Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:00 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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To the developers/maintainers of the DIAlignR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DIAlignR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 521/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DIAlignR 2.7.0 (landing page) Shubham Gupta
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: DIAlignR |
Version: 2.7.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DIAlignR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings DIAlignR_2.7.0.tar.gz |
StartedAt: 2023-02-06 23:50:19 -0000 (Mon, 06 Feb 2023) |
EndedAt: 2023-02-06 23:55:24 -0000 (Mon, 06 Feb 2023) |
EllapsedTime: 304.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: DIAlignR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DIAlignR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings DIAlignR_2.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/DIAlignR.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘DIAlignR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DIAlignR’ version ‘2.7.0’ * package encoding: UTF-8 * 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 ... NOTE Found the following hidden files and directories: .dockerignore These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘DIAlignR’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ * checking installed package size ... NOTE installed size is 27.6Mb sub-directories of 1Mb or more: extdata 4.0Mb libs 16.8Mb metabo 4.1Mb ptms 1.5Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * 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 Namespace in Imports field not imported from: ‘magrittr’ 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 alignTargetedRuns: no visible binding for global variable ‘peptide_id’ alignTargetedRuns : <anonymous>: no visible global function definition for ‘.’ alignTargetedRuns: no visible binding for global variable ‘intensity’ alignToRoot4: no visible binding for global variable ‘trees’ alignToRoot4: no visible binding for global variable ‘precursors’ alignToRoot4: no visible binding for global variable ‘intensity’ childXICs: possible error in cummax(v = cummax(ifelse(is.na(x), -Inf, x))): unused argument (v = cummax(ifelse(is.na(x), -Inf, x))) dist4split: no visible global function definition for ‘as.dist’ distMat.rSqrd : <anonymous> : <anonymous>: no visible binding for global variable ‘RT.ref’ distMat.rSqrd : <anonymous> : <anonymous>: no visible binding for global variable ‘RT.eXp’ fetchPrecursorsInfo: no visible binding for global variable ‘transition_id’ fetchPrecursorsInfo: no visible global function definition for ‘.’ fetchPrecursorsInfo: no visible binding for global variable ‘transition_group_id’ fetchTransitionsFromRun: no visible binding for global variable ‘intensity’ fetchTransitionsFromRun: no visible global function definition for ‘.’ fetchTransitionsFromRun: no visible binding for global variable ‘transition_group_id’ fetchTransitionsFromRun: no visible binding for global variable ‘peak_group_rank’ fetchTransitionsFromRun: no visible global function definition for ‘head’ getNativeIDs: no visible binding for global variable ‘peptide_id’ getPeptideScores: no visible binding for global variable ‘col2’ getPeptideScores: no visible binding for global variable ‘run’ getQuery: no visible binding for global variable ‘identifying.transitionPEPfilter’ getRTdf: no visible binding for global variable ‘peak_group_rank’ getRTdf: no visible binding for global variable ‘m_score’ getRTdf: no visible global function definition for ‘.’ getRTdf: no visible binding for global variable ‘transition_group_id’ getRTdf: no visible binding for global variable ‘RT’ getRefRun : <anonymous>: no visible binding for global variable ‘pvalue’ ipfReassignFDR: no visible binding for global variable ‘ref_run’ ipfReassignFDR: no visible binding for global variable ‘run’ ipfReassignFDR: no visible global function definition for ‘.’ ipfReassignFDR: no visible binding for global variable ‘i.to’ ipfReassignFDR: no visible binding for global variable ‘m_score_new’ ipfReassignFDR: no visible binding for global variable ‘ms2_m_score’ ipfReassignFDR: no visible binding for global variable ‘m_score’ mstAlignRuns: no visible binding for global variable ‘ropenms’ mstAlignRuns: no visible binding for global variable ‘peptide_id’ mstAlignRuns : <anonymous>: no visible global function definition for ‘.’ mstAlignRuns: no visible binding for global variable ‘intensity’ mstScript1: no visible binding for global variable ‘ropenms’ mstScript2: no visible binding for global variable ‘fileInfo’ mstScript2: no visible binding for global variable ‘peptide_id’ mstScript2: no visible binding for global variable ‘features’ mstScript2 : <anonymous>: no visible global function definition for ‘.’ mstScript2 : <anonymous>: no visible binding for global variable ‘features’ mstScript2: no visible binding for global variable ‘intensity’ progAlignRuns: no visible binding for global variable ‘peptide_id’ progAlignRuns : <anonymous>: no visible global function definition for ‘.’ progAlignRuns: no visible binding for global variable ‘intensity’ progComb3: no visible binding for global variable ‘precursors’ progComb3: no visible binding for global variable ‘ropenms’ progSplit2: no visible binding for global variable ‘trees’ progSplit2: no visible binding for global variable ‘scoreFile’ progSplit2: no visible binding for global variable ‘precursors’ progSplit2 : <anonymous>: no visible global function definition for ‘.’ progSplit2: no visible binding for global variable ‘ropenms’ progSplit4: no visible binding for global variable ‘precursors’ progSplit4 : <anonymous>: no visible global function definition for ‘.’ progSplit4: no visible binding for global variable ‘intensity’ progTree1: no visible binding for global variable ‘ropenms’ progTree1: no visible binding for global variable ‘peptide_id’ reIntensity: no visible binding for global variable ‘run’ reIntensity: no visible binding for global variable ‘alignment_rank’ recalculateIntensity: no visible binding for global variable ‘peptide_id’ recalculateIntensity: no visible binding for global variable ‘chromatogramIndex’ script2: no visible binding for global variable ‘fileInfo’ script2: no visible binding for global variable ‘peptide_id’ script2 : <anonymous>: no visible global function definition for ‘.’ script2: no visible binding for global variable ‘features’ script2: no visible binding for global variable ‘globalFits’ script2: no visible binding for global variable ‘RSE’ script2: no visible binding for global variable ‘intensity’ setRootRank : <anonymous>: no visible global function definition for ‘.’ writeTables: no visible binding for global variable ‘peptide_id’ writeTables: no visible binding for global variable ‘run’ writeTables: no visible binding for global variable ‘precursor’ Undefined global functions or variables: . RSE RT RT.eXp RT.ref alignment_rank as.dist chromatogramIndex col2 features fileInfo globalFits head i.to identifying.transitionPEPfilter intensity m_score m_score_new ms2_m_score peak_group_rank peptide_id precursor precursors pvalue ref_run ropenms run scoreFile transition_group_id transition_id trees Consider adding importFrom("datasets", "trees") importFrom("stats", "as.dist") importFrom("utils", "head") 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 compiled code ... NOTE Note: information on .o files is not available File ‘/home/biocbuild/bbs-3.17-bioc/R/library/DIAlignR/libs/DIAlignR.so’: 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed alignTargetedRuns 10.293 10.016 9.506 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Unable to locate conda environment 'TricEnvr'. [ FAIL 1 | WARN 9 | SKIP 8 | PASS 626 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • empty test (5) • ropenms not available for testing. A conda environment with name TricEnvr is MUST for testing. (3) ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_utils.R:170'): test_ipfReassignFDR ─────────────────────────── `finalTbl` not equal to `expData`. Column 'RT': 'is.NA' value mismatch: 2 in current 0 in target [ FAIL 1 | WARN 9 | SKIP 8 | PASS 626 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘DIAlignR-vignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 5 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/DIAlignR.Rcheck/00check.log’ for details.
DIAlignR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL DIAlignR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘DIAlignR’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++14 g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ChromatogramPeak.cpp -o ChromatogramPeak.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c DPosition.cpp -o DPosition.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c MSChromatogram.cpp -o MSChromatogram.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c PeakIntegrator.cpp -o PeakIntegrator.