| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-23 01:33:55 -0000 (Thu, 23 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4245 |
| 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 | ||||
|
To the developers/maintainers of the DIAlignR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DIAlignR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 521/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DIAlignR 2.7.0 (landing page) Shubham Gupta
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: DIAlignR |
| Version: 2.7.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DIAlignR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings DIAlignR_2.7.0.tar.gz |
| StartedAt: 2023-02-22 03:55:31 -0000 (Wed, 22 Feb 2023) |
| EndedAt: 2023-02-22 04:00:01 -0000 (Wed, 22 Feb 2023) |
| EllapsedTime: 269.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: DIAlignR.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DIAlignR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings DIAlignR_2.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/DIAlignR.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘DIAlignR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DIAlignR’ version ‘2.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.dockerignore
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DIAlignR’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
installed size is 27.7Mb
sub-directories of 1Mb or more:
extdata 4.0Mb
libs 16.8Mb
metabo 4.1Mb
ptms 1.5Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘magrittr’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
alignTargetedRuns: no visible binding for global variable ‘peptide_id’
alignTargetedRuns : <anonymous>: no visible global function definition
for ‘.’
alignTargetedRuns: no visible binding for global variable ‘intensity’
alignToRoot4: no visible binding for global variable ‘trees’
alignToRoot4: no visible binding for global variable ‘precursors’
alignToRoot4: no visible binding for global variable ‘intensity’
childXICs: possible error in cummax(v = cummax(ifelse(is.na(x), -Inf,
x))): unused argument (v = cummax(ifelse(is.na(x), -Inf, x)))
dist4split: no visible global function definition for ‘as.dist’
distMat.rSqrd : <anonymous> : <anonymous>: no visible binding for
global variable ‘RT.ref’
distMat.rSqrd : <anonymous> : <anonymous>: no visible binding for
global variable ‘RT.eXp’
fetchPrecursorsInfo: no visible binding for global variable
‘transition_id’
fetchPrecursorsInfo: no visible global function definition for ‘.’
fetchPrecursorsInfo: no visible binding for global variable
‘transition_group_id’
fetchTransitionsFromRun: no visible binding for global variable
‘intensity’
fetchTransitionsFromRun: no visible global function definition for ‘.’
fetchTransitionsFromRun: no visible binding for global variable
‘transition_group_id’
fetchTransitionsFromRun: no visible binding for global variable
‘peak_group_rank’
fetchTransitionsFromRun: no visible global function definition for
‘head’
getNativeIDs: no visible binding for global variable ‘peptide_id’
getPeptideScores: no visible binding for global variable ‘col2’
getPeptideScores: no visible binding for global variable ‘run’
getQuery: no visible binding for global variable
‘identifying.transitionPEPfilter’
getRTdf: no visible binding for global variable ‘peak_group_rank’
getRTdf: no visible binding for global variable ‘m_score’
getRTdf: no visible global function definition for ‘.’
getRTdf: no visible binding for global variable ‘transition_group_id’
getRTdf: no visible binding for global variable ‘RT’
getRefRun : <anonymous>: no visible binding for global variable
‘pvalue’
ipfReassignFDR: no visible binding for global variable ‘ref_run’
ipfReassignFDR: no visible binding for global variable ‘run’
ipfReassignFDR: no visible global function definition for ‘.’
ipfReassignFDR: no visible binding for global variable ‘i.to’
ipfReassignFDR: no visible binding for global variable ‘m_score_new’
ipfReassignFDR: no visible binding for global variable ‘ms2_m_score’
ipfReassignFDR: no visible binding for global variable ‘m_score’
mstAlignRuns: no visible binding for global variable ‘ropenms’
mstAlignRuns: no visible binding for global variable ‘peptide_id’
mstAlignRuns : <anonymous>: no visible global function definition for
‘.’
mstAlignRuns: no visible binding for global variable ‘intensity’
mstScript1: no visible binding for global variable ‘ropenms’
mstScript2: no visible binding for global variable ‘fileInfo’
mstScript2: no visible binding for global variable ‘peptide_id’
mstScript2: no visible binding for global variable ‘features’
mstScript2 : <anonymous>: no visible global function definition for ‘.’
mstScript2 : <anonymous>: no visible binding for global variable
‘features’
mstScript2: no visible binding for global variable ‘intensity’
progAlignRuns: no visible binding for global variable ‘peptide_id’
progAlignRuns : <anonymous>: no visible global function definition for
‘.’
progAlignRuns: no visible binding for global variable ‘intensity’
progComb3: no visible binding for global variable ‘precursors’
progComb3: no visible binding for global variable ‘ropenms’
progSplit2: no visible binding for global variable ‘trees’
progSplit2: no visible binding for global variable ‘scoreFile’
progSplit2: no visible binding for global variable ‘precursors’
progSplit2 : <anonymous>: no visible global function definition for ‘.’
