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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch snapCGH_1.36.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/snapCGH.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘snapCGH/DESCRIPTION’ ... OK
* this is package ‘snapCGH’ version ‘1.36.0’
* 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 ‘snapCGH’ can be installed ... [17s/18s] 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:
‘DNAcopy’ ‘limma’ ‘methods’
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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
MergeLevels.new: warning in matrix(1:ncol(dst), nrow = nrow(dst), ncol
= ncol(dst), b = TRUE): partial argument match of 'b' to 'byrow'
Viterbi.five: warning in matrix(nrow = K, ncol = n, b = TRUE): partial
argument match of 'b' to 'byrow'
Viterbi.four: warning in matrix(nrow = K, ncol = n, b = TRUE): partial
argument match of 'b' to 'byrow'
Viterbi.three: warning in matrix(nrow = K, ncol = n, b = TRUE): partial
argument match of 'b' to 'byrow'
Viterbi.two: warning in matrix(nrow = K, ncol = n, b = TRUE): partial
argument match of 'b' to 'byrow'
find.param.five: warning in matrix(c(1 - p1 - p2 - p3 - p4, p1, p2, p3,
p4, p5, 1 - p5 - p6 - p7 - p8, p6, p7, p8, p9, p10, 1 - p9 - p10 -
p11 - p12, p11, p12, p13, p14, p15, 1 - p13 - p14 - p15 - p16, p16,
p17, p18, p19, p20, 1 - p17 - p18 - p19 - p20), ncol = 5, b = TRUE):
partial argument match of 'b' to 'byrow'
find.param.five: warning in matrix(c(p1 + p2 + p3 + p4, -p1, -p2, -p3,
-p4, -p5, p5 + p6 + p7 + p8, -p6, -p7, -p8, -p9, -p10, p9 + p10 + p11
+ p12, -p11, -p12, -p13, -p14, -p15, p13 + p14 + p15 + p16, -p16,
-p17, -p18, -p19, -p20, p17 + p18 + p19 + p20), ncol = 5, b = TRUE):
partial argument match of 'b' to 'byrow'
find.param.four: warning in matrix(c(abs(1 - p1 - p2 - p3), p1, p2, p3,
p4, abs(1 - p4 - p5 - p6), p5, p6, p7, p8, abs(1 - p7 - p8 - p9), p9,
p10, p11, p12, abs(1 - p10 - p11 - p12)), ncol = 4, b = TRUE):
partial argument match of 'b' to 'byrow'
find.param.four: warning in matrix(c(p1 + p2 + p3, -p1, -p2, -p3, -p4,
p4 + p5 + p6, -p5, -p6, -p7, -p8, p7 + p8 + p9, -p9, -p10, -p11,
-p12, p10 + p11 + p12), ncol = 4, b = TRUE): partial argument match
of 'b' to 'byrow'
find.param.three: warning in matrix(c(abs(1 - p1 - p2), p1, p2, p3,
abs(1 - p3 - p4), p4, p5, p6, abs(1 - p5 - p6)), ncol = 3, b = TRUE):
partial argument match of 'b' to 'byrow'
find.param.three: warning in matrix(c(p1 + p2, -p1, -p2, -p3, p3 + p4,
-p4, -p5, -p6, p5 + p6), ncol = 3, b = TRUE): partial argument match
of 'b' to 'byrow'
find.param.two: warning in matrix(c(1 - p1, p1, p2, 1 - p2), ncol = 2,
b = TRUE): partial argument match of 'b' to 'byrow'
find.param.two: warning in matrix(c(p1, -p1, -p2, p2), ncol = 2, b =
TRUE): partial argument match of 'b' to 'byrow'
genomePlot: warning in matrix(data[ord, ], nrow =
nrow(as.matrix(data[ord, ])), ncol = ncol(data), b = FALSE, dimnames
= dimnames(data)): partial argument match of 'b' to 'byrow'
genomePlot: warning in matrix(data[chrom == nchr, ], nrow =
nrow(as.matrix(data[chrom == nchr, ])), ncol = ncol(data), b = FALSE,
dimnames = dimnames(data[chrom == nchr, ])): partial argument match
of 'b' to 'byrow'
simulateData: warning in generate.data(mid.point.short[[i]],
short.tiled[i], length.short.tiled[i], end.pos.short[[i]],
start.short.tiled[i], length.chrom.short[i],
zero.length.distr.non.tiled = zero.length.distr.non.tiled,
non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
zero.length.distr.tiled = zero.length.distr.tiled,
non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
argument match of 'zero.length.distr.non.tiled' to
'zero.length.distr.non.tiled.'
simulateData: warning in generate.data(mid.point.short[[i]],
short.tiled[i], length.short.tiled[i], end.pos.short[[i]],
start.short.tiled[i], length.chrom.short[i],
zero.length.distr.non.tiled = zero.length.distr.non.tiled,
non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
zero.length.distr.tiled = zero.length.distr.tiled,
non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
argument match of 'non.zero.length.distr.non.tiled' to
'non.zero.length.distr.non.tiled.'
simulateData: warning in generate.data(mid.point.short[[i]],
short.tiled[i], length.short.tiled[i], end.pos.short[[i]],
start.short.tiled[i], length.chrom.short[i],
zero.length.distr.non.tiled = zero.length.distr.non.tiled,
non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
zero.length.distr.tiled = zero.length.distr.tiled,
non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
argument match of 'zero.length.distr.tiled' to
'zero.length.distr.tiled.'
