Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:00 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the ChemmineR package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 285/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChemmineR 3.44.0 (landing page) Thomas Girke
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: ChemmineR |
Version: 3.44.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChemmineR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ChemmineR_3.44.0.tar.gz |
StartedAt: 2021-10-14 20:56:48 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 21:00:14 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 205.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ChemmineR.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChemmineR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ChemmineR_3.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ChemmineR.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'ChemmineR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ChemmineR' version '3.44.0' * 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 whether package 'ChemmineR' can be installed ... WARNING Found the following significant warnings: formats.cc:237:10: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 4 bytes from a string of length 100001 [-Wstringop-truncation] See 'C:/Users/biocbuild/bbs-3.13-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 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 ... WARNING Invalid citation information in 'inst/CITATION': Failed with error: 'there is no package called 'bibtex'' Error in (function (bibtype, textVersion = NULL, header = NULL, footer = NULL, key = NULL, ..., other = list(), mheader = NULL, mfooter = NULL) { BibTeX_names <- names(BibLaTeX_entry_field_db) args <- c(list(...), other) if (!length(args)) return(structure(list(), class = "bibentry")) if (any(vapply(names(args), .is_not_nonempty_text, FALSE))) stop("all fields have to be named") args <- c(list(bibtype = bibtype, textVersion = textVersion, header = header, footer = footer, key = key), list(...)) args <- lapply(args, .listify) other <- lapply(other, .listify) max_length <- max(vapply(c(args, other), length, 0L)) args_length <- vapply(args, length, 0L) if (!all(args_length_ok <- args_length %in% c(1L, max_length))) warning(gettextf("Not all arguments are of the same length, %s: %s", "the following need to be recycled", paste(names(args)[!args_length_ok], collapse = ", ")), domain = NA) args <- lapply(args, function(x) rep(x, length.out = max_length)) other_length <- vapply(other, length, 0L) if (!all(other_length_ok <- other_length %in% c(1L, max_length))) warning(gettextf("Not all arguments are of the same length, %s: %s", "the following need to be recycled", paste(names(other)[!other_length_ok], collapse = ", ")), domain = NA) other <- lapply(other, function(x) rep(x, length.out = max_length)) bibentry1 <- function(bibtype, textVersion, header = NULL, footer = NULL, key = NULL, ..., other = list()) { bibtype <- as.character(bibtype) stopifnot(length(bibtype) == 1L) pos <- match(tolower(bibtype), tolower(BibTeX_names)) if (is.na(pos)) stop(gettextf("%s has to be one of %s", sQuote("bibtype"), paste(BibTeX_names, collapse = ", ")), domain = NA) bibtype <- BibTeX_names[pos] rval <- c(list(...), other) rval <- rval[!vapply(rval, .is_not_nonempty_text, FALSE)] fields <- tolower(names(rval)) names(rval) <- fields attr(rval, "bibtype") <- bibtype .BibEntryCheckBibEntry1(rval) pos <- fields %in% .BibEntryNameList if (any(pos)) { for (i in which(pos)) if (!inherits(rval[[i]], "person")) rval[[i]] <- ArrangeAuthors(rval[[i]]) } pos <- fields %in% c("dateobj") | pos if (any(!pos)) { for (i in which(!pos)) rval[[i]] <- as.character(rval[[i]]) } attr(rval, "key") <- if (is.null(key)) NULL else as.character(key) if (is.null(rval[["dateobj"]])) { tdate <- try(ProcessDates(rval), TRUE) if (!inherits(tdate, "try-error")) attr(rval, "dateobj") <- tdate } else { attr(rval, "dateobj") <- rval[["dateobj"]] rval[["dateobj"]] <- NULL } if (!is.null(textVersion)) attr(rval, "textVersion") <- as.character(textVersion) if (!.is_not_nonempty_text(header)) attr(rval, "header") <- paste(header, collapse = "\n") if (!.is_not_nonempty_text(footer)) attr(rval, "footer") <- paste(footer, collapse = "\n") return(rval) } rval <- lapply(seq_along(args$bibtype), function(i) do.call("bibentry1", c(lapply(args, "[[", i), list(other = lapply(other, "[[", i))))) if (!.is_not_nonempty_text(mheader)) attr(rval, "mheader") <- paste(mheader, collapse = "\n") if (!.is_not_nonempty_text(mfooter)) attr(rval, "mfooter") <- paste(mfooter, collapse = "\n") class(rval) <- c("BibEntry", "bibentry") rval})(year = "2021", key = "_2021"): argument "bibtype" is missing, with no default * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/ChemmineR/libs/i386/ChemmineR.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/ChemmineR/libs/x64/ChemmineR.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed AP-class 0.44 0.11 6.11 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... 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: 2 WARNINGs, 4 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ChemmineR.Rcheck/00check.log' for details.
