Mark Robinson
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/Repitools |
| Branch: RELEASE_3_7 |
| Last Commit: 0f94299 |
| Last Changed Date: 2018-04-30 10:35:19 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:35:28 -0400 (Wed, 17 Oct 2018).
| Package 1221/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Repitools 1.26.0 Mark Robinson
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: Repitools |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Repitools.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Repitools_1.26.0.tar.gz |
| StartedAt: 2018-10-17 04:21:27 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 04:37:29 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 961.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Repitools.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Repitools.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Repitools_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/Repitools.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Repitools/DESCRIPTION' ... OK
* this is package 'Repitools' version '1.26.0'
* 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 'Repitools' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpWYTpBQ/R.INSTALL15782c1657b/Repitools/man/BAM2GRanges.Rd:27: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/Repitools.Rcheck/00install.out' for details.
* checking installed package size ... OK
* 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
* 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.cpgBoxplots: no visible global function definition for 'pdf'
.cpgBoxplots: no visible global function definition for 'par'
.cpgBoxplots: no visible global function definition for 'dev.off'
.diracBetaDirac: no visible global function definition for 'dbeta'
.doBiasPlot: no visible global function definition for 'plot'
.doBiasPlot: no visible global function definition for 'lines'
.doBiasPlot: no visible global function definition for 'lowess'
.doChrPlot: no visible global function definition for 'plot'
.doChrPlot: no visible global function definition for 'points'
.doChrPlot: no visible global function definition for 'abline'
.drawSegs : <anonymous>: no visible global function definition for
'lines'
.makeClusters : clusterScores: no visible global function definition
for 'embed'
.makeClusters : clusterScores: no visible global function definition
for 'filter'
.methylEstbeta: no visible global function definition for 'qnorm'
.mydmarginal: no visible global function definition for 'dbeta'
.mydmarginalDBD: no visible global function definition for 'dbeta'
.plotFreqs: no visible global function definition for 'layout'
.plotFreqs : <anonymous>: no visible global function definition for
'matplot'
.plotFreqs : <anonymous>: no visible global function definition for
'abline'
.plotFreqs : <anonymous>: no visible global function definition for
'legend'
determineOffset: no visible global function definition for 'par'
determineOffset: no visible global function definition for 'grid'
determineOffset: no visible global function definition for 'abline'
determineOffset: no visible global function definition for 'text'
getSampleOffsets: no visible global function definition for 'grid'
getSampleOffsets: no visible global function definition for 'abline'
loadPairFile: no visible global function definition for 'read.table'
plotQdnaByCN: no visible global function definition for 'layout'
plotQdnaByCN: no visible global function definition for 'grid'
plotQdnaByCN: no visible global function definition for 'abline'
plotQdnaByCN: no visible global function definition for 'plot'
processNDF: no visible global function definition for 'read.table'
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
definition for 'nbrOfArrays'
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
definition for 'extract'
.blocksStats,AffymetrixCelSet-GRanges: no visible binding for global
variable 'verbose'
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
definition for 'getCdf'
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
definition for 'extractMatrix'
.blocksStats,GRangesList-GRanges: no visible global function definition
for 'p.adjust'
.blocksStats,matrix-GRanges: no visible global function definition for
't.test'
.blocksStats,matrix-GRanges: no visible global function definition for
'pt'
.blocksStats,matrix-GRanges: no visible global function definition for
'p.adjust'
.featureScores,AffymetrixCelSet-GRanges: no visible global function
definition for 'getCdf'
.featureScores,AffymetrixCelSet-GRanges: no visible binding for global
variable 'verbose'
.featureScores,AffymetrixCelSet-GRanges: no visible global function
definition for 'extractMatrix'
GCadjustCopy,GRanges-matrix-GCAdjustParams : <anonymous>: no visible
global function definition for 'lm'
GCadjustCopy,GRanges-matrix-GCAdjustParams : <anonymous>: no visible
global function definition for 'predict'
GCbiasPlots,AdjustedCopyEstimate: no visible global function definition
for 'par'
GCbiasPlots,AdjustedCopyEstimate : <anonymous>: no visible global
function definition for 'abline'
binPlots,ScoresList: no visible global function definition for 'par'
binPlots,ScoresList : <anonymous>: no visible global function
definition for 'layout'
