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This page was generated on 2022-03-18 11:08:50 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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

CHECK results for TargetSearch on riesling1


To the developers/maintainers of the TargetSearch package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TargetSearch.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1938/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TargetSearch 1.51.1  (landing page)
Alvaro Cuadros-Inostroza
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/TargetSearch
git_branch: master
git_last_commit: d523a36
git_last_commit_date: 2022-01-31 09:14:00 -0400 (Mon, 31 Jan 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TargetSearch
Version: 1.51.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TargetSearch.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings TargetSearch_1.51.1.tar.gz
StartedAt: 2022-03-17 20:27:13 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 20:28:24 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 71.5 seconds
RetCode: 0
Status:   OK  
CheckDir: TargetSearch.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TargetSearch.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings TargetSearch_1.51.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/TargetSearch.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TargetSearch/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TargetSearch' version '1.51.1'
* 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 whether package 'TargetSearch' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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 for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/TargetSearch/libs/x64/TargetSearch.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
RIcorrect 7.88   2.27   10.17
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'tinytest.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: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/TargetSearch.Rcheck/00check.log'
for details.



Installation output

TargetSearch.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL TargetSearch
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'TargetSearch' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Rinit.c -o Rinit.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c baseline.c -o baseline.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c detection.c -o detection.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c file.c -o file.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c find_peaks.c -o find_peaks.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c getLine.c -o getLine.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c hpf.c -o hpf.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c matrix.c -o matrix.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ncdf.c -o ncdf.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c peak.c -o peak.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c utils.c -o utils.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o TargetSearch.dll tmp.def Rinit.o baseline.o detection.o file.o find_peaks.o getLine.o hpf.o matrix.o ncdf.o peak.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-TargetSearch/00new/TargetSearch/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TargetSearch'
    finding HTML links ... done
    FAMEoutliers                            html  
    FindAllPeaks                            html  
    FindPeaks                               html  
    ImportFameSettings                      html  
    ImportLibrary                           html  
    ImportSamples                           html  
    NetCDFPeakFinding                       html  
    Profile                                 html  
    ProfileCleanUp                          html  
    RIcorrect                               html  
    TSExample                               html  
    TargetSearch-defunct                    html  
    TargetSearch-package                    html  
    Write.Results                           html  
    baseline                                html  
    baselineCorrection                      html  
    baselineCorrectionQuant                 html  
    checkRimLim                             html  
    file                                    html  
    fixRI                                   html  
    medianRILib                             html  
    ncdf4Convert-method                     html  
    ncdf4_convert                           html  
    ncdf4_convert_from_path                 html  
    ncdf4_data_extract                      html  
    ncdf4_plot_peak                         html  
    ncdf4_update_ri                         html  
    peakCDFextraction                       html  
    peakFind                                html  
    plotFAME                                html  
    plotPeak                                html  
    plotPeakRI                              html  
    plotPeakSimple                          html  
    plotRIdev                               html  
    plotSpectra                             html  
    quantMatrix                             html  
    ri2rt                                   html  
    riMatrix                                html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-TargetSearch/00new/TargetSearch/help/riMatrix.html
    ri_data_extract                         html  
    ri_plot_peak                            html  
    rt2ri                                   html  
    sampleRI                                html  
    tsLib-class                             html  
    tsMSdata-class                          html  
    tsProfile-class                         html  
    tsRim-class                             html  
    tsSample-class                          html  
    tsUpdate-method                         html  
    updateRI                                html  
    writeLibText                            html  
    writeMSP                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TargetSearch)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'sparseMatrixStats' is missing or broken
 done

Tests output

TargetSearch.Rcheck/tests/tinytest.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> if ( requireNamespace("tinytest", quietly=TRUE) && requireNamespace("TargetSearchData", quietly=TRUE)) {
+     tinytest::test_package("TargetSearch")
+ }
Loading required package: TargetSearchData

test_file.R...................    0 tests    
test_file.R...................    0 tests    
test_file.R...................    0 tests    
test_file.R...................    0 tests    
test_file.R...................    1 tests OK 
test_file.R...................    1 tests OK 
test_file.R...................    1 tests OK 
test_file.R...................    2 tests OK 
test_file.R...................    2 tests OK 
test_file.R...................    3 tests OK 
test_file.R...................    3 tests OK 
test_file.R...................    3 tests OK 
test_file.R...................    4 tests OK 0.2s

