##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:snapCGH.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings snapCGH_1.54.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/snapCGH.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'snapCGH/DESCRIPTION' ... OK
* this is package 'snapCGH' version '1.54.0'
* 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 whether package 'snapCGH' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
cbind.SegList dim.SegList dimnames.SegList length.SegList
rbind.SegList
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* 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'
Undefined global functions or variables:
RGList floor.func non.zero.length.distr.non.tiled
non.zero.length.distr.tiled zero.length.distr.non.tiled
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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/snapCGH/libs/i386/snapCGH.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/snapCGH/libs/x64/snapCGH.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
Status: 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/snapCGH.Rcheck/00check.log'
for details.
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/snapCGH_1.54.0.tar.gz && rm -rf snapCGH.buildbin-libdir && mkdir snapCGH.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=snapCGH.buildbin-libdir snapCGH_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL snapCGH_1.54.0.zip && rm snapCGH_1.54.0.tar.gz snapCGH_1.54.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 620k 100 620k 0 0 8125k 0 --:--:-- --:--:-- --:--:-- 8867k
install for i386
* installing *source* package 'snapCGH' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c optimizer.c -o optimizer.o
optimizer.c: In function 'fr_two':
optimizer.c:26:30: warning: unused variable 'temp3' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c: In function 'fr_three':
optimizer.c:195:30: warning: unused variable 'temp3' [-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: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: In function 'fr_four':
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: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: In function 'fr_five':
optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:687:10: warning: unused variable 'denom' [-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: In function 'fr_two':
optimizer.c:150:58: warning: 'gammaC[1][1]' may be used uninitialized in this function [-Wmaybe-uninitialized]
alpha[k][t] = alpha[k][t] + alpha[d][t-1]*gammaC[d][k];
^
optimizer.c:150:58: warning: 'gammaC[1][0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
optimizer.c:150:58: warning: 'gammaC[0][1]' may be used uninitialized in this function [-Wmaybe-uninitialized]
optimizer.c:150:58: warning: 'gammaC[0][0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/snapCGH.buildbin-libdir/00LOCK-snapCGH/00new/snapCGH/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: more than one default provided in switch() call
** help
*** installing help indices
converting help for package 'snapCGH'
finding HTML links ... done
IDProbes html
LargeDataObject html
SegList html
Viterbi.five html
Viterbi.four html
Viterbi.three html
Viterbi.two html
cbind html
chrominfo.Mb html
compareSegmentations html
convert.output html
dim html
dimnames html
filter html
find.param.five html
find.param.four html
find.param.one html
find.param.three html
find.param.two html
findBreakPoints html
fit.model html
genomePlot html
heatmapGenome html
imputeMissingValues html
log2ratios html
mergeStates html
non.zero.length.distr.non.tiled html
non.zero.length.distr.tiled html
plotSegmentedGenome html
processCGH html
read.clonesinfo html
readPositionalInfo html
removeByWeights html
runBioHMM html
runDNAcopy html
runGLAD html
runHMM html
runTilingArray html
sim.structure html
zero.length.distr.non.tiled html
zero.length.distr.tiled html
zoomChromosome html
zoomGenome html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'snapCGH' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c optimizer.c -o optimizer.o
optimizer.c: In function 'fr_two':
optimizer.c:26:30: warning: unused variable 'temp3' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c: In function 'fr_three':
optimizer.c:195:30: warning: unused variable 'temp3' [-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: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: In function 'fr_four':
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: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: In function 'fr_five':
optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable]
double denom, temp, temp2, temp3;
^
optimizer.c:687:10: warning: unused variable 'denom' [-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:943:4: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
for(t = 1; t < nrow1; t++){
^
optimizer.c: In function 'fr_four':
optimizer.c:585:1: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
for(t = 1; t < nrow1; t++){
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/snapCGH.buildbin-libdir/snapCGH/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'snapCGH' as snapCGH_1.54.0.zip
* DONE (snapCGH)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'snapCGH' successfully unpacked and MD5 sums checked