binPlots,ScoresList : <anonymous>: no visible global function
definition for 'par'
binPlots,ScoresList : <anonymous>: no visible global function
definition for 'matplot'
binPlots,ScoresList : <anonymous>: no visible global function
definition for 'plot.new'
binPlots,ScoresList : <anonymous>: no visible global function
definition for 'legend'
binPlots,ScoresList : <anonymous>: no visible global function
definition for 'mtext'
binPlots,ScoresList : <anonymous>: no visible global function
definition for 'axis'
binPlots,ScoresList : <anonymous>: no visible global function
definition for 'plot'
binPlots,ScoresList : <anonymous>: no visible global function
definition for 'plot.window'
binPlots,ScoresList : <anonymous>: no visible global function
definition for 'text'
binPlots,ScoresList : <anonymous>: no visible global function
definition for 'title'
binPlots,ScoresList : <anonymous>: no visible global function
definition for 'persp'
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
definition for 'par'
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
definition for 'matplot'
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
definition for 'axis'
checkProbes,GRanges-GRanges : <anonymous> : <anonymous>: no visible
global function definition for 'matlines'
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
definition for 'plot'
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
definition for 'text'
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
definition for 'mtext'
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
definition for 'abline'
chromosomeCNplots,AdjustedCopyEstimate: no visible global function
definition for 'par'
chromosomeCNplots,CopyEstimate : <anonymous>: no visible global
function definition for 'str'
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
function definition for 'layout'
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
function definition for 'par'
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
function definition for 'plot.new'
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
function definition for 'legend'
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
function definition for 'matplot'
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
function definition for 'axis'
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
function definition for 'mtext'
clusterPlots,ClusteredScoresList: no visible global function definition
for 'par'
clusterPlots,ClusteredScoresList: no visible global function definition
for 'layout'
clusterPlots,ClusteredScoresList: no visible global function definition
for 'matplot'
clusterPlots,ClusteredScoresList: no visible global function definition
for 'axis'
clusterPlots,ClusteredScoresList: no visible global function definition
for 'mtext'
clusterPlots,ClusteredScoresList: no visible global function definition
for 'title'
clusterPlots,ClusteredScoresList: no visible global function definition
for 'plot.new'
clusterPlots,ClusteredScoresList: no visible global function definition
for 'plot.window'
clusterPlots,ClusteredScoresList: no visible global function definition
for 'text'
clusterPlots,ClusteredScoresList: no visible global function definition
for 'bxp'
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
function definition for 'rect'
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
function definition for 'abline'
clusterPlots,ClusteredScoresList: no visible global function definition
for 'plot'
clusterPlots,ScoresList: no visible global function definition for
'kmeans'
cpgBoxplots,AffymetrixCelSet: no visible binding for global variable
'Arguments'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
'pushState'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
'popState'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
'nbrOfArrays'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
'getCdf'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
'getMainCdf'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
'nbrOfUnits'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
'indexOf'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
'enter'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
'getCellIndices'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
'exit'
cpgBoxplots,AffymetrixCelSet: no visible binding for global variable
'AromaCellSequenceFile'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
'getChipType'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
'countBases'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
'extract'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
'getNames'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
'extractMatrix'
cpgBoxplots,AffymetrixCelSet: no visible binding for global variable
'AromaCellCpgFile'
cpgBoxplots,matrix: no visible binding for global variable 'Arguments'
cpgBoxplots,matrix: no visible global function definition for
'pushState'
cpgBoxplots,matrix: no visible global function definition for
'popState'
cpgBoxplots,matrix: no visible global function definition for 'enter'
cpgBoxplots,matrix: no visible global function definition for 'exit'
cpgDensityCalc,GRanges-BSgenome: no visible global function definition
for 'DNAString'
cpgDensityPlot,GRangesList: no visible global function definition for
'rainbow'
