############################################################################## ############################################################################## ### ### 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_3.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/ChemmineR.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ChemmineR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ChemmineR’ version ‘3.48.0’ * 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: r_wrap.cc:563:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] r_wrap.cc:564:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] r_wrap.cc:567:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] r_wrap.cc:570:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] r_wrap.cc:614:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] r_wrap.cc:633:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] r_wrap.cc:634:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] r_wrap.cc:636:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] r_wrap.cc:648:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] r_wrap.cc:649:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] r_wrap.cc:651:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] r_wrap.cc:652:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] r_wrap.cc:1689:14: warning: explicitly assigning value of variable of type 'void *' to itself [-Wself-assign] See ‘/Users/biocbuild/bbs-3.15-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 ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘ChemmineDrugs’ ‘ChemmineOB’ ‘RPostgreSQL’ ‘RSQLite’ ‘fmcsR’ ‘png’ ‘snow’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespace in Imports field not imported from: ‘BiocGenerics’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Found the following possibly unsafe calls: File ‘ChemmineR/R/sim.R’: unlockBinding(".progress_bar_int_cnt", environment(.progress_bar)) .data.frame.to.str: no visible global function definition for ‘write.table’ .data.frame.to.str: no visible binding for global variable ‘string’ .parseV3000: no visible binding for global variable ‘AW’ .rings: no visible global function definition for ‘combn’ DUD: no visible global function definition for ‘download.file’ DUD: no visible global function definition for ‘untar’ applyOptions: no visible global function definition for ‘convertFormat’ browseJob: no visible global function definition for ‘browseURL’ canonicalNumbering: no visible global function definition for ‘canonicalNumbering_OB’ canonicalNumberingOB: no visible global function definition for ‘canonicalNumbering_OB’ cluster.visualize: no visible global function definition for ‘rainbow’ cluster.visualize: no visible global function definition for ‘pdf’ cluster.visualize: no visible global function definition for ‘postscript’ cluster.visualize: no visible global function definition for ‘dev.off’ desc2fp: no visible global function definition for ‘data’ draw_sdf: no visible global function definition for ‘rgb’ draw_sdf: no visible global function definition for ‘fmcs’ exactMassOB: no visible global function definition for ‘exactMass_OB’ fingerprintOB: no visible global function definition for ‘fingerprint_OB’ getCompoundFeatures : : 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 is not available File ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ChemmineR/libs/ChemmineR.so’: Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++) Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed addNewFeatures 6.095 0.177 6.300 loadSdf 5.705 0.035 5.864 findCompounds 5.331 0.025 5.365 getCompoundFeatures 5.085 0.026 5.128 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 4 NOTEs See ‘/Users/biocbuild/bbs-3.15-bioc/meat/ChemmineR.Rcheck/00check.log’ for details.