| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-28 11:47 -0500 (Tue, 28 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4659 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4454 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4465 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4419 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4409 |
| 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 559/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Shubham Gupta
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the DIAlignR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DIAlignR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: DIAlignR |
| Version: 2.15.1 |
| 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_2.15.1.tar.gz |
| StartedAt: 2025-01-28 09:57:20 -0000 (Tue, 28 Jan 2025) |
| EndedAt: 2025-01-28 10:00:53 -0000 (Tue, 28 Jan 2025) |
| EllapsedTime: 213.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: DIAlignR.Rcheck |
| Warnings: NA |
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### 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_2.15.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/DIAlignR.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DIAlignR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DIAlignR’ version ‘2.15.1’
* 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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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 10.211 10.407 7.159
* 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 2 | WARN 0 | SKIP 8 | PASS 630 ]
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
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL DIAlignR
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘DIAlignR’ ...
** 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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/Core:214,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/Dense:1,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/RcppEigenForward.h:28,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/Core:172:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c SavitzkyGolayFilter.cpp -o SavitzkyGolayFilter.o
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/Core:214,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/Dense:1,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/RcppEigenForward.h:28,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/RcppEigen.h:25,
from SavitzkyGolayFilter.cpp:1:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/Core:172:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/site-library/RcppEigen/include/Eigen/Core:341:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/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) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(DIAlignR)
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 0.05764866 secs
Time difference of 0.2612989 secs
Time difference of 0.2196741 secs
Time difference of 0.02903795 secs
Time difference of 0.01093006 secs
Time difference of 0.1196508 secs
Time difference of 2.315256 secs
Time difference of 0.03657508 secs
Time difference of 0.4939179 secs
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"
Time difference of 0.01798081 secs
Time difference of 0.2349548 secs
Time difference of 0.1408749 secs
Time difference of 0.01786876 secs
Time difference of 0.007152796 secs
Time difference of 0.06836367 secs
Time difference of 1.016358 secs
Time difference of 0.01062036 secs
Time difference of 1.018265 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 0.01752424 secs
Time difference of 0.2526085 secs