cpgDensityPlot,GRangesList: no visible global function definition for
'plot'
cpgDensityPlot,GRangesList: no visible global function definition for
'lines'
cpgDensityPlot,GRangesList: no visible global function definition for
'legend'
enrichmentPlot,GRangesList: no visible global function definition for
'rainbow'
enrichmentPlot,GRangesList: no visible global function definition for
'plot'
enrichmentPlot,GRangesList: no visible global function definition for
'lines'
enrichmentPlot,GRangesList: no visible global function definition for
'legend'
genQC,SequenceQCSet: no visible global function definition for
'matplot'
genQC,SequenceQCSet: no visible global function definition for 'legend'
genQC,SequenceQCSet: no visible global function definition for 'par'
genQC,SequenceQCSet: no visible global function definition for 'layout'
genQC,SequenceQCSet : <anonymous>: no visible global function
definition for 'par'
genQC,SequenceQCSet : <anonymous>: no visible global function
definition for 'matplot'
genQC,SequenceQCSet : <anonymous>: no visible global function
definition for 'abline'
genQC,SequenceQCSet : <anonymous>: no visible global function
definition for 'plot.new'
genQC,SequenceQCSet : <anonymous>: no visible global function
definition for 'legend'
genQC,SequenceQCSet : <anonymous>: no visible global function
definition for 'barplot'
genQC,SequenceQCSet : <anonymous>: no visible global function
definition for 'axis'
getProbePositionsDf,AffymetrixCdfFile: no visible global function
definition for 'getCellIndices'
getProbePositionsDf,AffymetrixCdfFile: no visible binding for global
variable 'AromaCellPositionFile'
getProbePositionsDf,AffymetrixCdfFile: no visible global function
definition for 'getChipType'
plotClusters,GRanges : <anonymous>: no visible global function
definition for 'par'
plotClusters,GRanges : <anonymous>: no visible global function
definition for 'plot'
plotClusters,GRanges : <anonymous>: no visible global function
definition for 'title'
plotClusters,GRanges : <anonymous>: no visible global function
definition for 'mtext'
plotClusters,GRanges : <anonymous>: no visible global function
definition for 'axis'
profilePlots,ScoresList: no visible global function definition for
'rainbow'
profilePlots,ScoresList : <anonymous>: no visible global function
definition for 'matplot'
profilePlots,ScoresList : <anonymous>: no visible global function
definition for 'polygon'
profilePlots,ScoresList : <anonymous>: no visible global function
definition for 'legend'
regionStats,AffymetrixCelSet: no visible global function definition for
'getCdf'
regionStats,AffymetrixCelSet: no visible global function definition for
'getCellIndices'
regionStats,AffymetrixCelSet: no visible global function definition for
'nbrOfArrays'
regionStats,AffymetrixCelSet: no visible binding for global variable
'AromaCellPositionFile'
regionStats,AffymetrixCelSet: no visible global function definition for
'getChipType'
regionStats,AffymetrixCelSet: no visible global function definition for
'extract'
regionStats,AffymetrixCelSet: no visible global function definition for
'extractMatrix'
sequenceCalc,GRanges-BSgenome : <anonymous>: no visible global function
definition for 'matchPattern'
writeWig,AffymetrixCelSet: no visible global function definition for
'getNames'
writeWig,AffymetrixCelSet: no visible global function definition for
'extract'
writeWig,AffymetrixCelSet: no visible global function definition for
'getCdf'
writeWig,AffymetrixCelSet: no visible global function definition for
'extractMatrix'
Undefined global functions or variables:
Arguments AromaCellCpgFile AromaCellPositionFile
AromaCellSequenceFile DNAString abline axis barplot bxp countBases
dbeta dev.off embed enter exit extract extractMatrix filter getCdf
getCellIndices getChipType getMainCdf getNames grid indexOf kmeans
layout legend lines lm lowess matchPattern matlines matplot mtext
nbrOfArrays nbrOfUnits p.adjust par pdf persp plot plot.new
plot.window points polygon popState predict pt pushState qnorm
rainbow read.table rect str t.test text title verbose
Consider adding
importFrom("grDevices", "dev.off", "pdf", "rainbow")
importFrom("graphics", "abline", "axis", "barplot", "bxp", "grid",
"layout", "legend", "lines", "matlines", "matplot", "mtext",
"par", "persp", "plot", "plot.new", "plot.window", "points",
"polygon", "rect", "text", "title")
importFrom("stats", "dbeta", "embed", "filter", "kmeans", "lm",
"lowess", "p.adjust", "predict", "pt", "qnorm", "t.test")
importFrom("utils", "read.table", "str")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
methylEst 98.93 1.31 100.25
empBayes 37.53 2.89 40.42
BayMethList-class 9.91 1.48 11.39
sequenceCalc 10.39 0.63 11.05
cpgDensityCalc 9.89 0.58 10.47
determineOffset 6.32 0.47 6.80
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
methylEst 63.60 0.25 63.84
empBayes 33.42 1.81 35.23
cpgDensityCalc 11.44 0.93 12.37
sequenceCalc 9.50 0.60 10.09
BayMethList-class 9.09 0.37 9.47
determineOffset 7.42 0.57 8.00
maskOut 5.08 0.13 5.21
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'tests.R'
OK
** running tests for arch 'x64' ...
Running 'tests.R'
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: 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/Repitools.Rcheck/00check.log'
for details.
