Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-10-05 11:45 -0400 (Sat, 05 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4466 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4498 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4446 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
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 561/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DIAlignR 2.13.0 (landing page) Shubham Gupta
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the DIAlignR package: - 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 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: DIAlignR |
Version: 2.13.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:DIAlignR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DIAlignR_2.13.0.tar.gz |
StartedAt: 2024-10-05 04:39:20 -0000 (Sat, 05 Oct 2024) |
EndedAt: 2024-10-05 04:42:48 -0000 (Sat, 05 Oct 2024) |
EllapsedTime: 208.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: DIAlignR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:DIAlignR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DIAlignR_2.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/DIAlignR.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 ‘DIAlignR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DIAlignR’ version ‘2.13.0’ * 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 ... OK * 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++ (GCC) 10.3.1’ * checking C++ specification ... NOTE Specified C++14: please drop specification unless essential * checking installed package size ... NOTE installed size is 30.2Mb sub-directories of 1Mb or more: extdata 4.0Mb libs 19.3Mb 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 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 dependencies in R code ... OK * 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))) 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’ populateReferenceExperimentFeatureAlignmentMap: no visible binding for global variable ‘run’ populateReferenceExperimentFeatureAlignmentMap: no visible binding for global variable ‘transition_group_id’ populateReferenceExperimentFeatureAlignmentMap: no visible binding for global variable ‘feature_id’ 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 ‘.’ writeOutFeatureAlignmentMap: no visible binding for global variable ‘reference_feature_id’ writeOutFeatureAlignmentMap: no visible binding for global variable ‘experiment_feature_id’ writeOutFeatureAlignmentMap: no visible binding for global variable ‘ALIGNMENT_GROUP_ID’ writeOutFeatureAlignmentMap: no visible binding for global variable ‘REFERENCE’ writeOutFeatureAlignmentMap: no visible global function definition for ‘.’ writeOutFeatureAlignmentMap: no visible binding for global variable ‘i.to’ 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: . ALIGNMENT_GROUP_ID REFERENCE RSE RT RT.eXp RT.ref alignment_rank chromatogramIndex col2 experiment_feature_id feature_id 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 reference_feature_id ropenms run scoreFile transition_group_id transition_id trees Consider adding importFrom("datasets", "trees") 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 ... NOTE Documented arguments not in \usage in Rd file 'alignToRef.Rd': ‘feature_alignment_mapping’ Documented arguments not in \usage in Rd file 'blobXICs.Rd': ‘nativeId’ Documented arguments not in \usage in Rd file 'extractXIC_group2.Rd': ‘mz’ Documented arguments not in \usage in Rd file 'getOswAnalytes.Rd': ‘dataPath’ ‘filenames’ Documented arguments not in \usage in Rd file 'getOswFiles.Rd': ‘dataPath’ ‘filenames’ Documented arguments not in \usage in Rd file 'perBatch.Rd': ‘rownum’ Documented arguments not in \usage in Rd file 'readSqMassHeader.Rd': ‘mzmlName’ Documented arguments not in \usage in Rd file 'setAlignmentRank.Rd': ‘XICs.eXp’ Documented arguments not in \usage in Rd file 'traverseDown.Rd': ‘analytes’ Documented arguments not in \usage in Rd file 'writeTables.Rd': ‘filename’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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/R/R-4.4.1/site-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 9.932 10.385 6.647 * 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: 2. ├─testthat::compare(act$val, exp$val, ..., tolerance = tolerance) 3. └─testthat:::compare.default(act$val, exp$val, ..., tolerance = tolerance) 4. ├─base::all.equal(x, y, ...) 5. └─data.table:::all.equal.data.table(x, y, ...) 6. ├─base::all.equal(x, y, tolerance = tolerance, ..., check.attributes = check.attributes) 7. └─bit64::all.equal.integer64(...) 8. ├─base::is.na(current) 9. └─bit64::is.na.integer64(current) ── Failure ('test_utils.R:276:3'): test_ipfReassignFDR ───────────────────────── `finalTbl` not equal to `expData`. Column 'RT': 'is.NA' value mismatch: 2 in current 0 in target [ FAIL 3 | WARN 0 | SKIP 8 | PASS 629 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 5 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/DIAlignR.Rcheck/00check.log’ for details.