Time difference of 0.1417353 secs
Time difference of 0.09805727 secs
Time difference of 0.01081204 secs
Time difference of 0.09442282 secs
Time difference of 1.398763 secs
Time difference of 0.02683377 secs
Time difference of 0.3881037 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 0.0188098 secs
Time difference of 0.01640868 secs
Time difference of 0.0004136562 secs
Time difference of 0.09620786 secs
Time difference of 0.01046848 secs
Time difference of 0.06370187 secs
Time difference of 0.01818085 secs
Time difference of 0.0104022 secs
Time difference of 0.1321971 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 0.01043057 secs
Time difference of 0.03546047 secs
Time difference of 0.01361394 secs
Time difference of 0.01269197 secs
Time difference of 0.009011507 secs
Time difference of 0.04607224 secs
Time difference of 0.1055942 secs
Time difference of 0.009168386 secs
Time difference of 0.2672825 secs
[1] "chludwig_K150309_004b_SW_1_16" "chludwig_K150309_008_SW_1_4"
[3] "chludwig_K150309_013_SW_0"
Time difference of 0.01596689 secs
Time difference of 0.0136416 secs
Time difference of 0.001429319 secs
Time difference of 0.02193403 secs
Time difference of 0.01448631 secs
Time difference of 0.09396482 secs
Time difference of 0.008056879 secs
Time difference of 0.02516603 secs
Time difference of 0.3112788 secs
<simpleWarning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, drop.square = drop.square, normalize = normalize, statistics = control$statistics, surface = control$surface, cell = control$cell, iterations = iterations, iterTrace = control$iterTrace, trace.hat = control$trace.hat): span too small. fewer data values than degrees of freedom.>
<simpleWarning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, drop.square = drop.square, normalize = normalize, statistics = control$statistics, surface = control$surface, cell = control$cell, iterations = iterations, iterTrace = control$iterTrace, trace.hat = control$trace.hat): span too small. fewer data values than degrees of freedom.>
<simpleWarning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, drop.square = drop.square, normalize = normalize, statistics = control$statistics, surface = control$surface, cell = control$cell, iterations = iterations, iterTrace = control$iterTrace, trace.hat = control$trace.hat): Chernobyl! trL>n 10>
<simpleError in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, drop.square = drop.square, normalize = normalize, statistics = control$statistics, surface = control$surface, cell = control$cell, iterations = iterations, iterTrace = control$iterTrace, trace.hat = control$trace.hat): span is too small>
runName
run0 hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt
run1 hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt
run2 hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt
Time difference of 0.1011362 secs
Time difference of 0.01728725 secs
Time difference of 0.002585649 secs
Time difference of 0.01122522 secs
Time difference of 0.05752587 secs
Time difference of 0.01728106 secs
Time difference of 0.01982617 secs
Time difference of 0.1130221 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 0.02832794 secs
[1] "run0 run1\nrun2 run2"
Time difference of 0.2605608 secs
Time difference of 0.146045 secs
Time difference of 0.01096344 secs
Time difference of 0.1048443 secs
Time difference of 1.470509 secs
Time difference of 0.02005124 secs
Time difference of 0.4332297 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 0.1229529 secs
Time difference of 0.9275823 secs
Time difference of 6.498818 secs
Time difference of 0.5672483 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 0.1003404 secs