Repitools.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/Repitools_1.26.0.tar.gz && rm -rf Repitools.buildbin-libdir && mkdir Repitools.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Repitools.buildbin-libdir Repitools_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL Repitools_1.26.0.zip && rm Repitools_1.26.0.tar.gz Repitools_1.26.0.zip
###
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% 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 1420k 100 1420k 0 0 16.5M 0 --:--:-- --:--:-- --:--:-- 18.2M
install for i386
* installing *source* package 'Repitools' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D R_NO_REMAP -I. -O3 -Wall -std=gnu99 -mtune=generic -c const.c -o const.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D R_NO_REMAP -I. -O3 -Wall -std=gnu99 -mtune=generic -c hyp2f1.c -o hyp2f1.o
In file included from hyp2f1.c:81:0:
./mconf.h:100:0: warning: "DOMAIN" redefined
#define DOMAIN 1 /* argument domain error */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:29:0: note: this is the location of the previous definition
#define DOMAIN _DOMAIN
^
In file included from hyp2f1.c:81:0:
./mconf.h:101:0: warning: "SING" redefined
#define SING 2 /* argument singularity */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:30:0: note: this is the location of the previous definition
#define SING _SING
^
In file included from hyp2f1.c:81:0:
./mconf.h:102:0: warning: "OVERFLOW" redefined
#define OVERFLOW 3 /* overflow range error */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:31:0: note: this is the location of the previous definition
#define OVERFLOW _OVERFLOW
^
In file included from hyp2f1.c:81:0:
./mconf.h:103:0: warning: "UNDERFLOW" redefined
#define UNDERFLOW 4 /* underflow range error */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:32:0: note: this is the location of the previous definition
#define UNDERFLOW _UNDERFLOW
^
In file included from hyp2f1.c:81:0:
./mconf.h:104:0: warning: "TLOSS" redefined
#define TLOSS 5 /* total loss of precision */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:33:0: note: this is the location of the previous definition
#define TLOSS _TLOSS
^
In file included from hyp2f1.c:81:0:
./mconf.h:105:0: warning: "PLOSS" redefined
#define PLOSS 6 /* partial loss of precision */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:34:0: note: this is the location of the previous definition
#define PLOSS _PLOSS
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D R_NO_REMAP -I. -O3 -Wall -std=gnu99 -mtune=generic -c mtherr.c -o mtherr.o
In file included from mtherr.c:58:0:
./mconf.h:100:0: warning: "DOMAIN" redefined
#define DOMAIN 1 /* argument domain error */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:29:0: note: this is the location of the previous definition
#define DOMAIN _DOMAIN
^
In file included from mtherr.c:58:0:
./mconf.h:101:0: warning: "SING" redefined
#define SING 2 /* argument singularity */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:30:0: note: this is the location of the previous definition
#define SING _SING
^
In file included from mtherr.c:58:0:
./mconf.h:102:0: warning: "OVERFLOW" redefined
#define OVERFLOW 3 /* overflow range error */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:31:0: note: this is the location of the previous definition
#define OVERFLOW _OVERFLOW
^
In file included from mtherr.c:58:0:
./mconf.h:103:0: warning: "UNDERFLOW" redefined
#define UNDERFLOW 4 /* underflow range error */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:32:0: note: this is the location of the previous definition
#define UNDERFLOW _UNDERFLOW
^
In file included from mtherr.c:58:0:
./mconf.h:104:0: warning: "TLOSS" redefined
#define TLOSS 5 /* total loss of precision */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:33:0: note: this is the location of the previous definition
#define TLOSS _TLOSS
^
In file included from mtherr.c:58:0:
./mconf.h:105:0: warning: "PLOSS" redefined
#define PLOSS 6 /* partial loss of precision */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:34:0: note: this is the location of the previous definition
#define PLOSS _PLOSS
^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o Repitools.dll tmp.def const.o hyp2f1.o mtherr.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/Repitools.buildbin-libdir/Repitools/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Repitools'
finding HTML links ... done
AdjustedCopyEstimate-class html
finding level-2 HTML links ... done
AffymetrixCdfFile-class html
AffymetrixCelSet-class html
BAM2GRanges html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpWYTpBQ/R.INSTALL15782c1657b/Repitools/man/BAM2GRanges.Rd:27: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
BayMethList-class html
ChromaBlocks html
ChromaResults-class html
ClusteredScoresList-class html
CopyEstimate-class html
FastQC-class html
GCAdjustParams-class html
GCadjustCopy html
GCbiasPlots html
MappabilitySource-class html
QdnaData html
ScoresList-class html
abcdDNA html
absoluteCN html
annoDF2GR html
annoGR2DF html
annotationBlocksCounts html
annotationBlocksLookup html
annotationCounts html
annotationLookup html
binPlots html
blocksStats html
checkProbes html
chr21genes html
chromosomeCNplots html
clusterPlots html
cpgBoxPlots html
cpgDensityCalc html
cpgDensityPlot html
determineOffset html
empBayes html
enrichmentCalc html
enrichmentPlot html
expr html
featureBlocks html
featureScores html
findClusters html
gcContentCalc html
genQC html
genomeBlocks html
getProbePositionsDf html
getSampleOffsets html
hcRegions html
hyper html
loadPairFile html
loadSampleDirectory html
makeWindowLookupTable html
mappabilityCalc html
maskOut html
mergeReplicates html
