Shubham Gupta
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/DIAlignR |
| Branch: RELEASE_3_12 |
| Last Commit: 25b9e1a |
| Last Changed Date: 2020-10-27 11:52:59 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:27:20 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the DIAlignR package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 473/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DIAlignR 1.2.0 (landing page) Shubham Gupta
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: DIAlignR |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:DIAlignR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings DIAlignR_1.2.0.tar.gz |
| StartedAt: 2021-05-06 00:56:17 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 00:57:27 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 70.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DIAlignR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:DIAlignR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings DIAlignR_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/DIAlignR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DIAlignR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DIAlignR’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DIAlignR’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 8.1Mb
sub-directories of 1Mb or more:
extdata 3.6Mb
libs 4.0Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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-3.12-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. 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.12-bioc/meat/DIAlignR.Rcheck/00check.log’
for details.
DIAlignR.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL DIAlignR
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘DIAlignR’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c ChromatogramPeak.cpp -o ChromatogramPeak.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c DPosition.cpp -o DPosition.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c MSChromatogram.cpp -o MSChromatogram.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c PeakIntegrator.cpp -o PeakIntegrator.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c Rmain.cpp -o Rmain.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c affinealignment.cpp -o affinealignment.o
affinealignment.cpp: In function ‘void DIAlign::AffineAlignment::getAffineAlignedIndices(DIAlign::AffineAlignObj&, int)’:
affinealignment.cpp:260:11: warning: enumeration value ‘SS’ not handled in switch [-Wswitch]
switch(TracebackPointer){
^
affinealignment.cpp: In function ‘double DIAlign::AffineAlignment::getOlapAffineAlignStartIndices(double*, double*, double*, int, int, int&, int&, DIAlign::Traceback::tbJump&)’:
affinealignment.cpp:483:16: warning: ‘MaxColIndex’ may be used uninitialized in this function [-Wmaybe-uninitialized]
OlapStartCol = MaxColIndex;
~~~~~~~~~~~~~^~~~~~~~~~~~~
affinealignment.cpp:482:16: warning: ‘MaxRowIndex’ may be used uninitialized in this function [-Wmaybe-uninitialized]
OlapStartRow = MaxRowIndex;
~~~~~~~~~~~~~^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c affinealignobj.cpp -o affinealignobj.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c alignment.cpp -o alignment.o
alignment.cpp: In function ‘void DIAlign::Alignment::getAlignedIndices(DIAlign::AlignObj&)’:
alignment.cpp:194:11: warning: enumeration value ‘SS’ not handled in switch [-Wswitch]
switch(TracebackPointer){
^
alignment.cpp:194:11: warning: enumeration value ‘DA’ not handled in switch [-Wswitch]
alignment.cpp:194:11: warning: enumeration value ‘DB’ not handled in switch [-Wswitch]
alignment.cpp:194:11: warning: enumeration value ‘TA’ not handled in switch [-Wswitch]
alignment.cpp:194:11: warning: enumeration value ‘TB’ not handled in switch [-Wswitch]
alignment.cpp:194:11: warning: enumeration value ‘LA’ not handled in switch [-Wswitch]
alignment.cpp:194:11: warning: enumeration value ‘LB’ not handled in switch [-Wswitch]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/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 between signed and unsigned integer expressions [-Wsign-compare]
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 between signed and unsigned integer expressions [-Wsign-compare]
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 between signed and unsigned integer expressions [-Wsign-compare]
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 between signed and unsigned integer expressions [-Wsign-compare]
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::__cxx11::string, std::__cxx11::string, double, double)’:
