############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:netresponse.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings netresponse_1.66.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/netresponse.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 ‘netresponse/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘netresponse’ version ‘1.66.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' NOTE Depends: includes the non-default packages: 'BiocStyle', 'Rgraphviz', 'rmarkdown', 'minet', 'mclust', 'reshape2' 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 for sufficient/correct file permissions ... OK * checking whether package ‘netresponse’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * 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 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 ... OK * checking Rd files ... NOTE checkRd: (-1) vdp.mixt.Rd:88: Lost braces; missing escapes or markup? 88 | 'Nc' = \\sum_{n=1}^N q_{z_n} (z_n = c) (larger is better). | ^ checkRd: (-1) vdp.mixt.Rd:88: Lost braces; missing escapes or markup? 88 | 'Nc' = \\sum_{n=1}^N q_{z_n} (z_n = c) (larger is better). | ^ checkRd: (-1) vdp.mixt.Rd:92: Lost braces; missing escapes or markup? 92 | q_{z_n}(z_n = c_1) and q_{z_n}(z_n = c_2). | ^ checkRd: (-1) vdp.mixt.Rd:92: Lost braces; missing escapes or markup? 92 | q_{z_n}(z_n = c_1) and q_{z_n}(z_n = c_2). | ^ checkRd: (-1) vdp.mixt.Rd:94: Lost braces 94 | belonged to c, and determine the new value for the free energy, F{T+1}. | ^ checkRd: (-1) vdp.mixt.Rd:97: Lost braces 97 | 4. Select the split that lead to the maximal reduction of free energy, F{T+1}. | ^ checkRd: (-1) vdp.mixt.Rd:99: Lost braces 99 | 6. If FT - F{T+1} < \\epsilon then halt, else set T := T +1 and go to step 2. | ^ * 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 ... NOTE Documented arguments not in \usage in Rd file 'generate.toydata.Rd': ‘Dim’ ‘Nc’ ‘Ns’ ‘sd0’ ‘rgam.shape’ ‘rgam.scale’ Assignments in \usage in Rd file 'generate.toydata.Rd': D <- generate.toydata() 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 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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘bicmixture.R’ Running ‘mixture.model.test.R’ Running ‘mixture.model.test.multimodal.R’ Running ‘mixture.model.test.singlemode.R’ Running ‘timing.R’ Running ‘toydata2.R’ Running ‘validate.netresponse.R’ Running ‘vdpmixture.R’ OK * 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/netresponse.Rcheck/00check.log’ for details.