methylEst html
multiHeatmap html
plotClusters html
plotQdnaByCN html
processNDF html
profilePlots html
regionStats html
relativeCN html
samplesList html
sequenceCalc html
setCNVOffsets html
summarizeScores html
writeWig html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'Repitools' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D R_NO_REMAP -I. -O2 -Wall -std=gnu99 -mtune=generic -c const.c -o const.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D R_NO_REMAP -I. -O2 -Wall -std=gnu99 -mtune=generic -c hyp2f1.c -o hyp2f1.o
In file included from hyp2f1.c:81:0:
./mconf.h:100:0: warning: "DOMAIN" redefined
#define DOMAIN 1 /* argument domain error */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:29:0: note: this is the location of the previous definition
#define DOMAIN _DOMAIN
^
In file included from hyp2f1.c:81:0:
./mconf.h:101:0: warning: "SING" redefined
#define SING 2 /* argument singularity */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:30:0: note: this is the location of the previous definition
#define SING _SING
^
In file included from hyp2f1.c:81:0:
./mconf.h:102:0: warning: "OVERFLOW" redefined
#define OVERFLOW 3 /* overflow range error */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:31:0: note: this is the location of the previous definition
#define OVERFLOW _OVERFLOW
^
In file included from hyp2f1.c:81:0:
./mconf.h:103:0: warning: "UNDERFLOW" redefined
#define UNDERFLOW 4 /* underflow range error */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:32:0: note: this is the location of the previous definition
#define UNDERFLOW _UNDERFLOW
^
In file included from hyp2f1.c:81:0:
./mconf.h:104:0: warning: "TLOSS" redefined
#define TLOSS 5 /* total loss of precision */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:33:0: note: this is the location of the previous definition
#define TLOSS _TLOSS
^
In file included from hyp2f1.c:81:0:
./mconf.h:105:0: warning: "PLOSS" redefined
#define PLOSS 6 /* partial loss of precision */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0,
from hyp2f1.c:80:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:34:0: note: this is the location of the previous definition
#define PLOSS _PLOSS
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D R_NO_REMAP -I. -O2 -Wall -std=gnu99 -mtune=generic -c mtherr.c -o mtherr.o
In file included from mtherr.c:58:0:
./mconf.h:100:0: warning: "DOMAIN" redefined
#define DOMAIN 1 /* argument domain error */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:29:0: note: this is the location of the previous definition
#define DOMAIN _DOMAIN
^
In file included from mtherr.c:58:0:
./mconf.h:101:0: warning: "SING" redefined
#define SING 2 /* argument singularity */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:30:0: note: this is the location of the previous definition
#define SING _SING
^
In file included from mtherr.c:58:0:
./mconf.h:102:0: warning: "OVERFLOW" redefined
#define OVERFLOW 3 /* overflow range error */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:31:0: note: this is the location of the previous definition
#define OVERFLOW _OVERFLOW
^
In file included from mtherr.c:58:0:
./mconf.h:103:0: warning: "UNDERFLOW" redefined
#define UNDERFLOW 4 /* underflow range error */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:32:0: note: this is the location of the previous definition
#define UNDERFLOW _UNDERFLOW
^
In file included from mtherr.c:58:0:
./mconf.h:104:0: warning: "TLOSS" redefined
#define TLOSS 5 /* total loss of precision */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:33:0: note: this is the location of the previous definition
#define TLOSS _TLOSS
^
In file included from mtherr.c:58:0:
./mconf.h:105:0: warning: "PLOSS" redefined
#define PLOSS 6 /* partial loss of precision */
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0,
from mtherr.c:56:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:34:0: note: this is the location of the previous definition
#define PLOSS _PLOSS
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o Repitools.dll tmp.def const.o hyp2f1.o mtherr.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/Repitools.buildbin-libdir/Repitools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Repitools' as Repitools_1.26.0.zip
* DONE (Repitools)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'Repitools' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
Repitools.Rcheck/tests_i386/tests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("Repitools")
Loading required package: Repitools
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
> require("BSgenome.Hsapiens.UCSC.hg18")
Loading required package: BSgenome.Hsapiens.UCSC.hg18
Loading required package: BSgenome
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
Attaching package: 'rtracklayer'
The following object is masked from 'package:Repitools':
blocks
> options(warn = -1)
>
> probes <- data.frame(chr = c("chr1", "chr9", "chrY", "chr1", "chr21", "chr6", "chr6", "chr2", "chrX", "chr11"), position = c(10000, 5500, 100000, 11000, 20000000, 500100, 499900, 700000, 9900, 90000), strand = c('+', '+', '+', '+', '-', '-', '-', '+', '-', '+'), stringsAsFactors = FALSE)
> genes <- data.frame(chr = c("chr1", "chr9", "chr11", "chr1", "chr11", "chr6", "chr6", "chr22", "chrY", "chr21"), start = c(10000, 7900, 950000, 10500, 74000000, 450000, 5000000, 44000000, 1500, 9800000), end = c(12500, 9500, 1000000, 14500, 75000000, 500000, 9000000, 45000000, 3000, 10000000), strand = c('+', '-', '-', '+', '-', '-', '-', '+', '+', '-'), name = paste("Gene", 1:10), stringsAsFactors = FALSE)
>
> crossMatch <- annotationLookup(probes, genes, 5000, 5000)
Processing mapping between probes and features.
