Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:56 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 tofsims on machv2


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

raw results

Package 1970/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tofsims 1.22.0  (landing page)
Lorenz Gerber
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/tofsims
git_branch: RELEASE_3_14
git_last_commit: 6cfbd33
git_last_commit_date: 2021-10-26 12:24:38 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: tofsims
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tofsims.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tofsims_1.22.0.tar.gz
StartedAt: 2022-04-12 19:27:47 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 19:33:20 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 333.0 seconds
RetCode: 0
Status:   OK  
CheckDir: tofsims.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tofsims.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tofsims_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/tofsims.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tofsims/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tofsims’ version ‘1.22.0’
* 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 ‘tofsims’ 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
bwApply       9.316  0.261   9.587
findPeakWidth 8.416  0.812   9.237
peakWidths    7.953  0.530   8.515
pcaScores     6.741  0.160   6.939
image         6.444  0.114   6.561
pcaLoadings   6.361  0.186   6.555
smoothScatter 6.324  0.094   6.422
nComp         6.053  0.162   6.216
analysis      6.127  0.069   6.199
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/tofsims.Rcheck/00check.log’
for details.



Installation output

tofsims.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL tofsims
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘tofsims’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c LapackEigen.cpp -o LapackEigen.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c c_importer.cpp -o c_importer.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c nn.cpp -o nn.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c readRawPhi.cpp -o readRawPhi.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c utilities.cpp -o utilities.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o tofsims.so LapackEigen.o RcppExports.o c_importer.o nn.o readRawPhi.o utilities.o -llapack -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-tofsims/00new/tofsims/libs
** R
** 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 (tofsims)

Tests output

tofsims.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(tofsims)
Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

The following object is masked from 'package:stats':

    smooth

> library(tofsimsData)
> 
> test_check("tofsims")
                                             analysisName instrument no.spectra
1 /Users/loge/Data/ULVACPHI/RAW/080414/trift_test_001.RAW   ulvacphi     65'536
  spectra.points total.ion.count x.image.dimension y.image.dimention analysis
1            200       1'859'292               256               256     none
                                             analysisName instrument no.spectra
1 /Users/loge/Data/ULVACPHI/RAW/080414/trift_test_001.RAW   ulvacphi          1
  spectra.points total.ion.count analysis
1        162'255       2'033'289     none
[ FAIL 0 | WARN 53 | SKIP 0 | PASS 73 ]

[ FAIL 0 | WARN 53 | SKIP 0 | PASS 73 ]
> 
> proc.time()
   user  system elapsed 
116.434   6.621 123.217 

Example timings

tofsims.Rcheck/tofsims-Ex.timings

nameusersystemelapsed
MAF1.8190.0701.892
MCR0.1480.0230.171
MNF0.0830.0120.095
MassImage0.0120.0030.016
MassSpectra0.0240.0040.028
PCAnalysis0.0290.0050.035
PeakList3.5761.0774.656
PrComp0.0380.0020.041
PrinComp0.0420.0130.055
addFixedWidth3.6550.7184.375
addPeaks2.0060.0882.096
analysis6.1270.0696.199
analysisName1.7700.0211.792
binning0.4600.0440.511
bwApply9.3160.2619.587
calibPointNew2.1170.0482.171
calibPoints1.7840.0331.819
calibration1.8580.0471.909
changePeakWidth1.8580.0121.871
findPeakWidth8.4160.8129.237
getTOFs1.7580.0091.768
image6.4440.1146.561
imageMatrix2.8270.1362.966
instrument1.7890.0121.802
mz1.7740.0111.785
nComp6.0530.1626.216
nPeaks3.4031.1314.535
nnMNF0.1450.0160.162
nz1.8360.2102.049
overlayPlot2.1370.1512.289
pcaLoadings6.3610.1866.555
pcaScores6.7410.1606.939
peakIDs3.4161.2064.630
peakMzs3.4091.1934.603
peakPick4.4410.1384.588
peakWidths7.9530.5308.515
peaks2Spectra2.4990.4592.959
plot1.9670.0312.000
points2.2900.1452.438
poissonScaling0.0120.0000.013
recalibrate2.0790.1132.196
reduceSpectrumResolution1.8910.0211.915
removePeaks1.8190.0331.853
scale0.0390.0030.041
smoothScatter6.3240.0946.422
smootherGolay1.8720.0091.882
smootherSpline3.2971.0014.300
subset1.9120.0261.944
unitMassPeaks3.5001.0284.534
xy1.8810.1902.072
xySpec1.9650.0231.989