Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:55:47 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE SMAP PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1686/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
SMAP 1.52.0 Robin Andersson
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | NA | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK |
Package: SMAP |
Version: 1.52.0 |
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:SMAP.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings SMAP_1.52.0.tar.gz |
StartedAt: 2020-10-17 05:38:08 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 05:38:49 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 40.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SMAP.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:SMAP.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings SMAP_1.52.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/SMAP.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SMAP/DESCRIPTION’ ... OK * this is package ‘SMAP’ version ‘1.52.0’ * 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 ‘SMAP’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R 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 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 ‘SMAP/R/AllClasses.R’: .onLoad calls: require("methods", quietly = TRUE) Package startup functions should not change the search path. See section ‘Good practice’ in '?.onAttach'. .draw.dist,gaussparam: no visible global function definition for ‘abline’ plot,SMAPObservations-missing: no visible global function definition for ‘par’ plot,SMAPObservations-missing: no visible global function definition for ‘points’ plot,SMAPObservations-missing: no visible global function definition for ‘abline’ plot,SMAPObservations-missing: no visible global function definition for ‘box’ plot,SMAPObservations-missing: no visible global function definition for ‘axis’ profilePlot,SMAPProfile: no visible global function definition for ‘par’ profilePlot,SMAPProfile: no visible global function definition for ‘points’ profilePlot,SMAPProfile: no visible global function definition for ‘abline’ profilePlot,SMAPProfile: no visible global function definition for ‘box’ profilePlot,SMAPProfile: no visible global function definition for ‘axis’ profilePlot,SMAPProfiles: no visible global function definition for ‘par’ profilePlot,SMAPProfiles: no visible global function definition for ‘abline’ profilePlot,SMAPProfiles: no visible global function definition for ‘box’ profilePlot,SMAPProfiles: no visible global function definition for ‘axis’ Undefined global functions or variables: abline axis box par points Consider adding importFrom("graphics", "abline", "axis", "box", "par", "points") 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 ... 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 C/C++/Fortran sources/headers ... 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 smap 9.996 0.056 10.052 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.11-bioc/meat/SMAP.Rcheck/00check.log’ for details.
SMAP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL SMAP ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘SMAP’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c gradient.c -o gradient.o gradient.c: In function ‘prior_gradient’: gradient.c:142:7: warning: variable ‘lower’ set but not used [-Wunused-but-set-variable] int lower; ^~~~~ gradient.c: In function ‘hmm_update’: gradient.c:247:10: warning: unused variable ‘tmp’ [-Wunused-variable] double tmp; ^~~ gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c overlap.c -o overlap.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c prob.c -o prob.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c viterbi.c -o viterbi.o gcc -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o SMAP.so gradient.o init.o overlap.o prob.o viterbi.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-SMAP/00new/SMAP/libs ** R ** data ** 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 (SMAP)
SMAP.Rcheck/SMAP-Ex.timings
name | user | system | elapsed | |
GBM | 1.006 | 0.036 | 1.042 | |
SMAPObservations | 2.632 | 0.032 | 2.664 | |
smap | 9.996 | 0.056 | 10.052 | |