Mapping done.
> correctCrossMatch <- list(indexes = list(`Gene 1` = as.integer(c(1, 4)), `Gene 2` = as.integer(2), `Gene 3` = integer(), `Gene 4` = as.integer(c(1, 4)), `Gene 5` = integer(), `Gene 6` = as.integer(c(6, 7)), `Gene 7` = integer(), `Gene 8` = integer(), `Gene 9` = integer(), `Gene 10` = integer()), offsets = list(`Gene 1` = as.integer(c(0, 1000)), `Gene 2` = as.integer(4000), `Gene 3` = numeric(), `Gene 4` = as.integer(c(-500, 500)), `Gene 5` = numeric(), `Gene 6` = as.integer(c(-100, 100)), `Gene 7` = numeric(), `Gene 8` = numeric(), `Gene 9` = numeric(), `Gene 10` = numeric()))
> names(correctCrossMatch$offsets$`Gene 1`) <- c(1, 4)
> names(correctCrossMatch$offsets$`Gene 2`) <- c(2)
> names(correctCrossMatch$offsets$`Gene 4`) <- c(1, 4)
> names(correctCrossMatch$offsets$`Gene 6`) <- c(6, 7)
> names(correctCrossMatch$offsets$`Gene 8`) <- character()
> names(correctCrossMatch$offsets$`Gene 9`) <- character()
>
> if(!isTRUE(all.equal(crossMatch, correctCrossMatch)))
+ stop("Error in annotationLookup function.")
> cat("anontationLookup tested fine.\n")
anontationLookup tested fine.
>
> lookupTable <- makeWindowLookupTable(crossMatch$indexes, crossMatch$offsets, starts = seq(-5000, 4900, 100), ends = seq(-4900, 5000, 100))
> correctLookupTable <- matrix(NA, nrow = 10, ncol = 100, dimnames = list(genes$names, seq(-4950, 4950, 100)))
> correctLookupTable[1, c(50, 51)] <- 1
> correctLookupTable[1, c(60, 61)] <- 4
> correctLookupTable[2, c(90, 91)] <- 2
> correctLookupTable[4, c(45, 46)] <- 1
> correctLookupTable[4, c(55, 56)] <- 4
> correctLookupTable[6, c(49, 50)] <- 6
> correctLookupTable[6, c(51, 52)] <- 7
>
> if(!all(lookupTable == correctLookupTable, na.rm = TRUE))
+ stop("Error in makeWindowLookupTable function")
> cat("makeWindowLookupTable tested fine.\n")
makeWindowLookupTable tested fine.
>
> cpgDensity <- cpgDensityCalc(genes, organism = Hsapiens, window = 500, w.function="linear")
CpG density calculated for a sample.
> if(!isTRUE(all.equal(cpgDensity, c(5.784, 7.620, 5.828, 2.928, 2.080, 1.252, 0.000, 7.404, 3.928, 0.000))))
+ stop("cpgDensityCalc not working for window = 500, scaling = linear")
> cpgDensity <- cpgDensityCalc(genes, window = 100, w.function = "log", organism = Hsapiens)
CpG density calculated for a sample.
> if(!isTRUE(all.equal(round(cpgDensity, 3), c(2.424, 1.882, 1.436, 0.084, 0.379, 0.000, 0.000, 0.263, 1.392, 0.000))))
+ stop("cpgDensityCalc not working for window = 100, scaling = log")
> cpgDensity <- cpgDensityCalc(genes, window = 1000, w.function = "exp", organism = Hsapiens)
CpG density calculated for a sample.
