Multiple platform build/check report for BioC 3.9 - CHECK report for ChemmineR on tokay2

Package: ChemmineR

Version: 3.36.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChemmineR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ChemmineR_3.36.0.tar.gz

StartedAt: 2019-10-16 02:35:21 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:40:06 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 285.4 seconds

RetCode: 0

Status: OK

CheckDir: ChemmineR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChemmineR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ChemmineR_3.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ChemmineR.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChemmineR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChemmineR' version '3.36.0'
* 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 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
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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'
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 : : 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 ... 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/ChemmineR/libs/i386/ChemmineR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/ChemmineR/libs/x64/ChemmineR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/ChemmineR.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ChemmineR_3.36.0.tar.gz && rm -rf ChemmineR.buildbin-libdir && mkdir ChemmineR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChemmineR.buildbin-libdir ChemmineR_3.36.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ChemmineR_3.36.0.zip && rm ChemmineR_3.36.0.tar.gz ChemmineR_3.36.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  776k  100  776k    0     0   9.7M      0 --:--:-- --:--:-- --:--:-- 10.5M

install for i386

* installing *source* package 'ChemmineR' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include"   -I"C:/extsoft/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mtune=generic -c DisjointSets.cpp -o DisjointSets.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include"   -I"C:/extsoft/include"  -DNO_MAIN -DNO_DEBUG   -O2 -Wall  -mtune=generic -c cluster.cc -o cluster.o
cluster.cc: In function 'int nbr_intersect(std::vector&, std::vector&)':
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&)':
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&, std::vector&)':
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&)':
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


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 for (i in seq_along(snames)) { :
  closing unused connection 6 (<-TOKAY2:11855)
2: In for (i in seq_along(snames)) { :
  closing unused connection 5 (<-TOKAY2:11855)
3: In for (i in seq_along(snames)) { :
  closing unused connection 4 (<-TOKAY2:11855)
==============================
*** Open Babel Warning  in Init
  Cannot initialize database 'types.txt' which may cause further errors.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
test.formatConversions
Timing stopped at: 0 0 0
Error in DEACTIVATED("removed old version of function") : 
  removed old version of function
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
cid to sdf, length: 2
smiles search, length: 13
sdf search, length: 90
[1] "rotable bonds: "
CMP1 CMP2 CMP3 CMP4 CMP5 
  24   20   14   30   10 
[1] "650001" "650002" "650003" "650004" "650005"


RUNIT TEST PROTOCOL -- Wed Oct 16 02:39:08 2019 
*********************************************** 
Number of test functions: 24 
Number of deactivated test functions: 7 
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: 7 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In .Internal(paste(list(...), sep, collapse)) :
  closing unused connection 5 (https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastsimilarity_2d/smiles/C1CCCCCC1/SDF)
2: In .Internal(paste(list(...), sep, collapse)) :
  closing unused connection 4 (https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/434,435/SDF)
> 
> proc.time()
   user  system elapsed 
  19.62    1.21   46.81


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 for (i in seq_along(snames)) { :
  closing unused connection 6 (<-TOKAY2:11223)
2: In for (i in seq_along(snames)) { :
  closing unused connection 5 (<-TOKAY2:11223)
3: In for (i in seq_along(snames)) { :
  closing unused connection 4 (<-TOKAY2:11223)
==============================
*** Open Babel Warning  in Init
  Cannot initialize database 'types.txt' which may cause further errors.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
test.formatConversions
Timing stopped at: 0 0 0
Error in DEACTIVATED("removed old version of function") : 
  removed old version of function
Timing stopped at: 0 0 0
Error in DEACTIVATED("just for manual testing") : just for manual testing
Timing stopped at: 0.01 0 0.02
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: 13
sdf search, length: 90
[1] "rotable bonds: "
CMP1 CMP2 CMP3 CMP4 CMP5 
  24   20   14   30   10 
[1] "650001" "650002" "650003" "650004" "650005"


RUNIT TEST PROTOCOL -- Wed Oct 16 02:39:55 2019 
*********************************************** 
Number of test functions: 24 
Number of deactivated test functions: 7 
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: 7 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In cl :
  closing unused connection 5 (https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastsimilarity_2d/smiles/C1CCCCCC1/SDF)
2: In cl :
  closing unused connection 4 (https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/434,435/SDF)
3: In for (i in seq_along(methods)) { :
  closing unused connection 3 (C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpaGMGAw\file20b81e561044)
> 
> proc.time()
   user  system elapsed 
  19.98    1.35   46.92