test_ncdf4_plot_peak.R........    0 tests    
test_ncdf4_plot_peak.R........    0 tests    
test_ncdf4_plot_peak.R........    0 tests    
test_ncdf4_plot_peak.R........    0 tests    
test_ncdf4_plot_peak.R........    0 tests    
test_ncdf4_plot_peak.R........    0 tests    
test_ncdf4_plot_peak.R........    0 tests    
test_ncdf4_plot_peak.R........    0 tests    
test_ncdf4_plot_peak.R........    0 tests    
test_ncdf4_plot_peak.R........    5 tests OK 
test_ncdf4_plot_peak.R........    6 tests OK 
test_ncdf4_plot_peak.R........    7 tests OK 
test_ncdf4_plot_peak.R........    7 tests OK 0.4s

test_ri_data_extract.R........    0 tests    
test_ri_data_extract.R........    0 tests    
test_ri_data_extract.R........    0 tests    
test_ri_data_extract.R........    0 tests    
test_ri_data_extract.R........    1 tests OK 
test_ri_data_extract.R........    1 tests OK 
test_ri_data_extract.R........    1 tests OK 
test_ri_data_extract.R........    2 tests OK 
test_ri_data_extract.R........    2 tests OK 
test_ri_data_extract.R........    2 tests OK 
test_ri_data_extract.R........    3 tests OK 
test_ri_data_extract.R........    3 tests OK 
test_ri_data_extract.R........    4 tests OK 
test_ri_data_extract.R........    4 tests OK 
test_ri_data_extract.R........    4 tests OK 
test_ri_data_extract.R........    4 tests OK 
test_ri_data_extract.R........    4 tests OK 
test_ri_data_extract.R........    4 tests OK 
test_ri_data_extract.R........    5 tests OK 
test_ri_data_extract.R........    5 tests OK 
test_ri_data_extract.R........    6 tests OK 0.5s

test_ri_plot_peak.R...........    0 tests    
test_ri_plot_peak.R...........    0 tests    
test_ri_plot_peak.R...........    0 tests    
test_ri_plot_peak.R...........    0 tests    
test_ri_plot_peak.R...........    0 tests    
test_ri_plot_peak.R...........    0 tests    
test_ri_plot_peak.R...........    0 tests    
test_ri_plot_peak.R...........    0 tests    
test_ri_plot_peak.R...........    0 tests    
test_ri_plot_peak.R...........    0 tests    
test_ri_plot_peak.R...........   10 tests OK 
test_ri_plot_peak.R...........   11 tests OK 
test_ri_plot_peak.R...........   12 tests OK 
test_ri_plot_peak.R...........   12 tests OK 78ms
All ok, 29 results (1.2s)
> 
> proc.time()
   user  system elapsed 
   1.28    0.10    1.42 

Example timings

TargetSearch.Rcheck/TargetSearch-Ex.timings

nameusersystemelapsed
FAMEoutliers0.060.000.06
FindAllPeaks0.840.081.33
FindPeaks0.330.000.33
ImportFameSettings000
ImportLibrary0.030.000.03
ImportSamples000
NetCDFPeakFinding0.140.030.18
Profile1.210.001.20
ProfileCleanUp0.840.030.88
RIcorrect 7.88 2.2710.17
TSExample1.170.511.69
checkRimLim0.720.110.83
file0.120.000.14
fixRI0.910.070.97
medianRILib0.440.030.46
ncdf4Convert-method0.060.010.08
ncdf4_convert0.010.000.02
ncdf4_convert_from_path000
ncdf4_data_extract000
ncdf4_plot_peak0.580.130.70
peakFind0.250.000.25
plotFAME0.000.010.02
plotPeak0.080.050.12
plotPeakRI0.800.020.81
plotPeakSimple0.170.040.22
plotRIdev0.390.000.44
plotSpectra0.260.020.28
quantMatrix0.750.010.77
ri2rt000
riMatrix0.460.160.61
ri_data_extract0.040.000.04
ri_plot_peak1.400.021.41
rt2ri000
sampleRI0.50.00.5
tsLib-class0.010.000.02
tsMSdata-class000
tsProfile-class000
tsRim-class000
tsSample-class0.000.010.01
tsUpdate-method000
updateRI0.640.270.91
writeLibText0.020.000.01