Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 367/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cliqueMS 1.20.0 (landing page) Oriol Senan Campos
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the cliqueMS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cliqueMS.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: cliqueMS |
Version: 1.20.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cliqueMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cliqueMS_1.20.0.tar.gz |
StartedAt: 2024-12-20 14:47:08 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 14:54:17 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 428.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: cliqueMS.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cliqueMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cliqueMS_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/cliqueMS.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘cliqueMS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cliqueMS’ version ‘1.20.0’ * 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 ‘cliqueMS’ can be installed ... WARNING Found the following significant warnings: ./annotationCliqueMSR.h:739:5: warning: variable 'completeroundscore' is uninitialized when used here [-Wuninitialized] See ‘/Users/biocbuild/bbs-3.20-bioc/meat/cliqueMS.Rcheck/00install.out’ for details. * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * 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 ... 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 line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed createNetwork 9.404 2.407 11.822 anClique-class 9.443 1.076 10.540 createanClique 8.024 2.224 10.308 computeCliques 5.728 0.408 6.160 getCliques 5.147 0.309 5.476 anClique 4.185 1.161 5.351 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/cliqueMS.Rcheck/00check.log’ for details.
cliqueMS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cliqueMS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘cliqueMS’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c findAnnotationR.cpp -o findAnnotationR.o In file included from findAnnotationR.cpp:1: ./annotationCliqueMSR.h:739:5: warning: variable 'completeroundscore' is uninitialized when used here [-Wuninitialized] completeroundscore += *ritv; ^~~~~~~~~~~~~~~~~~ ./annotationCliqueMSR.h:733:28: note: initialize the variable 'completeroundscore' to silence this warning double completeroundscore,remainderroundscore = 0; ^ = 0.0 1 warning generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c findCliquesR.cpp -o findCliquesR.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c findIsotopesR.cpp -o findIsotopesR.o clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o cliqueMS.so RcppExports.o findAnnotationR.o findCliquesR.o findIsotopesR.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-cliqueMS/00new/cliqueMS/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 (cliqueMS)
cliqueMS.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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. > library(testthat) > library(cliqueMS) > > test_check("cliqueMS") adduct log10freq massdiff nummol charge 1 [M+2H-NH3]2+ -3.5129044 -15.012016600 1 2 2 [Cat]3+ -3.5129044 -0.001645737 1 3 3 [Cat]2+ -3.5129044 -0.001040400 1 2 4 [Cat+H]2+ -3.3368132 1.006178842 1 2 5 [M+2H]2+ -1.8139344 2.014552000 1 2 6 [M+H+Na]2+ -2.6999911 23.996494000 1 2 7 [M+2H+Na]3+ -3.8139344 25.003770000 1 3 8 [M+H+K]2+ -2.2341508 39.970434000 1 2 9 [M+2Na]2+ -2.6678064 45.978436000 1 2 10 [M+H+2Na]3+ -3.5129044 46.985730000 1 3 11 [M+3Na]3+ -3.5129044 68.967654000 1 3 12 [M+H]+ -0.2689987 1.007276000 1 1 13 [M+H-H2O]+ -0.7476085 -17.003277800 1 1 14 [M+Na]+ -0.9632882 22.989218000 1 1 15 [M+H-NH3]+ -1.5886251 -16.019274320 1 1 16 [M-H+2Na]+ -1.8596919 44.971164440 1 1 17 [Cat]+ -1.8948563 -0.000548579 1 1 18 [M-2H+3Na]+ -1.9108444 66.953081400 1 1 19 [M+H+H2O]+ -2.3225727 19.017868210 1 1 20 [M+K]+ -2.4159944 38.963158000 1 1 21 [M+NH4]+ -2.4917151 18.033823000 1 1 22 [M-H+2K]+ -3.1149644 76.919040000 1 1 23 [Cat+H2O]+ -3.2118744 18.010011000 1 1 24 [M+H-OH]+ -3.2118744 -15.995481930 1 1 25 [Cat-H2O]+ -3.5129044 -18.011087900 1 1 26 [Cat-H]+ -3.5129044 -1.008340400 1 1 27 [M+Na-H2O]+ -3.5129044 4.978142219 1 1 28 [M-2H+3K]+ -3.5129044 114.874881400 1 1 29 [M+K-H2O]+ -3.8139344 20.952042220 1 1 30 [M-CO2H+H]+ -4.8139344 -43.989863780 1 1 31 [3M+H-H2O]+ -4.8139344 -17.003277800 3 1 32 [2M+H]+ -1.2239848 1.007276000 2 1 33 [3M+H]+ -2.2698664 1.007276000 3 1 34 [2M+Na-H2O]+ -3.8139344 4.978142219 2 1 35 [2M+K-H2O]+ -3.8139344 20.952042220 2 1 36 [3M+K-H2O]+ -4.8139344 20.952042220 3 1 37 [2M+Na]+ -2.9688364 22.989218000 2 1 38 [2M+K]+ -3.8139344 38.963142220 2 1 39 [3M+K]+ -3.8139344 38.963142220 3 1 [1] -1.31290442 -1.31290442 -1.31290442 -1.13681316 0.38606558 -0.49999107 [7] -1.61393442 -0.03415082 -0.46780638 -1.31290442 -1.31290442 1.93100135 [13] 1.45239151 1.23671182 0.61137486 0.34030809 0.30514367 0.28915557 [19] -0.12257272 -0.21599441 -0.29171512 -0.91496441 -1.01187443 -1.01187443 [25] -1.31290442 -1.31290442 -1.31290442 -1.31290442 -1.61393442 -2.61393442 [31] -2.61393442 0.97601518 -0.06986637 -1.61393442 -1.61393442 -2.61393442 [37] -0.76883638 -1.61393442 -1.61393442 Beggining value of logl is -712.347 Aggregate cliques done, with 145 rounds Kernighan-Lin done with 2 rounds Finishing value of logl is -164.568 [ FAIL 0 | WARN 4 | SKIP 0 | PASS 14 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 14 ] > > proc.time() user system elapsed 32.322 3.196 35.614
cliqueMS.Rcheck/cliqueMS-Ex.timings
name | user | system | elapsed | |
anClique-class | 9.443 | 1.076 | 10.540 | |
anClique | 4.185 | 1.161 | 5.351 | |
computeCliques | 5.728 | 0.408 | 6.160 | |
createNetwork | 9.404 | 2.407 | 11.822 | |
createanClique | 8.024 | 2.224 | 10.308 | |
getAnnotation | 0.268 | 0.083 | 0.354 | |
getCliques | 5.147 | 0.309 | 5.476 | |
getIsotopes | 0.117 | 0.004 | 0.121 | |