progSplit2: no visible binding for global variable ‘ropenms’
progSplit4: no visible binding for global variable ‘precursors’
progSplit4 : <anonymous>: no visible global function definition for ‘.’
progSplit4: no visible binding for global variable ‘intensity’
progTree1: no visible binding for global variable ‘ropenms’
progTree1: no visible binding for global variable ‘peptide_id’
reIntensity: no visible binding for global variable ‘run’
reIntensity: no visible binding for global variable ‘alignment_rank’
recalculateIntensity: no visible binding for global variable
‘peptide_id’
recalculateIntensity: no visible binding for global variable
‘chromatogramIndex’
script2: no visible binding for global variable ‘fileInfo’
script2: no visible binding for global variable ‘peptide_id’
script2 : <anonymous>: no visible global function definition for ‘.’
script2: no visible binding for global variable ‘features’
script2: no visible binding for global variable ‘globalFits’
script2: no visible binding for global variable ‘RSE’
script2: no visible binding for global variable ‘intensity’
setRootRank : <anonymous>: no visible global function definition for
‘.’
writeTables: no visible binding for global variable ‘peptide_id’
writeTables: no visible binding for global variable ‘run’
writeTables: no visible binding for global variable ‘precursor’
Undefined global functions or variables:
. RSE RT RT.eXp RT.ref alignment_rank as.dist chromatogramIndex col2
features fileInfo globalFits head i.to
identifying.transitionPEPfilter intensity m_score m_score_new
ms2_m_score peak_group_rank peptide_id precursor precursors pvalue
ref_run ropenms run scoreFile transition_group_id transition_id trees
Consider adding
importFrom("datasets", "trees")
importFrom("stats", "as.dist")
importFrom("utils", "head")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.17-bioc/R/library/DIAlignR/libs/DIAlignR.so’:
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
alignTargetedRuns 10.018 11.893 7.065
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Unable to locate conda environment 'TricEnvr'.
[ FAIL 1 | WARN 9 | SKIP 8 | PASS 626 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (5)
• ropenms not available for testing. A conda environment with name TricEnvr is MUST for testing. (3)
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_utils.R:170'): test_ipfReassignFDR ───────────────────────────
`finalTbl` not equal to `expData`.
Column 'RT': 'is.NA' value mismatch: 2 in current 0 in target
[ FAIL 1 | WARN 9 | SKIP 8 | PASS 626 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘DIAlignR-vignette.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 5 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/DIAlignR.Rcheck/00check.log’
for details.
DIAlignR.Rcheck/00install.out
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL DIAlignR
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘DIAlignR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++14
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ChromatogramPeak.cpp -o ChromatogramPeak.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c DPosition.cpp -o DPosition.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c MSChromatogram.cpp -o MSChromatogram.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c PeakIntegrator.cpp -o PeakIntegrator.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c Rmain.cpp -o Rmain.o
Rmain.cpp: In function ‘Rcpp::NumericVector areaIntegrator(Rcpp::List, Rcpp::List, double, double, std::string, std::string, bool, bool, int, int)’:
Rmain.cpp:273:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
273 | for(int i = 0; i<vov2.size(); i++) sgolay.smoothChroms(vov2[i]);
| ~^~~~~~~~~~~~
Rmain.cpp: In function ‘Rcpp::NumericMatrix sgolayCpp(Rcpp::NumericMatrix, int, int)’:
Rmain.cpp:305:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
305 | for(int i = 0; i<d.size(); i++){
| ~^~~~~~~~~
Rmain.cpp: In function ‘Rcpp::NumericMatrix getAlignedTimesCpp(Rcpp::List, Rcpp::List, int, int, std::string, double, std::string, std::string, const std::vector<double>&, double, double, double, bool, double, double, int, bool, double)’:
Rmain.cpp:368:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
368 | for(int i = 0; i<intensity1.size(); i++){
| ~^~~~~~~~~~~~~~~~~~
Rmain.cpp: In function ‘Rcpp::List getChildXICpp(Rcpp::List, Rcpp::List, int, int, std::string, double, std::string, std::string, const std::vector<double>&, double, double, double, bool, double, double, int, bool, double, double, std::string, std::string, bool)’:
Rmain.cpp:771:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
771 | for(int i = 0; i<intensity1.size(); i++){
| ~^~~~~~~~~~~~~~~~~~
Rmain.cpp:818:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
818 | for(int i = 0; i < keep.size(); i++){
| ~~^~~~~~~~~~~~~
Rmain.cpp:824:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
824 | for(int j = 0; j <intensity1NN.size(); j++){
| ~~^~~~~~~~~~~~~~~~~~~~
Rmain.cpp:827:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
827 | for(int i = 0; i < keep.size(); i++){
| ~~^~~~~~~~~~~~~
Rmain.cpp:837:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
