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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings DECIPHER_2.0.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/DECIPHER.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-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 ‘2.0.2’
* 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 ... NOTE
installed size is 9.2Mb
sub-directories of 1Mb or more:
data 2.5Mb
doc 3.9Mb
extdata 1.4Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.CalculateEfficiencyFISH: no visible global function definition for
‘uniroot’
.midpointRoot : .containsZero: no visible global function definition
for ‘is.leaf’
.midpointRoot : .findMax: no visible global function definition for
‘is.leaf’
.midpointRoot : .containsMax: no visible global function definition for
‘is.leaf’
.midpointRoot : .findMidpoint: no visible global function definition
for ‘is.leaf’
.midpointRoot : .adjustHeight: no visible global function definition
for ‘is.leaf’
.midpointRoot : .revertList: no visible global function definition for
‘is.leaf’
.midpointRoot : .adjustMidpoints: no visible global function definition
for ‘is.leaf’
.optimizeModel: no visible global function definition for ‘optimize’
.optimizeModel: no visible global function definition for ‘nlminb’
AdjustAlignment: no visible global function definition for ‘data’
AlignDB: no visible global function definition for ‘data’
AlignDB: no visible global function definition for ‘txtProgressBar’
AlignDB: no visible global function definition for ‘setTxtProgressBar’
AlignProfiles: no visible global function definition for ‘data’
AlignSeqs: no visible global function definition for ‘data’
AlignSeqs: no visible global function definition for ‘flush.console’
AlignSeqs: no visible global function definition for ‘txtProgressBar’
AlignSeqs: no visible global function definition for
‘setTxtProgressBar’
AlignSynteny: no visible global function definition for
‘txtProgressBar’
AlignSynteny: no visible global function definition for
‘setTxtProgressBar’
Array2Matrix: no visible global function definition for
‘txtProgressBar’
Array2Matrix: no visible global function definition for
‘setTxtProgressBar’
BrowseDB: no visible global function definition for ‘browseURL’
BrowseSeqs: no visible global function definition for ‘rainbow’
BrowseSeqs: no visible global function definition for ‘browseURL’
CalculateEfficiencyArray: no visible global function definition for
‘data’
CalculateEfficiencyFISH: no visible global function definition for
‘step’
CalculateEfficiencyFISH: no visible global function definition for
‘uniroot’
CorrectFrameshifts: no visible global function definition for ‘data’
CorrectFrameshifts: no visible global function definition for
‘flush.console’
CorrectFrameshifts: no visible global function definition for
‘txtProgressBar’
CorrectFrameshifts: no visible global function definition for
‘setTxtProgressBar’
CorrectFrameshifts: no visible binding for global variable ‘setNames’
CreateChimeras: no visible global function definition for
‘txtProgressBar’
CreateChimeras: no visible global function definition for
‘setTxtProgressBar’
DB2Seqs: no visible global function definition for ‘txtProgressBar’
DB2Seqs: no visible global function definition for ‘setTxtProgressBar’
DesignArray: no visible global function definition for ‘txtProgressBar’
DesignPrimers: no visible global function definition for
‘flush.console’
DesignPrimers: no visible global function definition for
‘txtProgressBar’
DesignPrimers: no visible global function definition for
‘setTxtProgressBar’
DesignProbes: no visible global function definition for ‘flush.console’
DesignProbes: no visible global function definition for
‘txtProgressBar’
DesignProbes: no visible global function definition for
‘setTxtProgressBar’
DesignSignatures: no visible global function definition for ‘data’
DesignSignatures: no visible binding for global variable ‘deltaHrules’
DesignSignatures: no visible global function definition for
‘flush.console’
DesignSignatures: no visible global function definition for
‘txtProgressBar’
DesignSignatures: no visible global function definition for
‘setTxtProgressBar’
DesignSignatures: no visible global function definition for ‘dist’
DigestDNA: no visible global function definition for ‘setNames’
DistanceMatrix: no visible global function definition for
‘txtProgressBar’