simulateData: warning in generate.data(mid.point.short[[i]],
short.tiled[i], length.short.tiled[i], end.pos.short[[i]],
start.short.tiled[i], length.chrom.short[i],
zero.length.distr.non.tiled = zero.length.distr.non.tiled,
non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
zero.length.distr.tiled = zero.length.distr.tiled,
non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
argument match of 'non.zero.length.distr.tiled' to
'non.zero.length.distr.tiled.'
simulateData: warning in generate.data(mid.point.long[[i]],
long.tiled[i], length.long.tiled[i], end.pos.long[[i]],
start.long.tiled[i], length.chrom.long[i],
zero.length.distr.non.tiled = zero.length.distr.non.tiled,
non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
zero.length.distr.tiled = zero.length.distr.tiled,
non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
argument match of 'zero.length.distr.non.tiled' to
'zero.length.distr.non.tiled.'
simulateData: warning in generate.data(mid.point.long[[i]],
long.tiled[i], length.long.tiled[i], end.pos.long[[i]],
start.long.tiled[i], length.chrom.long[i],
zero.length.distr.non.tiled = zero.length.distr.non.tiled,
non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
zero.length.distr.tiled = zero.length.distr.tiled,
non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
argument match of 'non.zero.length.distr.non.tiled' to
'non.zero.length.distr.non.tiled.'
simulateData: warning in generate.data(mid.point.long[[i]],
long.tiled[i], length.long.tiled[i], end.pos.long[[i]],
start.long.tiled[i], length.chrom.long[i],
zero.length.distr.non.tiled = zero.length.distr.non.tiled,
non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
zero.length.distr.tiled = zero.length.distr.tiled,
non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
argument match of 'zero.length.distr.tiled' to
'zero.length.distr.tiled.'
simulateData: warning in generate.data(mid.point.long[[i]],
long.tiled[i], length.long.tiled[i], end.pos.long[[i]],
start.long.tiled[i], length.chrom.long[i],
zero.length.distr.non.tiled = zero.length.distr.non.tiled,
non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
zero.length.distr.tiled = zero.length.distr.tiled,
non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
argument match of 'non.zero.length.distr.tiled' to
'non.zero.length.distr.tiled.'
generate.data: no visible binding for global variable
‘zero.length.distr.non.tiled’
generate.data: no visible binding for global variable
‘non.zero.length.distr.non.tiled’
generate.data: no visible binding for global variable
‘zero.length.distr.tiled’
generate.data: no visible binding for global variable
‘non.zero.length.distr.tiled’
heatmapGenome: no visible binding for global variable ‘floor.func’
readPositionalInfo: no visible binding for global variable ‘RGList’
simulateData: no visible binding for global variable
‘zero.length.distr.non.tiled’
simulateData: no visible binding for global variable
‘zero.length.distr.tiled’
simulateData: no visible binding for global variable
‘non.zero.length.distr.non.tiled’
simulateData: no visible binding for global variable
‘non.zero.length.distr.tiled’
* checking Rd files ... NOTE
prepare_Rd: genomePlot.Rd:51-57: Dropping empty section \examples
prepare_Rd: heatmapGenome.Rd:76-77: Dropping empty section \examples
prepare_Rd: plotSegmentedGenome.Rd:52-58: Dropping empty section \examples
prepare_Rd: sim.structure.Rd:57-58: Dropping empty section \examples
* 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 ... [8s/8s] OK
* 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
NOTE: There were 3 notes.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/snapCGH.Rcheck/00check.log’
for details.
* installing *source* package ‘snapCGH’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c optimizer.c -o optimizer.o
optimizer.c:26:30: warning: unused variable 'temp3' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:195:23: warning: unused variable 'temp2' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:195:10: warning: unused variable 'denom' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:195:30: warning: unused variable 'temp3' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:194:69: warning: unused variable 'alphahat' [-Wunused-variable]
double gammaA[3][3], gammaB[3][3], gammaC[3][3], alpha[3][nrow1], alphahat[3][nrow1], emis_prob[3][nrow1];
^
optimizer.c:412:69: warning: unused variable 'alphahat' [-Wunused-variable]
double gammaA[4][4], gammaB[4][4], gammaC[4][4], alpha[4][nrow1], alphahat[4][nrow1], emis_prob[4][nrow1];
^
optimizer.c:413:30: warning: unused variable 'temp3' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:413:23: warning: unused variable 'temp2' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:413:10: warning: unused variable 'denom' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:687:10: warning: unused variable 'denom' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:686:69: warning: unused variable 'alphahat' [-Wunused-variable]
double gammaA[5][5], gammaB[5][5], gammaC[5][5], alpha[5][nrow1], alphahat[5][nrow1], emis_prob[5][nrow1];
^
optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
15 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o snapCGH.so optimizer.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/snapCGH.Rcheck/snapCGH/libs
** R
** data
** inst
** preparing package for lazy loading
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc, :
No generic function found corresponding to requested imported methods for "as.list" from package "multtest" (malformed exports?)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc, :
No generic function found corresponding to requested imported methods for "as.list" from package "multtest" (malformed exports?)
* DONE (snapCGH)