Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-06 11:41 -0400 (Mon, 06 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4832 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4613 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4554 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4585 |
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 576/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Shubham Gupta
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / 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: 2.16.0 |
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_2.16.0.tar.gz |
StartedAt: 2025-10-03 08:34:02 -0000 (Fri, 03 Oct 2025) |
EndedAt: 2025-10-03 08:37:36 -0000 (Fri, 03 Oct 2025) |
EllapsedTime: 214.1 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_2.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/DIAlignR.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (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 ‘2.16.0’ * 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 ... WARNING Found the following significant warnings: /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] See ‘/home/biocbuild/bbs-3.21-bioc/meat/DIAlignR.Rcheck/00install.out’ for details. * used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ * checking C++ specification ... NOTE Specified C++14: please drop specification unless essential * checking installed package size ... INFO installed size is 27.9Mb sub-directories of 1Mb or more: extdata 4.0Mb libs 17.0Mb 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 whether startup messages can be suppressed ... 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-devel_2025-02-19/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 9.73 9.626 6.334 * 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 10 | WARN 3 | SKIP 8 | PASS 622 ] 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, 1 WARNING, 4 NOTEs See ‘/home/biocbuild/bbs-3.21-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-devel_2025-02-19/site-library’ * installing *source* package ‘DIAlignR’ ... ** this is package ‘DIAlignR’ version ‘2.16.0’ ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ using C++14 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ChromatogramPeak.cpp -o ChromatogramPeak.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c DPosition.cpp -o DPosition.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c MSChromatogram.cpp -o MSChromatogram.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c PeakIntegrator.cpp -o PeakIntegrator.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/Core:214, from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/Dense:1, from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/RcppEigenForward.h:28, from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/RcppEigen.h:25, from RcppExports.cpp:4: /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’: /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/Core:172: /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’: /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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: 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(bd_type, double, bd_type, double, bool)’ defined but not used [-Wunused-function] 261 | void spline::set_boundary(spline::bd_type left, double left_value, | ^~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c SavitzkyGolayFilter.cpp -o SavitzkyGolayFilter.o In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/Core:214, from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/Dense:1, from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/RcppEigenForward.h:28, from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/RcppEigen.h:25, from SavitzkyGolayFilter.cpp:1: /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’: /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/Core:172: /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’: /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/Core:341: /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/products/TriangularMatrixVector.h: In 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/R/R-devel_2025-02-19/site-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/R/R-devel_2025-02-19/site-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, 