TitanCNA 1.14.0
Gavin Ha , Sohrab P Shah
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/TitanCNA | | Branch: RELEASE_3_5 | | Last Commit: fd54f7f | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf TitanCNA.buildbin-libdir TitanCNA.Rcheck && mkdir TitanCNA.buildbin-libdir TitanCNA.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TitanCNA.buildbin-libdir TitanCNA_1.14.0.tar.gz >TitanCNA.Rcheck\00install.out 2>&1 && cp TitanCNA.Rcheck\00install.out TitanCNA-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=TitanCNA.buildbin-libdir --install="check:TitanCNA-install.out" --force-multiarch --no-vignettes --timings TitanCNA_1.14.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/TitanCNA.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TitanCNA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TitanCNA' version '1.14.0'
* 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 'TitanCNA' can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.2Mb
sub-directories of 1Mb or more:
data 1.7Mb
extdata 4.9Mb
* 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
* 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
** checking loading without being on the library search path ... 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 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
correctReadDepth: no visible global function definition for 'queryHits'
correctReadcount: no visible global function definition for 'loess'
correctReadcount: no visible global function definition for 'predict'
correctReadcount: no visible global function definition for 'approxfun'
correctReadcount: no visible global function definition for 'lowess'
extractAlleleReadCounts: no visible global function definition for
'xtabs'
extractAlleleReadCounts: no visible global function definition for
'write.table'
getPositionOverlap: no visible global function definition for 'as'
getPositionOverlap: no visible global function definition for
'queryHits'
getPositionOverlap: no visible global function definition for
'subjectHits'
getSubcloneProfiles: no visible global function definition for
'read.delim'
loadAlleleCounts: no visible global function definition for
'read.delim'
outlierObslik: no visible global function definition for 'dunif'
outputModelParameters: no visible global function definition for
'write.table'
outputTitanResults: no visible global function definition for
'write.table'
outputTitanResults: no visible binding for global variable 'Chr'
outputTitanResults: no visible binding for global variable 'RefCount'
outputTitanResults: no visible binding for global variable 'NRefCount'
outputTitanResults: no visible binding for global variable 'Depth'
outputTitanResults: no visible binding for global variable
'AllelicRatio'
outputTitanResults: no visible binding for global variable 'LogRatio'
outputTitanResults: no visible binding for global variable 'CopyNumber'
outputTitanResults: no visible binding for global variable 'TITANstate'
outputTitanResults: no visible binding for global variable
'ClonalCluster'
outputTitanResults: no visible binding for global variable
'CellularPrevalence'
outputTitanSegments: no visible global function definition for
'write.table'
plotAllelicCN: no visible global function definition for 'par'
plotAllelicCN: no visible global function definition for 'plot'
plotAllelicCN: no visible global function definition for 'lines'
plotAllelicRatio: no visible global function definition for 'par'
plotAllelicRatio: no visible global function definition for 'plot'
plotAllelicRatio: no visible global function definition for 'lines'
plotCNlogRByChr: no visible global function definition for 'par'
plotCNlogRByChr: no visible global function definition for 'plot'
plotCNlogRByChr: no visible global function definition for 'lines'
plotCNlogRByChr : <anonymous>: no visible global function definition
for 'lines'
plotChrLines: no visible global function definition for 'lines'
plotChrLines: no visible global function definition for 'axis'
plotClonalFrequency: no visible global function definition for 'par'
plotClonalFrequency: no visible global function definition for 'plot'
plotClonalFrequency: no visible global function definition for 'lines'
plotClonalFrequency: no visible global function definition for 'mtext'
plotGeneAnnotation: no visible global function definition for 'abline'
plotGeneAnnotation: no visible global function definition for 'mtext'
plotSegmentMedians: no visible global function definition for 'par'
plotSegmentMedians: no visible global function definition for 'plot'
plotSegmentMedians : <anonymous>: no visible global function definition
for 'lines'
plotSegmentMedians: no visible global function definition for 'lines'
plotSubcloneProfiles: no visible global function definition for 'par'
plotSubcloneProfiles: no visible global function definition for 'plot'
plotSubcloneProfiles: no visible global function definition for 'axis'
plotSubcloneProfiles: no visible global function definition for
'points'
plotSubcloneProfiles: no visible global function definition for 'mtext'
plotSubcloneProfiles: no visible global function definition for 'lines'
printSDbw: no visible global function definition for 'write.table'
removeEmptyClusters: no visible global function definition for 'tail'
updateParameters: no visible global function definition for 'uniroot'
Undefined global functions or variables:
AllelicRatio CellularPrevalence Chr ClonalCluster CopyNumber Depth
LogRatio NRefCount RefCount TITANstate abline approxfun as axis dunif
lines loess lowess mtext par plot points predict queryHits read.delim
subjectHits tail uniroot write.table xtabs
Consider adding
importFrom("graphics", "abline", "axis", "lines", "mtext", "par",
"plot", "points")
importFrom("methods", "as")
importFrom("stats", "approxfun", "dunif", "loess", "lowess", "predict",
"uniroot", "xtabs")
importFrom("utils", "read.delim", "tail", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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-3.5-bioc/meat/TitanCNA.buildbin-libdir/TitanCNA/libs/i386/TitanCNA.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 the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
TitanCNA-package 27.83 0.40 28.23
runEMclonalCN 25.89 0.23 26.13
getPositionOverlap 9.76 0.11 9.88
filterData 9.35 0.20 9.55
correctReadDepth 9.26 0.14 9.40
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
TitanCNA-package 24.66 0.56 25.22
runEMclonalCN 20.36 0.15 20.52
filterData 11.22 0.08 11.29
getPositionOverlap 10.01 0.17 10.19
correctReadDepth 9.06 0.19 9.25
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/TitanCNA.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'TitanCNA' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c fwd_backC_clonalCN.c -o fwd_backC_clonalCN.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c getPositionOverlapC.c -o getPositionOverlapC.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c register.c -o register.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c viterbiC_clonalCN.c -o viterbiC_clonalCN.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o TitanCNA.dll tmp.def fwd_backC_clonalCN.o getPositionOverlapC.o register.o viterbiC_clonalCN.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/TitanCNA.buildbin-libdir/TitanCNA/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'TitanCNA' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c fwd_backC_clonalCN.c -o fwd_backC_clonalCN.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c getPositionOverlapC.c -o getPositionOverlapC.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c register.c -o register.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c viterbiC_clonalCN.c -o viterbiC_clonalCN.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o TitanCNA.dll tmp.def fwd_backC_clonalCN.o getPositionOverlapC.o register.o viterbiC_clonalCN.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/TitanCNA.buildbin-libdir/TitanCNA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TitanCNA' as TitanCNA_1.14.0.zip
* DONE (TitanCNA)