chromSimMatrix.cpp:368:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0; i < MASK.size(); i++){
~~^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c constrainMat.cpp -o constrainMat.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/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::__cxx11::string)’:
gapPenalty.cpp:26:10: warning: ‘gapPenalty’ may be used uninitialized in this function [-Wmaybe-uninitialized]
return gapPenalty;
^~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c integrateArea.cpp -o integrateArea.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c interface.cpp -o interface.o
interface.cpp: In function ‘void DIAlign::printVecOfVec(Rcpp::List)’:
interface.cpp:17:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j = 0; j < VecOfVec.size(); j++){
~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c run_alignment.cpp -o run_alignment.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c simpleFcn.cpp -o simpleFcn.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/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]
int idx = n*(1-p);
^~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o DIAlignR.so ChromatogramPeak.o DPosition.o MSChromatogram.o PeakIntegrator.o RcppExports.o Rmain.o affinealignment.o affinealignobj.o alignment.o chromSimMatrix.o constrainMat.o gapPenalty.o integrateArea.o interface.o run_alignment.o simpleFcn.o utils.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-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
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(DIAlignR)
>
> test_check("DIAlignR")
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"
[3] "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"
Time difference of 0.6407087 secs
[1] "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"
[2] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"
Time difference of 0.3784342 secs
[1] "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"
[2] "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 182 ]
>
> proc.time()
user system elapsed
11.124 0.148 11.284
DIAlignR.Rcheck/DIAlignR-Ex.timings
| name | user | system | elapsed | |
| alignChromatogramsCpp | 0.012 | 0.008 | 0.020 | |
| alignTargetedRuns | 3.564 | 0.056 | 3.803 | |
| analytesFromFeatures | 0.032 | 0.000 | 0.029 | |
| areaIntegrator | 0.000 | 0.000 | 0.002 | |
| calculateIntensity | 0.004 | 0.000 | 0.002 | |
| constrainSimCpp | 0.000 | 0.000 | 0.001 | |
| doAffineAlignmentCpp | 0.000 | 0.000 | 0.001 | |
| doAlignmentCpp | 0.000 | 0.000 | 0.001 | |
| extractXIC_group | 0.008 | 0.000 | 0.008 | |
| fetchAnalytesInfo | 0.008 | 0.000 | 0.006 | |
| fetchFeaturesFromRun | 0.012 | 0.000 | 0.012 | |
| fetchPrecursorsInfo | 0.000 | 0.000 | 0.001 | |
| filenamesFromMZML | 0 | 0 | 0 | |
| filenamesFromOSW | 0 | 0 | 0 | |
| getAlignObj | 0.020 | 0.000 | 0.021 | |
| getAlignObjs | 1.304 | 0.020 | 1.328 | |
| getAlignedFigs | 0.236 | 0.004 | 0.237 | |
| getAlignedIndices | 0.028 | 0.004 | 0.035 | |
| getBaseGapPenaltyCpp | 0 | 0 | 0 | |
| getChromSimMatCpp | 0.000 | 0.004 | 0.004 | |
| getChromatogramIndices | 0.268 | 0.004 | 0.273 | |
| getFeatures | 0.008 | 0.000 | 0.006 | |
| getGlobalAlignMaskCpp | 0 | 0 | 0 | |
| getGlobalAlignment | 0.016 | 0.000 | 0.016 | |
| getGlobalFits | 0.028 | 0.000 | 0.028 | |
| getLOESSfit | 0.004 | 0.000 | 0.001 | |
| getLinearfit | 0.000 | 0.000 | 0.001 | |
| getMZMLpointers | 0.028 | 0.004 | 0.031 | |
| getMappedRT | 0.016 | 0.000 | 0.016 | |
| getMultipeptide | 1.048 | 0.008 | 1.056 | |
| getOswAnalytes | 0.008 | 0.000 | 0.009 | |
| getOswFiles | 0.008 | 0.000 | 0.009 | |
| getPrecursorByID | 0.032 | 0.000 | 0.030 | |
| getPrecursors | 0.008 | 0.000 | 0.009 | |
| getRSE | 0.000 | 0.000 | 0.002 | |
| getRefRun | 0.000 | 0.004 | 0.001 | |
| getRunNames | 0.012 | 0.000 | 0.012 | |
| getSeqSimMatCpp | 0 | 0 | 0 | |
| getXICs | 0.188 | 0.000 | 0.187 | |
| getXICs4AlignObj | 0.144 | 0.000 | 0.143 | |
| mapIdxToTime | 0.000 | 0.000 | 0.001 | |
| mappedRTfromAlignObj | 0.004 | 0.000 | 0.003 | |
| pickNearestFeature | 0.000 | 0.000 | 0.002 | |
| plotAlignedAnalytes | 0.544 | 0.004 | 0.548 | |
| plotAlignmentPath | 0.376 | 0.012 | 0.388 | |
| plotAnalyteXICs | 0.416 | 0.000 | 0.415 | |
| plotXICgroup | 0.396 | 0.000 | 0.397 | |
| readChromatogramHeader | 0 | 0 | 0 | |
| setAlignmentRank | 0.004 | 0.000 | 0.005 | |
| smoothSingleXIC | 0.000 | 0.000 | 0.001 | |
| smoothXICs | 0.000 | 0.000 | 0.001 | |
| trimXICs | 0.000 | 0.000 | 0.001 | |
| updateFileInfo | 0.004 | 0.000 | 0.008 | |
| writeTables | 0.000 | 0.000 | 0.001 | |