Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:45 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 325/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChemmineR 3.57.0 (landing page) Thomas Girke
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: ChemmineR |
Version: 3.57.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ChemmineR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ChemmineR_3.57.0.tar.gz |
StartedAt: 2024-08-21 03:23:14 -0000 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 03:25:26 -0000 (Wed, 21 Aug 2024) |
EllapsedTime: 131.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ChemmineR.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:ChemmineR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ChemmineR_3.57.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ChemmineR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ChemmineR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ChemmineR’ version ‘3.57.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ChemmineR’ can be installed ... WARNING Found the following significant warnings: 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/ChemmineR.Rcheck/00install.out’ for details. * used C++ compiler: ‘g++ (GCC) 10.3.1’ * 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’: 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 = "2024", key = "_2024"): argument "bibtype" is missing, with no default * 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 loading without being on the library search path ... 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. * 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 ‘/home/biocbuild/R/R-4.4.1/site-library/ChemmineR/libs/ChemmineR.so’: Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++) Found ‘_ZSt4cout’, 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: 3 WARNINGs, 6 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/ChemmineR.Rcheck/00check.log’ for details.
ChemmineR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL ChemmineR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘ChemmineR’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -Wall -c DisjointSets.cpp -o DisjointSets.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -Wall -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 unsigned int’} [-Wsign-compare] 118 | 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 unsigned int’} [-Wsign-compare] 118 | 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 unsigned int’} [-Wsign-compare] 131 | 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 unsigned int’} [-Wsign-compare] 267 | 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] 284 | 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 unsigned int’} and ‘int’ [-Wsign-compare] 298 | 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] 314 | 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 unsigned int’} and ‘int’ [-Wsign-compare] 332 | 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] 390 | 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] 49 | void static prepare_neighbors(const char* nbr_file, int skip, int p) | ^~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -Wall -c cstrsplit.cc -o cstrsplit.o In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/range/iterator_range.hpp:13, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/range/as_literal.hpp:18, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/trim.hpp:19, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string.hpp:19, from cstrsplit.cc:7: /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/bind/mem_fn.hpp:25, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mem_fn.hpp:22, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/function/detail/prologue.hpp:19, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/function.hpp:30, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/iter_find.hpp:27, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/split.hpp:16, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string.hpp:23, from cstrsplit.cc:7: /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:54, from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27, from cstrsplit.cc:2: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -Wall -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 unsigned int’} [-Wsign-compare] 249 | for(int i=0; i < descs.size(); i++) | ~~^~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -Wall -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 unsigned int’} [-Wsign-compare] 138 | 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 unsigned int’} [-Wsign-compare] 145 | 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 unsigned int’} [-Wsign-compare] 158 | for(int i=0; i < aps.size(); i++){ | ~~^~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -Wall -c formats.cc -o formats.o formats.cc: In function ‘int sdf_iter(std::fstream&, std::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] 237 | strncpy(buf_4, line, 4); | ~~~~~~~^~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -Wall -c molecule.cc -o molecule.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -Wall -c r_wrap.cc -o r_wrap.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -Wall -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] 39 | static char elements[112][3] = { | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -Wall -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] 39 | static char elements[112][3] = { | ^~~~~~~~ g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o ChemmineR.so DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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: 0.001 0 0 Error in DEACTIVATED("local test") : local test In addition: There were 14 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 Timing stopped at: 0.001 0 0.001 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 0 0.001 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 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 -- Wed Aug 21 03:25:19 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 13.344 0.357 14.659
ChemmineR.Rcheck/ChemmineR-Ex.timings
name | user | system | elapsed | |
AP-class | 0.359 | 0.024 | 0.388 | |
APset-class | 0.383 | 0.028 | 0.416 | |
ExtSDF-class | 0.001 | 0.000 | 0.001 | |
FP-class | 0.082 | 0.000 | 0.083 | |
FPset-class | 0.320 | 0.011 | 0.335 | |
SDF-class | 0.053 | 0.004 | 0.057 | |
SDF2apcmp | 0.162 | 0.008 | 0.170 | |
SDFDataTable | 0 | 0 | 0 | |
SDFset-class | 0.339 | 0.028 | 0.370 | |
SDFset2SDF | 0.079 | 0.000 | 0.079 | |
SDFset2list | 0.032 | 0.016 | 0.049 | |
SDFstr-class | 0.305 | 0.004 | 0.310 | |
SMI-class | 0.002 | 0.000 | 0.002 | |
SMIset-class | 0.004 | 0.000 | 0.004 | |
addDescriptorType | 0 | 0 | 0 | |
addNewFeatures | 4.044 | 0.048 | 4.109 | |
ap | 0.078 | 0.004 | 0.083 | |
apfp | 0.002 | 0.000 | 0.002 | |
apset | 0.004 | 0.000 | 0.004 | |
apset2descdb | 0.287 | 0.052 | 0.339 | |
atomblock | 0.088 | 0.004 | 0.092 | |
atomcount | 0.197 | 0.000 | 0.197 | |
atomprop | 0.004 | 0.000 | 0.003 | |
atomsubset | 0.025 | 0.000 | 0.024 | |
batchByIndex | 0 | 0 | 0 | |
bondblock | 0.087 | 0.011 | 0.098 | |
bonds | 0.028 | 0.004 | 0.032 | |
browseJob | 0 | 0 | 0 | |
bufferLines | 0.000 | 0.000 | 0.001 | |
bufferResultSet | 0.001 | 0.000 | 0.001 | |
byCluster | 0.862 | 0.004 | 0.867 | |