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> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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:484:16: warning: ‘MaxRowIndex’ may be used uninitialized [-Wmaybe-uninitialized] 484 | OlapStartRow = MaxRowIndex; | ~~~~~~~~~~~~~^~~~~~~~~~~~~ affinealignment.cpp:436:7: note: ‘MaxRowIndex’ was declared here 436 | int MaxRowIndex, MaxColIndex; | ^~~~~~~~~~~ affinealignment.cpp:485:16: warning: ‘MaxColIndex’ may be used uninitialized [-Wmaybe-uninitialized] 485 | OlapStartCol = MaxColIndex; | ~~~~~~~~~~~~~^~~~~~~~~~~~~ affinealignment.cpp:436:20: note: ‘MaxColIndex’ was declared here 436 | int MaxRowIndex, MaxColIndex; | ^~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c affinealignobj.cpp -o affinealignobj.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c alignment.cpp -o alignment.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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++){ | ~~^~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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; | ^~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c gapPenalty.cpp -o gapPenalty.o gapPenalty.cpp: In function ‘double DIAlign::getGapPenalty(const SimMatrix&, double, std::string)’: gapPenalty.cpp:6:10: warning: ‘gapPenalty’ may be used uninitialized [-Wmaybe-uninitialized] 6 | double gapPenalty; | ^~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c integrateArea.cpp -o integrateArea.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c interface.cpp -o interface.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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(bd_type, double, bd_type, double, bool)’ defined but not used [-Wunused-function] 261 | void spline::set_boundary(spline::bd_type left, double left_value, | ^~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c run_alignment.cpp -o run_alignment.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c simpleFcn.cpp -o simpleFcn.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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(bd_type, double, bd_type, double, bool)’ defined but not used [-Wunused-function] 261 | void spline::set_boundary(spline::bd_type left, double left_value, | ^~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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); | ^~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -shared -L/home/biocbuild/R/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/R/R/lib -lR installing to /home/biocbuild/R/R-devel_2025-02-19/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 Warning in fun(libname, pkgname) : Package 'DIAlignR' is deprecated and will be removed from Bioconductor version 3.22 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'DIAlignR' is deprecated and will be removed from Bioconductor version 3.22 ** testing if installed package keeps a record of temporary installation path * DONE (DIAlignR)
DIAlignR.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" Copyright (C) 2025 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) Warning message: In fun(libname, pkgname) : Package 'DIAlignR' is deprecated and will be removed from Bioconductor version 3.22 > > 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 0.07907057 secs Time difference of 0.2327285 secs Time difference of 0.2185192 secs Time difference of 0.02692223 secs Time difference of 0.0093894 secs Time difference of 0.1102579 secs Time difference of 1.973056 secs Time difference of 0.03386545 secs Time difference of 0.4886851 secs [1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt" [2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt" Time difference of 0.02032423 secs Time difference of 0.2827864 secs Time difference of 0.1738896 secs Time difference of 0.02145433 secs Time difference of 0.009232044 secs Time difference of 0.07533979 secs Time difference of 1.026657 secs Time difference of 0.01105714 secs Time difference of 1.093407 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 0.01804829 secs Time difference of 0.2646358 secs Time difference of 0.1694355 secs Time difference of 0.1072297 