837 | for(int i = 0; i < keep.size(); i++) alignedChildTime[keep[i]] = t1NN[i];
| ~~^~~~~~~~~~~~~
Rmain.cpp:862:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
862 | for (int i = 0; i < intensity1NN.size(); i++){
| ~~^~~~~~~~~~~~~~~~~~~~~
Rmain.cpp:873:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
873 | for(int i =0, j = 0; i < alignedChildTime.size(); i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~
Rmain.cpp: In function ‘Rcpp::List otherChildXICpp(Rcpp::List, Rcpp::List, int, int, Rcpp::NumericMatrix, std::vector<double>, double, std::string)’:
Rmain.cpp:944:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
944 | for(int i = 0; i<intensity1.size(); i++){
| ~^~~~~~~~~~~~~~~~~~
Rmain.cpp:972:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
972 | for(int j = 0; j <intensity1NN.size(); j++){
| ~~^~~~~~~~~~~~~~~~~~~~
Rmain.cpp:975:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
975 | for(int i = 0; i < keep.size(); i++){
| ~~^~~~~~~~~~~~~
Rmain.cpp:1008:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1008 | for (int i = 0; i < intensity1NN.size(); i++){
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from Rmain.cpp:19:
miscell.h: At global scope:
miscell.h:14:19: warning: ‘const bool DIAlign::detect_end_na(double, double)’ declared ‘static’ but never defined [-Wunused-function]
14 | static bool const detect_end_na(double a, double b);
| ^~~~~~~~~~~~~
miscell.h:16:19: warning: ‘const bool DIAlign::detect_start_na(double, double)’ declared ‘static’ but never defined [-Wunused-function]
16 | static bool const detect_start_na(double a, double b);
| ^~~~~~~~~~~~~~~
miscell.h:18:19: warning: ‘const bool DIAlign::lessZero(double)’ declared ‘static’ but never defined [-Wunused-function]
18 | static bool const lessZero(double a);
| ^~~~~~~~
In file included from miscell.h:9,
from Rmain.cpp:19:
spline.h:390:10: warning: ‘double DIAlign::{anonymous}::tk::spline::deriv(int, double) const’ defined but not used [-Wunused-function]
390 | double spline::deriv(int order, double x) const
| ^~~~~~
spline.h:364:10: warning: ‘double DIAlign::{anonymous}::tk::spline::operator()(double) const’ defined but not used [-Wunused-function]
364 | double spline::operator() (double x) const
| ^~~~~~
spline.h:273:8: warning: ‘void DIAlign::{anonymous}::tk::spline::set_points(const std::vector<double>&, const std::vector<double>&, bool)’ defined but not used [-Wunused-function]
273 | void spline::set_points(const std::vector<double>& x,
| ^~~~~~
spline.h:261:8: warning: ‘void DIAlign::{anonymous}::tk::spline::set_boundary(DIAlign::{anonymous}::tk::spline::bd_type, double, DIAlign::{anonymous}::tk::spline::bd_type, double, bool)’ defined but not used [-Wunused-function]
261 | void spline::set_boundary(spline::bd_type left, double left_value,
| ^~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SavitzkyGolayFilter.cpp -o SavitzkyGolayFilter.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/Core:507,
from /home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
from /home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
from /home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
from SavitzkyGolayFilter.cpp:1:
/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/src/Core/products/TriangularMatrixVector.h: In static member function ‘static void Eigen::internal::trmv_selector<Mode, 1>::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<const Eigen::Block<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose<Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1, 1, -1, -1>, 1, -1, true>, 1, -1, false> >; int Mode = 6]’:
/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized]
327 | internal::triangular_matrix_vector_product
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
328 | <Index,Mode,
| ~~~~~~~~~~~~
329 | LhsScalar, LhsBlasTraits::NeedToConjugate,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
330 | RhsScalar, RhsBlasTraits::NeedToConjugate,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
331 | RowMajor>
| ~~~~~~~~~
332 | ::run(actualLhs.rows(),actualLhs.cols(),
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
333 | actualLhs.data(),actualLhs.outerStride(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
334 | actualRhsPtr,1,
| ~~~~~~~~~~~~~~~
335 | dest.data(),dest.innerStride(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
336 | actualAlpha);
| ~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type ‘const double*’ to ‘static void Eigen::internal::triangular_matrix_vector_product<Index, Mode, LhsScalar, ConjLhs, RhsScalar, ConjRhs, 1, Version>::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, Eigen::internal::triangular_matrix_vector_product<Index, Mode, LhsScalar, ConjLhs, RhsScalar, ConjRhs, 1, Version>::ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]’ declared here
105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product<Index,Mode,LhsScalar,ConjLhs,RhsScalar,ConjRhs,RowMajor,Version>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c affinealignment.cpp -o affinealignment.o