FindChimeras: no visible global function definition for ‘flush.console’
FindChimeras: no visible global function definition for
‘txtProgressBar’
FindChimeras: no visible global function definition for
‘setTxtProgressBar’
FindSynteny: no visible global function definition for ‘setNames’
FindSynteny: no visible global function definition for ‘txtProgressBar’
FindSynteny: no visible global function definition for ‘object.size’
FindSynteny: no visible global function definition for
‘setTxtProgressBar’
FormGroups: no visible global function definition for ‘txtProgressBar’
FormGroups: no visible global function definition for
‘setTxtProgressBar’
IdClusters: no visible global function definition for ‘txtProgressBar’
IdClusters: no visible global function definition for
‘setTxtProgressBar’
IdClusters: no visible global function definition for ‘pbinom’
IdClusters: no visible global function definition for ‘flush.console’
IdClusters : printLine: no visible global function definition for
‘flush.console’
IdClusters: no visible global function definition for
‘order.dendrogram’
IdClusters: no visible global function definition for ‘colors’
IdClusters : colEdge: no visible global function definition for
‘is.leaf’
IdClusters: no visible global function definition for ‘dendrapply’
IdClusters: no visible global function definition for ‘reorder’
IdClusters: no visible global function definition for ‘plot’
IdConsensus: no visible global function definition for ‘txtProgressBar’
IdConsensus: no visible global function definition for
‘setTxtProgressBar’
IdLengths: no visible global function definition for ‘txtProgressBar’
IdLengths: no visible global function definition for
‘setTxtProgressBar’
MaskAlignment: no visible global function definition for ‘par’
MaskAlignment: no visible global function definition for ‘plot’
MaskAlignment: no visible global function definition for ‘points’
MaskAlignment: no visible global function definition for ‘abline’
MaskAlignment: no visible global function definition for ‘axis’
MaskAlignment: no visible global function definition for ‘mtext’
MaskAlignment: no visible global function definition for ‘legend’
MeltDNA: no visible global function definition for ‘step’
NNLS: no visible global function definition for ‘txtProgressBar’
OrientNucleotides: no visible global function definition for
‘txtProgressBar’
OrientNucleotides: no visible global function definition for
‘setTxtProgressBar’
PredictHEC: no visible global function definition for ‘data’
ReadDendrogram: no visible global function definition for ‘dendrapply’
Seqs2DB : .cat: no visible global function definition for
‘flush.console’
Seqs2DB: no visible global function definition for ‘flush.console’
StaggerAlignment: no visible global function definition for
‘flush.console’
StaggerAlignment : .assignIndels: no visible global function definition
for ‘is.leaf’
StaggerAlignment : .groupIns: no visible global function definition for
‘is.leaf’
StaggerAlignment: no visible global function definition for
‘txtProgressBar’
StaggerAlignment: no visible global function definition for
‘setTxtProgressBar’
TileSeqs: no visible global function definition for ‘txtProgressBar’
TileSeqs: no visible global function definition for ‘setTxtProgressBar’
WriteDendrogram : .dendrogram2newick: no visible global function
definition for ‘is.leaf’
pairs.Synteny: no visible global function definition for ‘par’
pairs.Synteny: no visible global function definition for ‘dev.hold’
pairs.Synteny: no visible global function definition for ‘dev.flush’
pairs.Synteny: no visible global function definition for ‘strwidth’
pairs.Synteny: no visible global function definition for ‘plot’
pairs.Synteny: no visible global function definition for ‘box’
pairs.Synteny: no visible global function definition for ‘axis’
pairs.Synteny: no visible global function definition for ‘text’
pairs.Synteny: no visible global function definition for ‘segments’
pairs.Synteny: no visible global function definition for ‘rect’
pairs.Synteny: no visible global function definition for ‘rainbow’
pairs.Synteny: no visible global function definition for ‘mtext’
plot.Synteny: no visible global function definition for
‘colorRampPalette’
plot.Synteny: no visible global function definition for ‘dev.hold’
plot.Synteny: no visible global function definition for ‘dev.flush’
plot.Synteny: no visible global function definition for ‘dev.size’
plot.Synteny: no visible global function definition for ‘plot’
