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This page was generated on 2024-12-07 15:24 -0500 (Sat, 07 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-11-14 r87333) -- "Unsuffered Consequences" | 861 |
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Package 146/216 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
multtest 2.63.0 (landing page) Katherine S. Pollard
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
To the developers/maintainers of the multtest package: - 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: multtest |
Version: 2.63.0 |
Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:multtest.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings multtest_2.63.0.tar.gz |
StartedAt: 2024-12-07 14:44:48 -0500 (Sat, 07 Dec 2024) |
EndedAt: 2024-12-07 14:45:39 -0500 (Sat, 07 Dec 2024) |
EllapsedTime: 51.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: multtest.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:multtest.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings multtest_2.63.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/multtest.Rcheck’ * using R Under development (unstable) (2024-11-14 r87333) * 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 ‘multtest/DESCRIPTION’ ... OK * this is package ‘multtest’ version ‘2.63.0’ * 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 ‘multtest’ 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 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 ... NOTE 'library' or 'require' call to ‘methods’ which was already attached by Depends. Please remove these calls from your code. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘multtest/R/zzz.R’: .onLoad calls: require(methods) Package startup functions should not change the search path. See section ‘Good practice’ in '?.onAttach'. EBMTP: no visible global function definition for ‘makeCluster’ EBMTP: no visible global function definition for ‘clusterEvalQ’ EBMTP: no visible global function definition for ‘stopCluster’ MTP: no visible global function definition for ‘makeCluster’ MTP: no visible global function definition for ‘clusterEvalQ’ MTP: no visible global function definition for ‘stopCluster’ boot.null: no visible global function definition for ‘clusterApply’ boot.null: no visible global function definition for ‘clusterApplyLB’ EBupdate,EBMTP: no visible binding for global variable ‘y’ update,MTP: no visible binding for global variable ‘y’ Undefined global functions or variables: clusterApply clusterApplyLB clusterEvalQ makeCluster stopCluster y * checking Rd files ... NOTE checkRd: (-1) mt.maxT.Rd:88: Escaped LaTeX specials: \# checkRd: (-1) mt.maxT.Rd:91: Escaped LaTeX specials: \& checkRd: (-1) mt.plot.Rd:37: Escaped LaTeX specials: \# * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic '[' and siglist 'EBMTP,ANY,ANY,ANY' generic '[' and siglist 'MTP,ANY,ANY,ANY' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... NOTE Documented arguments not in \usage in Rd file 'boot.null.Rd': ‘csnull’ Documented arguments not in \usage in Rd file 'meanX.Rd': ‘surv.object’ Objects in \usage without \alias in Rd file 'meanX.Rd': ‘corr.Tn’ Assignments in \usage in Rd file 'mt.internal.Rd': mt.niceres <- function(res, X, index) mt.legend(x, y = NULL, legend, fill = NULL, col = "black", lty, lwd, pch, angle = 45, density = NULL, bty = "o", bg = par("bg"), pt.bg = NA, cex = 1, pt.cex = cex, pt.lwd = lwd, xjust = 0, yjust = 1, x.intersp = 1, y.intersp = 1, adj = c(0, 0.5), text.width = NULL, text.col = par("col"), merge = do.lines && has.pch, trace = FALSE, plot = TRUE, ncol = 1, horiz = FALSE, ...) 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 ... WARNING Note: information on .o files is not available File ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/multtest/libs/multtest.so’: Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C) Found ‘stderr’, possibly from ‘stderr’ (C) 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 files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘MTP.pdf’ ‘MTP.tex’ ‘MTPALL.pdf’ ‘golub.R’ ‘multtest.bib’ ‘multtest.pdf’ Package has no Sweave vignette sources and no VignetteBuilder field. * checking examples ... OK * checking package vignettes ... NOTE Package has ‘vignettes’ subdirectory but apparently no vignettes. Perhaps the ‘VignetteBuilder’ information is missing from the DESCRIPTION file? * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 5 NOTEs See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/multtest.Rcheck/00check.log’ for details.
multtest.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL multtest ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’ * installing *source* package ‘multtest’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -Wall -c Rpack.c -o Rpack.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -Wall -c VScount.c -o VScount.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -Wall -c block_sampling_fixed.c -o block_sampling_fixed.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -Wall -c bootloop.c -o bootloop.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -Wall -c mt.c -o mt.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -Wall -c pairt_sampling.c -o pairt_sampling.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -Wall -c pairt_sampling_fixed.c -o pairt_sampling_fixed.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -Wall -c random.c -o random.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -Wall -c sampling.c -o sampling.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -Wall -c sampling_fixed.c -o sampling_fixed.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -Wall -c stat_func.c -o stat_func.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -Wall -c stat_order.c -o stat_order.o gcc -shared -L/usr/local/lib -o multtest.so Rpack.o VScount.o block_sampling_fixed.o bootloop.o mt.o pairt_sampling.o pairt_sampling_fixed.o random.o sampling.o sampling_fixed.o stat_func.o stat_order.o -lm installing to /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/00LOCK-multtest/00new/multtest/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 (multtest)
multtest.Rcheck/multtest-Ex.timings
name | user | system | elapsed | |
EBMTP-class | 0 | 0 | 0 | |
EBMTP | 0.114 | 0.020 | 0.134 | |
Hsets | 0.114 | 0.000 | 0.113 | |
MTP-class | 0 | 0 | 0 | |
MTP | 0.359 | 0.109 | 0.469 | |
boot.null | 0.017 | 0.000 | 0.016 | |
corr.null | 0.009 | 0.001 | 0.009 | |
fwer2gfwer | 1.336 | 0.000 | 1.335 | |
get.index | 0.155 | 0.014 | 0.168 | |
meanX | 0.005 | 0.000 | 0.005 | |
mt.maxT | 2.743 | 0.016 | 2.760 | |
mt.plot | 0.284 | 0.001 | 0.285 | |
mt.rawp2adjp | 0.264 | 0.003 | 0.267 | |
mt.reject | 0.261 | 0.001 | 0.263 | |
mt.sample.teststat | 0.070 | 0.009 | 0.079 | |
mt.teststat | 0.122 | 0.013 | 0.135 | |
ss.maxT | 0 | 0 | 0 | |
wapply | 0.001 | 0.000 | 0.000 | |