Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 328/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChemmineR 3.58.0 (landing page) Thomas Girke
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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. |
Package: ChemmineR |
Version: 3.58.0 |
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_3.58.0.tar.gz |
StartedAt: 2024-12-20 01:01:10 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 01:05:24 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 254.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ChemmineR.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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_3.58.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ChemmineR.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ChemmineR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ChemmineR’ version ‘3.58.0’ * checking package namespace information ... OK * checking package dependencies ... 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 14.0.0 (clang-1400.0.29.202)’ * 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-x86_64/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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed addNewFeatures 7.122 0.413 7.875 loadSdf 6.532 0.087 6.763 findCompounds 6.336 0.051 6.453 getCompoundFeatures 5.870 0.051 5.978 * 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.
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-x86_64/Resources/library’ * installing *source* package ‘ChemmineR’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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-x86_64/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)
ChemmineR.Rcheck/tests/runTests.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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: 0.001 0 0 Error in DEACTIVATED("local test only") : local test only found 100 ids [1] 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 [19] 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 [37] 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 [55] 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 [73] 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 [91] 291 292 293 294 295 296 297 298 299 300 starting parBatchByIndex Loading required package: snow int [1:100] 201 202 203 204 205 206 207 208 209 210 ... NULL [1] "results: parBench-sub-1,parBench-sub-2,parBench-sub-3,parBench-sub-4,parBench-sub-5,parBench-sub-6,parBench-sub-7,parBench-sub-8,parBench-sub-9,parBench-sub-10" [1] "loading duplications" loading 1 new compounds, updating 1 compounds fetching features: Timing stopped at: 0 0 0 Error in DEACTIVATED("causing timeout on bioc, disabling for now") : causing timeout on bioc, disabling for now In addition: Warning messages: 1: In for (i in seq_along(snames)) { : closing unused connection 6 (<-localhost:11316) 2: In for (i in seq_along(snames)) { : closing unused connection 5 (<-localhost:11316) 3: In for (i in seq_along(snames)) { : closing unused connection 4 (<-localhost:11316) Timing stopped at: 0 0 0.003 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("this test requires ChemmineOB, but not available") : this test requires ChemmineOB, but not available Timing stopped at: 0.001 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: 0.001 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 0.001 0 Error in DEACTIVATED("Causes SSL protocol version error on BioC") : Causes SSL protocol version error on BioC Timing stopped at: 0 0 0.001 Error in DEACTIVATED("this test requires ChemmineOB, but not available") : this test requires ChemmineOB, but not available Timing stopped at: 0.001 0 0.001 Error in DEACTIVATED("this test requires ChemmineOB, but not installed") : this test requires ChemmineOB, but not installed RUNIT TEST PROTOCOL -- Fri Dec 20 01:05:01 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 24.679 2.281 29.320
ChemmineR.Rcheck/ChemmineR-Ex.timings
name | user | system | elapsed | |
AP-class | 0.646 | 0.370 | 1.022 | |
APset-class | 0.558 | 0.371 | 0.937 | |
ExtSDF-class | 0.001 | 0.001 | 0.003 | |
FP-class | 0.096 | 0.016 | 0.113 | |
FPset-class | 0.466 | 0.094 | 0.568 | |
SDF-class | 0.096 | 0.032 | 0.129 | |
SDF2apcmp | 0.036 | 0.003 | 0.040 | |
SDFDataTable | 0.001 | 0.000 | 0.001 | |
SDFset-class | 0.661 | 0.143 | 0.810 | |
SDFset2SDF | 0.143 | 0.036 | 0.179 | |
SDFset2list | 0.102 | 0.162 | 0.265 | |
SDFstr-class | 0.525 | 0.016 | 0.548 | |
SMI-class | 0.003 | 0.002 | 0.006 | |
SMIset-class | 0.008 | 0.004 | 0.012 | |
addDescriptorType | 0.000 | 0.000 | 0.001 | |
addNewFeatures | 7.122 | 0.413 | 7.875 | |
ap | 0.131 | 0.067 | 0.197 | |
apfp | 0.004 | 0.003 | 0.007 | |
apset | 0.006 | 0.004 | 0.010 | |
apset2descdb | 0.545 | 0.375 | 0.928 | |
atomblock | 0.157 | 0.067 | 0.226 | |
atomcount | 0.353 | 0.017 | 0.372 | |
atomprop | 0.006 | 0.003 | 0.009 | |
atomsubset | 0.046 | 0.006 | 0.053 | |
batchByIndex | 0.000 | 0.000 | 0.001 | |
bondblock | 0.159 | 0.049 | 0.209 | |
bonds | 0.048 | 0.011 | 0.059 | |
browseJob | 0.000 | 0.001 | 0.001 | |
bufferLines | 0 | 0 | 0 | |
bufferResultSet | 0.001 | 0.000 | 0.001 | |
byCluster | 1.248 | 0.101 | 1.359 | |
canonicalNumbering | 0.000 | 0.001 | 0.001 | |
canonicalize | 0.001 | 0.000 | 0.000 | |
cid | 0.031 | 0.003 | 0.034 | |
cluster.sizestat | 0.840 | 0.071 | 0.921 | |
cluster.visualize | 1.071 | 0.061 | 1.203 | |
cmp.cluster | 3.660 | 0.168 | 3.877 | |
cmp.duplicated | 0.072 | 0.005 | 0.077 | |
cmp.parse | 0.037 | 0.004 | 0.040 | |
cmp.parse1 | 0.000 | 0.001 | 0.001 | |
cmp.search | 1.080 | 0.057 | 1.158 | |
cmp.similarity | 0.028 | 0.005 | 0.033 | |
conMA | 0.098 | 0.048 | 0.150 | |
connections | 0.408 | 0.008 | 0.421 | |
datablock | 0.456 | 0.036 | 0.495 | |
datablock2ma | 0.062 | 0.008 | 0.070 | |
db.explain | 0.070 | 0.024 | 0.094 | |
db.subset | 0.004 | 0.003 | 0.007 | |
dbTransaction | 0.043 | 0.013 | 0.091 | |
desc2fp | 0.134 | 0.010 | 0.145 | |
draw_sdf | 1.151 | 0.061 | 2.054 | |
exactMassOB | 0.000 | 0.000 | 0.001 | |
findCompounds | 6.336 | 0.051 | 6.453 | |
findCompoundsByName | 0.590 | 0.026 | 0.617 | |