ChemmineR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ChemmineR_3.44.0.tar.gz && rm -rf ChemmineR.buildbin-libdir && mkdir ChemmineR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChemmineR.buildbin-libdir ChemmineR_3.44.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ChemmineR_3.44.0.zip && rm ChemmineR_3.44.0.tar.gz ChemmineR_3.44.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 780k 100 780k 0 0 1165k 0 --:--:-- --:--:-- --:--:-- 1167k install for i386 * installing *source* package 'ChemmineR' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DisjointSets.cpp -o DisjointSets.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cluster.cc -o cluster.o cluster.cc: In function 'int nbr_intersect(std::vector<int>&, std::vector<int>&)': cluster.cc:118:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare] while (i < nbrs1.size() and j < nbrs2.size()) { ~~^~~~~~~~~~~~~~ cluster.cc:118:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare] while (i < nbrs1.size() and j < nbrs2.size()) { ~~^~~~~~~~~~~~~~ cluster.cc: In function 'int contains(int, std::vector<int>&)': cluster.cc:131:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int i=0; i < list.size(); i++) ~~^~~~~~~~~~~~~ cluster.cc: In function 'DisjointSets cluster(int, int, int, int)': cluster.cc:267:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j = 0; j < nbr_list[i].size(); j ++) { ~~^~~~~~~~~~~~~~~~~~~~ cluster.cc: In function 'void loadNNMatrix(int, int, int, SEXP)': cluster.cc:284:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] for(unsigned i=0; i<N; i++) //rows ~^~ cluster.cc:298:18: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if(nbrs.size() < minNbrs) // will end up a singleton ~~~~~~~~~~~~^~~~~~~~~ cluster.cc: In function 'void loadNNList(int, int, SEXP)': cluster.cc:314:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] for(unsigned i=0; i<N; i++) //rows ~^~ cluster.cc:332:18: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if(nbrs.size() < minNbrs) // will end up a singleton ~~~~~~~~~~~~^~~~~~~~~ cluster.cc: In function 'SEXPREC* jarvis_patrick(SEXP, SEXP, SEXP, SEXP, SEXP)': cluster.cc:390:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] for(unsigned i=0; i<N; i++){ ~^~ cluster.cc: At global scope: cluster.cc:49:13: warning: 'void prepare_neighbors(const char*, int, int)' defined but not used [-Wunused-function] void static prepare_neighbors(const char* nbr_file, int skip, int p) ^~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cstrsplit.cc -o cstrsplit.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from cstrsplit.cc:7: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from cstrsplit.cc:7: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template<class T> T * get_pointer(std::auto_ptr<T> const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27, from cstrsplit.cc:2: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c desc.cc -o desc.o desc.cc: In function 'SEXPREC* genAPDescriptor(SEXP)': desc.cc:249:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<unsigned int>::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int i=0; i < descs.size(); i++) ~~^~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fingerprints.cc -o fingerprints.o fingerprints.cc: In function 'SEXPREC* uniquifyAtomPairs(SEXP)': fingerprints.cc:138:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<IndexedValue*>::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int i=0; i < aps.size(); i++) ~~^~~~~~~~~~~~ fingerprints.cc:145:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<IndexedValue*>::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int i=0; i < aps.size(); i++){ ~~^~~~~~~~~~~~ fingerprints.cc:158:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<IndexedValue*>::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int i=0; i < aps.size(); i++){ ~~^~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c formats.cc -o formats.o formats.cc: In function 'int sdf_iter(std::fstream&, std::__cxx11::string&, int&)': formats.cc:237:10: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 4 bytes from a string of length 100001 [-Wstringop-truncation] strncpy(buf_4, line, 4); ~~~~~~~^~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c molecule.cc -o molecule.