[1] "Written /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/DIAlignR/extdata/temp_prog1.RData"
[1] "Written /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/DIAlignR/extdata/temp_0_2.rds"
[1] "progTree1 is done."
Time difference of 1.933596 secs
Time difference of 0.4356568 secs
[1] "Written /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.7396069 secs
[1] "Written /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.4254801 secs
Time difference of 0.2912083 secs
[1] "Written /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/DIAlignR/extdata/temp_all_2.rds"
Time difference of 0.2354376 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 0.1047294 secs
[1] "Written /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/DIAlignR/extdata/temp_prog1.RData"
[1] "Written /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/DIAlignR/extdata/temp_0_2.rds"
[1] "progTree1 is done."
Time difference of 1.287391 secs
Time difference of 0.384037 secs
[1] "Written /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/DIAlignR/extdata/temp_1_2.rds"
Time difference of 0.5666749 secs
[1] "Written /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/DIAlignR/extdata/temp_2_2.rds"
Time difference of 0.429302 secs
Time difference of 0.01700568 secs
[1] "Written /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 2 | WARN 0 | SKIP 8 | PASS 630 ]
══ Skipped tests (8) ═══════════════════════════════════════════════════════════
• empty test (5): 'test_get_filenames.R:77:1', 'test_get_filenames.R:82:1',
'test_utils.R:200:1', 'test_utils.R:203:1', 'test_utils.R:206:1'
• ropenms not available for testing. A conda environment with name TricEnvr is
MUST for testing. (3): 'test_pyopenms.R:4:3', 'test_pyopenms.R:8:3',
'test_pyopenms.R:27:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_utils.R: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 2 | WARN 0 | SKIP 8 | PASS 630 ]
Error: Test failures
Execution halted
DIAlignR.Rcheck/DIAlignR-Ex.timings
| name | user | system | elapsed | |
| MSTperBatch | 0.001 | 0.000 | 0.001 | |
| addFlankToLeft | 0.001 | 0.000 | 0.002 | |
| addFlankToRight | 0.001 | 0.000 | 0.001 | |
| addXIC | 0 | 0 | 0 | |
| alignChromatogramsCpp | 0.031 | 0.000 | 0.033 | |
| alignTargetedRuns | 10.211 | 10.407 | 7.159 | |
| alignToMaster | 1.917 | 0.178 | 2.099 | |
| alignToRef | 0.000 | 0.001 | 0.001 | |
| alignToRefMST | 0.000 | 0.001 | 0.001 | |
| alignedXIC | 0.093 | 0.000 | 0.093 | |
| analytesFromFeatures | 0.045 | 0.000 | 0.045 | |
| approxFill | 0.001 | 0.000 | 0.001 | |
| areaIntegrator | 0.003 | 0.000 | 0.003 | |
| blobXICs | 0.002 | 0.000 | 0.002 | |
| calculateIntensity | 0.003 | 0.000 | 0.003 | |
| checkOverlap | 0 | 0 | 0 | |
| checkParams | 0 | 0 | 0 | |
| childXIC | 0.089 | 0.004 | 0.092 | |
| childXICs | 0.622 | 0.056 | 0.679 | |
| constrainSimCpp | 0.001 | 0.000 | 0.001 | |
| createMZML | 0.003 | 0.000 | 0.003 | |
| createSqMass | 0.002 | 0.000 | 0.002 | |
| dialignrLoess | 0.001 | 0.000 | 0.000 | |
| doAffineAlignmentCpp | 0.001 | 0.000 | 0.001 | |
| doAlignmentCpp | 0.001 | 0.000 | 0.001 | |
| extractXIC_group | 0.977 | 0.030 | 1.045 | |
| extractXIC_group2 | 0.001 | 0.001 | 0.001 | |
| fetchAnalytesInfo | 0.010 | 0.000 | 0.009 | |
| fetchFeaturesFromRun | 0.005 | 0.004 | 0.009 | |
| fetchPeptidesInfo | 0.009 | 0.000 | 0.010 | |
| fetchPeptidesInfo2 | 0.009 | 0.000 | 0.010 | |
| fetchPrecursorsInfo | 0.001 | 0.000 | 0.001 | |
| fetchTransitionsFromRun | 0.009 | 0.000 | 0.009 | |
| filenamesFromMZML | 0.001 | 0.000 | 0.001 | |
| filenamesFromOSW | 0.001 | 0.000 | 0.001 | |