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c Rmain.cpp -o Rmain.o Rmain.cpp: In function ‘Rcpp::NumericVector areaIntegrator(Rcpp::List, Rcpp::List, double, double, std::string, std::string, bool, bool, int, int)’: Rmain.cpp:273:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 273 | for(int i = 0; i<vov2.size(); i++) sgolay.smoothChroms(vov2[i]); | ~^~~~~~~~~~~~ Rmain.cpp: In function ‘Rcpp::NumericMatrix sgolayCpp(Rcpp::NumericMatrix, int, int)’: Rmain.cpp:305:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 305 | for(int i = 0; i<d.size(); i++){ | ~^~~~~~~~~ Rmain.cpp: In function ‘Rcpp::NumericMatrix getAlignedTimesCpp(Rcpp::List, Rcpp::List, int, int, std::string, double, std::string, std::string, const std::vector<double>&, double, double, double, bool, double, double, int, bool, double)’: Rmain.cpp:368:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 368 | for(int i = 0; i<intensity1.size(); i++){ | ~^~~~~~~~~~~~~~~~~~ Rmain.cpp: In function ‘Rcpp::List getChildXICpp(Rcpp::List, Rcpp::List, int, int, std::string, double, std::string, std::string, const std::vector<double>&, double, double, double, bool, double, double, int, bool, double, double, std::string, std::string, bool)’: Rmain.cpp:771:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 771 | for(int i = 0; i<intensity1.size(); i++){ | ~^~~~~~~~~~~~~~~~~~ Rmain.cpp:818:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 818 | for(int i = 0; i < keep.size(); i++){ | ~~^~~~~~~~~~~~~ Rmain.cpp:824:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 824 | for(int j = 0; j <intensity1NN.size(); j++){ | ~~^~~~~~~~~~~~~~~~~~~~ Rmain.cpp:827:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 827 | for(int i = 0; i < keep.size(); i++){ | ~~^~~~~~~~~~~~~ Rmain.cpp:837:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 837 | for(int i = 0; i < keep.size(); i++) alignedChildTime[keep[i]] = t1NN[i]; | ~~^~~~~~~~~~~~~ Rmain.cpp:862:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 862 | for (int i = 0; i < intensity1NN.size(); i++){ | ~~^~~~~~~~~~~~~~~~~~~~~ Rmain.cpp:873:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 873 | for(int i =0, j = 0; i < alignedChildTime.size(); i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ Rmain.cpp: In function ‘Rcpp::List otherChildXICpp(Rcpp::List, Rcpp::List, int, int, Rcpp::NumericMatrix, std::vector<double>, double, std::string)’: Rmain.cpp:944:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 944 | for(int i = 0; i<intensity1.size(); i++){ | ~^~~~~~~~~~~~~~~~~~ Rmain.cpp:972:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 972 | for(int j = 0; j <intensity1NN.size(); j++){ | ~~^~~~~~~~~~~~~~~~~~~~ Rmain.cpp:975:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 975 | for(int i = 0; i < keep.size(); i++){ | ~~^~~~~~~~~~~~~ Rmain.cpp:1008:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1008 | for (int i = 0; i < intensity1NN.size(); i++){ | ~~^~~~~~~~~~~~~~~~~~~~~ In file included from Rmain.cpp:19: miscell.h: At global scope: miscell.h:14:19: warning: ‘const bool DIAlign::detect_end_na(double, double)’ declared ‘static’ but never defined [-Wunused-function] 14 | static bool const detect_end_na(double a, double b); | ^~~~~~~~~~~~~ miscell.h:16:19: warning: ‘const bool DIAlign::detect_start_na(double, double)’ declared ‘static’ but never defined [-Wunused-function] 16 | static bool const detect_start_na(double a, double b); | ^~~~~~~~~~~~~~~ miscell.h:18:19: warning: ‘const bool DIAlign::lessZero(double)’ declared ‘static’ but never defined [-Wunused-function] 18 | static bool const lessZero(double a); | ^~~~~~~~ In file included from miscell.h:9, from Rmain.cpp:19: spline.h:390:10: warning: ‘double DIAlign::{anonymous}::tk::spline::deriv(int, double) const’ defined but not used [-Wunused-function] 390 | double spline::deriv(int order, double x) const | ^~~~~~ spline.h:364:10: warning: ‘double DIAlign::{anonymous}::tk::spline::operator()(double) const’ defined but not used [-Wunused-function] 364 | double spline::operator() (double x) const | ^~~~~~ spline.h:273:8: warning: ‘void DIAlign::{anonymous}::tk::spline::set_points(const std::vector<double>&, const std::vector<double>&, bool)’ defined but not used [-Wunused-function] 273 | void spline::set_points(const std::vector<double>& x, | ^~~~~~ spline.h:261:8: warning: ‘void DIAlign::{anonymous}::tk::spline::set_boundary(DIAlign::{anonymous}::tk::spline::bd_type, double, DIAlign::{anonymous}::tk::spline::bd_type, double, bool)’ defined but not used [-Wunused-function] 261 | void spline::set_boundary(spline::bd_type left, double left_value, | ^~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SavitzkyGolayFilter.cpp -o SavitzkyGolayFilter.o In file included from /home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/Core:507, from /home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/Dense:1, from /home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30, from /home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/RcppEigen.h:25, from SavitzkyGolayFilter.cpp:1: /home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/src/Core/products/TriangularMatrixVector.h: In static member function ‘static void Eigen::internal::trmv_selector<Mode, 1>::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<const