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CHECK report for ChemmineR on malbec1

This page was generated on 2020-04-15 12:05:23 -0400 (Wed, 15 Apr 2020).

Package 264/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChemmineR 3.38.0
Thomas Girke
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/ChemmineR
Branch: RELEASE_3_10
Last Commit: 1cbe310
Last Changed Date: 2019-10-29 13:07:59 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChemmineR
Version: 3.38.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ChemmineR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ChemmineR_3.38.0.tar.gz
StartedAt: 2020-04-15 00:34:00 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:36:37 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 157.2 seconds
RetCode: 0
Status:  OK 
CheckDir: ChemmineR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ChemmineR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ChemmineR_3.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/ChemmineR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChemmineR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChemmineR’ version ‘3.38.0’
* 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
* 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’
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 ... 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 ‘/home/biocbuild/bbs-3.10-bioc/R/library/ChemmineR/libs/ChemmineR.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘_ZSt4cout’, 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.



Installation output

ChemmineR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL ChemmineR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘ChemmineR’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c DisjointSets.cpp -o DisjointSets.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c cluster.cc -o cluster.o
cluster.cc: In function ‘int nbr_intersect(std::vector<int>&, std::vector<int>&)’:
cluster.cc:118:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  while (i < nbrs1.size() and j < nbrs2.size()) {
         ~~^~~~~~~~~~~~~~
cluster.cc:118:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  while (i < nbrs1.size() and j < nbrs2.size()) {
                              ~~^~~~~~~~~~~~~~
cluster.cc: In function ‘int contains(int, std::vector<int>&)’:
cluster.cc:131:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i < list.size(); i++)
               ~~^~~~~~~~~~~~~
cluster.cc: In function ‘DisjointSets cluster(int, int, int, int)’:
cluster.cc:267:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int j = 0; j < nbr_list[i].size(); j ++) {
                   ~~^~~~~~~~~~~~~~~~~~~~
cluster.cc: In function ‘void loadNNMatrix(int, int, int, SEXP)’:
cluster.cc:284:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned i=0; i<N; i++) //rows
                    ~^~
cluster.cc:298:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(nbrs.size() < minNbrs) // will end up a singleton
      ~~~~~~~~~~~~^~~~~~~~~
cluster.cc: In function ‘void loadNNList(int, int, SEXP)’:
cluster.cc:314:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned i=0; i<N; i++) //rows
                    ~^~
cluster.cc:332:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(nbrs.size() < minNbrs) // will end up a singleton
      ~~~~~~~~~~~~^~~~~~~~~
cluster.cc: In function ‘SEXPREC* jarvis_patrick(SEXP, SEXP, SEXP, SEXP, SEXP)’:
cluster.cc:390:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned i=0; i<N; i++){
                    ~^~
cluster.cc: At global scope:
cluster.cc:49:13: warning: ‘void prepare_neighbors(const char*, int, int)’ defined but not used [-Wunused-function]
 void static prepare_neighbors(const char* nbr_file, int skip, int p)
             ^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c cstrsplit.cc -o cstrsplit.o
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from cstrsplit.cc:7:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from cstrsplit.cc:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c desc.cc -o desc.o
desc.cc: In function ‘SEXPREC* genAPDescriptor(SEXP)’:
desc.cc:249:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i < descs.size(); i++)
               ~~^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c fingerprints.cc -o fingerprints.o
fingerprints.cc: In function ‘SEXPREC* uniquifyAtomPairs(SEXP)’:
fingerprints.cc:138:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i < aps.size(); i++)
               ~~^~~~~~~~~~~~
fingerprints.cc:145:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i < aps.size(); i++){
               ~~^~~~~~~~~~~~
fingerprints.cc:158:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i < aps.size(); i++){
               ~~^~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c formats.cc -o formats.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c molecule.cc -o molecule.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c r_wrap.cc -o r_wrap.o
r_wrap.cc: In function ‘SEXPREC* SWIG_MakePtr(void*, const char*, R_SWIG_Owner)’:
r_wrap.cc:949:15: warning: variable ‘p’ set but not used [-Wunused-but-set-variable]
   const char *p = typeName;
               ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c script.cc -o script.o
In file included from script.cc:2:0:
desc.h:39:13: warning: ‘elements’ defined but not used [-Wunused-variable]
 static char elements[112][3] = {
             ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c similarity.cc -o similarity.o
In file included from similarity.cc:1:0:
desc.h:39:13: warning: ‘elements’ defined but not used [-Wunused-variable]
 static char elements[112][3] = {
             ^~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o ChemmineR.so DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
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: 14
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 Apr 15 00:36:30 2020 
*********************************************** 
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 8 (https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastsimilarity_2d/smiles/C1CCCCCC1/SDF)
2: In .Internal(paste(list(...), sep, collapse)) :
  closing unused connection 7 (https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/434,435/SDF)
3: In for (i in seq_along(methods)) { :
  closing unused connection 6 (<-localhost:11256)
4: In for (i in seq_along(methods)) { :
  closing unused connection 5 (<-localhost:11256)
5: In for (i in seq_along(methods)) { :
  closing unused connection 4 (<-localhost:11256)
6: In for (i in seq_along(methods)) { :
  closing unused connection 3 (/tmp/RtmpgauBrg/file8b9411d3ac4)
> 
> proc.time()
   user  system elapsed 
 16.540   0.368  46.102 

