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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MassSpecWavelet.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MassSpecWavelet_1.65.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MassSpecWavelet.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MassSpecWavelet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MassSpecWavelet’ version ‘1.65.0’
* 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 ‘MassSpecWavelet’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding
  Warning message:
  In utils::packageDescription(basename(dir), dirname(dir)) :
    no package 'MassSpecWavelet' was found
* 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 loading without being on the library search path ... WARNING
Error in library(MassSpecWavelet, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") : 
  there is no package called ‘MassSpecWavelet’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* 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 ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... SKIPPED
* 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 ...
  ‘FindingLocalMaxima.Rmd’ using ‘UTF-8’... OK
  ‘MassSpecWavelet.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘FindingLocalMaxima.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MassSpecWavelet.Rcheck/vign_test/MassSpecWavelet/vignettes/FindingLocalMaxima_files/figure-html/unnamed-chunk-2-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MassSpecWavelet.Rcheck/vign_test/MassSpecWavelet/vignettes/FindingLocalMaxima_files/figure-html/unnamed-chunk-3-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MassSpecWavelet.Rcheck/vign_test/MassSpecWavelet/vignettes/FindingLocalMaxima_files/figure-html/unnamed-chunk-4-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MassSpecWavelet.Rcheck/vign_test/MassSpecWavelet/vignettes/FindingLocalMaxima_files/figure-html/unnamed-chunk-5-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MassSpecWavelet.Rcheck/vign_test/MassSpecWavelet/vignettes/FindingLocalMaxima_files/figure-html/benchmark-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MassSpecWavelet.Rcheck/vign_test/MassSpecWavelet/vignettes/FindingLocalMaxima_files/figure-html/unnamed-chunk-8-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MassSpecWavelet.Rcheck/vign_test/MassSpecWavelet/vignettes/FindingLocalMaxima_files/figure-html/unnamed-chunk-9-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MassSpecWavelet.Rcheck/vign_test/MassSpecWavelet/vignettes/FindingLocalMaxima_files/figure-html/localMax-1.png" but not available.
--- finished re-building ‘FindingLocalMaxima.Rmd’

--- re-building ‘MassSpecWavelet.Rmd’ using rmarkdown
Quitting from lines 66-67 (MassSpecWavelet.Rmd) 
Error: processing vignette 'MassSpecWavelet.Rmd' failed with diagnostics:
object 'plotRange' not found
--- failed re-building ‘MassSpecWavelet.Rmd’

SUMMARY: processing the following file failed:
  ‘MassSpecWavelet.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/MassSpecWavelet.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MassSpecWavelet
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘MassSpecWavelet’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c find_local_maximum.c -o find_local_maximum.o
find_local_maximum.c: In function ‘localMaximumSlidingWindow’:
find_local_maximum.c:493:17: warning: ‘kmax’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  493 |             outi[kmax] = 1;
      |                 ^
find_local_maximum.c:471:17: warning: ‘kmax’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  471 |             outi[kmax] = 1;
      |                 ^
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o MassSpecWavelet.so find_local_maximum.o init.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-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)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> 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 -- Sun Jan 29 02:46:45 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: 
/home/biocbuild/bbs-3.17-bioc/R/site-library/MassSpecWavelet/tests 
--------------------------- 
Test file: /home/biocbuild/bbs-3.17-bioc/R/site-library/MassSpecWavelet/tests/runit.cwt.R 
test01_cwt: (1 checks) ... OK (0 seconds)
test02_cwt: (2 checks) ... OK (0.01 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.17-bioc/R/site-library/MassSpecWavelet/tests/runit.localMaximum.R 
test01_localMaximum: (1 checks) ... OK (0 seconds)
test02_checkIdenticalResults_classic_vs_faster: (240 checks) ... OK (2.24 seconds)
test03_check_new_does_not_miss_maxima: (240 checks) ... OK (0.25 seconds)
--------------------------- 
Test file: /home/biocbuild/bbs-3.17-bioc/R/site-library/MassSpecWavelet/tests/runit.peakDetectionCWT.R 
test01_peakDetection: (3 checks) ... OK (0.02 seconds)
test02_peakDetection: (2 checks) ... OK (0.02 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 
  2.741   0.059   2.793