Thomas Girke
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ChemmineR |
| Branch: master |
| Last Commit: 2906861 |
| Last Changed Date: 2019-03-18 13:12:04 -0400 (Mon, 18 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:24:33 -0400 (Tue, 09 Apr 2019).
| Package 245/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ChemmineR 3.35.6 Thomas Girke
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK |
| Package: ChemmineR |
| Version: 3.35.6 |
| 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_3.35.6.tar.gz |
| StartedAt: 2019-04-08 23:47:31 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 23:50:26 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 175.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ChemmineR.Rcheck |
| Warnings: 1 |
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### Running command:
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### /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_3.35.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ChemmineR.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘3.35.6’
* 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++1z [-Wdeprecated-register]
r_wrap.cc:564:7: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
r_wrap.cc:567:2: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
r_wrap.cc:570:4: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
r_wrap.cc:614:7: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
r_wrap.cc:633:3: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
r_wrap.cc:634:3: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
r_wrap.cc:636:5: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
r_wrap.cc:648:3: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
r_wrap.cc:649:3: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
r_wrap.cc:651:5: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
r_wrap.cc:652:5: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
r_wrap.cc:1689:14: warning: explicitly assigning value of variable of type 'void *' to itself [-Wself-assign]
See ‘/Users/biocbuild/bbs-3.9-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-3.9-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.
ChemmineR.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ChemmineR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ChemmineR’ ...
** 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" -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" -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" -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" -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" -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" -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" -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" -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++1z [-Wdeprecated-register]
register size_t l = 0;
^˜˜˜˜˜˜˜˜
r_wrap.cc:564:7: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-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++1z [-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++1z [-Wdeprecated-register]
register int compare = strcmp(name, iname);
^˜˜˜˜˜˜˜˜
r_wrap.cc:614:7: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
register size_t i = 0;
^˜˜˜˜˜˜˜˜
r_wrap.cc:633:3: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-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++1z [-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++1z [-Wdeprecated-register]
