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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MassSpecWavelet.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings MassSpecWavelet_1.70.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/MassSpecWavelet.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MassSpecWavelet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MassSpecWavelet' version '1.70.0'
* 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 whether package 'MassSpecWavelet' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* 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 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 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 ... NOTE
checkRd: (-1) exampleMS.Rd:16: Escaped LaTeX specials: \#
checkRd: (-1) extendNBase.Rd:13: Escaped LaTeX specials: \^
checkRd: (-1) getRidge.Rd:45: Escaped LaTeX specials: \_
* 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 'F:/biocbuild/bbs-3.19-bioc/R/library/MassSpecWavelet/libs/x64/MassSpecWavelet.dll':
  Found '_exit', possibly from '_exit' (C)
  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 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
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runit.R'
 OK
* 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: 2 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/MassSpecWavelet.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL MassSpecWavelet
###
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* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'MassSpecWavelet' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c find_local_maximum.c -o find_local_maximum.o
find_local_maximum.c: In function 'localMaximumSlidingWindow':
find_local_maximum.c:471:17: warning: 'kmax' may be used uninitialized [-Wmaybe-uninitialized]
  471 |             outi[kmax] = 1;
      |                 ^
find_local_maximum.c:461:13: note: 'kmax' was declared here
  461 |         int kmax;
      |             ^~~~
find_local_maximum.c:493:17: warning: 'kmax' may be used uninitialized [-Wmaybe-uninitialized]
  493 |             outi[kmax] = 1;
      |                 ^
find_local_maximum.c:479:13: note: 'kmax' was declared here
  479 |         int kmax;
      |             ^~~~
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
gcc -shared -s -static-libgcc -o MassSpecWavelet.dll tmp.def find_local_maximum.o init.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-MassSpecWavelet/00new/MassSpecWavelet/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MassSpecWavelet)

R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 -- Thu Jun 27 03:15:27 2024 
*********************************************** 
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: 
F:/biocbuild/bbs-3.19-bioc/R/library/MassSpecWavelet/tests 
--------------------------- 
Test file: F:/biocbuild/bbs-3.19-bioc/R/library/MassSpecWavelet/tests/runit.cwt.R 
test01_cwt: (1 checks) ... OK (0 seconds)
test02_cwt: (2 checks) ... OK (0 seconds)
--------------------------- 
Test file: F:/biocbuild/bbs-3.19-bioc/R/library/MassSpecWavelet/tests/runit.localMaximum.R 
test01_localMaximum: (1 checks) ... OK (0 seconds)
test02_checkIdenticalResults_classic_vs_faster: (240 checks) ... OK (2 seconds)
test03_check_new_does_not_miss_maxima: (240 checks) ... OK (0.42 seconds)
--------------------------- 
Test file: F:/biocbuild/bbs-3.19-bioc/R/library/MassSpecWavelet/tests/runit.peakDetectionCWT.R 
test01_peakDetection: (3 checks) ... OK (0.03 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 
   2.60    0.20    2.79