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c r_wrap.cc -o r_wrap.o r_wrap.cc: In function 'SEXPREC* SWIG_MakePtr(void*, const char*, R_SWIG_Owner)': r_wrap.cc:949:15: warning: variable 'p' set but not used [-Wunused-but-set-variable] const char *p = typeName; ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c script.cc -o script.o In file included from script.cc:2: desc.h:39:13: warning: 'elements' defined but not used [-Wunused-variable] static char elements[112][3] = { ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c similarity.cc -o similarity.o In file included from similarity.cc:1: desc.h:39:13: warning: 'elements' defined but not used [-Wunused-variable] static char elements[112][3] = { ^~~~~~~~ C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ChemmineR.dll tmp.def DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/ChemmineR.buildbin-libdir/00LOCK-ChemmineR/00new/ChemmineR/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'ChemmineR' finding HTML links ... done AP-class html APset-class html ExtSDF-class html FP-class html FPset-class html SDF-class html SDF2apcmp html SDFDataTable html SDFset-class html SDFset2SDF html SDFset2list html SDFstr-class html SMI-class html SMIset-class html addDescriptorType html addNewFeatures html ap html apfp html apset html apset2descdb html atomblock html atomcount html atomprop html atomsubset html batchByIndex html bondblock html bonds html browseJob html bufferLines html bufferResultSet html byCluster html canonicalNumbering html canonicalize html cid html cluster.sizestat html cluster.visualize html cmp.cluster html cmp.duplicated html cmp.parse html cmp.parse1 html cmp.search html cmp.similarity html conMA html connections html datablock html datablock2ma html db.explain html db.subset html dbTransaction html desc2fp html draw_sdf html exactMassOB html findCompounds html findCompoundsByName html fingerprintOB html fold html foldCount html fp2bit html fpSim html fptype html fromNNMatrix html genAPDescriptors html genParameters html generate3DCoords html getAllCompoundIds html getCompoundFeatures html getCompoundNames html getCompounds html getIds html grepSDFset html groups html header html initDb html jarvisPatrick html jarvisPatrick_c html jobToken-class html largestComponent html launchCMTool html listCMTools html listFeatures html loadSdf html makeUnique html maximallyDissimilar html nearestNeighbors html numBits html obmol html openBabelPlot html parBatchByIndex html plotStruc html propOB html pubchemCidToSDF html pubchemFPencoding html pubchemName2CID html pubchemSDFSearch html pubchemSmilesSearch html read.AP html read.SDFindex html read.SDFset html read.SDFstr html read.SMIset html regenerateCoords html result html rings html sdf.subset html sdf.visualize html sdf2ap html sdf2list html sdf2smiles html sdf2str html sdfStream html sdfid html sdfsample html sdfstr2list html searchSim html searchString html selectInBatches html setPriorities html smartsSearchOB html smiles2sdf html smisample html status html toolDetails html trimNeighbors html validSDF html view html write.SDF html write.SDFsplit html write.SMI html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'ChemmineR' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DisjointSets.cpp -o DisjointSets.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cluster.cc -o cluster.o cluster.cc: In function 'int nbr_intersect(std::vector<int>&, std::vector<int>&)': cluster.cc:118:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] while (i < nbrs1.size() and j < nbrs2.size()) { ~~^~~~~~~~~~~~~~ cluster.cc:118:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] while (i < nbrs1.size() and j < nbrs2.size()) { ~~^~~~~~~~~~~~~~ cluster.cc: In function 'int contains(int, std::vector<int>&)': cluster.cc:131:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(int i=0; i < list.size(); i++) ~~^~~~~~~~~~~~~ cluster.cc: In function 'DisjointSets cluster(int, int, int, int)': cluster.cc:267:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int j = 0; j < nbr_list[i].size(); j ++) { ~~^~~~~~~~~~~~~~~~~~~~ cluster.cc: In function 'void loadNNMatrix(int, int, int, SEXP)': cluster.cc:284:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] for(unsigned i=0; i<N; i++) //rows ~^~ cluster.cc:298:18: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] if(nbrs.size() < minNbrs) // will end up a singleton ~~~~~~~~~~~~^~~~~~~~~ cluster.cc: In function 'void loadNNList(int, int, SEXP)': cluster.cc:314:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] for(unsigned i=0; i<N; i++) //rows ~^~ cluster.cc:332:18: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] if(nbrs.size() < minNbrs) // will end up a singleton ~~~~~~~~~~~~^~~~~~~~~ cluster.cc: In function 'SEXPREC* jarvis_patrick(SEXP, SEXP, SEXP, SEXP, SEXP)': cluster.cc:390:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] for(unsigned i=0; i<N; i++){ ~^~ cluster.cc: At global scope: cluster.cc:49:13: warning: 'void prepare_neighbors(const char*, int, int)' defined but not used [-Wunused-function] void static prepare_neighbors(const char* nbr_file, int skip, int p) ^~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cstrsplit.cc -o cstrsplit.