Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 531/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DeMixT 1.21.0 (landing page) Shuai Guo
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the DeMixT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DeMixT.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: DeMixT |
Version: 1.21.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DeMixT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings DeMixT_1.21.0.tar.gz |
StartedAt: 2024-06-10 01:49:29 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 01:59:15 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 586.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: DeMixT.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DeMixT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings DeMixT_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/DeMixT.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 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 'DeMixT/DESCRIPTION' ... OK * this is package 'DeMixT' version '1.21.0' * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'parallel', 'Rcpp', 'SummarizedExperiment', 'knitr', 'KernSmooth', 'matrixcalc', 'rmarkdown', 'DSS', 'dendextend', 'psych', 'sva' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 'DeMixT' can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'ggplot2::%+%' by 'psych::%+%' when loading 'DeMixT' Warning: replacing previous import 'SummarizedExperiment::distance' by 'psych::distance' when loading 'DeMixT' Warning: replacing previous import 'ggplot2::alpha' by 'psych::alpha' when loading 'DeMixT' See 'F:/biocbuild/bbs-3.20-bioc/meat/DeMixT.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 13.2.0' * used C++ compiler: 'G__~1.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 whether startup messages can be suppressed ... 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 DeMixT_GS: no visible global function definition for 'qchisq' DeMixT_preprocessing: no visible global function definition for 'quantile_normalization' detect_suspicious_sample_by_hierarchical_clustering_2comp : <anonymous>: no visible global function definition for 'wilcox.test' detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible global function definition for 'prcomp' detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible global function definition for 'dist' detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible global function definition for 'hclust' detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible global function definition for 'par' detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible global function definition for 'as.dendrogram' detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible global function definition for 'legend' plot_dim: no visible global function definition for 'prcomp' plot_dim: no visible global function definition for 'rainbow' plot_dim: no visible global function definition for 'abline' plot_dim: no visible global function definition for 'segments' plot_dim: no visible global function definition for 'points' plot_dim: no visible global function definition for 'legend' plot_sd: no visible global function definition for 'par' scale_normalization_75th_percentile: no visible global function definition for 'median' simulate_2comp: no visible global function definition for 'SimpleList' simulate_2comp: no visible global function definition for 'DataFrame' simulate_3comp: no visible global function definition for 'SimpleList' simulate_3comp: no visible global function definition for 'DataFrame' Undefined global functions or variables: DataFrame SimpleList abline as.dendrogram dist hclust legend median par points prcomp qchisq quantile_normalization rainbow segments wilcox.test Consider adding importFrom("grDevices", "rainbow") importFrom("graphics", "abline", "legend", "par", "points", "segments") importFrom("stats", "as.dendrogram", "dist", "hclust", "median", "prcomp", "qchisq", "wilcox.test") to your NAMESPACE file. * 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 ... WARNING Undocumented arguments in Rd file 'detect_suspicious_sample_by_hierarchical_clustering_2comp.Rd' 'labels' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * 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 LazyData ... 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/DeMixT/libs/x64/DeMixT.dll': Found '_assert', possibly from 'assert' (C) Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed DeMixT_S2 267.57 0 135.85 * checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' call not declared from: 'calibrate' * 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 WARNINGs, 4 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/DeMixT.Rcheck/00check.log' for details.