plot.Synteny: no visible global function definition for ‘par’
plot.Synteny: no visible global function definition for ‘strheight’
plot.Synteny: no visible global function definition for ‘text’
plot.Synteny: no visible global function definition for ‘rect’
plot.Synteny: no visible global function definition for ‘segments’
Undefined global functions or variables:
abline axis box browseURL colorRampPalette colors data deltaHrules
dendrapply dev.flush dev.hold dev.size dist flush.console is.leaf
legend mtext nlminb object.size optimize order.dendrogram par pbinom
plot points rainbow rect reorder segments setNames setTxtProgressBar
step strheight strwidth text txtProgressBar uniroot
Consider adding
importFrom("grDevices", "colorRampPalette", "colors", "dev.flush",
"dev.hold", "dev.size", "rainbow")
importFrom("graphics", "abline", "axis", "box", "legend", "mtext",
"par", "plot", "points", "rect", "segments", "strheight",
"strwidth", "text")
importFrom("stats", "dendrapply", "dist", "is.leaf", "nlminb",
"optimize", "order.dendrogram", "pbinom", "reorder",
"setNames", "step", "uniroot")
importFrom("utils", "browseURL", "data", "flush.console",
"object.size", "setTxtProgressBar", "txtProgressBar")
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 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 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
CorrectFrameshifts 25.070 0.092 25.278
StaggerAlignment 22.090 0.111 22.854
AlignTranslation 13.902 0.036 14.040
AlignSeqs 9.949 0.092 10.156
TileSeqs 7.789 0.004 7.817
Array2Matrix 7.409 0.028 7.497
DesignArray 7.167 0.111 7.314
BrowseSeqs 6.153 0.020 6.211
* 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-3.3-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.
* installing *source* package ‘DECIPHER’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c AlignProfiles.c -o AlignProfiles.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c AppendXStringSets.c -o AppendXStringSets.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c AssignIndels.c -o AssignIndels.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-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-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c CalculateDeltaG.c -o CalculateDeltaG.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-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]
-11.5, -7.8, -7, -8.3,
^
CalculateFISH.c:26:3: warning: (near initialization for ‘dH_DR[0]’) [-Wmissing-braces]
CalculateFISH.c:32:3: warning: missing braces around initializer [-Wmissing-braces]
-36.4, -21.6, -19.7, -23.9,
^
CalculateFISH.c:32:3: warning: (near initialization for ‘dS_DR[0]’) [-Wmissing-braces]
CalculateFISH.c:38:3: warning: missing braces around initializer [-Wmissing-braces]
-7.9, -8.4, -7.8, -7.2,
^
CalculateFISH.c:38:3: warning: (near initialization for ‘dH_DD[0]’) [-Wmissing-braces]
CalculateFISH.c:44:3: warning: missing braces around initializer [-Wmissing-braces]
-22.2, -22.4, -21, -20.4,
^
CalculateFISH.c:44:3: warning: (near initialization for ‘dS_DD[0]’) [-Wmissing-braces]
CalculateFISH.c:50:3: warning: missing braces around initializer [-Wmissing-braces]
-6.6, -10.17, -7.65, -5.76,
^
CalculateFISH.c:50:3: warning: (near initialization for ‘dH_RR[0]’) [-Wmissing-braces]
CalculateFISH.c:56:3: warning: missing braces around initializer [-Wmissing-braces]
-18.38, -26.03, -19.18, -15.67,
^
CalculateFISH.c:56:3: warning: (near initialization for ‘dS_RR[0]’) [-Wmissing-braces]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function ‘chainSegments’:
ChainSegments.c:414:72: warning: ‘upY’ may be used uninitialized in this function [-Wmaybe-uninitialized]
int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
^
ChainSegments.c:462:8: warning: ‘upX’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (upX) { // new chain is last
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c ClusterML.c -o ClusterML.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-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 [-Wmaybe-uninitialized]
minCol = minC;
^
ClusterNJ.c:195:62: note: ‘minC’ was declared here
int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC;
^
ClusterNJ.c:280:12: warning: ‘minR’ may be used uninitialized in this function [-Wmaybe-uninitialized]
minRow = minR;
^
ClusterNJ.c:195:56: note: ‘minR’ was declared here
int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC;
