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This page was generated on 2015-10-09 09:24:47 -0700 (Fri, 09 Oct 2015).
Package 316/1024 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
fastseg 1.14.0 Guenter Klambauer
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | ||||||
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | ||||||
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | ||||||
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
Package: fastseg |
Version: 1.14.0 |
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings fastseg_1.14.0.tar.gz |
StartedAt: 2015-10-09 01:02:53 -0700 (Fri, 09 Oct 2015) |
EndedAt: 2015-10-09 01:04:41 -0700 (Fri, 09 Oct 2015) |
EllapsedTime: 108.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: fastseg.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings fastseg_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/fastseg.Rcheck’ * using R version 3.2.2 (2015-08-14) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘fastseg/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘fastseg’ version ‘1.14.0’ * 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 ‘fastseg’ can be installed ... [7s/10s] OK * 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 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘graphics’ ‘stats’ All declared Imports should be used. Packages in Depends field not imported from: ‘Biobase’ ‘GenomicRanges’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE fastseg: no visible global function definition for ‘assayData’ fastseg: no visible global function definition for ‘fData’ fastseg: no visible global function definition for ‘sampleNames’ fastseg: no visible global function definition for ‘featureData’ fastseg : <anonymous>: no visible global function definition for ‘featureData’ fastseg: no visible global function definition for ‘GRanges’ fastseg: no visible global function definition for ‘Rle’ fastseg: no visible global function definition for ‘IRanges’ fastseg: no visible global function definition for ‘seqnames’ fastseg: no visible global function definition for ‘elementMetadata’ fastseg: no visible global function definition for ‘width’ segPlot: no visible global function definition for ‘seqnames’ segPlot: no visible global function definition for ‘values’ segPlot: no visible global function definition for ‘ranges’ segmentGeneral: no visible global function definition for ‘IRanges’ toDNAcopyObj: no visible global function definition for ‘elementMetadata’ * 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 ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [9s/18s] OK Examples with CPU or elapsed time > 5s user system elapsed fastseg 2.567 0.012 5.193 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.1-bioc/meat/fastseg.Rcheck/00check.log’ for details.
fastseg.Rcheck/00install.out:
* installing *source* package ‘fastseg’ ... ** libs gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_init_fastseg.c -o R_init_fastseg.o g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c segment.cpp -o segment.o segment.cpp: In function ‘SEXPREC* segment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: segment.cpp:60:20: warning: variable ‘globalSd’ set but not used [-Wunused-but-set-variable] double globalMean,globalSd,diff,M2,globalVariance; ^ segment.cpp:61:9: warning: variable ‘oldStatistic’ set but not used [-Wunused-but-set-variable] double oldStatistic, meanLeft,meanRight,varLeft,varRight; ^ segment.cpp:62:31: warning: variable ‘maxStatistic’ set but not used [-Wunused-but-set-variable] double newStatistic,meanDiff,maxStatistic,DOF,a,b,eps1; ^ segment.cpp:63:40: warning: variable ‘maxIdx’ set but not used [-Wunused-but-set-variable] double newPValue, maxPValue,oldPValue,maxIdx; ^ In file included from segment.cpp:10:0: /home/biocbuild/bbs-3.1-bioc/R/include/Rmath.h:217:15: warning: unused variable ‘Rf_beta’ [-Wunused-variable] #define beta Rf_beta ^ segment.cpp:65:9: note: in expansion of macro ‘beta’ double beta,nn; ^ g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c segmentCyberT.cpp -o segmentCyberT.o segmentCyberT.cpp: In function ‘SEXPREC* segmentCyberT(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: segmentCyberT.cpp:59:20: warning: variable ‘globalSd’ set but not used [-Wunused-but-set-variable] double globalMean,globalSd,diff,M2,globalVariance; ^ segmentCyberT.cpp:60:9: warning: variable ‘oldStatistic’ set but not used [-Wunused-but-set-variable] double oldStatistic,meanLeft,meanRight,varLeft,varRight; ^ segmentCyberT.cpp:61:31: warning: variable ‘maxStatistic’ set but not used [-Wunused-but-set-variable] double newStatistic,meanDiff,maxStatistic,DOF,a,b,eps1; ^ In file included from segmentCyberT.cpp:10:0: /home/biocbuild/bbs-3.1-bioc/R/include/Rmath.h:217:15: warning: unused variable ‘Rf_beta’ [-Wunused-variable] #define beta Rf_beta ^ segmentCyberT.cpp:63:50: note: in expansion of macro ‘beta’ double newStatisticBptLeft,newStatisticBptRight,beta,nn; ^ g++ -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o fastseg.so R_init_fastseg.o segment.o segmentCyberT.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.1-bioc/meat/fastseg.Rcheck/fastseg/libs ** R ** data ** inst ** preparing package for lazy loading Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’ * DONE (fastseg)
fastseg.Rcheck/fastseg-Ex.timings:
name | user | system | elapsed | |
fastseg | 2.567 | 0.012 | 5.193 | |
segPlot | 1.376 | 0.005 | 2.423 | |
toDNAcopyObj | 2.454 | 0.013 | 4.863 | |