Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-10-28 11:48 -0400 (Mon, 28 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4501
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4761
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4504
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4535
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4483
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4491
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 328/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChemmineR 3.57.1  (landing page)
Thomas Girke
Snapshot Date: 2024-10-27 02:55 -0400 (Sun, 27 Oct 2024)
git_url: https://git.bioconductor.org/packages/ChemmineR
git_branch: devel
git_last_commit: 0dd0179
git_last_commit_date: 2024-09-26 11:02:20 -0400 (Thu, 26 Sep 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for ChemmineR on kjohnson3

To the developers/maintainers of the ChemmineR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChemmineR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ChemmineR
Version: 3.57.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChemmineR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChemmineR_3.57.1.tar.gz
StartedAt: 2024-10-27 11:29:11 -0400 (Sun, 27 Oct 2024)
EndedAt: 2024-10-27 11:33:33 -0400 (Sun, 27 Oct 2024)
EllapsedTime: 262.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChemmineR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChemmineR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChemmineR_3.57.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ChemmineR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChemmineR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChemmineR’ version ‘3.57.1’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 NOTE
Package which this enhances but not available for checking: ‘ChemmineOB’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ChemmineR’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘png’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘ChemmineDrugs’ ‘ChemmineOB’ ‘RPostgreSQL’ ‘RSQLite’ ‘fmcsR’ ‘png’
  ‘snow’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘BiocGenerics’
  All declared Imports should be used.
Unavailable namespace imported from by a ':::' call: ‘ChemmineOB’
  See the note in ?`:::` about the use of this operator.
* 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 ... NOTE
checkRd: (-1) cmp.duplicated.Rd:29: Escaped LaTeX specials: \$
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘sdfid<-’
Undocumented S4 methods:
  generic '$' and siglist '_p_Descriptors'
  generic '[' and siglist 'ExternalReferenceSwig'
  generic '[<-' and siglist 'ExternalReferenceSwig'
  generic 'coerce' and siglist 'ExternalReferenceSwig,character'
  generic 'length' and siglist 'SWIGArray'
  generic 'sdfid<-' and siglist 'SDFset'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... NOTE
Argument items with no description in Rd file 'cmp.search.Rd':
  ‘visualize’ ‘visualize.browse’ ‘visualize.query’
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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 nor [v]sprintf. 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 ... 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, 7 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.


Installation output

ChemmineR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘ChemmineR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fPIC  -falign-functions=64 -Wall -g -O2   -c DisjointSets.cpp -o DisjointSets.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fPIC  -falign-functions=64 -Wall -g -O2   -c cluster.cc -o cluster.o
cluster.cc:49:13: warning: unused function 'prepare_neighbors' [-Wunused-function]
void static prepare_neighbors(const char* nbr_file, int skip, int p)
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fPIC  -falign-functions=64 -Wall -g -O2   -c cstrsplit.cc -o cstrsplit.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fPIC  -falign-functions=64 -Wall -g -O2   -c desc.cc -o desc.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fPIC  -falign-functions=64 -Wall -g -O2   -c fingerprints.cc -o fingerprints.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fPIC  -falign-functions=64 -Wall -g -O2   -c formats.cc -o formats.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fPIC  -falign-functions=64 -Wall -g -O2   -c molecule.cc -o molecule.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fPIC  -falign-functions=64 -Wall -g -O2   -c r_wrap.cc -o r_wrap.o
r_wrap.cc:758:10: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
# define R_NO_REMAP
         ^
<command line>:5:9: note: previous definition is here
#define R_NO_REMAP 1
        ^
r_wrap.cc:761:10: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined]
# define STRICT_R_HEADERS
         ^
<command line>:4:9: note: previous definition is here
#define STRICT_R_HEADERS 1
        ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fPIC  -falign-functions=64 -Wall -g -O2   -c script.cc -o script.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include   -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fPIC  -falign-functions=64 -Wall -g -O2   -c similarity.cc -o similarity.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.4-arm64/Resources/library/00LOCK-ChemmineR/00new/ChemmineR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ChemmineR)

Tests output

ChemmineR.Rcheck/tests/runTests.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

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

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

> BiocGenerics:::testPackage("ChemmineR")
======= testing fpset ===============================================
======= folding... 
Loading required package: RSQLite
[1] "createing db"
[1] "createing db"
[1] "loading first half, no features"
[1] "createing db"
[1] "loading first half,with features"
adding new features to existing compounds. This could take a while
[1] "loading incomplete features"
[1] "loading second half"
adding new features to existing compounds. This could take a while
[1] "done loading"
[1] "createing db"
adding new features to existing compounds. This could take a while
[1] "found 70  compounds"
[1] "found 20  compounds"
Timing stopped at: 0 0 0
Error in DEACTIVATED("local test") : local test
In addition: There were 13 warnings (use warnings() to see them)
Timing stopped at: 0 0 0.001
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 (<-localhost:11751)
2: In for (i in seq_along(snames)) { :
  closing unused connection 5 (<-localhost:11751)
3: In for (i in seq_along(snames)) { :
  closing unused connection 4 (<-localhost:11751)
Timing stopped at: 0 0 0
Error in DEACTIVATED("this test requires ChemmineOB, but not available") : 
  this test requires ChemmineOB, but not available
Timing stopped at: 0 0 0
Error in DEACTIVATED("this test requires ChemmineOB, but not available") : 
  this test requires ChemmineOB, but not available
Timing stopped at: 0 0 0
Error in DEACTIVATED("this test requires ChemmineOB, but not available") : 
  this test requires ChemmineOB, but not available
Timing stopped at: 0 0 0
Error in DEACTIVATED("this test requires ChemmineOB, but not available") : 
  this test requires ChemmineOB, but not available
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("this test requires ChemmineOB, but not available") : 
  this test requires ChemmineOB, but not available
Timing stopped at: 0 0 0.001
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
Timing stopped at: 0 0 0
Error in DEACTIVATED("Causes SSL protocol version error on BioC") : 
  Causes SSL protocol version error on BioC
Timing stopped at: 0 0 0
Error in DEACTIVATED("this test requires ChemmineOB, but not available") : 
  this test requires ChemmineOB, but not available
Timing stopped at: 0 0 0
Error in DEACTIVATED("this test requires ChemmineOB, but not installed") : 
  this test requires ChemmineOB, but not installed