^
ClusterNJ.c: In function ‘clusterNJ’:
ClusterNJ.c:491:9: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
^
ClusterNJ.c:491:9: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ClusterNJ.c:487:29: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized]
*rPercentComplete = floor(100*soFar/total);
^
ClusterNJ.c:492:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
before = *rPercentComplete;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-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:200:12: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
minCol = minC;
^
ClusterUPGMA.c:124:62: note: ‘minC’ was declared here
int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC, met;
^
ClusterUPGMA.c:199:12: warning: ‘minR’ may be used uninitialized in this function [-Wmaybe-uninitialized]
minRow = minR;
^
ClusterUPGMA.c:124:56: note: ‘minR’ was declared here
int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC, met;
^
ClusterUPGMA.c: In function ‘clusterUPGMA’:
ClusterUPGMA.c:430:9: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
^
ClusterUPGMA.c:430:9: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ClusterUPGMA.c:426:29: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized]
*rPercentComplete = floor(100*soFar/total);
^
ClusterUPGMA.c:431:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
before = *rPercentComplete;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c CommonGaps.c -o CommonGaps.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c Compositions.c -o Compositions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c Compression.c -o Compression.o
Compression.c: In function ‘nbit._omp_fn.0’:
Compression.c:882:17: warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
p[c] = ((k - 1) >> 8) & 0xFF; // length of run
^
Compression.c:411:12: note: ‘k’ was declared here
int i, j, k, pos;
^
Compression.c:916:12: warning: ‘count’ may be used uninitialized in this function [-Wmaybe-uninitialized]
count++;
^
Compression.c:437:29: note: ‘count’ was declared here
unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
^
Compression.c:915:20: warning: ‘word’ may be used uninitialized in this function [-Wmaybe-uninitialized]
word = (word << 8) | (unsigned int)reorder(byte);
^
Compression.c:437:23: note: ‘word’ was declared here
unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
^
Compression.c:1077:16: warning: ‘lastHit’ may be used uninitialized in this function [-Wmaybe-uninitialized]
p[c++] = (unsigned char)lastHit;
^
Compression.c:437:36: note: ‘lastHit’ was declared here
unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
^
Compression.c:1073:14: warning: ‘rev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
p[c++] = rev==0 ? 254 : 255;
^
Compression.c:438:27: note: ‘rev’ was declared here
int lastTemp, currTemp, rev, len, len2, thresh = 1;
^
Compression.c:734:9: warning: ‘lastCase’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (lower==1)
^
Compression.c:535:25: note: ‘lastCase’ was declared here
int run, lastTriplet, lastCase;
^
Compression.c:1150:8: warning: ‘lastTriplet’ may be used uninitialized in this function [-Wmaybe-uninitialized]
j = lastTriplet + 1;
^
Compression.c:535:12: note: ‘lastTriplet’ was declared here
int run, lastTriplet, lastCase;
^
Compression.c:935:23: warning: ‘dict’ may be used uninitialized in this function [-Wmaybe-uninitialized]
lastHit = dict[(word >> k) & 0xFF];
^
Compression.c:437:17: note: ‘dict’ was declared here
unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c ConsensusSequence.c -o ConsensusSequence.o
ConsensusSequence.c: In function ‘consensusProfileAA’:
ConsensusSequence.c:1748:10: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
double *HEC, *s;
^
ConsensusSequence.c: In function ‘colScores’:
ConsensusSequence.c:1915:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
int do_DBN, n, l, d;
^
ConsensusSequence.c: In function ‘colScoresAA’:
ConsensusSequence.c:2040:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
int do_HEC, n, l, d;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c ConsolidateGaps.c -o ConsolidateGaps.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-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]
-0.816507461,-2.5401714,-1.647430026,-1.184658548
^
DesignProbes.c:71:3: warning: (near initialization for ‘NN[0]’) [-Wmissing-braces]