Example timings

ChemmineR.Rcheck/ChemmineR-Ex.timings

nameusersystemelapsed
AP-class0.3360.0680.404
APset-class0.2680.0440.314
ExtSDF-class0.0040.0000.001
FP-class0.0840.0000.086
FPset-class0.2960.0160.312
SDF-class0.0440.0040.050
SDF2apcmp0.0240.0000.022
SDFDataTable1.6200.1123.072
SDFset-class0.4400.0560.506
SDFset2SDF0.1440.0040.150
SDFset2list0.0640.0240.086
SDFstr-class0.4120.0040.415
SMI-class0.0040.0000.003
SMIset-class0.0080.0000.006
addDescriptorType000
addNewFeatures2.9440.0322.980
ap0.0760.0040.078
apfp0.0000.0000.002
apset0.0000.0040.004
apset2descdb0.2600.0560.313
atomblock0.0760.0080.082
atomcount0.1600.0000.161
atomprop0.0000.0040.003
atomsubset0.0240.0040.027
batchByIndex000
bondblock0.0960.0120.107
bonds0.0480.0000.047
browseJob000
bufferLines000
bufferResultSet0.0000.0000.001
byCluster0.8520.0000.853
canonicalNumbering0.0480.0000.061
canonicalize0.0600.0000.063
cid0.0320.0000.031
cluster.sizestat0.5880.0040.593
cluster.visualize0.7440.0080.758
cmp.cluster1.8000.0121.812
cmp.duplicated0.0720.0000.071
cmp.parse0.0200.0040.022
cmp.parse1000
cmp.search0.5040.0040.508
cmp.similarity0.0120.0000.013
conMA0.0440.0040.048
connections0.2800.0040.328
datablock0.2720.0120.287
datablock2ma0.0480.0040.051
db.explain0.0520.0040.056
db.subset0.0040.0000.004
dbTransaction0.0240.0000.023
desc2fp0.1360.0000.137
draw_sdf0.6400.0120.652
exactMassOB0.7560.0000.757
findCompounds3.9040.0083.926
findCompoundsByName0.4920.0120.533
fingerprintOB000
fold0.0000.0000.001
foldCount0.0000.0000.001
fp2bit0.3320.0080.343
fpSim0.3960.0000.400
fptype0.0000.0000.001
fromNNMatrix0.9800.0080.992
genAPDescriptors0.0240.0000.027
genParameters0.3360.0000.335
generate3DCoords0.0040.0000.000
getAllCompoundIds0.4720.0000.476
getCompoundFeatures3.8960.0043.916
getCompoundNames0.4520.0080.483
getCompounds0.4120.0000.423
getIds000
grepSDFset0.0680.0000.067
groups0.1480.0080.156
header0.0640.0000.064
initDb0.0200.0000.021
jarvisPatrick1.6120.0001.613
jobToken-class000
largestComponent0.2040.0000.202
launchCMTool000
listCMTools000
listFeatures0.3120.0040.313
loadSdf4.0200.0044.035
makeUnique0.0160.0000.015
maximallyDissimilar0.2560.0000.256
nearestNeighbors1.1160.0001.118
numBits0.0040.0000.001
obmol0.0480.0000.049
openBabelPlot000
parBatchByIndex0.0000.0000.001
plotStruc0.3320.0000.332
propOB0.0000.0000.001
pubchemCidToSDF0.0000.0000.001
pubchemFPencoding0.0040.0000.003
pubchemName2CID000
pubchemSDFSearch000
pubchemSmilesSearch000
read.AP0.0200.0040.025
read.SDFindex0.0280.0000.025
read.SDFset0.8560.0040.861
read.SDFstr1.1480.0001.147
read.SMIset0.0000.0000.001
regenerateCoords000
result000
rings0.7920.0080.802
sdf.subset000
sdf.visualize0.0160.0000.016
sdf2ap0.2840.0320.314
sdf2list0.0320.0080.040
sdf2smiles000
sdf2str0.0400.0040.044
sdfStream0.0240.0000.026
sdfid0.0280.0000.028
sdfsample0.0480.0040.052
sdfstr2list0.7520.2400.998
searchSim000
searchString0.0000.0000.001
selectInBatches0.0040.0000.000
setPriorities000
smartsSearchOB000
smiles2sdf000
smisample0.0000.0040.002
status000
toolDetails000
trimNeighbors1.3200.0001.321
validSDF0.0280.0000.028
view0.0680.0040.072
write.SDF0.1960.0080.206
write.SDFsplit0.0240.0000.025
write.SMI0.0000.0000.002