name	user	system	elapsed
AP-class	0.52	0.07	0.61
APset-class	0.34	0.00	0.34
ExtSDF-class	0	0	0
FP-class	0.10	0.01	0.11
FPset-class	0.36	0.00	0.36
SDF-class	0.04	0.02	0.06
SDF2apcmp	0.03	0.00	0.06
SDFDataTable	1.27	0.14	3.44
SDFset-class	0.31	0.06	0.38
SDFset2SDF	0.08	0.00	0.07
SDFset2list	0.05	0.02	0.07
SDFstr-class	0.20	0.04	0.25
SMI-class	0	0	0
SMIset-class	0	0	0
addDescriptorType	0	0	0
addNewFeatures	3.09	0.23	3.33
ap	0.08	0.04	0.11
apfp	0	0	0
apset	0	0	0
apset2descdb	0.42	0.08	0.50
atomblock	0.10	0.04	0.13
atomcount	0.23	0.00	0.23
atomprop	0	0	0
atomsubset	0.04	0.00	0.04
batchByIndex	0	0	0
bondblock	0.10	0.03	0.13
bonds	0.04	0.00	0.04
browseJob	0	0	0
bufferLines	0	0	0
bufferResultSet	0	0	0
byCluster	0.89	0.01	0.91
canonicalNumbering	0.04	0.00	0.22
canonicalize	0.05	0.00	0.06
cid	0.05	0.00	0.05
cluster.sizestat	0.56	0.02	0.58
cluster.visualize	0.66	0.00	0.65
cmp.cluster	1.67	0.01	1.69
cmp.duplicated	0.12	0.00	0.13
cmp.parse	0.03	0.00	0.03
cmp.parse1	0	0	0
cmp.search	0.75	0.02	0.76
cmp.similarity	0.02	0.00	0.02
conMA	0.06	0.02	0.07
connections	0.26	0.00	1.18
datablock	0.38	0.00	0.37
datablock2ma	0.03	0.01	0.05
db.explain	0.06	0.02	0.08
db.subset	0.00	0.01	0.01
dbTransaction	0.03	0.02	0.05
desc2fp	0.14	0.00	0.14
draw_sdf	0.43	1.14	1.56
exactMassOB	0.51	0.00	0.55
findCompounds	2.63	0.01	2.64
findCompoundsByName	0.49	0.02	0.50
fingerprintOB	0	0	0
fold	0.01	0.00	0.02
foldCount	0	0	0
fp2bit	0.46	0.06	0.52
fpSim	0.28	0.03	0.31
fptype	0	0	0
fromNNMatrix	0.97	0.02	0.99
genAPDescriptors	0.02	0.01	0.03
genParameters	0.37	0.02	0.39
generate3DCoords	0	0	0
getAllCompoundIds	0.25	0.02	0.27
getCompoundFeatures	0.42	0.00	0.42
getCompoundNames	0.46	0.01	0.47
getCompounds	0.43	0.00	0.43
getIds	0	0	0
grepSDFset	0.08	0.00	0.08
groups	0.17	0.00	0.17
header	0.08	0.00	0.08
initDb	0	0	0
jarvisPatrick	2.35	0.00	2.35
jobToken-class	0	0	0
largestComponent	0.56	0.00	0.64
launchCMTool	0	0	0
listCMTools	0	0	0
listFeatures	0.51	0.03	0.54
loadSdf	2.85	0.00	2.85
makeUnique	0.03	0.00	0.03
maximallyDissimilar	0.27	0.00	0.27
nearestNeighbors	1.2	0.0	1.2
numBits	0	0	0
obmol	0.03	0.02	0.04
openBabelPlot	0	0	0
parBatchByIndex	0	0	0
plotStruc	0.23	0.01	0.25
propOB	0	0	0
pubchemCidToSDF	0	0	0
pubchemFPencoding	0	0	0
pubchemName2CID	0	0	0
pubchemSDFSearch	0	0	0
pubchemSmilesSearch	0	0	0
read.AP	0.02	0.00	0.02
read.SDFindex	0.01	0.00	0.01
read.SDFset	0.5	0.0	0.5
read.SDFstr	0.75	0.02	0.77
read.SMIset	0.00	0.02	0.01
regenerateCoords	0	0	0
result	0	0	0
rings	0.56	0.00	0.57
sdf.subset	0	0	0
sdf.visualize	0.02	0.01	0.03
sdf2ap	0.29	0.03	0.33
sdf2list	0.02	0.02	0.03
sdf2smiles	0	0	0
sdf2str	0.04	0.00	0.05
sdfStream	0.02	0.00	0.01
sdfid	0.02	0.00	0.02
sdfsample	0.04	0.00	0.05
sdfstr2list	1.14	0.14	1.28
searchSim	0	0	0
searchString	0	0	0
selectInBatches	0	0	0
setPriorities	0	0	0
smartsSearchOB	0	0	0
smiles2sdf	0	0	0
smisample	0	0	0
status	0	0	0
toolDetails	0	0	0
trimNeighbors	1.24	0.00	1.24
validSDF	0.03	0.00	0.03
view	0.08	0.00	0.08
write.SDF	0.17	0.00	0.17
write.SDFsplit	0.04	0.00	0.04
write.SMI	0.00	0.02	0.01

