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CHECK report for ChemmineR on merida1

This page was generated on 2020-04-15 12:35:41 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChemmineR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChemmineR_3.38.0.tar.gz
StartedAt: 2020-04-15 01:05:08 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 01:08:27 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 198.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ChemmineR.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChemmineR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChemmineR_3.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/ChemmineR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChemmineR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChemmineR’ version ‘3.38.0’
* 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 ... WARNING
Found the following significant warnings:
  r_wrap.cc:563:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  r_wrap.cc:564:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  r_wrap.cc:567:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  r_wrap.cc:570:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  r_wrap.cc:614:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  r_wrap.cc:633:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  r_wrap.cc:634:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  r_wrap.cc:636:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  r_wrap.cc:648:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  r_wrap.cc:649:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  r_wrap.cc:651:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  r_wrap.cc:652:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  r_wrap.cc:1689:14: warning: explicitly assigning value of variable of type 'void *' to itself [-Wself-assign]
See ‘/Users/biocbuild/bbs-3.10-bioc/meat/ChemmineR.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘png’ ‘ChemmineOB’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘ChemmineDrugs’ ‘ChemmineOB’ ‘RPostgreSQL’ ‘RSQLite’ ‘fmcsR’ ‘png’
  ‘snow’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘BiocGenerics’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File ‘ChemmineR/R/sim.R’:
  unlockBinding(".progress_bar_int_cnt", environment(.progress_bar))

.data.frame.to.str: no visible global function definition for
  ‘write.table’
.data.frame.to.str: no visible binding for global variable ‘string’
.parseV3000: no visible binding for global variable ‘AW’
.rings: no visible global function definition for ‘combn’
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 ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ChemmineR/libs/ChemmineR.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.