DeMixT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL DeMixT ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'DeMixT' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DeMixT.c -o DeMixT.o DeMixT.c: In function 'Tdemix': DeMixT.c:37:45: warning: variable 'st2_sig_2' set but not used [-Wunused-but-set-variable] 37 | double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2; | ^~~~~~~~~ DeMixT.c:37:33: warning: variable 'st1_sig_2' set but not used [-Wunused-but-set-variable] 37 | double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2; | ^~~~~~~~~ DeMixT.c:37:22: warning: variable 'st2_mu_2' set but not used [-Wunused-but-set-variable] 37 | double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2; | ^~~~~~~~ DeMixT.c:37:11: warning: variable 'st1_mu_2' set but not used [-Wunused-but-set-variable] 37 | double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2; | ^~~~~~~~ DeMixT.c: In function 'gettumor': DeMixT.c:591:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable] 591 | double obj_old, obj_new; | ^~~~~~~ DeMixT.c:591:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable] 591 | double obj_old, obj_new; | ^~~~~~~ DeMixT.c: In function 'getpi': DeMixT.c:1280:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable] 1280 | double obj_old, obj_new; | ^~~~~~~ DeMixT.c:1280:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable] 1280 | double obj_old, obj_new; | ^~~~~~~ DeMixT.c: In function 'getspikeinpi': DeMixT.c:1307:25: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable] 1307 | double obj_old, obj_new; | ^~~~~~~ DeMixT.c:1307:16: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable] 1307 | double obj_old, obj_new; | ^~~~~~~ DeMixT.c: In function 'getpiT': DeMixT.c:1322:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable] 1322 | double obj_old, obj_new; | ^~~~~~~ DeMixT.c:1322:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable] 1322 | double obj_old, obj_new; | ^~~~~~~ DeMixT.c: In function 'Tdemix': DeMixT.c:195:11: warning: 'Tavgtmp' may be used uninitialized [-Wmaybe-uninitialized] 195 | if(Tavgtmp <= 0) Tavgtmp = exp(10*log(2.0) + p->Tsigma[j]/2.0*pow(log(2.0), 2.0)); | ^ DeMixT.c:177:12: note: 'Tavgtmp' was declared here 177 | double Tavgtmp; | ^~~~~~~ DeMixT.c:94:8: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 94 | FD = calloc(nS ,sizeof(double *)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from DeMixT.c:8: C:/rtools44/x86_64-w64-mingw32.static.posix/include/stdlib.h:536:17: note: in a call to allocation function 'calloc' declared here 536 | void *__cdecl calloc(size_t _NumOfElements,size_t _SizeOfElements); | ^~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Profile_2D.cpp -o Profile_2D.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c registerDynamicSymbol.c -o registerDynamicSymbol.o g++ -std=gnu++17 -shared -s -static-libgcc -o DeMixT.dll tmp.def DeMixT.o Profile_2D.o RcppExports.o init.o registerDynamicSymbol.o -fopenmp -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-DeMixT/00new/DeMixT/libs/x64 ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'ggplot2::%+%' by 'psych::%+%' when loading 'DeMixT' Warning: replacing previous import 'SummarizedExperiment::distance' by 'psych::distance' when loading 'DeMixT' Warning: replacing previous import 'ggplot2::alpha' by 'psych::alpha' when loading 'DeMixT' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'ggplot2::%+%' by 'psych::%+%' when loading 'DeMixT' Warning: replacing previous import 'SummarizedExperiment::distance' by 'psych::distance' when loading 'DeMixT' Warning: replacing previous import 'ggplot2::alpha' by 'psych::alpha' when loading 'DeMixT' ** testing if installed package can be loaded from final location Warning: replacing previous import 'ggplot2::%+%' by 'psych::%+%' when loading 'DeMixT' Warning: replacing previous import 'SummarizedExperiment::distance' by 'psych::distance' when loading 'DeMixT' Warning: replacing previous import 'ggplot2::alpha' by 'psych::alpha' when loading 'DeMixT' ** testing if installed package keeps a record of temporary installation path * DONE (DeMixT)
DeMixT.Rcheck/DeMixT-Ex.timings
name | user | system | elapsed | |
DeMixT | 0.00 | 0.04 | 0.05 | |
DeMixT_DE | 0.00 | 0.01 | 0.01 | |
DeMixT_GS | 0.00 | 0.02 | 0.02 | |
DeMixT_S2 | 267.57 | 0.00 | 135.85 | |
Optimum_KernelC | 0.00 | 0.01 | 0.02 | |
simulate_2comp | 0.13 | 0.03 | 0.26 | |
simulate_3comp | 0.11 | 0.05 | 0.16 | |