register unsigned char uu = *u;
^˜˜˜˜˜˜˜˜
r_wrap.cc:648:3: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-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++1z [-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++1z [-Wdeprecated-register]
register char d = *(c++);
^˜˜˜˜˜˜˜˜
r_wrap.cc:652:5: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-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" -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" -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/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
* DONE (ChemmineR)
ChemmineR.Rcheck/tests/runTests.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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: closing unused connection 5 (<-localhost:11067)
2: closing unused connection 4 (<-localhost:11067)
3: closing unused connection 3 (<-localhost:11067)
test.formatConversions
Timing stopped at: 0 0 0.001
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: 0.001 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: 92
[1] "rotable bonds: "
CMP1 CMP2 CMP3 CMP4 CMP5
24 20 14 30 10
[1] "650001" "650002" "650003" "650004" "650005"
RUNIT TEST PROTOCOL -- Mon Apr 8 23:50:15 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 matrix(as.numeric(ctma), nrow = length(ct), ncol = Ncol, dimnames = list(1:length(ct), :
closing unused connection 4 (https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastsimilarity_2d/smiles/C1CCCCCC1/SDF)
2: In matrix(as.numeric(ctma), nrow = length(ct), ncol = Ncol, dimnames = list(1:length(ct), :
closing unused connection 3 (https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/434,435/SDF)
>
> proc.time()
user system elapsed
22.529 1.382 52.189
ChemmineR.Rcheck/ChemmineR-Ex.timings
| name | user | system | elapsed | |
| AP-class | 0.439 | 0.106 | 0.547 | |
| APset-class | 0.404 | 0.099 | 0.509 | |
| ExtSDF-class | 0.002 | 0.000 | 0.002 | |
| FP-class | 0.069 | 0.004 | 0.075 | |
| FPset-class | 0.355 | 0.027 | 0.387 | |
| SDF-class | 0.088 | 0.010 | 0.099 | |
| SDF2apcmp | 0.026 | 0.001 | 0.028 | |
| SDFDataTable | 2.226 | 0.135 | 2.418 | |
| SDFset-class | 0.509 | 0.041 | 0.555 | |
| SDFset2SDF | 0.136 | 0.011 | 0.148 | |
| SDFset2list | 0.069 | 0.035 | 0.106 | |
| SDFstr-class | 0.332 | 0.007 | 0.343 | |
| SMI-class | 0.003 | 0.000 | 0.003 | |
| SMIset-class | 0.005 | 0.001 | 0.006 | |
| addDescriptorType | 0 | 0 | 0 | |
| addNewFeatures | 4.064 | 0.141 | 4.281 | |
| ap | 0.112 | 0.018 | 0.130 | |
| apfp | 0.003 | 0.000 | 0.003 | |
| apset | 0.004 | 0.001 | 0.005 | |
| apset2descdb | 0.384 | 0.105 | 0.496 | |
| atomblock | 0.113 | 0.020 | 0.134 | |
| atomcount | 0.183 | 0.008 | 0.191 | |
| atomprop | 0.005 | 0.001 | 0.006 | |
| atomsubset | 0.033 | 0.002 | 0.035 | |
| batchByIndex | 0 | 0 | 0 | |
| bondblock | 0.112 | 0.012 | 0.125 | |
| bonds | 0.045 | 0.003 | 0.049 | |
| browseJob | 0.000 | 0.000 | 0.001 | |
| bufferLines | 0 | 0 | 0 | |
| bufferResultSet | 0.000 | 0.001 | 0.001 | |
| byCluster | 0.777 | 0.062 | 0.850 | |
| canonicalNumbering | 0.041 | 0.001 | 0.042 | |
| canonicalize | 0.053 | 0.003 | 0.056 | |
| cid | 0.030 | 0.002 | 0.032 | |
| cluster.sizestat | 0.503 | 0.042 | 0.553 | |
| cluster.visualize | 0.696 | 0.039 | 0.746 | |
| cmp.cluster | 2.156 | 0.060 | 2.234 | |
| cmp.duplicated | 0.060 | 0.002 | 0.061 | |
| cmp.parse | 0.029 | 0.002 | 0.031 | |
| cmp.parse1 | 0 | 0 | 0 | |
| cmp.search | 0.641 | 0.049 | 0.695 | |