Eigen::Block<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose<Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1, 1, -1, -1>, 1, -1, true>, 1, -1, false> >; int Mode = 6]’: /home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | <Index,Mode, | ~~~~~~~~~~~~ 329 | LhsScalar, LhsBlasTraits::NeedToConjugate, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 | RhsScalar, RhsBlasTraits::NeedToConjugate, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 331 | RowMajor> | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type ‘const double*’ to ‘static void Eigen::internal::triangular_matrix_vector_product<Index, Mode, LhsScalar, ConjLhs, RhsScalar, ConjRhs, 1, Version>::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, Eigen::internal::triangular_matrix_vector_product<Index, Mode, LhsScalar, ConjLhs, RhsScalar, ConjRhs, 1, Version>::ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]’ declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product<Index,Mode,LhsScalar,ConjLhs,RhsScalar,ConjRhs,RowMajor,Version> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c affinealignment.cpp -o affinealignment.o affinealignment.cpp: In function ‘double DIAlign::AffineAlignment::getOlapAffineAlignStartIndices(double*, double*, double*, int, int, int&, int&, DIAlign::Traceback::tbJump&)’: affinealignment.cpp:485:16: warning: ‘MaxColIndex’ may be used uninitialized in this function [-Wmaybe-uninitialized] 485 | OlapStartCol = MaxColIndex; | ~~~~~~~~~~~~~^~~~~~~~~~~~~ affinealignment.cpp:484:16: warning: ‘MaxRowIndex’ may be used uninitialized in this function [-Wmaybe-uninitialized] 484 | OlapStartRow = MaxRowIndex; | ~~~~~~~~~~~~~^~~~~~~~~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c affinealignobj.cpp -o affinealignobj.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c alignment.cpp -o alignment.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c chromSimMatrix.cpp -o chromSimMatrix.o chromSimMatrix.cpp: In function ‘std::vector<double> DIAlign::SimilarityMatrix::perSampleEucLenVecOfVec(const std::vector<std::vector<double> >&)’: chromSimMatrix.cpp:32:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 32 | for (int i = 0; i < mag.size(); i++){ | ~~^~~~~~~~~~~~ chromSimMatrix.cpp: In function ‘std::vector<double> DIAlign::SimilarityMatrix::perSampleSqrSumVecOfVec(const std::vector<std::vector<double> >&)’: chromSimMatrix.cpp:45:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 45 | for (int i = 0; i < mag.size(); i++){ | ~~^~~~~~~~~~~~ chromSimMatrix.cpp: In function ‘std::vector<double> DIAlign::SimilarityMatrix::perSampleMeanVecOfVec(const std::vector<std::vector<double> >&)’: chromSimMatrix.cpp:57:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 57 | for (int i = 0; i < mean.size(); i++){ | ~~^~~~~~~~~~~~~ chromSimMatrix.cpp: In function ‘std::vector<double> DIAlign::SimilarityMatrix::perSampleSumVecOfVec(const std::vector<std::vector<double> >&)’: chromSimMatrix.cpp:70:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 70 | for (int i = 0; i < sum.size(); i++){ | ~~^~~~~~~~~~~~ chromSimMatrix.cpp: In function ‘DIAlign::SimMatrix DIAlign::SimilarityMatrix::getSimilarityMatrix(const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, std::string, std::string, double, double, int)’: chromSimMatrix.cpp:414:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 414 | for(int i = 0; i < MASK.size(); i++){ | ~~^~~~~~~~~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c constrainMat.cpp -o constrainMat.o constrainMat.cpp: In function ‘void DIAlign::ConstrainMatrix::calcNoBeefMask2(DIAlign::SimMatrix&, std::vector<double>, std::vector<double>, std::vector<double>, int, bool)’: constrainMat.cpp:78:10: warning: unused variable ‘mapped’ [-Wunused-variable] 78 | double mapped = 0.0; | ^~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c gapPenalty.cpp -o gapPenalty.o gapPenalty.cpp: In function ‘double DIAlign::getGapPenalty(const DIAlign::SimMatrix&, double, std::string)’: gapPenalty.cpp:26:35: warning: ‘gapPenalty’ may be used uninitialized in this function [-Wmaybe-uninitialized] 26 | return std::max(0.01, gapPenalty); // gapPenalty must be positive. | ^ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c integrateArea.cpp -o integrateArea.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c interface.cpp -o interface.