* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/DECIPHER.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.8.0’
* 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 ... [11s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘Biostrings’ ‘parallel’ ‘RSQLite’ ‘IRanges’ ‘stats’ ‘XVector’
A package should be listed in only one of these fields.
* 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
Namespaces in Imports field not imported from:
‘RSQLite’ ‘XVector’ ‘parallel’ ‘stats’
All declared Imports should be used.
Packages in Depends field not imported from:
‘RSQLite’ ‘XVector’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘DECIPHERing.Rnw’, ‘DesignMicroarray.Rnw’, ‘DesignPrimers.Rnw’,
‘DesignProbes.Rnw’, ‘FindChimeras.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [521s/202s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
AlignSeqs 437.472 0.984 154.745
AlignProfiles 40.174 0.160 15.872
TileSeqs 11.893 0.076 12.440
DesignArray 10.057 0.060 4.521
Array2Matrix 9.852 0.060 4.465
* 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
NOTE: There were 3 notes.
See
‘/home/biocbuild/bbs-2.13-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.
* installing *source* package ‘DECIPHER’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c AlignProfiles.c -o AlignProfiles.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c CalculateDeltaG.c -o CalculateDeltaG.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function ‘calculateFISH’:
CalculateFISH.c:26:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:26:3: warning: (near initialization for ‘dH_DR[0]’) [-Wmissing-braces]
CalculateFISH.c:32:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:32:3: warning: (near initialization for ‘dS_DR[0]’) [-Wmissing-braces]
CalculateFISH.c:38:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:38:3: warning: (near initialization for ‘dH_DD[0]’) [-Wmissing-braces]
CalculateFISH.c:44:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:44:3: warning: (near initialization for ‘dS_DD[0]’) [-Wmissing-braces]
CalculateFISH.c:50:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:50:3: warning: (near initialization for ‘dH_RR[0]’) [-Wmissing-braces]
CalculateFISH.c:56:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:56:3: warning: (near initialization for ‘dS_RR[0]’) [-Wmissing-braces]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c ClusterML.c -o ClusterML.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function ‘clusterNJ._omp_fn.0’:
ClusterNJ.c:281:12: warning: ‘minC’ may be used uninitialized in this function [-Wuninitialized]
ClusterNJ.c:195:62: note: ‘minC’ was declared here
ClusterNJ.c:280:12: warning: ‘minR’ may be used uninitialized in this function [-Wuninitialized]
ClusterNJ.c:195:56: note: ‘minR’ was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function ‘clusterUPGMA._omp_fn.0’:
ClusterUPGMA.c:198:12: warning: ‘minC’ may be used uninitialized in this function [-Wuninitialized]
ClusterUPGMA.c:124:62: note: ‘minC’ was declared here
ClusterUPGMA.c:197:12: warning: ‘minR’ may be used uninitialized in this function [-Wuninitialized]
ClusterUPGMA.c:124:56: note: ‘minR’ was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c CommonGaps.c -o CommonGaps.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c ConsensusSequence.c -o ConsensusSequence.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function ‘designProbes’:
DesignProbes.c:71:3: warning: missing braces around initializer [-Wmissing-braces]
DesignProbes.c:71:3: warning: (near initialization for ‘NN[0]’) [-Wmissing-braces]
DesignProbes.c:78:3: warning: missing braces around initializer [-Wmissing-braces]
DesignProbes.c:78:3: warning: (near initialization for ‘PM[0]’) [-Wmissing-braces]
DesignProbes.c:85:3: warning: missing braces around initializer [-Wmissing-braces]
DesignProbes.c:85:3: warning: (near initialization for ‘sMM[0]’) [-Wmissing-braces]
DesignProbes.c: In function ‘designProbes._omp_fn.0’:
DesignProbes.c:829:29: warning: ‘lastCycle’ may be used uninitialized in this function [-Wuninitialized]
DesignProbes.c:267:37: note: ‘lastCycle’ was declared here
DesignProbes.c:829:29: warning: ‘thisCycle’ may be used uninitialized in this function [-Wuninitialized]
DesignProbes.c:267:48: note: ‘thisCycle’ was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c DistanceMatrix.c -o DistanceMatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c MultiMatch.c -o MultiMatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c NNLS.c -o NNLS.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c R_init_decipher.c -o R_init_decipher.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c ReplaceChars.c -o ReplaceChars.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/parallel/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/stats/include" -I"/home/biocbuild/bbs-2.13-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c TerminalMismatch.c -o TerminalMismatch.o
gcc -std=gnu99 -shared -L/usr/local/lib -o DECIPHER.so AlignProfiles.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DesignProbes.o DistanceMatrix.o MultiMatch.o NNLS.o R_init_decipher.o ReplaceChars.o TerminalMismatch.o -fopenmp -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-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
** testing if installed package can be loaded
* DONE (DECIPHER)