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from cstrsplit.cc:7: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_<Pred>::************ ^ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from cstrsplit.cc:7: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template<class T> T * get_pointer(std::auto_ptr<T> const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27, from cstrsplit.cc:2: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c desc.cc -o desc.o desc.cc: In function 'SEXPREC* genAPDescriptor(SEXP)': desc.cc:249:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<unsigned int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(int i=0; i < descs.size(); i++) ~~^~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fingerprints.cc -o fingerprints.o fingerprints.cc: In function 'SEXPREC* uniquifyAtomPairs(SEXP)': fingerprints.cc:138:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<IndexedValue*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(int i=0; i < aps.size(); i++) ~~^~~~~~~~~~~~ fingerprints.cc:145:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<IndexedValue*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(int i=0; i < aps.size(); i++){ ~~^~~~~~~~~~~~ fingerprints.cc:158:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<IndexedValue*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(int i=0; i < aps.size(); i++){ ~~^~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c formats.cc -o formats.o formats.cc: In function 'int sdf_iter(std::fstream&, std::__cxx11::string&, int&)': formats.cc:237:10: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 4 bytes from a string of length 100001 [-Wstringop-truncation] strncpy(buf_4, line, 4); ~~~~~~~^~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c molecule.cc -o molecule.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c r_wrap.cc -o r_wrap.o r_wrap.cc: In function 'SEXPREC* SWIG_MakePtr(void*, const char*, R_SWIG_Owner)': r_wrap.cc:949:15: warning: variable 'p' set but not used [-Wunused-but-set-variable] const char *p = typeName; ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c script.cc -o script.o In file included from script.cc:2: desc.h:39:13: warning: 'elements' defined but not used [-Wunused-variable] static char elements[112][3] = { ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c similarity.cc -o similarity.o In file included from similarity.cc:1: desc.h:39:13: warning: 'elements' defined but not used [-Wunused-variable] static char elements[112][3] = { ^~~~~~~~ C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ChemmineR.dll tmp.def DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/ChemmineR.buildbin-libdir/ChemmineR/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'ChemmineR' as ChemmineR_3.44.0.zip * DONE (ChemmineR) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'ChemmineR' successfully unpacked and MD5 sums checked
ChemmineR.Rcheck/tests_i386/runTests.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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") ======= 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 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(slotTypes)) { : closing unused connection 5 (<-TOKAY2:11855) 2: In for (i in seq_along(slotTypes)) { : closing unused connection 4 (<-TOKAY2:11855) 3: In for (i in seq_along(slotTypes)) { : closing unused connection 3 (<-TOKAY2:11855) Timing stopped at: 0.41 0.02 0.42 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: 0.01 0 0.01 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("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 -- Thu Oct 14 20:59:46 2021 *********************************************** 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 12.40 0.75 14.82 |
ChemmineR.Rcheck/tests_x64/runTests.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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") ======= 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 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(slotTypes)) { : closing unused connection 5 (<-TOKAY2:11073) 2: In for (i in seq_along(slotTypes)) { : closing unused connection 4 (<-TOKAY2:11073) 3: In for (i in seq_along(slotTypes)) { : closing unused connection 3 (<-TOKAY2:11073) test.formatConversions Timing stopped at: 0 0 0 Error in DEACTIVATED("removed old version of function") : removed old version of function Timing stopped at: 0 0 0 Error in DEACTIVATED("just for manual testing") : just for manual testing Timing stopped at: 0 0 0 Error in DEACTIVATED("requires local files") : requires local files Timing stopped at: 0 0 0 Error in DEACTIVATED("fails on ubuntu 16.04") : fails on ubuntu 16.04 Timing stopped at: 0 0 0 Error in DEACTIVATED("Causes SSL protocol version error on BioC") : Causes SSL protocol version error on BioC [1] "rotable bonds: " CMP1 CMP2 CMP3 CMP4 CMP5 24 20 14 30 10 [1] "650001" "650002" "650003" "650004" "650005" RUNIT TEST PROTOCOL -- Thu Oct 14 21:00:02 2021 *********************************************** Number of test functions: 23 Number of deactivated test functions: 8 Number of errors: 0 Number of failures: 0 1 Test Suite : ChemmineR RUnit Tests - 23 test functions, 0 errors, 0 failures Number of test functions: 23 Number of deactivated test functions: 8 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 13.85 0.81 15.79 |
ChemmineR.Rcheck/examples_i386/ChemmineR-Ex.timings
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ChemmineR.Rcheck/examples_x64/ChemmineR-Ex.timings
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