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c miscell.cpp -o miscell.o miscell.cpp: In function ‘void DIAlign::xicIntersect(std::vector<std::vector<double> >&, std::vector<std::vector<double> >&)’: miscell.cpp:10:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 10 | for (unsigned int i = 0; i < len; i++){ | ~~^~~~~ miscell.cpp:15:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 15 | for(unsigned int i = 0; i < len; i++){ | ~~^~~~~ miscell.cpp:26:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 26 | for (unsigned int i = 0; i < len; i++){ | ~~^~~~~ miscell.cpp:39:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 39 | for (unsigned int i = 0; i < len; i++) len2[i] = intensity[i].size(); | ~~^~~~~ miscell.cpp: In function ‘std::vector<std::vector<double> > DIAlign::imputeChromatogram(const std::vector<std::vector<double> >&, const std::vector<double>&, const std::vector<int>&)’: miscell.cpp:125:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 125 | for(int i =0; i< middle.size(); i++){ | ~^~~~~~~~~~~~~~~ miscell.cpp:131:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 131 | for(int i =0; i < (Anew.size()-1); i++){ | ~~^~~~~~~~~~~~~~~~~ miscell.cpp:139:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 139 | for(int j=0; j<result.size(); j++){ | ~^~~~~~~~~~~~~~ miscell.cpp: In function ‘std::vector<int> DIAlign::getSkip(const std::vector<int>&, const std::vector<int>&)’: miscell.cpp:164:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 164 | for(int i = 0; i < index.size(); i++){ | ~~^~~~~~~~~~~~~~ miscell.cpp: In function ‘void DIAlign::mergeIntensity(std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, double)’: miscell.cpp:221:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 221 | for(int i = 0; i< A.size(); i++){ | ~^~~~~~~~~~ miscell.cpp: In function ‘void DIAlign::addFlankToLeft(const std::vector<double>&, std::vector<double>&, std::vector<double>&, const std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<int>&)’: miscell.cpp:250:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 250 | for(int i = 0; i< intenN.size(); i++){ | ~^~~~~~~~~~~~~~~ miscell.cpp: In function ‘void DIAlign::addFlankToRight(const std::vector<double>&, std::vector<double>&, std::vector<double>&, const std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<int>&)’: miscell.cpp:277:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 277 | for(int i = 0; i< intenN.size(); i++){ | ~^~~~~~~~~~~~~~~ miscell.cpp: In function ‘void DIAlign::addFlankToLeft1(const std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<int>&)’: miscell.cpp:288:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 288 | for(int i = 0; i< intenN.size(); i++){ | ~^~~~~~~~~~~~~~~ miscell.cpp: In function ‘void DIAlign::addFlankToRight1(const std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<int>&)’: miscell.cpp:307:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 307 | for(int i = 0; i< intenN.size(); i++){ | ~^~~~~~~~~~~~~~~ miscell.cpp: In function ‘std::vector<int> DIAlign::getMatchingIdx(const std::vector<double>&, const std::vector<double>&)’: miscell.cpp:318:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 318 | for(int i =0, j=0; i< tMain.size(); i++){ | ~^~~~~~~~~~~~~~ miscell.cpp:320:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 320 | for(; j<t.size();){ | ~^~~~~~~~~ miscell.cpp: In function ‘std::vector<std::vector<double> > DIAlign::imputeChromatogram1(const std::vector<std::vector<double> >&, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&)’: miscell.cpp:337:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 337 | for(int j = 0; j <A.size(); j++){ | ~~^~~~~~~~~ miscell.cpp:339:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 339 | for(int i = 0; i < temp.size(); i++){ | ~~^~~~~~~~~~~~~ miscell.cpp:353:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 353 | for(int i =0; i< middle.size(); i++){ | ~^~~~~~~~~~~~~~~ miscell.cpp:358:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 358 | for(int i =0; i < intensity.size(); i++){ | ~~^~~~~~~~~~~~~~~~~~ miscell.cpp:360:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 360 | for(int j=0; j<result.size(); j++){ | ~^~~~~~~~~~~~~~ miscell.cpp: At global scope: miscell.cpp:53:19: warning: ‘const bool DIAlign::lessZero(double)’ defined but not used [-Wunused-function] 53 | static bool const lessZero(double a){ | ^~~~~~~~ In file included from miscell.h:9, from miscell.cpp:3: spline.h:390:10: warning: ‘double DIAlign::{anonymous}::tk::spline::deriv(int, double) const’ defined but not used [-Wunused-function] 390 | double spline::deriv(int order, double x) const | ^~~~~~ spline.h:364:10: warning: ‘double DIAlign::{anonymous}::tk::spline::operator()(double) const’ defined but not used [-Wunused-function] 364 | double spline::operator() (double x) const | ^~~~~~ spline.h:273:8: warning: ‘void DIAlign::{anonymous}::tk::spline::set_points(const std::vector<double>&, const std::vector<double>&, bool)’ defined but not used [-Wunused-function] 273 | void spline::set_points(const std::vector<double>& x, | ^~~~~~ spline.h:261:8: warning: ‘void DIAlign::{anonymous}::tk::spline::set_boundary(DIAlign::{anonymous}::tk::spline::bd_type, double, DIAlign::{anonymous}::tk::spline::bd_type, double, bool)’ defined but not used [-Wunused-function] 261 | void spline::set_boundary(spline::bd_type left, double left_value, | ^~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c run_alignment.cpp -o run_alignment.