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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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

Package 1159/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MassSpecWavelet 1.72.0  (landing page)
Sergio Oller Moreno
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/MassSpecWavelet
git_branch: RELEASE_3_20
git_last_commit: 0628ed5
git_last_commit_date: 2024-10-29 09:27:42 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for MassSpecWavelet on teran2

To the developers/maintainers of the MassSpecWavelet package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: MassSpecWavelet
Version: 1.72.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MassSpecWavelet.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MassSpecWavelet_1.72.0.tar.gz
StartedAt: 2024-11-20 05:15:25 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 05:16:28 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 63.1 seconds
RetCode: 0
Status:   OK  
CheckDir: MassSpecWavelet.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MassSpecWavelet.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MassSpecWavelet_1.72.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/MassSpecWavelet.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MassSpecWavelet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MassSpecWavelet’ version ‘1.72.0’
* 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 13.2.0-23ubuntu4) 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 loading without being on the library search path ... 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 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/MassSpecWavelet.Rcheck/00check.log’
for details.


Installation output

MassSpecWavelet.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL MassSpecWavelet
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘MassSpecWavelet’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/home/biocbuild/bbs-3.20-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: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"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o MassSpecWavelet.so find_local_maximum.o init.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-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)

Tests output

MassSpecWavelet.Rcheck/tests/runit.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 -- Wed Nov 20 05:15:50 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: 
/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/MassSpecWavelet/tests 
--------------------------- 
Test file: /media/volume/teran2_disk/biocbuild/bbs-3.20-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: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/MassSpecWavelet/tests/runit.localMaximum.R 
test01_localMaximum: (1 checks) ... OK (0 seconds)
test02_checkIdenticalResults_classic_vs_faster: (240 checks) ... OK (1.07 seconds)
test03_check_new_does_not_miss_maxima: (240 checks) ... OK (0.14 seconds)
--------------------------- 
Test file: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/MassSpecWavelet/tests/runit.peakDetectionCWT.R 
test01_peakDetection: (3 checks) ... OK (0.01 seconds)
test02_peakDetection: (2 checks) ... OK (0.01 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 
  1.315   0.090   1.394 

Example timings

MassSpecWavelet.Rcheck/MassSpecWavelet-Ex.timings

nameusersystemelapsed
MassSpecWavelet-package0.4650.0540.521
cwt0.5050.0280.532
extendLength000
extendNBase000
getLocalMaximumCWT0.1420.0130.156
getRidge0.0720.0020.074
getRidgeLength0.0000.0000.001
identifyMajorPeaks1.0940.0141.109
localMaximum0.0400.0010.041
mexh000
peakDetectionCWT1.7680.0591.828
plotLocalMax0.0630.0000.063
plotPeak0.4650.0080.474
plotRidgeList0.1020.0020.104
prepareWavelets0.0010.0000.001
tuneInPeakInfo0.6230.0200.642