DesignProbes.c:78:3: warning: missing braces around initializer [-Wmissing-braces]
-0.141370102,-0.439805276,-0.285236035,-0.205111781
^
DesignProbes.c:78:3: warning: (near initialization for ‘PM[0]’) [-Wmissing-braces]
DesignProbes.c:85:3: warning: missing braces around initializer [-Wmissing-braces]
0,0,0,0
^
DesignProbes.c:85:3: warning: (near initialization for ‘sMM[0]’) [-Wmissing-braces]
DesignProbes.c: In function ‘designProbes._omp_fn.0’:
DesignProbes.c:834:29: warning: ‘lastCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
cycles += lastCycle - thisCycle;
^
DesignProbes.c:267:37: note: ‘lastCycle’ was declared here
int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
^
DesignProbes.c:834:29: warning: ‘thisCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
cycles += lastCycle - thisCycle;
^
DesignProbes.c:267:48: note: ‘thisCycle’ was declared here
int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c Diff.c -o Diff.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c DistanceMatrix.c -o DistanceMatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function ‘enumerateGappedSequence’:
EnumerateSequence.c:267:6: warning: variable ‘x_length’ set but not used [-Wunused-but-set-variable]
int x_length, i, j, k, wS, sum, ambiguous, *rans, *p;
^
EnumerateSequence.c: In function ‘enumerateGappedSequenceAA’:
EnumerateSequence.c:364:6: warning: variable ‘x_length’ set but not used [-Wunused-but-set-variable]
int x_length, i, j, k, wS, sum, ambiguous, *rans, *p;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function ‘findFrameshifts’:
FindFrameshifts.c:319:8: warning: ‘K’ may be used uninitialized in this function [-Wmaybe-uninitialized]
d = k - C[k*rc + j*r + i];
^
FindFrameshifts.c:317:22: warning: ‘J’ may be used uninitialized in this function [-Wmaybe-uninitialized]
while (i > 0 && j > 0) {
^
FindFrameshifts.c:317:13: warning: ‘I’ may be used uninitialized in this function [-Wmaybe-uninitialized]
while (i > 0 && j > 0) {
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c Import.c -o Import.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c InsertGaps.c -o InsertGaps.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c IntDist.c -o IntDist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function ‘meltPolymer’:
MeltPolymer.c:80:3: warning: missing braces around initializer [-Wmissing-braces]
-7.9,-8.4,-7.8,-7.2
^
MeltPolymer.c:80:3: warning: (near initialization for ‘dH[0]’) [-Wmissing-braces]
MeltPolymer.c:89:3: warning: missing braces around initializer [-Wmissing-braces]
-22.2,-22.4,-21.0,-20.4
^
MeltPolymer.c:89:3: warning: (near initialization for ‘dS[0]’) [-Wmissing-braces]
MeltPolymer.c:54:10: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
double *rans;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c MultiMatch.c -o MultiMatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c NNLS.c -o NNLS.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c Order.c -o Order.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c PredictHEC.c -o PredictHEC.o
PredictHEC.c: In function ‘predictHEC’:
PredictHEC.c:41:24: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
double H, E, C, sum, *rans;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-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-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c RemoveGaps.c -o RemoveGaps.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c ReplaceChars.c -o ReplaceChars.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c SubsetXStringSet.c -o SubsetXStringSet.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c TerminalMismatch.c -o TerminalMismatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c Translate.c -o Translate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -fopenmp -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o DECIPHER.so AlignProfiles.o AppendXStringSets.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o Compositions.o Compression.o ConsensusSequence.o ConsolidateGaps.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o Import.o InsertGaps.o IntDist.o MeltPolymer.o MultiMatch.o NNLS.o Order.o PredictHEC.o R_init_decipher.o RemoveGaps.o ReplaceChars.o SubsetXStringSet.o TerminalMismatch.o Translate.o XVector_stubs.o -fopenmp -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/DECIPHER.Rcheck/DECIPHER/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DECIPHER)