affinealignment.cpp: In function ‘double DIAlign::AffineAlignment::getOlapAffineAlignStartIndices(double*, double*, double*, int, int, int&, int&, DIAlign::Traceback::tbJump&)’:
affinealignment.cpp:485:16: warning: ‘MaxColIndex’ may be used uninitialized in this function [-Wmaybe-uninitialized]
485 | OlapStartCol = MaxColIndex;
| ~~~~~~~~~~~~~^~~~~~~~~~~~~
affinealignment.cpp:484:16: warning: ‘MaxRowIndex’ may be used uninitialized in this function [-Wmaybe-uninitialized]
484 | OlapStartRow = MaxRowIndex;
| ~~~~~~~~~~~~~^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c affinealignobj.cpp -o affinealignobj.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c alignment.cpp -o alignment.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c chromSimMatrix.cpp -o chromSimMatrix.o
chromSimMatrix.cpp: In function ‘std::vector<double> DIAlign::SimilarityMatrix::perSampleEucLenVecOfVec(const std::vector<std::vector<double> >&)’:
chromSimMatrix.cpp:32:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
32 | for (int i = 0; i < mag.size(); i++){
| ~~^~~~~~~~~~~~
chromSimMatrix.cpp: In function ‘std::vector<double> DIAlign::SimilarityMatrix::perSampleSqrSumVecOfVec(const std::vector<std::vector<double> >&)’:
chromSimMatrix.cpp:45:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
45 | for (int i = 0; i < mag.size(); i++){
| ~~^~~~~~~~~~~~
chromSimMatrix.cpp: In function ‘std::vector<double> DIAlign::SimilarityMatrix::perSampleMeanVecOfVec(const std::vector<std::vector<double> >&)’:
chromSimMatrix.cpp:57:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
57 | for (int i = 0; i < mean.size(); i++){
| ~~^~~~~~~~~~~~~
chromSimMatrix.cpp: In function ‘std::vector<double> DIAlign::SimilarityMatrix::perSampleSumVecOfVec(const std::vector<std::vector<double> >&)’:
chromSimMatrix.cpp:70:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
70 | for (int i = 0; i < sum.size(); i++){
| ~~^~~~~~~~~~~~
chromSimMatrix.cpp: In function ‘DIAlign::SimMatrix DIAlign::SimilarityMatrix::getSimilarityMatrix(const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, std::string, std::string, double, double, int)’:
chromSimMatrix.cpp:414:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
414 | for(int i = 0; i < MASK.size(); i++){
| ~~^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c constrainMat.cpp -o constrainMat.o
constrainMat.cpp: In function ‘void DIAlign::ConstrainMatrix::calcNoBeefMask2(DIAlign::SimMatrix&, std::vector<double>, std::vector<double>, std::vector<double>, int, bool)’:
constrainMat.cpp:78:10: warning: unused variable ‘mapped’ [-Wunused-variable]
78 | double mapped = 0.0;
| ^~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c gapPenalty.cpp -o gapPenalty.o
gapPenalty.cpp: In function ‘double DIAlign::getGapPenalty(const DIAlign::SimMatrix&, double, std::string)’:
gapPenalty.cpp:26:35: warning: ‘gapPenalty’ may be used uninitialized in this function [-Wmaybe-uninitialized]
26 | return std::max(0.01, gapPenalty); // gapPenalty must be positive.
| ^
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c integrateArea.cpp -o integrateArea.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c interface.cpp -o interface.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c miscell.cpp -o miscell.o
miscell.cpp: In function ‘void DIAlign::xicIntersect(std::vector<std::vector<double> >&, std::vector<std::vector<double> >&)’:
miscell.cpp:10:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
10 | for (unsigned int i = 0; i < len; i++){
| ~~^~~~~
miscell.cpp:15:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
15 | for(unsigned int i = 0; i < len; i++){
| ~~^~~~~
miscell.cpp:26:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
26 | for (unsigned int i = 0; i < len; i++){
| ~~^~~~~
miscell.cpp:39:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
39 | for (unsigned int i = 0; i < len; i++) len2[i] = intensity[i].size();
| ~~^~~~~
miscell.cpp: In function ‘std::vector<std::vector<double> > DIAlign::imputeChromatogram(const std::vector<std::vector<double> >&, const std::vector<double>&, const std::vector<int>&)’:
miscell.cpp:125:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
125 | for(int i =0; i< middle.size(); i++){
| ~^~~~~~~~~~~~~~~
miscell.cpp:131:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
131 | for(int i =0; i < (Anew.size()-1); i++){
| ~~^~~~~~~~~~~~~~~~~
miscell.cpp:139:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
139 | for(int j=0; j<result.size(); j++){
| ~^~~~~~~~~~~~~~
miscell.cpp: In function ‘std::vector<int> DIAlign::getSkip(const std::vector<int>&, const std::vector<int>&)’:
miscell.cpp:164:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
164 | for(int i = 0; i < index.size(); i++){
| ~~^~~~~~~~~~~~~~
miscell.cpp: In function ‘void DIAlign::mergeIntensity(std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, double)’:
miscell.cpp:221:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
221 | for(int i = 0; i< A.size(); i++){
| ~^~~~~~~~~~
miscell.cpp: In function ‘void DIAlign::addFlankToLeft(const std::vector<double>&, std::vector<double>&, std::vector<double>&, const std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<int>&)’:
miscell.cpp:250:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
250 | for(int i = 0; i< intenN.size(); i++){
| ~^~~~~~~~~~~~~~~
miscell.cpp: In function ‘void DIAlign::addFlankToRight(const std::vector<double>&, std::vector<double>&, std::vector<double>&, const std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<int>&)’:
miscell.cpp:277:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
277 | for(int i = 0; i< intenN.size(); i++){
| ~^~~~~~~~~~~~~~~
miscell.cpp: In function ‘void DIAlign::addFlankToLeft1(const std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<int>&)’:
miscell.cpp:288:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
288 | for(int i = 0; i< intenN.size(); i++){
| ~^~~~~~~~~~~~~~~
miscell.cpp: In function ‘void DIAlign::addFlankToRight1(const std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, std::vector<int>&)’:
miscell.cpp:307:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
307 | for(int i = 0; i< intenN.size(); i++){
| ~^~~~~~~~~~~~~~~
miscell.cpp: In function ‘std::vector<int> DIAlign::getMatchingIdx(const std::vector<double>&, const std::vector<double>&)’:
miscell.cpp:318:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
318 | for(int i =0, j=0; i< tMain.size(); i++){
| ~^~~~~~~~~~~~~~
miscell.cpp:320:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
320 | for(; j<t.size();){
| ~^~~~~~~~~
miscell.cpp: In function ‘std::vector<std::vector<double> > DIAlign::imputeChromatogram1(const std::vector<std::vector<double> >&, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&)’:
miscell.cpp:337:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
337 | for(int j = 0; j <A.size(); j++){
| ~~^~~~~~~~~
miscell.cpp:339:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
339 | for(int i = 0; i < temp.size(); i++){
| ~~^~~~~~~~~~~~~
miscell.cpp:353:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
353 | for(int i =0; i< middle.size(); i++){
| ~^~~~~~~~~~~~~~~
miscell.cpp:358:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
358 | for(int i =0; i < intensity.size(); i++){
| ~~^~~~~~~~~~~~~~~~~~
miscell.cpp:360:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
360 | for(int j=0; j<result.size(); j++){
| ~^~~~~~~~~~~~~~
miscell.cpp: At global scope:
miscell.cpp:53:19: warning: ‘const bool DIAlign::lessZero(double)’ defined but not used [-Wunused-function]
53 | static bool const lessZero(double a){
| ^~~~~~~~
In file included from miscell.h:9,
from miscell.cpp:3:
spline.h:390:10: warning: ‘double DIAlign::{anonymous}::tk::spline::deriv(int, double) const’ defined but not used [-Wunused-function]
390 | double spline::deriv(int order, double x) const
| ^~~~~~
spline.h:364:10: warning: ‘double DIAlign::{anonymous}::tk::spline::operator()(double) const’ defined but not used [-Wunused-function]
364 | double spline::operator() (double x) const
| ^~~~~~
spline.h:273:8: warning: ‘void DIAlign::{anonymous}::tk::spline::set_points(const std::vector<double>&, const std::vector<double>&, bool)’ defined but not used [-Wunused-function]
273 | void spline::set_points(const std::vector<double>& x,
| ^~~~~~
spline.h:261:8: warning: ‘void DIAlign::{anonymous}::tk::spline::set_boundary(DIAlign::{anonymous}::tk::spline::bd_type, double, DIAlign::{anonymous}::tk::spline::bd_type, double, bool)’ defined but not used [-Wunused-function]
261 | void spline::set_boundary(spline::bd_type left, double left_value,
| ^~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c run_alignment.cpp -o run_alignment.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c simpleFcn.cpp -o simpleFcn.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c spline.cpp -o spline.o
In file included from spline.cpp:1:
spline.h:390:10: warning: ‘double DIAlign::{anonymous}::tk::spline::deriv(int, double) const’ defined but not used [-Wunused-function]
390 | double spline::deriv(int order, double x) const
| ^~~~~~
spline.h:261:8: warning: ‘void DIAlign::{anonymous}::tk::spline::set_boundary(DIAlign::{anonymous}::tk::spline::bd_type, double, DIAlign::{anonymous}::tk::spline::bd_type, double, bool)’ defined but not used [-Wunused-function]
261 | void spline::set_boundary(spline::bd_type left, double left_value,
| ^~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c utils.cpp -o utils.o
utils.cpp: In function ‘double DIAlign::Utils::getQuantile(std::vector<double>, double)’:
utils.cpp:48:9: warning: unused variable ‘idx’ [-Wunused-variable]
48 | int idx = n*(1-p);
| ^~~
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o DIAlignR.so ChromatogramPeak.o DPosition.o MSChromatogram.o PeakIntegrator.o RcppExports.o Rmain.o SavitzkyGolayFilter.o affinealignment.o affinealignobj.o alignment.o chromSimMatrix.o constrainMat.o gapPenalty.o integrateArea.o interface.o miscell.o run_alignment.o simpleFcn.o spline.o utils.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-DIAlignR/00new/DIAlignR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DIAlignR)
DIAlignR.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
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Platform: aarch64-unknown-linux-gnu (64-bit)
