BioC 2.12: CHECK report for DECIPHER on lamb2

Package: DECIPHER

Version: 1.5.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings DECIPHER_1.5.0.tar.gz

StartedAt: 2013-01-16 01:58:37 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 02:03:11 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 274.1 seconds

RetCode: 0

Status: OK

CheckDir: DECIPHER.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/DECIPHER.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘1.5.0’
* 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 ‘DECIPHER’ can be installed ... OK
* 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 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 for unstated 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 ... NOTE
DB2FASTA: warning in writeXStringSet(myDNAStringSet, file = file,
  append = append): partial argument match of 'file' to 'filepath'
CreateChimeras: no visible binding for global variable ‘s1’
CreateChimeras: no visible binding for global variable ‘d’
CreateChimeras: no visible binding for global variable ‘myName’
* 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 line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
TileSeqs       145.157  0.036 145.774
CreateChimeras   7.924  0.024   3.957
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.

* installing *source* package ‘DECIPHER’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/stats/include"  -fopenmp -fpic  -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/stats/include"  -fopenmp -fpic  -g -O2  -c CalculateDeltaG.c -o CalculateDeltaG.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/stats/include"  -fopenmp -fpic  -g -O2  -c ClusterML.c -o ClusterML.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/stats/include"  -fopenmp -fpic  -g -O2  -c ClusterNJ.c -o ClusterNJ.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/stats/include"  -fopenmp -fpic  -g -O2  -c ClusterUPGMA.c -o ClusterUPGMA.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/stats/include"  -fopenmp -fpic  -g -O2  -c CommonGaps.c -o CommonGaps.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/stats/include"  -fopenmp -fpic  -g -O2  -c ConsensusSequence.c -o ConsensusSequence.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/stats/include"  -fopenmp -fpic  -g -O2  -c DistanceMatrix.c -o DistanceMatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/stats/include"  -fopenmp -fpic  -g -O2  -c MultiMatch.c -o MultiMatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/stats/include"  -fopenmp -fpic  -g -O2  -c R_init_decipher.c -o R_init_decipher.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/stats/include"  -fopenmp -fpic  -g -O2  -c ReplaceChars.c -o ReplaceChars.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/RSQLite/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/stats/include"  -fopenmp -fpic  -g -O2  -c TerminalMismatch.c -o TerminalMismatch.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o DECIPHER.so Biostrings_stubs.o CalculateDeltaG.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DistanceMatrix.o MultiMatch.o R_init_decipher.o ReplaceChars.o TerminalMismatch.o -fopenmp -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/DECIPHER.Rcheck/DECIPHER/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘DECIPHERing.Rnw’ 
   ‘DesignPrimers.Rnw’ 
   ‘FindChimeras.Rnw’ 
** testing if installed package can be loaded

* DONE (DECIPHER)

name	user	system	elapsed
Add2DB	0.596	0.028	0.627
BrowseDB	0.076	0.012	0.094
BrowseSequences	0.136	0.020	0.162
CalculateEfficiencyArray	0.516	0.020	0.569
CalculateEfficiencyPCR	0.020	0.008	0.028
ConsensusSequence	0.020	0.004	0.038
CreateChimeras	7.924	0.024	3.957
DB2FASTA	0.024	0.020	0.086
DesignPrimers	0.016	0.000	0.019
DistanceMatrix	0.128	0.000	0.075
FindChimeras	0.856	0.028	0.730
FormGroups	0.060	0.000	0.062
IdClusters	0.156	0.000	0.065
IdConsensus	2.085	0.044	1.951
IdLengths	0.040	0.004	0.048
IdentifyByRank	0.040	0.004	0.044
SearchDB	0.036	0.000	0.038
Seqs2DB	0.512	0.008	0.529
TerminalChar	0.052	0.000	0.055
TileSeqs	145.157	0.036	145.774
deltaGrules	0.024	0.008	0.036

Summary

Command output