DIAlignR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL DIAlignR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘DIAlignR’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ using C++14 g++ -std=gnu++14 -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/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ChromatogramPeak.cpp -o ChromatogramPeak.o g++ -std=gnu++14 -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/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c DPosition.cpp -o DPosition.o g++ -std=gnu++14 -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/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c MSChromatogram.cpp -o MSChromatogram.o g++ -std=gnu++14 -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/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c PeakIntegrator.cpp -o PeakIntegrator.o g++ -std=gnu++14 -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/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -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/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/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/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SavitzkyGolayFilter.cpp -o SavitzkyGolayFilter.o g++ -std=gnu++14 -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/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/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/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c affinealignobj.cpp -o affinealignobj.o g++ -std=gnu++14 -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/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c alignment.cpp -o alignment.o g++ -std=gnu++14 -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/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/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/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/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/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/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/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c integrateArea.cpp -o integrateArea.o g++ -std=gnu++14 -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/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c interface.cpp -o interface.o g++ -std=gnu++14 -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/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/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/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/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/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c simpleFcn.cpp -o simpleFcn.o g++ -std=gnu++14 -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/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/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/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/R/R-4.4.1/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/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-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
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. > 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 0.0557549 secs Time difference of 0.2679627 secs Time difference of 0.2098486 secs Time difference of 0.02932334 secs Time difference of 0.01189518 secs Time difference of 0.1168265 secs Time difference of 2.036949 secs Time difference of 0.02990532 secs Time difference of 0.4930694 secs [1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt" [2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" Time difference of 0.01792121 secs Time difference of 0.2327704 secs Time difference of 0.1365068 secs Time difference of 0.01848841 secs Time difference of 0.007199764 secs Time difference