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This page was generated on 2023-04-12 11:06:13 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 MassSpecWavelet on lconway


To the developers/maintainers of the MassSpecWavelet package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MassSpecWavelet.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 1101/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MassSpecWavelet 1.64.1  (landing page)
Sergio Oller Moreno
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/MassSpecWavelet
git_branch: RELEASE_3_16
git_last_commit: 3d555a8
git_last_commit_date: 2023-01-30 13:37:34 -0400 (Mon, 30 Jan 2023)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MassSpecWavelet
Version: 1.64.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MassSpecWavelet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MassSpecWavelet_1.64.1.tar.gz
StartedAt: 2023-04-10 21:00:13 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 21:00:51 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 37.6 seconds
RetCode: 0
Status:   OK  
CheckDir: MassSpecWavelet.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MassSpecWavelet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MassSpecWavelet_1.64.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/MassSpecWavelet.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MassSpecWavelet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MassSpecWavelet’ version ‘1.64.1’
* 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 ‘MassSpecWavelet’ 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runit.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-3.16-bioc/meat/MassSpecWavelet.Rcheck/00check.log’
for details.



Installation output

MassSpecWavelet.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘MassSpecWavelet’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c find_local_maximum.c -o find_local_maximum.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -mmacosx-version-min=10.13 -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 MassSpecWavelet.so find_local_maximum.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-MassSpecWavelet/00new/MassSpecWavelet/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 (MassSpecWavelet)

Tests output

MassSpecWavelet.Rcheck/tests/runit.Rout


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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.

> stopifnot(require(RUnit, quietly = TRUE))
> stopifnot(require(MassSpecWavelet, quietly = TRUE))
> ## Define tests
> testSuite <- defineTestSuite(name = "MassSpecWavelet Unit Tests",
+                              dirs = system.file("tests", package = "MassSpecWavelet"),
+                              testFuncRegexp = "^[Tt]est+",
+                              rngKind = "Mersenne-Twister",
+                              rngNormalKind = "Inversion"
+ )
> tests <- runTestSuite(testSuite) # Run tests


Executing test function test01_cwt  ...  done successfully.



Executing test function test02_cwt  ...  done successfully.



Executing test function test01_localMaximum  ...  done successfully.



Executing test function test02_checkIdenticalResults_classic_vs_faster  ...  done successfully.



Executing test function test03_check_new_does_not_miss_maxima  ...  done successfully.



Executing test function test01_peakDetection  ...  done successfully.



Executing test function test02_peakDetection  ...  done successfully.

> printTextProtocol(tests) # Print results
RUNIT TEST PROTOCOL -- Mon Apr 10 21:00:41 2023 
*********************************************** 
Number of test functions: 7 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MassSpecWavelet Unit Tests - 7 test functions, 0 errors, 0 failures



Details 
*************************** 
Test Suite: MassSpecWavelet Unit Tests 
Test function regexp: ^[Tt]est+ 
Test file regexp: ^runit.+\.[rR]$ 
Involved directory: 
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/MassSpecWavelet/tests 
--------------------------- 
Test file: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/MassSpecWavelet/tests/runit.cwt.R 
test01_cwt: (1 checks) ... OK (0 seconds)
test02_cwt: (2 checks) ... OK (0.01 seconds)
--------------------------- 
Test file: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/MassSpecWavelet/tests/runit.localMaximum.R 
test01_localMaximum: (1 checks) ... OK (0 seconds)
test02_checkIdenticalResults_classic_vs_faster: (240 checks) ... OK (1.47 seconds)
test03_check_new_does_not_miss_maxima: (240 checks) ... OK (0.26 seconds)
--------------------------- 
Test file: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/MassSpecWavelet/tests/runit.peakDetectionCWT.R 
test01_peakDetection: (3 checks) ... OK (0.02 seconds)
test02_peakDetection: (2 checks) ... OK (0.03 seconds)
> # Return success or failure to R CMD CHECK
> if (getErrors(tests)$nFail > 0) stop("TEST FAILED!")
> if (getErrors(tests)$nErr > 0) stop("TEST HAD ERRORS!")
> if (getErrors(tests)$nTestFunc < 1) stop("NO TEST FUNCTIONS RUN!")
> 
> proc.time()
   user  system elapsed 
  1.894   0.179   2.082 

Example timings

MassSpecWavelet.Rcheck/MassSpecWavelet-Ex.timings

nameusersystemelapsed
MassSpecWavelet-package0.6270.1040.734
cwt0.7030.0910.799
extendLength000
extendNBase000
getLocalMaximumCWT0.1910.0260.218
getRidge0.1020.0130.117
getRidgeLength0.0000.0000.001
identifyMajorPeaks1.4080.1321.547
localMaximum0.0540.0020.057
mexh0.0000.0010.002
peakDetectionCWT2.1340.2442.385
plotLocalMax0.0830.0060.089
plotPeak0.5420.1020.646
plotRidgeList0.1360.0110.149
prepareWavelets0.0010.0010.002
tuneInPeakInfo0.7130.0810.801