> if(!isTRUE(all.equal(round(cpgDensity, 3), c(4.874, 5.835, 4.999, 2.239, 1.567, 0.851, 0.054, 5.589, 3.229,0.062))))
+ stop("cpgDensityCalc not working for window = 1000, scaling = exp")
> cpgDensity <- cpgDensityCalc(genes, window = 500, w.function = "none", organism = Hsapiens)
CpG density calculated for a sample.
> if(!isTRUE(all.equal(cpgDensity, c(11, 14, 16, 6, 4, 2, 0, 15, 9, 0))))
+ stop("cpgDensityCalc not working for window = 500, scaling = none")
> cat("cpgDensityCalc tested fine.\n")
cpgDensityCalc tested fine.
>
> GCpercent <- gcContentCalc(genes, Hsapiens, 500)
Calculating GC content.
> if(!isTRUE(all.equal(GCpercent, c(0.504, 0.586, 0.560, 0.470, 0.540, 0.304, 0.356, 0.638, 0.444, 0.388))))
+ stop("Error in gcContentCalc function")
> cat("gcContentCalc tested fine.\n")
gcContentCalc tested fine.
>
> findsCount <- sequenceCalc(genes, Hsapiens, 500, pattern = "AATT")
> if(!isTRUE(all.equal(findsCount, c(1, 1, 0, 2, 1, 8, 2, 0, 4, 10))))
+ stop("Error in sequenceCalc function counting task")
>
> findsPlaces <- sequenceCalc(genes, Hsapiens, 500, pattern = "AATT", positions = TRUE)
> correctPlaces <- list(-62, 181, NULL, c(-140, -98), 231, c(-219, -146, -88, -12, 12, 182, 209, 214), c(-61, 60), NULL, c(-115, -30, 11, 80), c(-238, -228, -202, -189, -177, -106, -21, 148, 158, 238))
> if(!isTRUE(all.equal(findsPlaces, correctPlaces)))
+ stop("Error in sequenceCalc function positions task")
> cat("sequenceCalc tested fine.\n")
sequenceCalc tested fine.
> cat("All tests passed.\n")
All tests passed.
>
> proc.time()
user system elapsed
106.37 9.18 116.07
|
Repitools.Rcheck/tests_x64/tests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("Repitools")
Loading required package: Repitools
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
> require("BSgenome.Hsapiens.UCSC.hg18")
Loading required package: BSgenome.Hsapiens.UCSC.hg18
Loading required package: BSgenome
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
Attaching package: 'rtracklayer'
The following object is masked from 'package:Repitools':
blocks
> options(warn = -1)
>
> probes <- data.frame(chr = c("chr1", "chr9", "chrY", "chr1", "chr21", "chr6", "chr6", "chr2", "chrX", "chr11"), position = c(10000, 5500, 100000, 11000, 20000000, 500100, 499900, 700000, 9900, 90000), strand = c('+', '+', '+', '+', '-', '-', '-', '+', '-', '+'), stringsAsFactors = FALSE)
> genes <- data.frame(chr = c("chr1", "chr9", "chr11", "chr1", "chr11", "chr6", "chr6", "chr22", "chrY", "chr21"), start = c(10000, 7900, 950000, 10500, 74000000, 450000, 5000000, 44000000, 1500, 9800000), end = c(12500, 9500, 1000000, 14500, 75000000, 500000, 9000000, 45000000, 3000, 10000000), strand = c('+', '-', '-', '+', '-', '-', '-', '+', '+', '-'), name = paste("Gene", 1:10), stringsAsFactors = FALSE)
>
> crossMatch <- annotationLookup(probes, genes, 5000, 5000)
Processing mapping between probes and features.
Mapping done.
> correctCrossMatch <- list(indexes = list(`Gene 1` = as.integer(c(1, 4)), `Gene 2` = as.integer(2), `Gene 3` = integer(), `Gene 4` = as.integer(c(1, 4)), `Gene 5` = integer(), `Gene 6` = as.integer(c(6, 7)), `Gene 7` = integer(), `Gene 8` = integer(), `Gene 9` = integer(), `Gene 10` = integer()), offsets = list(`Gene 1` = as.integer(c(0, 1000)), `Gene 2` = as.integer(4000), `Gene 3` = numeric(), `Gene 4` = as.integer(c(-500, 500)), `Gene 5` = numeric(), `Gene 6` = as.integer(c(-100, 100)), `Gene 7` = numeric(), `Gene 8` = numeric(), `Gene 9` = numeric(), `Gene 10` = numeric()))
> names(correctCrossMatch$offsets$`Gene 1`) <- c(1, 4)
> names(correctCrossMatch$offsets$`Gene 2`) <- c(2)
> names(correctCrossMatch$offsets$`Gene 4`) <- c(1, 4)
> names(correctCrossMatch$offsets$`Gene 6`) <- c(6, 7)
> names(correctCrossMatch$offsets$`Gene 8`) <- character()
> names(correctCrossMatch$offsets$`Gene 9`) <- character()
>
> if(!isTRUE(all.equal(crossMatch, correctCrossMatch)))
+ stop("Error in annotationLookup function.")