RUNIT TEST PROTOCOL -- Sun Oct 27 11:33:28 2024 
*********************************************** 
Number of test functions: 16 
Number of deactivated test functions: 15 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ChemmineR RUnit Tests - 16 test functions, 0 errors, 0 failures
Number of test functions: 16 
Number of deactivated test functions: 15 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  3.277   0.354   3.935 

Example timings

ChemmineR.Rcheck/ChemmineR-Ex.timings

nameusersystemelapsed
AP-class0.0890.0350.124
APset-class0.1140.0330.147
ExtSDF-class0.0010.0000.001
FP-class0.0170.0020.019
FPset-class0.0680.0100.079
SDF-class0.0130.0040.016
SDF2apcmp0.0080.0000.008
SDFDataTable000
SDFset-class0.0750.0150.090
SDFset2SDF0.0190.0040.022
SDFset2list0.0140.0150.030
SDFstr-class0.0720.0020.075
SMI-class0.0000.0010.001
SMIset-class0.0010.0010.002
addDescriptorType000
addNewFeatures0.8000.0580.861
ap0.0220.0060.029
apfp0.0000.0010.001
apset0.0020.0000.002
apset2descdb0.0840.0340.118
atomblock0.0200.0070.028
atomcount0.0440.0040.048
atomprop0.0010.0000.001
atomsubset0.0080.0010.009
batchByIndex000
bondblock0.0190.0050.024
bonds0.0100.0010.010
browseJob000
bufferLines000
bufferResultSet000
byCluster0.2450.0240.270
canonicalNumbering000
canonicalize000
cid0.0070.0000.008
cluster.sizestat0.1670.0160.182
cluster.visualize0.2120.0170.229
cmp.cluster0.5630.0580.621
cmp.duplicated0.0140.0010.016
cmp.parse0.0140.0010.015
cmp.parse1000
cmp.search0.2200.0270.247
cmp.similarity0.0120.0030.015
conMA0.0150.0050.020
connections0.0560.0020.059
datablock0.0580.0040.061
datablock2ma0.0120.0010.013
db.explain0.0110.0020.014
db.subset0.0010.0010.001
dbTransaction0.0070.0020.009
desc2fp0.0270.0020.029
draw_sdf0.1750.0110.388
exactMassOB000
findCompounds0.7340.0200.754
findCompoundsByName0.0840.0050.090
fingerprintOB000
fold0.0010.0010.001
foldCount000
fp2bit0.0840.0120.097
fpSim0.0880.0150.103
fptype000
fromNNMatrix0.2360.0320.268
genAPDescriptors0.0060.0000.007
genParameters0.0850.0100.095
generate3DCoords0.0000.0000.001
getAllCompoundIds0.0790.0050.084
getAtomAttr000
getBondAttr0.0010.0000.000
getCompoundFeatures0.6230.0200.643
getCompoundNames0.0740.0040.078
getCompounds0.0830.0050.087
getIds000
grepSDFset0.0140.0010.015
groups0.0290.0020.031
header0.0230.0020.024
initDb0.0060.0020.008
jarvisPatrick0.5080.0560.564
jobToken-class000
largestComponent000
launchCMTool0.0000.0010.000
listCMTools000
listFeatures0.0800.0040.084
loadSdf0.6570.0200.678
makeUnique0.0060.0010.006
maximallyDissimilar0.0480.0030.051
nearestNeighbors0.2940.0200.313
numBits000
obmol000
openBabelPlot000
parBatchByIndex000
plotStruc0.0540.0020.057
propOB000
pubchemCidToSDF000
pubchemFPencoding0.0010.0010.002
pubchemInchi2cid000
pubchemInchikey2sdf000
pubchemName2CID000
pubchemSDFSearch000
pubchemSmilesSearch000
read.AP0.0060.0000.006
read.SDFindex0.0060.0010.006
read.SDFset0.1340.0020.136
read.SDFstr0.1900.0020.192
read.SMIset0.0010.0010.001
regenerateCoords000
result000
rings0.1420.0030.146
sdf.subset000
sdf.visualize0.0060.0000.006
sdf2ap0.0830.0340.119
sdf2list0.0070.0040.012
sdf2smiles000
sdf2str0.0090.0020.011
sdfStream0.0060.0010.006
sdfid0.0060.0000.006
sdfsample0.0090.0010.010
sdfstr2list0.1750.1470.323
searchSim000
searchString000
selectInBatches000
setPriorities000
smartsSearchOB0.0000.0010.000
smiles2sdf000
smisample0.0000.0000.002
status000
toolDetails000
trimNeighbors0.4190.0280.449
validSDF0.0080.0000.008
view0.0120.0020.014
write.SDF0.0350.0020.036
write.SDFsplit0.0060.0010.007
write.SMI0.0010.0000.001