fingerprintOB | 0.001 | 0.000 | 0.001 | |
fold | 0.001 | 0.000 | 0.002 | |
foldCount | 0.002 | 0.001 | 0.002 | |
fp2bit | 0.584 | 0.045 | 0.641 | |
fpSim | 0.57 | 0.06 | 0.63 | |
fptype | 0.001 | 0.000 | 0.002 | |
fromNNMatrix | 1.200 | 0.034 | 1.270 | |
genAPDescriptors | 0.027 | 0.003 | 0.031 | |
genParameters | 0.737 | 0.018 | 0.759 | |
generate3DCoords | 0.000 | 0.000 | 0.001 | |
getAllCompoundIds | 0.592 | 0.027 | 0.624 | |
getAtomAttr | 0.000 | 0.000 | 0.001 | |
getBondAttr | 0.000 | 0.000 | 0.001 | |
getCompoundFeatures | 5.870 | 0.051 | 5.978 | |
getCompoundNames | 0.581 | 0.027 | 0.635 | |
getCompounds | 0.638 | 0.029 | 0.842 | |
getIds | 0.000 | 0.000 | 0.001 | |
grepSDFset | 0.071 | 0.003 | 0.078 | |
groups | 0.272 | 0.031 | 0.374 | |
header | 0.172 | 0.019 | 0.199 | |
initDb | 0.041 | 0.013 | 0.058 | |
jarvisPatrick | 3.305 | 0.067 | 3.594 | |
jobToken-class | 0.001 | 0.002 | 0.003 | |
largestComponent | 0.000 | 0.001 | 0.001 | |
launchCMTool | 0.001 | 0.001 | 0.002 | |
listCMTools | 0.000 | 0.001 | 0.001 | |
listFeatures | 0.664 | 0.027 | 0.794 | |
loadSdf | 6.532 | 0.087 | 6.763 | |
makeUnique | 0.027 | 0.003 | 0.030 | |
maximallyDissimilar | 0.358 | 0.002 | 0.361 | |
nearestNeighbors | 1.556 | 0.039 | 1.615 | |
numBits | 0.001 | 0.001 | 0.002 | |
obmol | 0.001 | 0.001 | 0.002 | |
openBabelPlot | 0.000 | 0.001 | 0.002 | |
parBatchByIndex | 0.000 | 0.001 | 0.001 | |
plotStruc | 0.489 | 0.033 | 0.532 | |
propOB | 0.001 | 0.001 | 0.001 | |
pubchemCidToSDF | 0 | 0 | 0 | |
pubchemFPencoding | 0.004 | 0.003 | 0.007 | |
pubchemInchi2cid | 0.001 | 0.001 | 0.001 | |
pubchemInchikey2sdf | 0.000 | 0.001 | 0.001 | |
pubchemName2CID | 0.000 | 0.000 | 0.002 | |
pubchemSDFSearch | 0.001 | 0.001 | 0.001 | |
pubchemSmilesSearch | 0.000 | 0.001 | 0.000 | |
read.AP | 0.025 | 0.004 | 0.030 | |
read.SDFindex | 0.025 | 0.004 | 0.029 | |
read.SDFset | 1.070 | 0.010 | 1.122 | |
read.SDFstr | 1.578 | 0.016 | 1.770 | |
read.SMIset | 0.002 | 0.002 | 0.003 | |
regenerateCoords | 0.000 | 0.001 | 0.000 | |
result | 0.000 | 0.001 | 0.001 | |
rings | 1.436 | 0.031 | 1.503 | |
sdf.subset | 0.000 | 0.001 | 0.001 | |
sdf.visualize | 0.025 | 0.003 | 0.028 | |
sdf2ap | 0.557 | 0.520 | 1.116 | |
sdf2list | 0.043 | 0.069 | 0.112 | |
sdf2smiles | 0.000 | 0.001 | 0.001 | |
sdf2str | 0.047 | 0.027 | 0.075 | |
sdfStream | 0.026 | 0.004 | 0.030 | |
sdfid | 0.027 | 0.004 | 0.032 | |
sdfsample | 0.066 | 0.021 | 0.087 | |
sdfstr2list | 1.248 | 1.571 | 2.884 | |
searchSim | 0.000 | 0.001 | 0.001 | |
searchString | 0.000 | 0.000 | 0.001 | |
selectInBatches | 0.001 | 0.001 | 0.001 | |
setPriorities | 0.001 | 0.000 | 0.001 | |
smartsSearchOB | 0.000 | 0.000 | 0.001 | |
smiles2sdf | 0.000 | 0.001 | 0.001 | |
smisample | 0.004 | 0.003 | 0.007 | |
status | 0.000 | 0.001 | 0.001 | |
toolDetails | 0.000 | 0.001 | 0.001 | |
trimNeighbors | 2.018 | 0.052 | 2.092 | |
validSDF | 0.032 | 0.003 | 0.036 | |
view | 0.079 | 0.026 | 0.141 | |
write.SDF | 0.302 | 0.019 | 0.323 | |
write.SDFsplit | 0.026 | 0.004 | 0.029 | |
write.SMI | 0.002 | 0.003 | 0.005 | |