| getAlignObj | 0.021 | 0.003 | 0.025 | |
| getAlignObjs | 1.345 | 0.059 | 1.409 | |
| getAlignedFigs | 0.165 | 0.000 | 0.165 | |
| getAlignedIndices | 0.008 | 0.004 | 0.012 | |
| getAlignedTimes | 0.023 | 0.000 | 0.023 | |
| getAlignedTimesCpp | 0.009 | 0.000 | 0.008 | |
| getAlignedTimesFast | 0.018 | 0.000 | 0.018 | |
| getBaseGapPenaltyCpp | 0.000 | 0.000 | 0.001 | |
| getChildFeature | 0.047 | 0.000 | 0.047 | |
| getChildXICpp | 0.005 | 0.004 | 0.009 | |
| getChildXICs | 0.860 | 0.028 | 0.890 | |
| getChromSimMatCpp | 0.005 | 0.000 | 0.005 | |
| getChromatogramIndices | 0.123 | 0.004 | 0.126 | |
| getFeatures | 0.044 | 0.000 | 0.045 | |
| getGlobalAlignMaskCpp | 0.001 | 0.000 | 0.001 | |
| getGlobalAlignment | 0.008 | 0.000 | 0.008 | |
| getGlobalFits | 0.467 | 0.015 | 0.481 | |
| getLOESSfit | 0.004 | 0.000 | 0.004 | |
| getLinearfit | 0.000 | 0.003 | 0.003 | |
| getMST | 0 | 0 | 0 | |
| getMZMLpointers | 0.021 | 0.000 | 0.021 | |
| getMappedRT | 0.013 | 0.000 | 0.013 | |
| getMultipeptide | 2.215 | 0.156 | 2.375 | |
| getNativeIDs | 0.018 | 0.003 | 0.022 | |
| getNodeIDs | 0 | 0 | 0 | |
| getNodeRun | 0.484 | 0.005 | 0.489 | |
| getOswAnalytes | 0.006 | 0.004 | 0.010 | |
| getOswFiles | 0.007 | 0.004 | 0.011 | |
| getPeptideScores | 0.043 | 0.000 | 0.043 | |
| getPrecursorByID | 0.014 | 0.003 | 0.018 | |
| getPrecursorIndices | 0.052 | 0.005 | 0.057 | |
| getPrecursors | 0.027 | 0.000 | 0.027 | |
| getRSE | 0.003 | 0.000 | 0.003 | |
| getRTdf | 0.007 | 0.000 | 0.008 | |
| getRefExpFeatureMap | 0.335 | 0.008 | 0.344 | |
| getRefRun | 0.410 | 0.007 | 0.419 | |
| getRunNames | 0.007 | 0.004 | 0.011 | |
| getSeqSimMatCpp | 0.000 | 0.000 | 0.001 | |
| getTransitions | 0.156 | 0.000 | 0.155 | |
| getTree | 0.033 | 0.000 | 0.035 | |
| getXICs | 0.098 | 0.004 | 0.102 | |
| getXICs4AlignObj | 0.07 | 0.00 | 0.07 | |
| get_ropenms | 0 | 0 | 0 | |
| imputeChromatogram | 0.015 | 0.000 | 0.016 | |
| ipfReassignFDR | 0 | 0 | 0 | |
| mapIdxToTime | 0.001 | 0.000 | 0.001 | |
| mappedRTfromAlignObj | 0.003 | 0.000 | 0.003 | |
| mergeXIC | 0.003 | 0.000 | 0.003 | |
| mstAlignRuns | 2.091 | 0.087 | 2.182 | |
| mstScript1 | 0.528 | 0.299 | 0.594 | |
| mstScript2 | 2.762 | 0.711 | 3.093 | |
| nrDesc | 0 | 0 | 0 | |
| otherChildXICpp | 0.006 | 0.004 | 0.010 | |
| paramsDIAlignR | 0 | 0 | 0 | |
| perBatch | 0.002 | 0.000 | 0.001 | |
| pickNearestFeature | 0.004 | 0.000 | 0.004 | |
| plotAlignedAnalytes | 0.713 | 0.020 | 0.734 | |
| plotAlignmentPath | 0.420 | 0.028 | 0.449 | |
| plotAnalyteXICs | 0.509 | 0.032 | 0.542 | |
| plotXICgroup | 0.430 | 0.015 | 0.447 | |
| populateReferenceExperimentFeatureAlignmentMap | 0.012 | 0.001 | 0.012 | |
| progAlignRuns | 0.000 | 0.001 | 0.001 | |
| readMzMLHeader | 0.001 | 0.000 | 0.001 | |
| readSqMassHeader | 0.001 | 0.000 | 0.001 | |
| recalculateIntensity | 0.301 | 0.000 | 0.303 | |
| reduceXICs | 0.085 | 0.004 | 0.089 | |
| script1 | 0.812 | 1.067 | 1.069 | |
| script2 | 3.051 | 1.607 | 3.472 | |
| setAlignmentRank | 0.013 | 0.000 | 0.013 | |
| sgolayCpp | 0.002 | 0.001 | 0.003 | |
| sgolayFill | 0.000 | 0.001 | 0.001 | |
| smoothSingleXIC | 0.002 | 0.001 | 0.002 | |
| smoothXICs | 0.009 | 0.000 | 0.009 | |
| splineFill | 0.000 | 0.001 | 0.001 | |
| splineFillCpp | 0.000 | 0.005 | 0.005 | |
| traverseDown | 1.828 | 0.128 | 1.960 | |
| traverseMST | 0 | 0 | 0 | |
| traverseUp | 1.834 | 0.016 | 1.855 | |
| trfrParentFeature | 0.050 | 0.000 | 0.051 | |
| trimXICs | 0.001 | 0.002 | 0.002 | |
| uncompressVec | 0.005 | 0.001 | 0.007 | |
| updateFileInfo | 0.012 | 0.000 | 0.011 | |
| writeOutFeatureAlignmentMap | 0.001 | 0.004 | 0.005 | |
| writeTables | 0.003 | 0.000 | 0.003 | |