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> 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 0.05411792 secs
Time difference of 0.3151178 secs
Time difference of 0.1171496 secs
Time difference of 0.02737427 secs
Time difference of 0.01211095 secs
Time difference of 0.638696 secs
Time difference of 2.047955 secs
Time difference of 0.02989841 secs
Time difference of 0.4967346 secs
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"
Time difference of 0.01928782 secs
Time difference of 0.2888987 secs
Time difference of 0.112848 secs
Time difference of 0.01959658 secs
Time difference of 0.007301569 secs
Time difference of 0.2655652 secs
Time difference of 1.298981 secs
Time difference of 0.01047277 secs
Time difference of 1.099794 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 0.01919937 secs
Time difference of 0.3219631 secs
Time difference of 0.1273792 secs
Time difference of 0.1009865 secs
Time difference of 0.01220822 secs
Time difference of 0.3677354 secs
Time difference of 1.774662 secs
Time difference of 0.03204608 secs
Time difference of 0.4600854 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 0.02015042 secs
Time difference of 0.01899123 secs
Time difference of 0.0005688667 secs
Time difference of 0.105154 secs
Time difference of 0.01253867 secs
Time difference of 0.358969 secs
Time difference of 0.02189922 secs
Time difference of 0.009905338 secs
Time difference of 0.1163011 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 0.009734869 secs
Time difference of 0.04085684 secs
Time difference of 0.01239729 secs
Time difference of 0.0147903 secs
Time difference of 0.009810686 secs
Time difference of 0.2725832 secs
Time difference of 0.114589 secs
Time difference of 0.009434462 secs
Time difference of 0.2806873 secs
[1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4"
[3] "chludwig_K150309_013_SW_0"
Time difference of 0.01394439 secs
Time difference of 0.01526546 secs
Time difference of 0.001549959 secs
Time difference of 0.01998901 secs
Time difference of 0.01442122 secs
Time difference of 0.3541846 secs
Time difference of 0.007796526 secs
Time difference of 0.02321982 secs
Time difference of 0.3425775 secs
<simpleWarning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, drop.square = drop.square, normalize = normalize, statistics = control$statistics, surface = control$surface, cell = control$cell, iterations = iterations, iterTrace = control$iterTrace, trace.hat = control$trace.hat): span too small. fewer data values than degrees of freedom.>
<simpleWarning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, drop.square = drop.square, normalize = normalize, statistics = control$statistics, surface = control$surface, cell = control$cell, iterations = iterations, iterTrace = control$iterTrace, trace.hat = control$trace.hat): span too small. fewer data values than degrees of freedom.>
<simpleWarning in sqrt(sum.squares/one.delta): NaNs produced>
<simpleError in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, drop.square = drop.square, normalize = normalize, statistics = control$statistics, surface = control$surface, cell = control$cell, iterations = iterations, iterTrace = control$iterTrace, trace.hat = control$trace.hat): span is too small>
runName
run0 hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt
run1 hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt
run2 hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt
Time difference of 0.1064222 secs
Time difference of 0.02269173 secs
Time difference of 0.002971649 secs
Time difference of 0.01526093 secs
Time difference of 0.3918374 secs
Time difference of 0.02612615 secs
Time difference of 0.02018118 secs
Time difference of 0.1157844 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 0.0295465 secs
[1] "run0 run1\nrun2 run2"
Time difference of 0.3105404 secs
Time difference of 0.1405332 secs
Time difference of 0.01194048 secs
Time difference of 0.3843393 secs
Time difference of 1.793248 secs
Time difference of 0.01963639 secs
Time difference of 0.4381099 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 0.1226168 secs
Time difference of 1.047569 secs
Time difference of 5.627768 secs
Time difference of 0.6905961 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 0.1093419 secs
[1] "Written /home/biocbuild/bbs-3.17-bioc/R/library/DIAlignR/extdata/temp_prog1.RData"
[1] "Written /home/biocbuild/bbs-3.17-bioc/R/library/DIAlignR/extdata/temp_0_2.rds"
[1] "progTree1 is done."
Time difference of 1.856067 secs
Time difference of 0.6065333 secs
[1] "Written /home/biocbuild/bbs-3.17-bioc/R/library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 1.266315 secs
[1] "Written /home/biocbuild/bbs-3.17-bioc/R/library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.5512626 secs
Time difference of 0.2609038 secs
[1] "Written /home/biocbuild/bbs-3.17-bioc/R/library/DIAlignR/extdata/temp_all_2.rds"
Time difference of 0.2429647 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 0.1002812 secs
[1] "Written /home/biocbuild/bbs-3.17-bioc/R/library/DIAlignR/extdata/temp_prog1.RData"
[1] "Written /home/biocbuild/bbs-3.17-bioc/R/library/DIAlignR/extdata/temp_0_2.rds"
[1] "progTree1 is done."