> cat("anontationLookup tested fine.\n")
anontationLookup tested fine.
>
> lookupTable <- makeWindowLookupTable(crossMatch$indexes, crossMatch$offsets, starts = seq(-5000, 4900, 100), ends = seq(-4900, 5000, 100))
> correctLookupTable <- matrix(NA, nrow = 10, ncol = 100, dimnames = list(genes$names, seq(-4950, 4950, 100)))
> correctLookupTable[1, c(50, 51)] <- 1
> correctLookupTable[1, c(60, 61)] <- 4
> correctLookupTable[2, c(90, 91)] <- 2
> correctLookupTable[4, c(45, 46)] <- 1
> correctLookupTable[4, c(55, 56)] <- 4
> correctLookupTable[6, c(49, 50)] <- 6
> correctLookupTable[6, c(51, 52)] <- 7
>
> if(!all(lookupTable == correctLookupTable, na.rm = TRUE))
+ stop("Error in makeWindowLookupTable function")
> cat("makeWindowLookupTable tested fine.\n")
makeWindowLookupTable tested fine.
>
> cpgDensity <- cpgDensityCalc(genes, organism = Hsapiens, window = 500, w.function="linear")
CpG density calculated for a sample.
> if(!isTRUE(all.equal(cpgDensity, c(5.784, 7.620, 5.828, 2.928, 2.080, 1.252, 0.000, 7.404, 3.928, 0.000))))
+ stop("cpgDensityCalc not working for window = 500, scaling = linear")
> cpgDensity <- cpgDensityCalc(genes, window = 100, w.function = "log", organism = Hsapiens)
CpG density calculated for a sample.
> if(!isTRUE(all.equal(round(cpgDensity, 3), c(2.424, 1.882, 1.436, 0.084, 0.379, 0.000, 0.000, 0.263, 1.392, 0.000))))
+ stop("cpgDensityCalc not working for window = 100, scaling = log")
> cpgDensity <- cpgDensityCalc(genes, window = 1000, w.function = "exp", organism = Hsapiens)
CpG density calculated for a sample.
> if(!isTRUE(all.equal(round(cpgDensity, 3), c(4.874, 5.835, 4.999, 2.239, 1.567, 0.851, 0.054, 5.589, 3.229,0.062))))
+ stop("cpgDensityCalc not working for window = 1000, scaling = exp")
> cpgDensity <- cpgDensityCalc(genes, window = 500, w.function = "none", organism = Hsapiens)
CpG density calculated for a sample.
> if(!isTRUE(all.equal(cpgDensity, c(11, 14, 16, 6, 4, 2, 0, 15, 9, 0))))
+ stop("cpgDensityCalc not working for window = 500, scaling = none")
> cat("cpgDensityCalc tested fine.\n")
cpgDensityCalc tested fine.
>
> GCpercent <- gcContentCalc(genes, Hsapiens, 500)
Calculating GC content.
> if(!isTRUE(all.equal(GCpercent, c(0.504, 0.586, 0.560, 0.470, 0.540, 0.304, 0.356, 0.638, 0.444, 0.388))))
+ stop("Error in gcContentCalc function")
> cat("gcContentCalc tested fine.\n")
gcContentCalc tested fine.
>
> findsCount <- sequenceCalc(genes, Hsapiens, 500, pattern = "AATT")
> if(!isTRUE(all.equal(findsCount, c(1, 1, 0, 2, 1, 8, 2, 0, 4, 10))))
+ stop("Error in sequenceCalc function counting task")
>
> findsPlaces <- sequenceCalc(genes, Hsapiens, 500, pattern = "AATT", positions = TRUE)
> correctPlaces <- list(-62, 181, NULL, c(-140, -98), 231, c(-219, -146, -88, -12, 12, 182, 209, 214), c(-61, 60), NULL, c(-115, -30, 11, 80), c(-238, -228, -202, -189, -177, -106, -21, 148, 158, 238))
> if(!isTRUE(all.equal(findsPlaces, correctPlaces)))
+ stop("Error in sequenceCalc function positions task")
> cat("sequenceCalc tested fine.\n")
sequenceCalc tested fine.
> cat("All tests passed.\n")
All tests passed.
>
> proc.time()
user system elapsed
98.40 8.42 107.06
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Repitools.Rcheck/examples_i386/Repitools-Ex.timings
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Repitools.Rcheck/examples_x64/Repitools-Ex.timings
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