name	user	system	elapsed
AP-class	0.30	0.05	0.34
APset-class	0.34	0.03	0.37
ExtSDF-class	0	0	0
FP-class	0.12	0.02	0.14
FPset-class	0.52	0.03	0.55
SDF-class	0.07	0.01	0.09
SDF2apcmp	0.04	0.00	0.14
SDFDataTable	1.15	0.11	1.91
SDFset-class	0.52	0.03	0.54
SDFset2SDF	0.17	0.00	0.18
SDFset2list	0.09	0.00	0.09
SDFstr-class	0.46	0.00	0.45
SMI-class	0.01	0.00	0.02
SMIset-class	0	0	0
addDescriptorType	0	0	0
addNewFeatures	3.81	0.21	4.01
ap	0.11	0.00	0.11
apfp	0	0	0
apset	0.02	0.00	0.02
apset2descdb	0.42	0.04	0.47
atomblock	0.08	0.02	0.09
atomcount	0.22	0.01	0.24
atomprop	0	0	0
atomsubset	0.04	0.02	0.06
batchByIndex	0	0	0
bondblock	0.15	0.00	0.14
bonds	0.04	0.00	0.05
browseJob	0	0	0
bufferLines	0	0	0
bufferResultSet	0	0	0
byCluster	0.94	0.00	0.93
canonicalNumbering	0.03	0.02	0.05
canonicalize	0.05	0.00	0.05
cid	0.01	0.00	0.01
cluster.sizestat	0.5	0.0	0.5
cluster.visualize	0.49	0.04	0.53
cmp.cluster	1.61	0.00	1.61
cmp.duplicated	0.11	0.00	0.11
cmp.parse	0.04	0.00	0.05
cmp.parse1	0	0	0
cmp.search	0.60	0.00	0.59
cmp.similarity	0.01	0.02	0.04
conMA	0.07	0.00	0.06
connections	0.18	0.00	0.19
datablock	0.21	0.00	0.20
datablock2ma	0.01	0.01	0.03
db.explain	0.03	0.00	0.03
db.subset	0.00	0.02	0.02
dbTransaction	0.03	0.00	0.03
desc2fp	0.14	0.03	0.17
draw_sdf	0.63	1.53	2.16
exactMassOB	0.92	0.00	0.92
findCompounds	2.89	0.00	2.95
findCompoundsByName	0.52	0.03	0.77
fingerprintOB	0	0	0
fold	0	0	0
foldCount	0	0	0
fp2bit	0.47	0.03	0.50
fpSim	0.65	0.05	0.70
fptype	0	0	0
fromNNMatrix	0.99	0.00	0.99
genAPDescriptors	0.02	0.00	0.02
genParameters	0.53	0.02	0.54
generate3DCoords	0	0	0
getAllCompoundIds	0.48	0.00	0.49
getCompoundFeatures	0.47	0.00	0.47
getCompoundNames	0.51	0.01	0.53
getCompounds	0.52	0.03	0.55
getIds	0	0	0
grepSDFset	0.08	0.00	0.08
groups	0.2	0.0	0.2
header	0.13	0.00	0.13
initDb	0.01	0.00	0.01
jarvisPatrick	2.69	0.02	2.72
jobToken-class	0	0	0
largestComponent	0.38	0.00	0.37
launchCMTool	0	0	0
listCMTools	0	0	0
listFeatures	0.56	0.00	0.56
loadSdf	3.56	0.00	3.56
makeUnique	0.02	0.00	0.02
maximallyDissimilar	0.18	0.00	0.19
nearestNeighbors	0.77	0.01	0.78
numBits	0	0	0
obmol	0.03	0.00	0.03
openBabelPlot	0	0	0
parBatchByIndex	0	0	0
plotStruc	0.2	0.0	0.2
propOB	0	0	0
pubchemCidToSDF	0	0	0
pubchemFPencoding	0	0	0
pubchemName2CID	0	0	0
pubchemSDFSearch	0	0	0
pubchemSmilesSearch	0	0	0
read.AP	0.01	0.00	0.01
read.SDFindex	0.02	0.00	0.02
read.SDFset	0.55	0.02	0.56
read.SDFstr	0.81	0.02	0.83
read.SMIset	0	0	0
regenerateCoords	0	0	0
result	0	0	0
rings	0.59	0.00	0.59
sdf.subset	0	0	0
sdf.visualize	0.02	0.00	0.02
sdf2ap	0.28	0.03	0.31
sdf2list	0.02	0.00	0.02
sdf2smiles	0	0	0
sdf2str	0.00	0.03	0.03
sdfStream	0.01	0.00	0.01
sdfid	0.02	0.01	0.03
sdfsample	0.03	0.00	0.04
sdfstr2list	0.70	0.24	0.93
searchSim	0	0	0
searchString	0	0	0
selectInBatches	0	0	0
setPriorities	0	0	0
smartsSearchOB	0	0	0
smiles2sdf	0	0	0
smisample	0.02	0.00	0.02
status	0	0	0
toolDetails	0	0	0
trimNeighbors	1.06	0.00	1.06
validSDF	0.02	0.00	0.02
view	0.04	0.00	0.04
write.SDF	0.14	0.01	0.16
write.SDFsplit	0.02	0.00	0.02
write.SMI	0	0	0

CHECK report for ChemmineR on tokay2

Summary

Command output

Installation output

Tests output

Example timings