############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:affy.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings affy_1.85.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/affy.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * 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 ‘affy/DESCRIPTION’ ... OK * this is package ‘affy’ version ‘1.85.0’ * 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' 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 ‘affy’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: Things done: 0 (wh:) moved everything related to Cdf-class from 'affy' to 'makecdfenv': R/Cdf.R, R/getLocationsData.Cdf.R, locate.name.R, pmormm.R R/read.cdffile.R, data/cdf.example.rda, man/Cdf-class.Rd man/getLocationsData.Cdf.Rd, man/locate.name.Rd, man/pmormm.Rd man/read.cdffile.Rd, src/read_cdffile.c o read.affybatch2 reads all cel files together in one big hit into an affybatch o the baseline in normalize.AffyBatch,invariant can be selected using a baseline.type parameter. Also changed "progress" to the more standard "verbose". Seemed to be an error since both PM and MM probes were normalized by only PM's where used to establish the normalization, now follows same standard as been introduced for normalize.AffyBatch.quantiles. o Most normalization routines can now be called with the parameter type which specifies whether to be pmonly, mmonly, both together or both separately. This introduces more consistency to the how the normalization routines are actually applied to affybatchs. o express() has been completely removed. * 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 ... NOTE Unexported objects imported by ':::' calls: ‘stats:::C_loess_raw’ ‘stats:::C_lowesp’ ‘stats:::C_lowesw’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... WARNING Foreign function calls to a base package: .C(stats:::C_loess_raw, ...) .Fortran(stats:::C_lowesp, ...) .Fortran(stats:::C_lowesw, ...) Packages should not make .C/.Call/.External/.Fortran calls to a base package. They are not part of the API, for use only by R itself and subject to change without notice. * checking R code for possible problems ... OK * checking Rd files ... NOTE checkRd: (-1) xy2indices.Rd:51: Escaped LaTeX specials: \_ \_ * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: AffyBatch-class.Rd: normalize normalize-methods.Rd: normalize normalize.invariantset.Rd: normalize normalize.loess.Rd: normalize normalize.quantiles.Rd: normalize normalize.quantiles.robust.Rd: normalize Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 shell scripts ... 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 mas5 16.975 0.205 17.185 MAplot 10.988 0.373 11.363 expresso 7.580 0.135 7.718 ProgressBarText-class 0.775 0.029 16.297 * 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: 1 WARNING, 5 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/affy.Rcheck/00check.log’ for details.