| cmp.similarity | 0.018 | 0.001 | 0.022 | |
| conMA | 0.071 | 0.011 | 0.088 | |
| connections | 0.246 | 0.004 | 0.260 | |
| datablock | 0.275 | 0.010 | 0.291 | |
| datablock2ma | 0.041 | 0.001 | 0.044 | |
| db.explain | 0.066 | 0.006 | 0.074 | |
| db.subset | 0.002 | 0.001 | 0.003 | |
| dbTransaction | 0.020 | 0.003 | 0.024 | |
| desc2fp | 0.096 | 0.004 | 0.099 | |
| draw_sdf | 0.539 | 0.039 | 0.601 | |
| exactMassOB | 0.596 | 0.002 | 0.606 | |
| findCompounds | 3.467 | 0.027 | 3.526 | |
| findCompoundsByName | 0.310 | 0.007 | 0.323 | |
| fingerprintOB | 0.000 | 0.001 | 0.001 | |
| fold | 0.001 | 0.000 | 0.002 | |
| foldCount | 0.002 | 0.000 | 0.001 | |
| fp2bit | 0.375 | 0.041 | 0.420 | |
| fpSim | 0.557 | 0.053 | 0.612 | |
| fptype | 0.001 | 0.000 | 0.001 | |
| fromNNMatrix | 0.719 | 0.034 | 0.760 | |
| genAPDescriptors | 0.025 | 0.002 | 0.026 | |
| genParameters | 0.629 | 0.006 | 0.643 | |
| generate3DCoords | 0.000 | 0.000 | 0.001 | |
| getAllCompoundIds | 0.364 | 0.007 | 0.373 | |
| getCompoundFeatures | 3.315 | 0.022 | 3.369 | |
| getCompoundNames | 0.355 | 0.007 | 0.363 | |
| getCompounds | 0.406 | 0.009 | 0.420 | |
| getIds | 0 | 0 | 0 | |
| grepSDFset | 0.066 | 0.002 | 0.069 | |
| groups | 0.189 | 0.006 | 0.198 | |
| header | 0.093 | 0.003 | 0.096 | |
| initDb | 0.029 | 0.005 | 0.037 | |
| jarvisPatrick | 1.878 | 0.063 | 1.965 | |
| jobToken-class | 0.001 | 0.000 | 0.001 | |
| largestComponent | 0.580 | 0.001 | 0.588 | |
| launchCMTool | 0.001 | 0.000 | 0.000 | |
| listCMTools | 0.000 | 0.001 | 0.000 | |
| listFeatures | 0.424 | 0.009 | 0.439 | |
| loadSdf | 3.887 | 0.031 | 3.973 | |
| makeUnique | 0.026 | 0.001 | 0.027 | |
| maximallyDissimilar | 0.256 | 0.001 | 0.261 | |
| nearestNeighbors | 1.159 | 0.043 | 1.215 | |
| numBits | 0.000 | 0.000 | 0.001 | |
| obmol | 0.037 | 0.001 | 0.039 | |
| openBabelPlot | 0 | 0 | 0 | |
| parBatchByIndex | 0.000 | 0.000 | 0.001 | |
| plotStruc | 0.380 | 0.009 | 0.397 | |
| propOB | 0 | 0 | 0 | |
| pubchemCidToSDF | 0.000 | 0.000 | 0.001 | |
| pubchemFPencoding | 0.004 | 0.001 | 0.005 | |
| pubchemName2CID | 0 | 0 | 0 | |
| pubchemSDFSearch | 0.000 | 0.000 | 0.001 | |
| pubchemSmilesSearch | 0.000 | 0.000 | 0.001 | |
| read.AP | 0.018 | 0.001 | 0.019 | |
| read.SDFindex | 0.016 | 0.001 | 0.018 | |
| read.SDFset | 0.730 | 0.002 | 0.744 | |
| read.SDFstr | 1.090 | 0.004 | 1.100 | |
| read.SMIset | 0.002 | 0.001 | 0.004 | |
| regenerateCoords | 0.001 | 0.001 | 0.000 | |
| result | 0.001 | 0.000 | 0.001 | |
| rings | 0.894 | 0.009 | 0.915 | |
| sdf.subset | 0.001 | 0.000 | 0.001 | |
| sdf.visualize | 0.025 | 0.002 | 0.028 | |
| sdf2ap | 0.362 | 0.068 | 0.433 | |
| sdf2list | 0.035 | 0.014 | 0.049 | |
| sdf2smiles | 0.000 | 0.000 | 0.001 | |
| sdf2str | 0.044 | 0.011 | 0.056 | |
| sdfStream | 0.018 | 0.001 | 0.018 | |
| sdfid | 0.019 | 0.001 | 0.021 | |
| sdfsample | 0.055 | 0.003 | 0.058 | |
| sdfstr2list | 1.372 | 0.449 | 1.841 | |
| searchSim | 0 | 0 | 0 | |
| searchString | 0 | 0 | 0 | |
| selectInBatches | 0.001 | 0.000 | 0.001 | |
| setPriorities | 0 | 0 | 0 | |
| smartsSearchOB | 0 | 0 | 0 | |
| smiles2sdf | 0.000 | 0.001 | 0.000 | |
| smisample | 0.004 | 0.001 | 0.005 | |
| status | 0 | 0 | 0 | |
| toolDetails | 0.000 | 0.000 | 0.001 | |
| trimNeighbors | 1.301 | 0.065 | 1.383 | |
| validSDF | 0.026 | 0.001 | 0.027 | |
| view | 0.063 | 0.005 | 0.068 | |
| write.SDF | 0.218 | 0.003 | 0.226 | |
| write.SDFsplit | 0.015 | 0.000 | 0.016 | |
| write.SMI | 0.002 | 0.000 | 0.002 | |