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c simpleFcn.cpp -o simpleFcn.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c spline.cpp -o spline.o In file included from spline.cpp:1: spline.h:390:10: warning: ‘double DIAlign::{anonymous}::tk::spline::deriv(int, double) const’ defined but not used [-Wunused-function] 390 | double spline::deriv(int order, double x) const | ^~~~~~ spline.h:261:8: warning: ‘void DIAlign::{anonymous}::tk::spline::set_boundary(DIAlign::{anonymous}::tk::spline::bd_type, double, DIAlign::{anonymous}::tk::spline::bd_type, double, bool)’ defined but not used [-Wunused-function] 261 | void spline::set_boundary(spline::bd_type left, double left_value, | ^~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c utils.cpp -o utils.o utils.cpp: In function ‘double DIAlign::Utils::getQuantile(std::vector<double>, double)’: utils.cpp:48:9: warning: unused variable ‘idx’ [-Wunused-variable] 48 | int idx = n*(1-p); | ^~~ g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o DIAlignR.so ChromatogramPeak.o DPosition.o MSChromatogram.o PeakIntegrator.o RcppExports.o Rmain.o SavitzkyGolayFilter.o affinealignment.o affinealignobj.o alignment.o chromSimMatrix.o constrainMat.o gapPenalty.o integrateArea.o interface.o miscell.o run_alignment.o simpleFcn.o spline.o utils.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-DIAlignR/00new/DIAlignR/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 (DIAlignR)
DIAlignR.Rcheck/tests/testthat.Rout.fail
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Type 'q()' to quit R. > library(testthat) > library(DIAlignR) > > test_check("DIAlignR") [1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt" [2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" [3] "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt" Time difference of 0.1167641 secs Time difference of 0.3294697 secs Time difference of 0.1180341 secs Time difference of 0.06699276 secs Time difference of 0.0154407 secs Time difference of 0.6986387 secs Time difference of 1.998069 secs Time difference of 0.02999091 secs Time difference of 0.4851508 secs [1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt" [2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" Time difference of 0.01982498 secs Time difference of 0.2864611 secs Time difference of 0.1189706 secs Time difference of 0.01955938 secs Time difference of 0.007932901 secs Time difference of 0.283283 secs Time difference of 1.240523 secs Time difference of 0.01004028 secs Time difference of 1.080069 secs [1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt" [2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" [3] "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt" Time difference of 0.02019 secs Time difference of 0.3162768 secs Time difference of 0.1284649 secs Time difference of 0.121551 secs Time difference of 0.01233721 secs Time difference of 0.3855598 secs Time difference of 14.04402 secs Time difference of 0.02684093 secs Time difference of 0.447794 secs [1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt" [2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" [3] "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt" Time difference of 0.02374554 secs Time difference of 0.0180037 secs Time difference of 0.0005099773 secs Time difference of 0.1196363 secs Time difference of 0.01204586 secs Time difference of 0.3470778 secs Time difference of 0.02120042 secs Time difference of 0.009685516 secs Time difference of 0.1143157 secs [1] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" [2] "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt" [1] "PestMix1_8Step1Plasma1SWATH20-50" "PestMix1_8Step8Plasma1SWATH20-50" Time difference of 0.009912968 secs Time difference of 0.04104781 secs Time difference of 0.01224756 secs Time difference of 0.01574111 secs Time difference of 0.00935626 secs Time difference of 0.304482 secs Time difference of 0.1162853 secs Time difference of 0.009232998 secs Time difference of 0.275717 secs [1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4" [3] "chludwig_K150309_013_SW_0" Time difference of 0.01195908 secs Time difference of 0.01265502 secs Time difference of 0.001308203 secs Time difference of 0.01855326 secs Time difference of 0.01324081 secs Time difference of 0.3472397 secs Time difference of 0.00762701 secs Time difference of 0.02295709 secs Time difference of 0.3322229 secs <simpleWarning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, drop.square = drop.square, normalize = normalize, statistics = control$statistics, surface = control$surface, cell = control$cell, iterations = iterations, iterTrace = control$iterTrace, trace.hat = control$trace.hat): span too small. fewer data values than degrees of freedom.