of 0.06937361 secs Time difference of 1.0514 secs Time difference of 0.01056409 secs Time difference of 1.114033 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 0.0189569 secs Time difference of 0.2677698 secs Time difference of 0.145997 secs Time difference of 0.1017151 secs Time difference of 0.01200986 secs Time difference of 0.1012735 secs Time difference of 1.518452 secs Time difference of 0.0314393 secs Time difference of 0.4305072 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 0.02009988 secs Time difference of 0.01907611 secs Time difference of 0.000494957 secs Time difference of 0.1016088 secs Time difference of 0.01201558 secs Time difference of 0.06056643 secs Time difference of 0.01816702 secs Time difference of 0.01056147 secs Time difference of 0.1372669 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 0.01140261 secs Time difference of 0.04181123 secs Time difference of 0.01348591 secs Time difference of 0.01553822 secs Time difference of 0.01027584 secs Time difference of 0.05090499 secs Time difference of 0.1197336 secs Time difference of 0.01017356 secs Time difference of 0.2718027 secs [1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4" [3] "chludwig_K150309_013_SW_0" Time difference of 0.01737022 secs Time difference of 0.01354814 secs Time difference of 0.001396656 secs Time difference of 0.02370119 secs Time difference of 0.01583219 secs Time difference of 0.08660722 secs Time difference of 0.00840354 secs Time difference of 0.0259788 secs Time difference of 0.3214347 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 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$trace.hat): Chernobyl! trL>n 10> <simpleError in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, drop.square = drop.square, normalize = normalize, statistics = control$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 0.1160309 secs Time difference of 0.01746583 secs Time difference of 0.002563 secs Time difference of 0.01171708 secs Time difference of 0.05750918 secs Time difference of 0.01754236 secs Time difference of 0.01996017 secs Time difference of 0.1169279 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 0.02885175 secs [1] "run0 run1\nrun2 run2" Time difference of 0.2617054 secs Time difference of 0.1387606 secs Time difference of 0.01221943 secs Time difference of 0.1046662 secs Time difference of 1.50527 secs Time difference of 0.02005982 secs Time difference of 0.4403274 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 0.1218634 secs Time difference of 0.8724587 secs Time difference of 7.398869 secs Time difference of 0.5854599 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 0.1104693 secs [1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_prog1.RData" [1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_0_2.rds" [1] "progTree1 is done." Time difference of 1.656526 secs Time difference of 0.4454074 secs [1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_1_2.rds" Time difference of 0.8179736 secs [1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_2_2.rds" Time difference of 0.43993 secs Time difference of 0.2779517 secs [1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_all_2.rds" Time difference of 0.2252522 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 0.1056826 secs [1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_prog1.RData" [1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_0_2.rds" [1] "progTree1 is done." Time difference of 1.374873 secs Time difference of 0.4246218 secs [1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_1_2.rds" Time difference of 0.6356618 secs [1] "Written /home/biocbuild/R/R-4.4.1/site-library/DIAlignR/extdata/temp_2_2.rds" Time difference of 0.4250684 secs Time difference of 0.01906395 secs [1] "Written /home/biocbuild/R/R-4.4.1/site-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 3 | WARN 0 | SKIP 8 | PASS 629 ] ══ Skipped tests (8) ═══════════════════════════════════════════════════════════ • empty test (5): 'test_get_filenames.R:77:1', 'test_get_filenames.R:82:1', 'test_utils.R:200:1', 'test_utils.R:203:1', 'test_utils.R:206:1' • ropenms not available for testing. A conda environment with name TricEnvr is MUST for testing. (3): 'test_pyopenms.R:4:3', 'test_pyopenms.R:8:3', 'test_pyopenms.R:27:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_utils.R:61:3'): test_getMultipeptide ─────────────────────────── Error in `sum.integer64(structure(c(8.12925173103238e+105, 7.07020651020428e+62, 2.87322374279237e+166, 3.16623447292931e-138, 2.73500684933996e-275, 3.15239881785171e+291, 4.67202095363214e+123, 8.27712377546863e-298, 264730160634500, 4.29832987800134e+292, 1.24545021916353e-79, 6.68432480390972e-210, 5.77682771166528e-16, 7.69829720567834e+172, 1.44901952004469e-19, 4.589273630966e+269, 1.43016762562436e-297 ), class = "integer64"), na.rm = FALSE)`: (converted from warning) NAs produced by integer64 overflow Backtrace: ▆ 1. └─testthat::expect_equal(outData[[1]], expData, tolerance = 1e-04) at test_utils.R:61:3 2. ├─testthat::compare(act$val, exp$val, ..., tolerance = tolerance) 3. └─testthat:::compare.default(act$val, exp$val, ..., tolerance = tolerance) 4. ├─base::all.equal(x, y, ...) 5. └─data.table:::all.equal.data.table(x, y, ...) 6. ├─base::all.equal(x, y, tolerance = tolerance, ..., check.attributes = check.attributes) 7. └─bit64::all.equal.integer64(...) ── Error ('test_utils.R:76:13'): test_getRefExpFeatureMap ────────────────────── Error in `is.na.integer64(current)`: REAL() can only be applied to a 'numeric', not a 'integer' Backtrace: ▆ 1. └─testthat::expect_equal(outData[[1]], expData, tolerance = 1e-04) at test_utils.R:76:13 2. ├─testthat::compare(act$val, exp$val, ..., tolerance = tolerance) 3. └─testthat:::compare.default(act$val, exp$val, ..., tolerance = tolerance) 4. ├─base::all.equal(x, y, ...) 5. └─data.table:::all.equal.data.table(x, y, ...) 6. ├─base::all.equal(x, y, tolerance = tolerance, ..., check.attributes = check.attributes) 7. └─bit64::all.equal.integer64(...) 8. ├─base::is.na(current) 9. └─bit64::is.na.integer64(current) ── Failure ('test_utils.R:276:3'): test_ipfReassignFDR ───────────────────────── `finalTbl` not equal to `expData`. Column 'RT': 'is.NA' value mismatch: 2 in current 0 in target [ FAIL 3 | WARN 0 | SKIP 8 | PASS 629 ] Error: Test failures Execution halted
DIAlignR.Rcheck/DIAlignR-Ex.timings
name | user | system | elapsed | |
MSTperBatch | 0.001 | 0.000 | 0.001 | |
addFlankToLeft | 0.002 | 0.000 | 0.002 | |
addFlankToRight | 0.001 | 0.000 | 0.001 | |
addXIC | 0 | 0 | 0 | |
alignChromatogramsCpp | 0.021 | 0.008 | 0.028 | |
alignTargetedRuns | 9.932 | 10.385 | 6.647 | |
alignToMaster | 1.966 | 0.080 | 2.051 | |
alignToRef | 0.001 | 0.000 | 0.001 | |
alignToRefMST | 0.001 | 0.000 | 0.001 | |
alignedXIC | 0.090 | 0.004 | 0.093 | |
analytesFromFeatures | 0.041 | 0.004 | 0.045 | |
approxFill | 0.001 | 0.000 | 0.001 | |
areaIntegrator | 0.003 | 0.000 | 0.003 | |
blobXICs | 0.002 | 0.000 | 0.002 | |
calculateIntensity | 0.003 | 0.000 | 0.003 | |
checkOverlap | 0.001 | 0.000 | 0.000 | |
checkParams | 0 | 0 | 0 | |
childXIC | 0.087 | 0.012 | 0.099 | |
childXICs | 0.689 | 0.130 | 0.821 | |
constrainSimCpp | 0 | 0 | 0 | |
createMZML | 0.003 | 0.000 | 0.003 | |
createSqMass | 0.002 | 0.000 | 0.002 | |
dialignrLoess | 0.001 | 0.000 | 0.001 | |
doAffineAlignmentCpp | 0.001 | 0.000 | 0.001 | |
doAlignmentCpp | 0.001 | 0.000 | 0.002 | |
extractXIC_group | 0.945 | 0.075 | 1.026 | |
extractXIC_group2 | 0.001 | 0.001 | 0.001 | |
fetchAnalytesInfo | 0.011 | 0.000 | 0.011 | |
