smiles2sdf(smiles[c(2, 3)]) :
  Could not convert FailingSmile2'. Skipping.
Timing stopped at: 0.001 0 0
Error in DEACTIVATED("requires local files") : requires local files
Timing stopped at: 0 0 0.001
Error in DEACTIVATED("fails on ubuntu 16.04") : fails on ubuntu 16.04
Timing stopped at: 0 0 0
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"
2025-09-30 20:12:56.168 R[23544:420694142] XType: com.apple.fonts is not accessible.
2025-09-30 20:12:56.168 R[23544:420694142] XType: XTFontStaticRegistry is enabled.


RUNIT TEST PROTOCOL -- Tue Sep 30 20:12:56 2025 
*********************************************** 
Number of test functions: 24 
Number of deactivated test functions: 8 
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: 8 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 15.593   1.536  18.595 

Example timings

ChemmineR.Rcheck/ChemmineR-Ex.timings

nameusersystemelapsed
AP-class0.3750.1470.525
APset-class0.3570.1350.527
ExtSDF-class0.0010.0010.001
FP-class0.0660.0080.073
FPset-class0.2240.0470.273
SDF-class0.0480.0210.069
SDF2apcmp0.0220.0010.024
SDFDataTable000
SDFset-class0.3240.0500.377
SDFset2SDF0.0670.0130.081
SDFset2list0.0560.0520.108
SDFstr-class0.2420.0070.250
SMI-class0.0030.0010.004
SMIset-class0.0040.0020.007
addDescriptorType000
addNewFeatures3.0770.2663.426
ap0.0550.0160.072
apfp0.0020.0010.004
apset0.0040.0020.006
apset2descdb0.3440.1260.472
atomblock0.0690.0260.095
atomcount0.1610.0070.168
atomprop0.0020.0010.003
atomsubset0.0210.0020.024
batchByIndex000
bondblock0.0840.0160.099
bonds0.0280.0050.032
browseJob0.0000.0000.001
bufferLines000
bufferResultSet000
byCluster1.2470.0371.288
canonicalNumbering0.0000.0000.001
canonicalize000
cid0.0190.0020.020
cluster.sizestat0.8190.0230.845
cluster.visualize0.9780.0361.017
cmp.cluster2.6630.0652.740
cmp.duplicated0.0320.0020.034
cmp.parse0.0270.0030.030
cmp.parse1000
cmp.search1.0900.0381.132
cmp.similarity0.0320.0030.035
conMA0.0450.0160.062
connections0.2250.0060.234
datablock0.1820.0120.195
datablock2ma0.0320.0030.035
db.explain0.0290.0080.037
db.subset0.0030.0020.005
dbTransaction0.0260.0080.036
desc2fp0.0730.0050.079
draw_sdf0.7860.0340.846
exactMassOB000
findCompounds2.5340.0292.581
findCompoundsByName0.3140.0160.333
fingerprintOB0.0000.0000.001
fold0.0010.0000.001
foldCount0.0010.0010.001
fp2bit0.3160.0310.350
fpSim0.3390.0350.375
fptype0.0010.0000.000
fromNNMatrix1.2210.0291.254
genAPDescriptors0.0160.0020.017
genParameters0.2980.0040.302
generate3DCoords0.0000.0000.001
getAllCompoundIds0.3090.0180.331
getAtomAttr0.0000.0000.001
getBondAttr000
getCompoundFeatures2.5560.0312.603
getCompoundNames0.3650.0170.390
getCompounds0.3350.0190.359
getIds0.0010.0000.000
grepSDFset0.0590.0030.061
groups0.1360.0090.147
header0.0650.0050.070
initDb0.0260.0070.036
jarvisPatrick2.6820.0462.745
jobToken-class0.0000.0010.000
largestComponent0.0000.0010.000
launchCMTool000
listCMTools0.0000.0000.001
listFeatures0.3340.0170.356
loadSdf2.9740.0493.051
makeUnique0.0170.0020.018
maximallyDissimilar0.2790.0040.285
nearestNeighbors1.4770.0321.519
numBits0.0010.0000.001
obmol0.4570.0830.547
openBabelPlot000
parBatchByIndex0.0000.0000.001
plotStruc0.2620.0180.284
propOB0.0000.0010.000
pubchemCidToSDF0.0000.0010.001
pubchemFPencoding0.0030.0020.004
pubchemInchi2cid0.0000.0000.001
pubchemInchikey2sdf0.0000.0000.001
pubchemName2CID0.0000.0010.000
pubchemSDFSearch0.0000.0010.000
pubchemSmilesSearch000
read.AP0.0120.0020.014
read.SDFindex0.0140.0020.015
read.SDFset0.5310.0060.542
read.SDFstr0.7680.0080.781
read.SMIset0.0010.0020.002
regenerateCoords000
result000
rings0.5320.0140.550
sdf.subset000
sdf.visualize0.0150.0020.017
sdf2ap0.3350.1970.537
sdf2list0.0210.0260.046
sdf2smiles0.0000.0000.001
sdf2str0.0260.0120.039
sdfStream0.0180.0020.021
sdfid0.0180.0020.021
sdfsample0.0270.0070.034
sdfstr2list0.5680.5391.118
searchSim000
searchString0.0000.0010.001
selectInBatches000
setPriorities0.0000.0010.000
smartsSearchOB000
smiles2sdf0.0010.0000.000
smisample0.0030.0010.004
status0.0000.0000.001
toolDetails000
trimNeighbors2.1330.0422.189
validSDF0.0160.0010.017
view0.0370.0070.044
write.SDF0.1470.0070.157
write.SDFsplit0.0140.0020.015
write.SMI0.0010.0020.002