Time difference of 1.599661 secs
Time difference of 0.5350609 secs
[1] "Written /home/biocbuild/bbs-3.17-bioc/R/library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.6712005 secs
[1] "Written /home/biocbuild/bbs-3.17-bioc/R/library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.612077 secs
Time difference of 0.01779652 secs
[1] "Written /home/biocbuild/bbs-3.17-bioc/R/library/DIAlignR/extdata/temp_all_2.rds"
Error in reticulate::use_condaenv(condaEnv, required = TRUE) :
Unable to locate conda environment 'TricEnvr'.
Error in reticulate::use_condaenv(condaEnv, required = TRUE) :
Unable to locate conda environment 'TricEnvr'.
Error in reticulate::use_condaenv(condaEnv, required = TRUE) :
Unable to locate conda environment 'TricEnvr'.
[ FAIL 1 | WARN 9 | SKIP 8 | PASS 626 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (5)
• ropenms not available for testing. A conda environment with name TricEnvr is MUST for testing. (3)
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_utils.R:170'): test_ipfReassignFDR ───────────────────────────
`finalTbl` not equal to `expData`.
Column 'RT': 'is.NA' value mismatch: 2 in current 0 in target
[ FAIL 1 | WARN 9 | SKIP 8 | PASS 626 ]
Error: Test failures
Execution halted
DIAlignR.Rcheck/DIAlignR-Ex.timings
| name | user | system | elapsed | |
| MSTperBatch | 0.000 | 0.000 | 0.001 | |
| addFlankToLeft | 0.003 | 0.000 | 0.003 | |
| addFlankToRight | 0.002 | 0.000 | 0.002 | |
| addXIC | 0 | 0 | 0 | |
| alignChromatogramsCpp | 0.026 | 0.003 | 0.031 | |
| alignTargetedRuns | 10.018 | 11.893 | 7.065 | |
| alignToMaster | 4.487 | 0.260 | 4.747 | |
| alignToRef | 0.001 | 0.000 | 0.001 | |
| alignToRefMST | 0.001 | 0.000 | 0.000 | |
| alignedXIC | 0.091 | 0.004 | 0.094 | |
| analytesFromFeatures | 0.057 | 0.000 | 0.057 | |
| approxFill | 0.001 | 0.000 | 0.001 | |
| areaIntegrator | 0.003 | 0.000 | 0.003 | |
| blobXICs | 0.002 | 0.000 | 0.002 | |
| calculateIntensity | 0.002 | 0.000 | 0.003 | |
| checkOverlap | 0 | 0 | 0 | |
| checkParams | 0 | 0 | 0 | |
| childXIC | 0.094 | 0.000 | 0.094 | |
| childXICs | 0.63 | 0.00 | 0.63 | |
| constrainSimCpp | 0.000 | 0.000 | 0.001 | |
| createMZML | 0.003 | 0.000 | 0.003 | |
| createSqMass | 0.002 | 0.000 | 0.002 | |
| dialignrLoess | 0.001 | 0.000 | 0.001 | |
| doAffineAlignmentCpp | 0.002 | 0.000 | 0.001 | |
| doAlignmentCpp | 0.002 | 0.000 | 0.002 | |
| extractXIC_group | 0.936 | 0.006 | 0.950 | |
| extractXIC_group2 | 0.001 | 0.000 | 0.001 | |
| fetchAnalytesInfo | 0.009 | 0.000 | 0.010 | |
| fetchFeaturesFromRun | 0.008 | 0.000 | 0.009 | |
| fetchPeptidesInfo | 0.008 | 0.000 | 0.008 | |
| fetchPeptidesInfo2 | 0.008 | 0.000 | 0.008 | |
| fetchPrecursorsInfo | 0.001 | 0.000 | 0.001 | |
| fetchTransitionsFromRun | 0.008 | 0.000 | 0.008 | |
| filenamesFromMZML | 0.000 | 0.000 | 0.001 | |
| filenamesFromOSW | 0.001 | 0.000 | 0.000 | |
| getAlignObj | 0.025 | 0.000 | 0.025 | |
| getAlignObjs | 1.593 | 0.035 | 1.629 | |
| getAlignedFigs | 0.287 | 0.001 | 0.288 | |
| getAlignedIndices | 0.01 | 0.00 | 0.01 | |
| getAlignedTimes | 0.022 | 0.000 | 0.022 | |
| getAlignedTimesCpp | 0.004 | 0.004 | 0.008 | |
| getAlignedTimesFast | 0.013 | 0.003 | 0.017 | |
