TitanCNA 1.13.1
Gavin Ha , Sohrab P Shah
| Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TitanCNA | | Last Changed Rev: 126021 / Revision: 127142 | | Last Changed Date: 2017-01-19 09:28:52 -0500 (Thu, 19 Jan 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TitanCNA_1.13.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/TitanCNA.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TitanCNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TitanCNA’ version ‘1.13.1’
* 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 ‘TitanCNA’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.4Mb
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
* 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 ... 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
TitanCNA-package 21.350 0.438 21.816
runEMclonalCN 15.899 0.406 16.319
filterData 11.005 0.407 11.417
correctReadDepth 9.115 0.237 9.354
getPositionOverlap 8.547 0.319 8.869
* 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
‘/Users/biocbuild/bbs-3.5-bioc/meat/TitanCNA.Rcheck/00check.log’
for details.
* installing *source* package ‘TitanCNA’ ...
** 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 fwd_backC_clonalCN.c -o fwd_backC_clonalCN.o
fwd_backC_clonalCN.c:257:21: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((iZS==jZS)){
˜˜˜^˜˜˜˜
fwd_backC_clonalCN.c:257:21: note: remove extraneous parentheses around the comparison to silence this warning
if ((iZS==jZS)){
˜ ^ ˜
fwd_backC_clonalCN.c:257:21: note: use '=' to turn this equality comparison into an assignment
if ((iZS==jZS)){
^˜
=
1 warning generated.
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 getPositionOverlapC.c -o getPositionOverlapC.o
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 register.c -o register.o
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 viterbiC_clonalCN.c -o viterbiC_clonalCN.o
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 TitanCNA.so fwd_backC_clonalCN.o getPositionOverlapC.o register.o viterbiC_clonalCN.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/TitanCNA.Rcheck/TitanCNA/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 (TitanCNA)