Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
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 1137/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MassSpecWavelet 1.71.0 (landing page) Sergio Oller Moreno
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
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. |
Package: MassSpecWavelet |
Version: 1.71.0 |
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MassSpecWavelet.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MassSpecWavelet_1.71.0.tar.gz |
StartedAt: 2024-07-16 01:24:56 -0400 (Tue, 16 Jul 2024) |
EndedAt: 2024-07-16 01:25:37 -0400 (Tue, 16 Jul 2024) |
EllapsedTime: 40.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MassSpecWavelet.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MassSpecWavelet.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MassSpecWavelet_1.71.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/MassSpecWavelet.Rcheck' * using R version 4.4.1 (2024-06-14 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 '1.71.0' * 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 'C:/Users/biocbuild/bbs-3.20-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 'C:/Users/biocbuild/bbs-3.20-bioc/meat/MassSpecWavelet.Rcheck/00check.log' for details.
MassSpecWavelet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL MassSpecWavelet ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'MassSpecWavelet' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-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 -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.20-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)
MassSpecWavelet.Rcheck/tests/runit.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 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 -- Tue Jul 16 01:25:28 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: C:/Users/biocbuild/bbs-3.20-bioc/R/library/MassSpecWavelet/tests --------------------------- Test file: C:/Users/biocbuild/bbs-3.20-bioc/R/library/MassSpecWavelet/tests/runit.cwt.R test01_cwt: (1 checks) ... OK (0.01 seconds) test02_cwt: (2 checks) ... OK (0 seconds) --------------------------- Test file: C:/Users/biocbuild/bbs-3.20-bioc/R/library/MassSpecWavelet/tests/runit.localMaximum.R test01_localMaximum: (1 checks) ... OK (0 seconds) test02_checkIdenticalResults_classic_vs_faster: (240 checks) ... OK (1.29 seconds) test03_check_new_does_not_miss_maxima: (240 checks) ... OK (0.21 seconds) --------------------------- Test file: C:/Users/biocbuild/bbs-3.20-bioc/R/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 1.65 0.17 1.76
MassSpecWavelet.Rcheck/MassSpecWavelet-Ex.timings
name | user | system | elapsed | |
MassSpecWavelet-package | 0.63 | 0.09 | 0.72 | |
cwt | 0.77 | 0.11 | 0.90 | |
extendLength | 0 | 0 | 0 | |
extendNBase | 0 | 0 | 0 | |
getLocalMaximumCWT | 0.16 | 0.00 | 0.17 | |
getRidge | 0.09 | 0.03 | 0.12 | |
getRidgeLength | 0 | 0 | 0 | |
identifyMajorPeaks | 1.24 | 0.27 | 1.50 | |
localMaximum | 0.05 | 0.00 | 0.05 | |
mexh | 0 | 0 | 0 | |
peakDetectionCWT | 2.46 | 0.47 | 2.95 | |
plotLocalMax | 0.1 | 0.0 | 0.1 | |
plotPeak | 0.59 | 0.08 | 0.67 | |
plotRidgeList | 0.14 | 0.01 | 0.16 | |
prepareWavelets | 0 | 0 | 0 | |
tuneInPeakInfo | 0.63 | 0.35 | 0.96 | |