| getBaseGapPenaltyCpp | 0 | 0 | 0 | |
| getChildFeature | 0.044 | 0.003 | 0.047 | |
| getChildXICpp | 0.008 | 0.000 | 0.008 | |
| getChildXICs | 3.143 | 0.016 | 3.159 | |
| getChromSimMatCpp | 0.001 | 0.002 | 0.002 | |
| getChromatogramIndices | 0.155 | 0.010 | 0.164 | |
| getFeatures | 0.059 | 0.000 | 0.059 | |
| getGlobalAlignMaskCpp | 0.000 | 0.001 | 0.001 | |
| getGlobalAlignment | 0.006 | 0.002 | 0.008 | |
| getGlobalFits | 2.409 | 0.000 | 2.409 | |
| getLOESSfit | 0.000 | 0.004 | 0.003 | |
| getLinearfit | 0.002 | 0.000 | 0.003 | |
| getMST | 0.001 | 0.000 | 0.001 | |
| getMZMLpointers | 0.019 | 0.000 | 0.019 | |
| getMappedRT | 0.012 | 0.001 | 0.012 | |
| getMultipeptide | 1.721 | 0.071 | 1.792 | |
| getNativeIDs | 0.014 | 0.009 | 0.022 | |
| getNodeIDs | 0 | 0 | 0 | |
| getNodeRun | 0.557 | 0.004 | 0.561 | |
| getOswAnalytes | 0.009 | 0.000 | 0.010 | |
| getOswFiles | 0.009 | 0.000 | 0.009 | |
| getPeptideScores | 0.041 | 0.000 | 0.041 | |
| getPrecursorByID | 0.017 | 0.000 | 0.018 | |
| getPrecursorIndices | 0.056 | 0.000 | 0.056 | |
| getPrecursors | 0.027 | 0.000 | 0.026 | |
| getRSE | 0.003 | 0.000 | 0.003 | |
| getRTdf | 0.007 | 0.000 | 0.007 | |
| getRefRun | 0.444 | 0.000 | 0.444 | |
| getRunNames | 0.022 | 0.003 | 0.025 | |
| getSeqSimMatCpp | 0 | 0 | 0 | |
| getTransitions | 0.161 | 0.008 | 0.166 | |
| getTree | 0.034 | 0.000 | 0.034 | |
| getXICs | 0.161 | 0.003 | 0.164 | |
| getXICs4AlignObj | 0.107 | 0.000 | 0.107 | |
| get_ropenms | 0 | 0 | 0 | |
| imputeChromatogram | 0.034 | 0.000 | 0.034 | |
| ipfReassignFDR | 0 | 0 | 0 | |
| mapIdxToTime | 0.001 | 0.000 | 0.001 | |
| mappedRTfromAlignObj | 0.003 | 0.000 | 0.003 | |
| mergeXIC | 0.002 | 0.000 | 0.002 | |
| mstAlignRuns | 2.932 | 0.060 | 2.991 | |
| mstScript1 | 0.487 | 0.281 | 0.524 | |
| mstScript2 | 2.990 | 0.629 | 3.301 | |
| nrDesc | 0 | 0 | 0 | |
| otherChildXICpp | 0.009 | 0.000 | 0.009 | |
| paramsDIAlignR | 0 | 0 | 0 | |
| perBatch | 0.001 | 0.000 | 0.001 | |
| pickNearestFeature | 0.003 | 0.000 | 0.003 | |
| plotAlignedAnalytes | 0.794 | 0.012 | 0.806 | |
| plotAlignmentPath | 0.538 | 0.024 | 0.563 | |
| plotAnalyteXICs | 0.579 | 0.004 | 0.583 | |
| plotXICgroup | 0.513 | 0.020 | 0.533 | |
| progAlignRuns | 0.001 | 0.000 | 0.001 | |
| readMzMLHeader | 0.001 | 0.000 | 0.001 | |
| readSqMassHeader | 0.001 | 0.000 | 0.000 | |
| recalculateIntensity | 0.355 | 0.040 | 0.395 | |
| reduceXICs | 0.093 | 0.000 | 0.093 | |
| script1 | 0.774 | 1.061 | 1.034 | |
| script2 | 3.232 | 1.727 | 3.765 | |
| setAlignmentRank | 0.004 | 0.008 | 0.013 | |
| sgolayCpp | 0.000 | 0.002 | 0.002 | |
| sgolayFill | 0.000 | 0.001 | 0.001 | |
| smoothSingleXIC | 0.000 | 0.002 | 0.002 | |
| smoothXICs | 0.005 | 0.003 | 0.009 | |
| splineFill | 0.000 | 0.000 | 0.001 | |
| splineFillCpp | 0.005 | 0.000 | 0.005 | |
| traverseDown | 3.871 | 0.080 | 3.950 | |
| traverseMST | 0 | 0 | 0 | |
| traverseUp | 4.006 | 0.072 | 4.078 | |
| trfrParentFeature | 0.046 | 0.004 | 0.050 | |
| trimXICs | 0.003 | 0.000 | 0.002 | |
| uncompressVec | 0.006 | 0.000 | 0.006 | |
| updateFileInfo | 0.011 | 0.000 | 0.010 | |
| writeTables | 0.003 | 0.000 | 0.003 | |