fetchFeaturesFromRun | 0.009 | 0.000 | 0.009 | |
fetchPeptidesInfo | 0.009 | 0.000 | 0.009 | |
fetchPeptidesInfo2 | 0.006 | 0.003 | 0.009 | |
fetchPrecursorsInfo | 0.001 | 0.000 | 0.001 | |
fetchTransitionsFromRun | 0.009 | 0.000 | 0.009 | |
filenamesFromMZML | 0.001 | 0.000 | 0.001 | |
filenamesFromOSW | 0.001 | 0.000 | 0.001 | |
getAlignObj | 0.021 | 0.004 | 0.025 | |
getAlignObjs | 1.392 | 0.043 | 1.438 | |
getAlignedFigs | 0.178 | 0.009 | 0.187 | |
getAlignedIndices | 0.004 | 0.007 | 0.010 | |
getAlignedTimes | 0.023 | 0.000 | 0.023 | |
getAlignedTimesCpp | 0.008 | 0.000 | 0.008 | |
getAlignedTimesFast | 0.013 | 0.003 | 0.017 | |
getBaseGapPenaltyCpp | 0 | 0 | 0 | |
getChildFeature | 0.048 | 0.000 | 0.048 | |
getChildXICpp | 0.008 | 0.000 | 0.008 | |
getChildXICs | 0.842 | 0.023 | 0.868 | |
getChromSimMatCpp | 0.002 | 0.001 | 0.002 | |
getChromatogramIndices | 0.137 | 0.000 | 0.137 | |
getFeatures | 0.044 | 0.000 | 0.045 | |
getGlobalAlignMaskCpp | 0.001 | 0.000 | 0.000 | |
getGlobalAlignment | 0.008 | 0.000 | 0.008 | |
getGlobalFits | 0.477 | 0.011 | 0.489 | |
getLOESSfit | 0.004 | 0.000 | 0.004 | |
getLinearfit | 0.003 | 0.000 | 0.004 | |
getMST | 0.000 | 0.000 | 0.001 | |
getMZMLpointers | 0.023 | 0.000 | 0.023 | |
getMappedRT | 0.013 | 0.000 | 0.013 | |
getMultipeptide | 2.241 | 0.075 | 2.320 | |
getNativeIDs | 0.021 | 0.004 | 0.025 | |
getNodeIDs | 0 | 0 | 0 | |
getNodeRun | 0.489 | 0.035 | 0.525 | |
getOswAnalytes | 0.009 | 0.000 | 0.009 | |
getOswFiles | 0.009 | 0.000 | 0.009 | |
getPeptideScores | 0.037 | 0.004 | 0.040 | |
getPrecursorByID | 0.017 | 0.000 | 0.017 | |
getPrecursorIndices | 0.057 | 0.000 | 0.056 | |
getPrecursors | 0.027 | 0.000 | 0.027 | |
getRSE | 0.003 | 0.000 | 0.003 | |
getRTdf | 0.007 | 0.000 | 0.007 | |
getRefExpFeatureMap | 0.313 | 0.008 | 0.322 | |
getRefRun | 0.408 | 0.000 | 0.409 | |
getRunNames | 0.011 | 0.000 | 0.011 | |
getSeqSimMatCpp | 0 | 0 | 0 | |
getTransitions | 0.149 | 0.004 | 0.151 | |
getTree | 0.032 | 0.000 | 0.033 | |
getXICs | 0.097 | 0.008 | 0.105 | |
getXICs4AlignObj | 0.075 | 0.000 | 0.075 | |
get_ropenms | 0.001 | 0.000 | 0.000 | |
imputeChromatogram | 0.017 | 0.000 | 0.016 | |
ipfReassignFDR | 0.001 | 0.000 | 0.000 | |
mapIdxToTime | 0 | 0 | 0 | |
mappedRTfromAlignObj | 0.003 | 0.000 | 0.002 | |
mergeXIC | 0.003 | 0.000 | 0.003 | |
mstAlignRuns | 2.249 | 0.072 | 2.326 | |
mstScript1 | 0.521 | 0.275 | 0.590 | |
mstScript2 | 2.680 | 0.599 | 2.935 | |
nrDesc | 0 | 0 | 0 | |
otherChildXICpp | 0.01 | 0.00 | 0.01 | |
paramsDIAlignR | 0 | 0 | 0 | |
perBatch | 0.001 | 0.000 | 0.002 | |
pickNearestFeature | 0.003 | 0.000 | 0.003 | |
plotAlignedAnalytes | 0.712 | 0.028 | 0.741 | |
plotAlignmentPath | 0.429 | 0.036 | 0.465 | |
plotAnalyteXICs | 0.504 | 0.016 | 0.520 | |
plotXICgroup | 0.448 | 0.012 | 0.461 | |
populateReferenceExperimentFeatureAlignmentMap | 0.010 | 0.004 | 0.013 | |
progAlignRuns | 0.001 | 0.000 | 0.001 | |
readMzMLHeader | 0.001 | 0.000 | 0.002 | |
readSqMassHeader | 0.001 | 0.000 | 0.001 | |
recalculateIntensity | 0.298 | 0.023 | 0.322 | |
reduceXICs | 0.092 | 0.004 | 0.096 | |
script1 | 0.837 | 1.022 | 1.020 | |
script2 | 2.921 | 1.431 | 3.258 | |
setAlignmentRank | 0.012 | 0.000 | 0.013 | |
sgolayCpp | 0.000 | 0.003 | 0.003 | |
sgolayFill | 0.000 | 0.000 | 0.001 | |
smoothSingleXIC | 0.002 | 0.000 | 0.002 | |
smoothXICs | 0.01 | 0.00 | 0.01 | |
splineFill | 0.001 | 0.000 | 0.001 | |
splineFillCpp | 0.005 | 0.000 | 0.004 | |
traverseDown | 1.716 | 0.080 | 1.799 | |
traverseMST | 0 | 0 | 0 | |
traverseUp | 2.123 | 0.087 | 2.213 | |
trfrParentFeature | 0.048 | 0.000 | 0.048 | |
trimXICs | 0.002 | 0.000 | 0.002 | |
uncompressVec | 0.006 | 0.000 | 0.006 | |
updateFileInfo | 0.012 | 0.000 | 0.012 | |
writeOutFeatureAlignmentMap | 0.004 | 0.000 | 0.004 | |
writeTables | 0.004 | 0.000 | 0.003 | |