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 12:04 -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 1957/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
signeR 2.8.0 (landing page) Renan Valieris
| 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 | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the signeR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/signeR.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: signeR |
Version: 2.8.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:signeR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings signeR_2.8.0.tar.gz |
StartedAt: 2024-12-20 05:29:45 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 05:38:38 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 533.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: signeR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:signeR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings signeR_2.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/signeR.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 ‘signeR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘signeR’ version ‘2.8.0’ * 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 ‘signeR’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * 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 loading without being on the library search path ... 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 covariate: no visible binding for global variable ‘.’ explorepage: no visible binding for global variable ‘.’ genCountMatrixFromMAF: no visible binding for global variable ‘Variant_Type’ genCountMatrixFromMAF: no visible binding for global variable ‘Reference_Allele’ genCountMatrixFromMAF: no visible binding for global variable ‘Tumor_Seq_Allele2’ genCountMatrixFromMAF: no visible binding for global variable ‘Tumor_Seq_Allele1’ genCountMatrixFromVcf: no visible global function definition for ‘alt<-’ signeRFlow : server : loadSig: no visible binding for global variable ‘sig’ signeRFlow : server : loadSig: no visible binding for global variable ‘sig_test’ tcgaexplorer : get_similarities_tcga: no visible binding for global variable ‘project’ tcgaexplorer: no visible binding for global variable ‘.’ DiffExp,SignExp-character: no visible binding for global variable ‘fc’ ExposureBarplot,SignExp: no visible binding for global variable ‘Samples’ ExposureBarplot,SignExp: no visible binding for global variable ‘Signatures’ ExposureBoxplot,SignExp: no visible binding for global variable ‘Signatures’ ExposureBoxplot,SignExp: no visible binding for global variable ‘Samples’ ExposureClassify,ANY-character: no visible binding for global variable ‘Col’ ExposureClassify,ANY-character: no visible binding for global variable ‘Frequency’ ExposureClassify,ANY-character: no visible binding for global variable ‘Row’ ExposureClassifyCV,ANY-character: no visible binding for global variable ‘Col’ ExposureClassifyCV,ANY-character: no visible binding for global variable ‘Frequency’ ExposureClassifyCV,ANY-character: no visible binding for global variable ‘Row’ ExposureCorrelation,SignExp-numeric: no visible binding for global variable ‘Feature’ ExposureCorrelation,SignExp-numeric: no visible binding for global variable ‘exposure’ ExposureCorrelation,matrix-numeric: no visible binding for global variable ‘Feature’ ExposureCorrelation,matrix-numeric: no visible binding for global variable ‘exposure’ Undefined global functions or variables: . Col Feature Frequency Reference_Allele Row Samples Signatures Tumor_Seq_Allele1 Tumor_Seq_Allele2 Variant_Type alt<- exposure fc project sig sig_test * checking Rd files ... NOTE prepare_Rd: cosmic_data.Rd:91-93: Dropping empty section \details prepare_Rd: cosmic_data.Rd:98-100: Dropping empty section \references prepare_Rd: cosmic_data.Rd:101-102: Dropping empty section \examples prepare_Rd: tcga_similarities.Rd:96-98: Dropping empty section \details prepare_Rd: tcga_similarities.Rd:99-101: Dropping empty section \source prepare_Rd: tcga_similarities.Rd:102-104: Dropping empty section \references prepare_Rd: tcga_similarities.Rd:105-106: Dropping empty section \examples prepare_Rd: tcga_tumors.Rd:18-20: Dropping empty section \details prepare_Rd: tcga_tumors.Rd:21-23: Dropping empty section \source prepare_Rd: tcga_tumors.Rd:24-26: Dropping empty section \references prepare_Rd: tcga_tumors.Rd:27-28: Dropping empty section \examples * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... 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 ExposureClassifyCV 5.247 0.142 5.390 ExposureFuzzyClustering 5.042 0.020 5.059 * 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: 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/signeR.Rcheck/00check.log’ for details.
signeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL signeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘signeR’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c fuzzy.cpp -o fuzzy.o fuzzy.cpp: In function ‘Rcpp::List FuzzyClusterCpp(arma::cube, arma::mat, int, int, double)’: fuzzy.cpp:143:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 143 | if(C>=j) C = j-1; | ~^~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c gibbs_2.cpp -o gibbs_2.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c signeR_init.c -o signeR_init.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o signeR.so RcppExports.o fuzzy.o gibbs_2.o signeR_init.o -Wl,-S -llapack -L/home/biocbuild/bbs-3.20-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-signeR/00new/signeR/libs ** R ** data *** moving datasets to lazyload DB ** 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 (signeR)
signeR.Rcheck/signeR-Ex.timings
name | user | system | elapsed | |
Diffexp | 2.690 | 0.055 | 2.746 | |
ExposureClassify | 3.347 | 0.087 | 3.436 | |
ExposureClassifyCV | 5.247 | 0.142 | 5.390 | |
ExposureCorrelation | 1.870 | 0.017 | 1.886 | |
ExposureFuzzyClustering | 5.042 | 0.020 | 5.059 | |
ExposureGLM | 1.640 | 0.061 | 1.701 | |
ExposureHierarchicalClustering | 1.451 | 0.002 | 1.453 | |
ExposureSurvModel | 3.322 | 0.054 | 3.378 | |
ExposureSurvival | 1.836 | 0.058 | 1.894 | |
genMatrix | 2.182 | 0.311 | 2.497 | |
methods | 2.458 | 0.180 | 2.638 | |
plots | 1.848 | 0.001 | 1.849 | |
signeR-package | 0.001 | 0.000 | 0.001 | |
signeR | 0.001 | 0.000 | 0.001 | |