> <simpleWarning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, drop.square = drop.square, normalize = normalize, statistics = control$statistics, surface = control$surface, cell = control$cell, iterations = iterations, iterTrace = control$iterTrace, trace.hat = control$trace.hat): span too small. fewer data values than degrees of freedom.> <simpleWarning in sqrt(sum.squares/one.delta): NaNs produced> <simpleError in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, drop.square = drop.square, normalize = normalize, statistics = control$statistics, surface = control$surface, cell = control$cell, iterations = iterations, iterTrace = control$iterTrace, trace.hat = control$trace.hat): span is too small> runName run0 hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt run1 hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt run2 hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt Time difference of 0.1125443 secs Time difference of 0.01823902 secs Time difference of 0.002462149 secs Time difference of 0.01263928 secs Time difference of 0.3815126 secs Time difference of 0.02398157 secs Time difference of 0.02068257 secs Time difference of 0.1226015 secs runName run0 hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt run1 hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt run2 hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt Time difference of 0.02940726 secs [1] "run0 run1\nrun2 run2" Time difference of 0.3357277 secs Time difference of 0.1437211 secs Time difference of 0.01123691 secs Time difference of 0.3839591 secs Time difference of 1.83621 secs Time difference of 0.0197649 secs Time difference of 0.4361048 secs runName run0 hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt run1 hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt run2 hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt Time difference of 0.1764166 secs Time difference of 1.614964 secs Time difference of 7.930198 secs Time difference of 0.5917578 secs runName run0 hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt run1 hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt run2 hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt Time difference of 0.1191332 secs [1] "Written /home/biocbuild/bbs-3.17-bioc/R/library/DIAlignR/extdata/temp_prog1.RData" [1] "Written /home/biocbuild/bbs-3.17-bioc/R/library/DIAlignR/extdata/temp_0_2.rds" [1] "progTree1 is done." Time difference of 1.711523 secs Time difference of 0.5538855 secs [1] "Written /home/biocbuild/bbs-3.17-bioc/R/library/DIAlignR/extdata/temp_1_2.rds" Time difference of 0.7604678 secs [1] "Written /home/biocbuild/bbs-3.17-bioc/R/library/DIAlignR/extdata/temp_2_2.rds" Time difference of 0.5787926 secs Time difference of 0.2802331 secs [1] "Written /home/biocbuild/bbs-3.17-bioc/R/library/DIAlignR/extdata/temp_all_2.rds" Time difference of 0.2415924 secs runName run0 hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt run1 hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt run2 hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt Time difference of 0.1360812 secs [1] "Written /home/biocbuild/bbs-3.17-bioc/R/library/DIAlignR/extdata/temp_prog1.RData" [1] "Written /home/biocbuild/bbs-3.17-bioc/R/library/DIAlignR/extdata/temp_0_2.rds" [1] "progTree1 is done." Time difference of 1.662446 secs Time difference of 0.5303667 secs [1] "Written /home/biocbuild/bbs-3.17-bioc/R/library/DIAlignR/extdata/temp_1_2.rds" Time difference of 0.7049334 secs [1] "Written /home/biocbuild/bbs-3.17-bioc/R/library/DIAlignR/extdata/temp_2_2.rds" Time difference of 0.5821109 secs Time difference of 0.02079725 secs [1] "Written /home/biocbuild/bbs-3.17-bioc/R/library/DIAlignR/extdata/temp_all_2.rds" Error in reticulate::use_condaenv(condaEnv, required = TRUE) : Unable to locate conda environment 'TricEnvr'. Error in reticulate::use_condaenv(condaEnv, required = TRUE) : Unable to locate conda environment 'TricEnvr'. Error in reticulate::use_condaenv(condaEnv, required = TRUE) : Unable to locate conda environment 'TricEnvr'. [ FAIL 1 | WARN 9 | SKIP 8 | PASS 626 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • empty test (5) • ropenms not available for testing. A conda environment with name TricEnvr is MUST for testing. (3) ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_utils.R:170'): test_ipfReassignFDR ─────────────────────────── `finalTbl` not equal to `expData`. Column 'RT': 'is.NA' value mismatch: 2 in current 0 in target [ FAIL 1 | WARN 9 | SKIP 8 | PASS 626 ] Error: Test failures Execution halted
DIAlignR.Rcheck/DIAlignR-Ex.timings
name | user | system | elapsed | |
MSTperBatch | 0.001 | 0.000 | 0.001 | |