secs Time difference of 0.01229095 secs Time difference of 0.1097291 secs Time difference of 1.423833 secs Time difference of 0.02745056 secs Time difference of 0.4146011 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 0.0189147 secs Time difference of 0.01688981 secs Time difference of 0.0004074574 secs Time difference of 0.09945488 secs Time difference of 0.0115788 secs Time difference of 0.05825543 secs Time difference of 0.01750994 secs Time difference of 0.01035309 secs Time difference of 0.1532836 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 0.01100183 secs Time difference of 0.03735137 secs Time difference of 0.01491714 secs Time difference of 0.01308322 secs Time difference of 0.00916791 secs Time difference of 0.06792665 secs Time difference of 0.08996296 secs Time difference of 0.009041309 secs Time difference of 0.2481666 secs [1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4" [3] "chludwig_K150309_013_SW_0" Time difference of 0.01579261 secs Time difference of 0.01625896 secs Time difference of 0.00163722 secs Time difference of 0.02267671 secs Time difference of 0.01488876 secs Time difference of 0.06878567 secs Time difference of 0.006637573 secs Time difference of 0.02551603 secs Time difference of 0.329463 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.> <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 0.1019306 secs Time difference of 0.01818562 secs Time difference of 0.002881289 secs Time difference of 0.01198959 secs Time difference of 0.06053615 secs Time difference of 0.01846385 secs Time difference of 0.021029 secs Time difference of 0.1363709 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 0.02998376 secs [1] "run0 run1\nrun2 run2" Time difference of 0.271004 secs Time difference of 0.2032666 secs Time difference of 0.01211739 secs Time difference of 0.08791423 secs Time difference of 1.782591 secs Time difference of 0.01996207 secs Time difference of 0.408829 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 0.1209569 secs Time difference of 0.8755052 secs Time difference of 5.566916 secs Time difference of 0.5767424 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 0.1050766 secs [1] "Written /home/biocbuild/R/R-devel_2025-02-19/site-library/DIAlignR/extdata/temp_prog1.RData" [1] "Written /home/biocbuild/R/R-devel_2025-02-19/site-library/DIAlignR/extdata/temp_0_2.rds" [1] "progTree1 is done." Time difference of 1.506169 secs Time difference of 0.4204931 secs [1] "Written /home/biocbuild/R/R-devel_2025-02-19/site-library/DIAlignR/extdata/temp_1_2.rds" Time difference of 0.7275276 secs [1] "Written /home/biocbuild/R/R-devel_2025-02-19/site-library/DIAlignR/extdata/temp_2_2.rds" Time difference of 0.3950324 secs Time difference of 0.2480431 secs [1] "Written /home/biocbuild/R/R-devel_2025-02-19/site-library/DIAlignR/extdata/temp_all_2.rds" Time difference of 0.2258751 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 0.1038785 secs [1] "Written /home/biocbuild/R/R-devel_2025-02-19/site-library/DIAlignR/extdata/temp_prog1.RData" [1] "Written /home/biocbuild/R/R-devel_2025-02-19/site-library/DIAlignR/extdata/temp_0_2.rds" [1] "progTree1 is done." Time difference of 1.252522 secs Time difference of 0.3758602 secs [1] "Written /home/biocbuild/R/R-devel_2025-02-19/site-library/DIAlignR/extdata/temp_1_2.rds" Time difference of 0.5662904 secs [1] "Written /home/biocbuild/R/R-devel_2025-02-19/site-library/DIAlignR/extdata/temp_2_2.rds" Time difference of 0.3836219 secs Time difference of 0.01631141 secs [1] "Written /home/biocbuild/R/R-devel_2025-02-19/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 10 | WARN 3 | SKIP 8 | PASS 622 ] ══ 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 ════════════════════════════════════════════════════════════════ ── Failure ('test_align_dia_runs.R:122:3'): test_getAlignObjs ────────────────── outData[[2]][["4618"]][["run1_run2"]][["ref"]] not equal to lapply(...). Component 1: Attributes: < Component 2: Component 2: 2 string mismatches > Component 2: Attributes: < Component 2: Component 2: 2 string mismatches > Component 3: Attributes: < Component 2: Component 2: 2 string mismatches > Component 4: Attributes: < Component 2: Component 2: 2 string mismatches > Component 5: Attributes: < Component 2: Component 2: 2 string mismatches > Component 6: Attributes: < Component 2: Component 2: 2 string mismatches > ── Failure ('test_align_dia_runs.R:124:3'): test_getAlignObjs ────────────────── outData[[2]][["4618"]][["run1_run2"]][["eXp"]] not equal to lapply(...). Component 1: Attributes: < Component 2: Component 2: 2 string mismatches > Component 2: Attributes: < Component 2: Component 2: 2 string mismatches > Component 3: Attributes: < Component 2: Component 2: 2 string mismatches > Component 4: Attributes: < Component 2: Component 2: 2 string mismatches > Component 5: Attributes: < Component 2: Component 2: 2 string mismatches > Component 6: Attributes: < Component 2: Component 2: 2 string mismatches > ── Failure ('test_get_global_fit.R:21:3'): test_dialignrLoess ────────────────── outData$pars$span not equal to 0.8. 1/1 mismatches [1] 0.4 - 0.8 == -0.4 ── Failure ('test_get_global_fit.R:22:3'): test_dialignrLoess ────────────────── predict(outData, newdata = data.frame(RT.ref = 13.5))[[1]] not equal to 5.5. 1/1 mismatches [1] 2.75 - 5.5 == -2.75 ── Failure ('test_get_peaks_chromatograms.R:48:3'): test_getXICs4AlignObj ────── outData[["hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"]][["4618"]] not equal to lapply(XICs[[runs[["run0"]]]][["4618"]], as.matrix). Component 1: Attributes: < Component 2: Component 2: 2 string mismatches > Component 2: Attributes: < Component 2: Component 2: 2 string mismatches > Component 3: Attributes: < Component 2: Component 2: 2 string mismatches > Component 4: Attributes: < Component 2: Component 2: 2 string mismatches > Component 5: Attributes: < Component 2: Component 2: 2 string mismatches > Component 6: Attributes: < Component 2: Component 2: 2 string mismatches > ── Failure ('test_get_peaks_chromatograms.R:49:3'): test_getXICs4AlignObj ────── outData[["hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]] not equal to lapply(XICs[[runs[["run1"]]]][["4618"]], as.matrix). Component 1: Attributes: < Component 2: Component 2: 2 string mismatches > Component 2: Attributes: < Component 2: Component 2: 2 string mismatches > Component 3: Attributes: < Component 2: Component 2: 2 string mismatches > Component 4: Attributes: < Component 2: Component 2: 2 string mismatches > Component 5: Attributes: < Component 2: Component 2: 2 string mismatches > Component 6: Attributes: < Component 2: Component 2: 2 string mismatches > ── Failure ('test_get_peaks_chromatograms.R:68:3'): test_getXICs ─────────────── outData[["hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"]][["4618"]] not equal to lapply(...). Component 1: Attributes: < Component 2: Component 2: 2 string mismatches > Component 2: Attributes: < Component 2: Component 2: 2 string mismatches > Component 3: Attributes: < Component 2: Component 2: 2 string mismatches > Component 4: Attributes: < Component 2: Component 2: 2 string mismatches > Component 5: Attributes: < Component 2: Component 2: 2 string mismatches > Component 6: Attributes: < Component 2: Component 2: 2 string mismatches > ── Failure ('test_get_peaks_chromatograms.R:70:3'): test_getXICs ─────────────── outData[["hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]] not equal to lapply(...). Component 1: Attributes: < Component 2: Component 2: 2 string mismatches > Component 2: Attributes: < Component 2: Component 2: 2 string mismatches > Component 3: Attributes: < Component 2: Component 2: 2 string mismatches > Component 4: Attributes: < Component 2: Component 2: 2 string mismatches > Component 5: Attributes: < Component 2: Component 2: 2 string mismatches > Component 6: Attributes: < Component 2: Component 2: 2 string mismatches > ── 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 10 | WARN 3 | SKIP 8 | PASS 622 ] 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 | 0.002 | |
addXIC | 0.001 | 0.000 | 0.000 | |
alignChromatogramsCpp | 0.025 | 0.004 | 0.031 | |
alignTargetedRuns | 9.730 | 9.626 | 6.334 | |
alignToMaster | 2.032 | 0.143 | 2.181 | |
alignToRef | 0.001 | 0.000 | 0.001 | |
alignToRefMST | 0.000 | 0.001 | 0.001 | |
alignedXIC | 0.082 | 0.010 | 0.092 | |
analytesFromFeatures | 0.046 | 0.001 | 0.046 | |
approxFill | 0.001 | 0.000 | 0.001 | |
areaIntegrator | 0.000 | 0.003 | 0.004 | |