canonicalNumbering | 0 | 0 | 0 | |
canonicalize | 0 | 0 | 0 | |
cid | 0.015 | 0.004 | 0.020 | |
cluster.sizestat | 0.573 | 0.007 | 0.581 | |
cluster.visualize | 0.699 | 0.011 | 0.713 | |
cmp.cluster | 2.417 | 0.016 | 2.437 | |
cmp.duplicated | 0.067 | 0.000 | 0.067 | |
cmp.parse | 0.017 | 0.000 | 0.017 | |
cmp.parse1 | 0.000 | 0.000 | 0.001 | |
cmp.search | 0.901 | 0.012 | 0.915 | |
cmp.similarity | 0.020 | 0.000 | 0.019 | |
conMA | 0.048 | 0.004 | 0.052 | |
connections | 0.248 | 0.004 | 0.257 | |
datablock | 0.256 | 0.004 | 0.261 | |
datablock2ma | 0.032 | 0.000 | 0.032 | |
db.explain | 0.040 | 0.000 | 0.041 | |
db.subset | 0.003 | 0.000 | 0.003 | |
dbTransaction | 0.023 | 0.004 | 0.026 | |
desc2fp | 0.097 | 0.000 | 0.098 | |
draw_sdf | 0.643 | 0.020 | 0.657 | |
exactMassOB | 0 | 0 | 0 | |
findCompounds | 3.489 | 0.024 | 3.521 | |
findCompoundsByName | 0.384 | 0.000 | 0.384 | |
fingerprintOB | 0 | 0 | 0 | |
fold | 0.001 | 0.000 | 0.002 | |
foldCount | 0.001 | 0.000 | 0.001 | |
fp2bit | 0.387 | 0.016 | 0.404 | |
fpSim | 0.392 | 0.004 | 0.398 | |
fptype | 0.001 | 0.000 | 0.001 | |
fromNNMatrix | 0.866 | 0.004 | 0.871 | |
genAPDescriptors | 0.012 | 0.004 | 0.016 | |
genParameters | 0.450 | 0.000 | 0.451 | |
generate3DCoords | 0 | 0 | 0 | |
getAllCompoundIds | 0.383 | 0.032 | 0.416 | |
getAtomAttr | 0 | 0 | 0 | |
getBondAttr | 0 | 0 | 0 | |
getCompoundFeatures | 3.510 | 0.016 | 3.536 | |
getCompoundNames | 0.384 | 0.004 | 0.388 | |
getCompounds | 0.398 | 0.000 | 0.398 | |
getIds | 0.000 | 0.000 | 0.001 | |
grepSDFset | 0.043 | 0.000 | 0.043 | |
groups | 0.166 | 0.000 | 0.166 | |
header | 0.093 | 0.004 | 0.097 | |
initDb | 0.021 | 0.004 | 0.025 | |
jarvisPatrick | 2.208 | 0.016 | 2.229 | |
jobToken-class | 0 | 0 | 0 | |
largestComponent | 0 | 0 | 0 | |
launchCMTool | 0.001 | 0.000 | 0.000 | |
listCMTools | 0 | 0 | 0 | |
listFeatures | 0.420 | 0.004 | 0.425 | |
loadSdf | 3.843 | 0.016 | 3.876 | |
makeUnique | 0.016 | 0.000 | 0.016 | |
maximallyDissimilar | 0.254 | 0.000 | 0.254 | |
nearestNeighbors | 1.102 | 0.007 | 1.111 | |
numBits | 0.001 | 0.000 | 0.001 | |
obmol | 0.001 | 0.000 | 0.000 | |
openBabelPlot | 0 | 0 | 0 | |
parBatchByIndex | 0 | 0 | 0 | |
plotStruc | 0.281 | 0.000 | 0.282 | |
propOB | 0 | 0 | 0 | |
pubchemCidToSDF | 0 | 0 | 0 | |
pubchemFPencoding | 0.003 | 0.000 | 0.003 | |
pubchemInchi2cid | 0 | 0 | 0 | |
pubchemInchikey2sdf | 0 | 0 | 0 | |
pubchemName2CID | 0.000 | 0.000 | 0.001 | |
pubchemSDFSearch | 0 | 0 | 0 | |
pubchemSmilesSearch | 0 | 0 | 0 | |
read.AP | 0.016 | 0.000 | 0.016 | |
read.SDFindex | 0.016 | 0.000 | 0.016 | |
read.SDFset | 0.676 | 0.012 | 0.690 | |
read.SDFstr | 0.960 | 0.008 | 0.970 | |
read.SMIset | 0.002 | 0.000 | 0.001 | |
regenerateCoords | 0 | 0 | 0 | |
result | 0 | 0 | 0 | |
rings | 0.848 | 0.000 | 0.850 | |
sdf.subset | 0 | 0 | 0 | |
sdf.visualize | 0.015 | 0.000 | 0.015 | |
sdf2ap | 0.309 | 0.032 | 0.341 | |
sdf2list | 0.022 | 0.000 | 0.022 | |
sdf2smiles | 0 | 0 | 0 | |
sdf2str | 0.022 | 0.004 | 0.026 | |
sdfStream | 0.015 | 0.000 | 0.015 | |
sdfid | 0.013 | 0.004 | 0.017 | |
sdfsample | 0.038 | 0.000 | 0.037 | |
sdfstr2list | 0.542 | 0.115 | 0.659 | |
searchSim | 0.001 | 0.000 | 0.000 | |
searchString | 0 | 0 | 0 | |
selectInBatches | 0 | 0 | 0 | |
setPriorities | 0 | 0 | 0 | |
smartsSearchOB | 0.001 | 0.000 | 0.000 | |
smiles2sdf | 0 | 0 | 0 | |
smisample | 0.003 | 0.000 | 0.002 | |
status | 0 | 0 | 0 | |
toolDetails | 0 | 0 | 0 | |
trimNeighbors | 1.609 | 0.004 | 1.616 | |
validSDF | 0.019 | 0.000 | 0.019 | |
view | 0.045 | 0.000 | 0.045 | |
write.SDF | 0.171 | 0.004 | 0.175 | |
write.SDFsplit | 0.015 | 0.000 | 0.014 | |
write.SMI | 0.002 | 0.000 | 0.001 | |