addFlankToLeft | 0.003 | 0.000 | 0.003 | |
addFlankToRight | 0.000 | 0.002 | 0.001 | |
addXIC | 0 | 0 | 0 | |
alignChromatogramsCpp | 0.025 | 0.005 | 0.031 | |
alignTargetedRuns | 10.293 | 10.016 | 9.506 | |
alignToMaster | 4.451 | 0.088 | 4.564 | |
alignToRef | 0.001 | 0.000 | 0.001 | |
alignToRefMST | 0.000 | 0.000 | 0.001 | |
alignedXIC | 0.095 | 0.000 | 0.096 | |
analytesFromFeatures | 0.056 | 0.003 | 0.059 | |
approxFill | 0.001 | 0.000 | 0.001 | |
areaIntegrator | 0.003 | 0.000 | 0.004 | |
blobXICs | 0.002 | 0.000 | 0.003 | |
calculateIntensity | 0.003 | 0.000 | 0.003 | |
checkOverlap | 0.000 | 0.000 | 0.001 | |
checkParams | 0.001 | 0.000 | 0.000 | |
childXIC | 0.091 | 0.004 | 0.095 | |
childXICs | 0.638 | 0.005 | 0.645 | |
constrainSimCpp | 0.001 | 0.000 | 0.001 | |
createMZML | 0.003 | 0.000 | 0.003 | |
createSqMass | 0.002 | 0.000 | 0.002 | |
dialignrLoess | 0.001 | 0.000 | 0.000 | |
doAffineAlignmentCpp | 0.002 | 0.000 | 0.001 | |
doAlignmentCpp | 0.001 | 0.001 | 0.001 | |
extractXIC_group | 0.935 | 0.025 | 1.053 | |
extractXIC_group2 | 0.001 | 0.000 | 0.001 | |
fetchAnalytesInfo | 0.006 | 0.004 | 0.010 | |
fetchFeaturesFromRun | 0.008 | 0.000 | 0.009 | |
fetchPeptidesInfo | 0.009 | 0.000 | 0.008 | |
fetchPeptidesInfo2 | 0.009 | 0.000 | 0.008 | |
fetchPrecursorsInfo | 0.001 | 0.000 | 0.001 | |
fetchTransitionsFromRun | 0.008 | 0.000 | 0.009 | |
filenamesFromMZML | 0.001 | 0.000 | 0.001 | |
filenamesFromOSW | 0 | 0 | 0 | |
getAlignObj | 0.018 | 0.006 | 0.024 | |
getAlignObjs | 1.613 | 0.005 | 1.625 | |
getAlignedFigs | 0.293 | 0.003 | 0.297 | |
getAlignedIndices | 0.010 | 0.000 | 0.011 | |
getAlignedTimes | 0.018 | 0.004 | 0.022 | |
getAlignedTimesCpp | 0.004 | 0.004 | 0.008 | |
getAlignedTimesFast | 0.017 | 0.000 | 0.016 | |
getBaseGapPenaltyCpp | 0.000 | 0.000 | 0.001 | |
getChildFeature | 0.047 | 0.000 | 0.048 | |
getChildXICpp | 0.008 | 0.000 | 0.008 | |
getChildXICs | 3.173 | 0.013 | 3.189 | |
getChromSimMatCpp | 0.002 | 0.000 | 0.002 | |
getChromatogramIndices | 0.179 | 0.004 | 0.183 | |
getFeatures | 0.044 | 0.004 | 0.048 | |
getGlobalAlignMaskCpp | 0.001 | 0.000 | 0.001 | |
getGlobalAlignment | 0.007 | 0.000 | 0.007 | |
getGlobalFits | 2.454 | 0.006 | 2.461 | |
getLOESSfit | 0.000 | 0.003 | 0.003 | |
getLinearfit | 0.003 | 0.000 | 0.003 | |
getMST | 0 | 0 | 0 | |
getMZMLpointers | 0.017 | 0.002 | 0.019 | |
getMappedRT | 0.008 | 0.004 | 0.012 | |
getMultipeptide | 1.866 | 0.012 | 1.879 | |
getNativeIDs | 0.024 | 0.000 | 0.024 | |
getNodeIDs | 0 | 0 | 0 | |
getNodeRun | 0.585 | 0.008 | 0.594 | |
getOswAnalytes | 0.007 | 0.004 | 0.010 | |
getOswFiles | 0.010 | 0.000 | 0.009 | |
getPeptideScores | 0.043 | 0.004 | 0.046 | |
getPrecursorByID | 0.021 | 0.000 | 0.021 | |
getPrecursorIndices | 0.066 | 0.000 | 0.066 | |
getPrecursors | 0.028 | 0.004 | 0.031 | |
getRSE | 0.004 | 0.000 | 0.003 | |
getRTdf | 0.008 | 0.000 | 0.008 | |
getRefRun | 0.486 | 0.004 | 0.490 | |
getRunNames | 0.012 | 0.000 | 0.012 | |
getSeqSimMatCpp | 0.001 | 0.000 | 0.000 | |
getTransitions | 0.180 | 0.004 | 0.184 | |
getTree | 0.030 | 0.004 | 0.035 | |
getXICs | 0.181 | 0.000 | 0.181 | |
getXICs4AlignObj | 0.132 | 0.004 | 0.136 | |
get_ropenms | 0 | 0 | 0 | |
imputeChromatogram | 0.021 | 0.000 | 0.021 | |
ipfReassignFDR | 0 | 0 | 0 | |
mapIdxToTime | 0.001 | 0.000 | 0.000 | |
mappedRTfromAlignObj | 0.003 | 0.000 | 0.003 | |
mergeXIC | 0.003 | 0.000 | 0.003 | |
mstAlignRuns | 3.009 | 0.028 | 3.066 | |
mstScript1 | 0.517 | 0.234 | 0.568 | |
mstScript2 | 3.129 | 0.527 | 3.518 | |
nrDesc | 0.000 | 0.000 | 0.001 | |
otherChildXICpp | 0.007 | 0.002 | 0.010 | |
paramsDIAlignR | 0.000 | 0.000 | 0.001 | |
perBatch | 0.001 | 0.000 | 0.001 | |
pickNearestFeature | 0.003 | 0.000 | 0.003 | |
plotAlignedAnalytes | 0.862 | 0.004 | 0.867 | |
plotAlignmentPath | 0.561 | 0.036 | 0.597 | |
plotAnalyteXICs | 0.587 | 0.000 | 0.586 | |
plotXICgroup | 0.506 | 0.008 | 0.514 | |
progAlignRuns | 0.001 | 0.000 | 0.001 | |
readMzMLHeader | 0.001 | 0.000 | 0.000 | |
readSqMassHeader | 0.000 | 0.000 | 0.001 | |
recalculateIntensity | 0.373 | 0.000 | 0.373 | |
reduceXICs | 0.098 | 0.000 | 0.097 | |
script1 | 0.733 | 0.979 | 1.276 | |
script2 | 3.355 | 1.430 | 4.077 | |
setAlignmentRank | 0.014 | 0.000 | 0.014 | |
sgolayCpp | 0.003 | 0.000 | 0.002 | |
sgolayFill | 0.001 | 0.000 | 0.001 | |
smoothSingleXIC | 0.002 | 0.000 | 0.002 | |
smoothXICs | 0.008 | 0.000 | 0.009 | |
splineFill | 0.001 | 0.000 | 0.001 | |
splineFillCpp | 0.004 | 0.000 | 0.004 | |
traverseDown | 4.054 | 0.013 | 4.075 | |
traverseMST | 0 | 0 | 0 | |
traverseUp | 4.141 | 0.023 | 4.171 | |
trfrParentFeature | 0.048 | 0.004 | 0.052 | |
trimXICs | 0.002 | 0.000 | 0.004 | |
uncompressVec | 0.005 | 0.002 | 0.006 | |
updateFileInfo | 0.009 | 0.001 | 0.011 | |
writeTables | 0.004 | 0.000 | 0.003 | |