Installation output

ChemmineR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ChemmineR’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c DisjointSets.cpp -o DisjointSets.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c cluster.cc -o cluster.o
cluster.cc:49:13: warning: unused function 'prepare_neighbors' [-Wunused-function]
void static prepare_neighbors(const char* nbr_file, int skip, int p)
            ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c cstrsplit.cc -o cstrsplit.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c desc.cc -o desc.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c fingerprints.cc -o fingerprints.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c formats.cc -o formats.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c molecule.cc -o molecule.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c r_wrap.cc -o r_wrap.o
r_wrap.cc:563:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
      register size_t l = 0;
      ^~~~~~~~~
r_wrap.cc:564:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
      register size_t r = iter->size - 1;
      ^~~~~~~~~
r_wrap.cc:567:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
        register size_t i = (l + r) >> 1; 
        ^~~~~~~~~
r_wrap.cc:570:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
          register int compare = strcmp(name, iname);
          ^~~~~~~~~
r_wrap.cc:614:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
      register size_t i = 0;
      ^~~~~~~~~
r_wrap.cc:633:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register const unsigned char *u = (unsigned char *) ptr;
  ^~~~~~~~~
r_wrap.cc:634:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register const unsigned char *eu =  u + sz;
  ^~~~~~~~~
r_wrap.cc:636:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register unsigned char uu = *u;
    ^~~~~~~~~
r_wrap.cc:648:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register unsigned char *u = (unsigned char *) ptr;
  ^~~~~~~~~
r_wrap.cc:649:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register const unsigned char *eu = u + sz;
  ^~~~~~~~~
r_wrap.cc:651:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register char d = *(c++);
    ^~~~~~~~~
r_wrap.cc:652:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register unsigned char uu;
    ^~~~~~~~~
r_wrap.cc:1689:14: warning: explicitly assigning value of variable of type 'void *' to itself [-Wself-assign]
  clientdata = clientdata;
  ~~~~~~~~~~ ^ ~~~~~~~~~~
13 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c script.cc -o script.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c similarity.cc -o similarity.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ChemmineR.so DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

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

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

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

> BiocGenerics:::testPackage("ChemmineR")
Loading required package: RSQLite
[1] "createing db"
[1] "createing db"
[1] "loading first half, no features"
[1] "createing db"
[1] "loading first half,with features"
adding new features to existing compounds. This could take a while
[1] "loading incomplete features"
[1] "loading second half"
adding new features to existing compounds. This could take a while
[1] "done loading"
[1] "createing db"
adding new features to existing compounds. This could take a while
[1] "found 70  compounds"
[1] "found 20  compounds"
Timing stopped at: 0 0 0.001
Error in DEACTIVATED("local test") : local test
In addition: There were 15 warnings (use warnings() to see them)
Timing stopped at: 0 0 0
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 5 (<-localhost:11047)
2: In for (i in seq_along(snames)) { :
  closing unused connection 4 (<-localhost:11047)
3: In for (i in seq_along(snames)) { :
  closing unused connection 3 (<-localhost:11047)
test.formatConversions
Timing stopped at: 0 0 0
Error in DEACTIVATED("removed old version of function") : 
  removed old version of function
Timing stopped at: 0.001 0 0.001
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 01:08:18 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 for (i in seq_along(snames)) { :
  closing unused connection 4 (https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastsimilarity_2d/smiles/C1CCCCCC1/SDF)
2: In for (i in seq_along(snames)) { :
  closing unused connection 3 (https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/434,435/SDF)
> 
> proc.time()
   user  system elapsed 
 22.325   1.338  69.218 

Example timings

ChemmineR.Rcheck/ChemmineR-Ex.timings

nameusersystemelapsed
AP-class0.4380.1200.563
APset-class0.4530.1090.565
ExtSDF-class0.0020.0010.002
FP-class0.0730.0030.076
FPset-class0.3550.0240.383
SDF-class0.0740.0080.083
SDF2apcmp0.0210.0010.023
SDFDataTable2.3290.1322.540
SDFset-class0.4700.0570.537
SDFset2SDF0.1170.0080.126
SDFset2list0.0610.0290.090
SDFstr-class0.3340.0060.349
SMI-class0.0020.0010.004
SMIset-class0.0060.0010.006
addDescriptorType000
addNewFeatures4.0560.1364.254
ap0.1050.0140.123
apfp0.0030.0010.003
apset0.0050.0020.008
apset2descdb0.3600.1040.471
atomblock0.1180.0180.136
atomcount0.1970.0090.206
atomprop0.0030.0010.004
atomsubset0.0250.0020.026
batchByIndex000
bondblock0.0740.0090.083
bonds0.0330.0030.037
browseJob000
bufferLines000
bufferResultSet0.0010.0000.001
byCluster0.7390.0690.818
canonicalNumbering0.0450.0020.048
canonicalize0.0420.0020.043
cid0.0360.0070.043
cluster.sizestat0.5300.0270.559
cluster.visualize0.7110.0430.763
cmp.cluster2.2480.0822.346
cmp.duplicated0.0540.0020.057
cmp.parse0.0310.0010.033
cmp.parse1000
cmp.search0.6840.0280.719
cmp.similarity0.0230.0020.025
conMA0.0870.0150.104
connections0.2500.0040.257
datablock0.3080.0100.320
datablock2ma0.0520.0020.056
db.explain0.0620.0060.068
db.subset0.0040.0010.005
dbTransaction0.0260.0030.029
desc2fp0.1220.0040.127
draw_sdf0.5900.0380.647
exactMassOB0.6640.0040.672
findCompounds3.6920.0233.773
findCompoundsByName0.3620.0080.373
fingerprintOB000
fold0.0020.0010.002
foldCount0.0010.0000.002
fp2bit0.3440.0380.385
fpSim0.3380.0410.382
fptype0.0010.0000.001
fromNNMatrix0.9460.0371.000
genAPDescriptors0.0160.0010.016
genParameters0.3380.0180.356
generate3DCoords000
getAllCompoundIds0.3410.0100.352
getCompoundFeatures3.5860.0203.639
getCompoundNames0.3540.0080.367
getCompounds0.3660.0080.378
getIds0.0000.0000.001
grepSDFset0.0530.0020.055
groups0.1770.0050.184
header0.0980.0030.101
initDb0.0250.0030.029
jarvisPatrick1.8070.0761.900
jobToken-class0.0010.0000.001
largestComponent0.5250.0020.531
launchCMTool0.0000.0010.001
listCMTools0.0000.0000.001
listFeatures0.3720.0080.383
loadSdf4.2250.0334.361
makeUnique0.0220.0010.022
maximallyDissimilar0.2570.0020.265
nearestNeighbors1.0600.0251.101
numBits0.0010.0000.002
obmol0.0380.0010.039
openBabelPlot000
parBatchByIndex0.0000.0000.001
plotStruc0.3510.0070.362
propOB0.0000.0010.001
pubchemCidToSDF0.0000.0000.001
pubchemFPencoding0.0030.0010.004
pubchemName2CID000
pubchemSDFSearch000
pubchemSmilesSearch000
read.AP0.0240.0010.026
read.SDFindex0.0220.0010.022
read.SDFset0.8590.0030.867
read.SDFstr1.1460.0031.166
read.SMIset0.0010.0010.002
regenerateCoords000
result0.0000.0000.001
rings0.8970.0090.918
sdf.subset000
sdf.visualize0.0260.0020.028
sdf2ap0.3840.0860.476
sdf2list0.0270.0110.038
sdf2smiles0.0000.0000.001
sdf2str0.0420.0050.047
sdfStream0.0160.0010.017
sdfid0.0290.0020.031
sdfsample0.0610.0050.067
sdfstr2list1.5810.4512.051
searchSim0.0000.0010.000
searchString0.0000.0000.001
selectInBatches0.0020.0000.002
setPriorities000
smartsSearchOB000
smiles2sdf0.0000.0010.000
smisample0.0040.0010.004
status000
toolDetails0.0010.0000.001
trimNeighbors1.3490.0561.415
validSDF0.0260.0010.027
view0.0780.0050.087
write.SDF0.2060.0110.224
write.SDFsplit0.0260.0020.028
write.SMI0.0020.0010.003