Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:46 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 2025/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sRACIPE 1.21.0 (landing page) Vivek Kohar
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | 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 | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the sRACIPE package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sRACIPE.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: sRACIPE |
Version: 1.21.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sRACIPE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sRACIPE_1.21.0.tar.gz |
StartedAt: 2024-08-27 00:42:59 -0400 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 00:44:08 -0400 (Tue, 27 Aug 2024) |
EllapsedTime: 69.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sRACIPE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sRACIPE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sRACIPE_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/sRACIPE.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sRACIPE/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sRACIPE’ version ‘1.21.0’ * 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 ‘sRACIPE’ can be installed ... OK * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * 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 ... NOTE License stub is invalid DCF. * 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 ... NOTE sracipeSimulate: no visible global function definition for ‘registerDoFuture’ sracipeSimulate: no visible global function definition for ‘plan’ sracipeSimulate: no visible global function definition for ‘%dopar%’ sracipeSimulate: no visible global function definition for ‘foreach’ sracipeSimulate: no visible binding for global variable ‘configurationTmp’ sracipeSimulate: no visible binding for global variable ‘outFileGETmp’ sracipeSimulate: no visible binding for global variable ‘outFileParamsTmp’ sracipeSimulate: no visible binding for global variable ‘outFileICTmp’ Undefined global functions or variables: %dopar% configurationTmp foreach outFileGETmp outFileICTmp outFileParamsTmp plan registerDoFuture * checking Rd files ... NOTE checkRd: (-1) sracipeHeatmapSimilarity.Rd:31: Lost braces 31 | If clusterCut is missing, hierarchical clustering using /code{ward.D2} | ^ checkRd: (-1) sracipeHeatmapSimilarity.Rd:32: Lost braces 32 | and /code{distance = (1-cor(x, method = "spear"))/2} will be used to | ^ * 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 sracipeSimulate 5.461 0.009 5.471 * 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: 5 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/sRACIPE.Rcheck/00check.log’ for details.
sRACIPE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sRACIPE ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘sRACIPE’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ 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/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/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c generateThresholds.cpp -o generateThresholds.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/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c header.cpp -o header.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/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c simulateGRC.cpp -o simulateGRC.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/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c steppers.cpp -o steppers.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 sRACIPE.so RcppExports.o generateThresholds.o header.o simulateGRC.o steppers.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-sRACIPE/00new/sRACIPE/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 (sRACIPE)
sRACIPE.Rcheck/sRACIPE-Ex.timings
name | user | system | elapsed | |
RacipeSE | 0.010 | 0.000 | 0.011 | |
annotation-RacipeSE-method | 0.361 | 0.005 | 0.366 | |
annotation-set-RacipeSE-ANY-method | 0.511 | 0.010 | 0.521 | |
sracipeCircuit-set | 0.010 | 0.003 | 0.013 | |
sracipeCircuit | 0.008 | 0.002 | 0.011 | |
sracipeConfig-set | 0.002 | 0.000 | 0.003 | |
sracipeConfig | 0.008 | 0.002 | 0.010 | |
sracipeGenParamNames | 0.008 | 0.003 | 0.010 | |
sracipeGetTS | 0.021 | 0.004 | 0.026 | |
sracipeIC-set | 0.038 | 0.004 | 0.043 | |
sracipeIC | 0.028 | 0.003 | 0.031 | |
sracipeKnockDown | 0.000 | 0.002 | 0.002 | |
sracipeNormalize | 0.027 | 0.002 | 0.029 | |
sracipeOverExp | 0.001 | 0.002 | 0.002 | |
sracipeParams-set | 0.024 | 0.003 | 0.027 | |
sracipeParams | 0.019 | 0.003 | 0.022 | |
sracipePlotCircuit | 0.000 | 0.002 | 0.002 | |
sracipePlotData | 0.001 | 0.001 | 0.001 | |
sracipePlotParamBifur | 0.000 | 0.001 | 0.001 | |
sracipeSimulate | 5.461 | 0.009 | 5.471 | |