blobXICs | 0.002 | 0.000 | 0.002 | |
calculateIntensity | 0.002 | 0.001 | 0.003 | |
checkOverlap | 0 | 0 | 0 | |
checkParams | 0 | 0 | 0 | |
childXIC | 0.089 | 0.003 | 0.092 | |
childXICs | 0.742 | 0.060 | 0.803 | |
constrainSimCpp | 0.001 | 0.000 | 0.000 | |
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 | 0.001 | |
extractXIC_group | 1.003 | 0.019 | 1.027 | |
extractXIC_group2 | 0.001 | 0.000 | 0.001 | |
fetchAnalytesInfo | 0.011 | 0.000 | 0.011 | |
fetchFeaturesFromRun | 0.01 | 0.00 | 0.01 | |
fetchPeptidesInfo | 0.009 | 0.000 | 0.010 | |
fetchPeptidesInfo2 | 0.01 | 0.00 | 0.01 | |
fetchPrecursorsInfo | 0.000 | 0.001 | 0.001 | |
fetchTransitionsFromRun | 0.008 | 0.002 | 0.010 | |
filenamesFromMZML | 0.001 | 0.000 | 0.001 | |
filenamesFromOSW | 0.002 | 0.000 | 0.002 | |
getAlignObj | 0.027 | 0.000 | 0.027 | |
getAlignObjs | 1.483 | 0.032 | 1.519 | |
getAlignedFigs | 0.162 | 0.016 | 0.178 | |
getAlignedIndices | 0.011 | 0.000 | 0.012 | |
getAlignedTimes | 0.023 | 0.000 | 0.024 | |
getAlignedTimesCpp | 0.008 | 0.000 | 0.008 | |
getAlignedTimesFast | 0.018 | 0.000 | 0.018 | |
getBaseGapPenaltyCpp | 0 | 0 | 0 | |
getChildFeature | 0.047 | 0.004 | 0.051 | |
getChildXICpp | 0.009 | 0.000 | 0.009 | |
getChildXICs | 0.885 | 0.020 | 0.907 | |
getChromSimMatCpp | 0.001 | 0.000 | 0.002 | |
getChromatogramIndices | 0.125 | 0.004 | 0.130 | |
getFeatures | 0.046 | 0.000 | 0.046 | |
getGlobalAlignMaskCpp | 0.000 | 0.000 | 0.001 | |
getGlobalAlignment | 0.008 | 0.000 | 0.008 | |
getGlobalFits | 0.482 | 0.012 | 0.494 | |
getLOESSfit | 0.004 | 0.000 | 0.003 | |
getLinearfit | 0.004 | 0.000 | 0.003 | |
getMST | 0.001 | 0.000 | 0.001 | |
getMZMLpointers | 0.021 | 0.000 | 0.022 | |
getMappedRT | 0.012 | 0.000 | 0.012 | |
getMultipeptide | 2.146 | 0.068 | 2.220 | |
getNativeIDs | 0.021 | 0.000 | 0.021 | |
getNodeIDs | 0 | 0 | 0 | |
getNodeRun | 0.486 | 0.008 | 0.495 | |
getOswAnalytes | 0.009 | 0.000 | 0.009 | |
getOswFiles | 0.009 | 0.000 | 0.009 | |
getPeptideScores | 0.041 | 0.000 | 0.040 | |
getPrecursorByID | 0.017 | 0.000 | 0.017 | |
getPrecursorIndices | 0.056 | 0.000 | 0.055 | |
getPrecursors | 0.028 | 0.000 | 0.028 | |
getRSE | 0.003 | 0.000 | 0.003 | |
getRTdf | 0.007 | 0.000 | 0.008 | |
getRefExpFeatureMap | 0.334 | 0.003 | 0.337 | |
getRefRun | 0.409 | 0.008 | 0.418 | |
getRunNames | 0.011 | 0.000 | 0.011 | |
getSeqSimMatCpp | 0.000 | 0.000 | 0.001 | |
getTransitions | 0.137 | 0.020 | 0.155 | |
getTree | 0.035 | 0.000 | 0.035 | |
getXICs | 0.111 | 0.000 | 0.110 | |
getXICs4AlignObj | 0.091 | 0.000 | 0.091 | |
get_ropenms | 0 | 0 | 0 | |
imputeChromatogram | 0.015 | 0.000 | 0.015 | |
ipfReassignFDR | 0 | 0 | 0 | |
mapIdxToTime | 0 | 0 | 0 | |
mappedRTfromAlignObj | 0.002 | 0.000 | 0.002 | |
mergeXIC | 0.002 | 0.000 | 0.002 | |
mstAlignRuns | 2.226 | 0.020 | 2.253 | |
mstScript1 | 0.550 | 0.265 | 0.575 | |
mstScript2 | 2.672 | 0.498 | 2.880 | |
nrDesc | 0.000 | 0.000 | 0.001 | |
otherChildXICpp | 0.005 | 0.005 | 0.010 | |
paramsDIAlignR | 0 | 0 | 0 | |
perBatch | 0.001 | 0.000 | 0.001 | |
pickNearestFeature | 0.003 | 0.000 | 0.003 | |
plotAlignedAnalytes | 0.716 | 0.011 | 0.730 | |
plotAlignmentPath | 0.435 | 0.040 | 0.476 | |
plotAnalyteXICs | 0.553 | 0.044 | 0.599 | |
plotXICgroup | 0.481 | 0.000 | 0.482 | |
populateReferenceExperimentFeatureAlignmentMap | 0.008 | 0.004 | 0.013 | |
progAlignRuns | 0.000 | 0.001 | 0.001 | |
readMzMLHeader | 0.000 | 0.001 | 0.002 | |
readSqMassHeader | 0.001 | 0.000 | 0.001 | |
recalculateIntensity | 0.336 | 0.008 | 0.345 | |
reduceXICs | 0.093 | 0.000 | 0.092 | |
script1 | 0.834 | 0.913 | 0.959 | |
script2 | 3.013 | 1.332 | 3.368 | |
setAlignmentRank | 0.013 | 0.001 | 0.013 | |
sgolayCpp | 0.003 | 0.000 | 0.003 | |
sgolayFill | 0.001 | 0.000 | 0.002 | |
smoothSingleXIC | 0.002 | 0.000 | 0.002 | |
smoothXICs | 0.010 | 0.000 | 0.009 | |
splineFill | 0.001 | 0.000 | 0.001 | |
splineFillCpp | 0.005 | 0.000 | 0.005 | |
traverseDown | 1.754 | 0.087 | 1.846 | |
traverseMST | 0 | 0 | 0 | |
traverseUp | 2.113 | 0.147 | 2.267 | |
trfrParentFeature | 0.044 | 0.004 | 0.048 | |
trimXICs | 0.002 | 0.000 | 0.002 | |
uncompressVec | 0.006 | 0.000 | 0.006 | |
updateFileInfo | 0.01 | 0.00 | 0.01 | |
writeOutFeatureAlignmentMap | 0.004 | 0.000 | 0.004 | |
writeTables | 0.003 | 0.000 | 0.003 | |