CHECK report for cn.farms on tokay2
This page was generated on 2019-04-09 11:59:09 -0400 (Tue, 09 Apr 2019).
cn.farms 1.31.0
Andreas Mitterecker
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/cn.farms |
| Branch: master |
| Last Commit: 1797438 |
| Last Changed Date: 2018-10-30 11:54:29 -0400 (Tue, 30 Oct 2018) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
Summary
Command output
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cn.farms.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings cn.farms_1.31.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/cn.farms.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cn.farms/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cn.farms' version '1.31.0'
* 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 'cn.farms' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/cn.farms.Rd:16: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/combineData.Rd:10: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/combineData.Rd:13: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/combineData.Rd:29: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/dnaCopySf.Rd:22: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/fragLengCorr.Rd:10: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/fragLengCorr.Rd:20: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/mlSummarization.Rd:10: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/mlSummarization.Rd:36: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/normalizeNone.Rd:29: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/normalizeNpData.Rd:25: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/normalizeSequenceEffect.Rd:11: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/normalizeSor.Rd:29: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/plotEvalIc.Rd:12: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/plotRegions.Rd:10: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/plotRegions.Rd:12: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/plotSmoothScatter.Rd:9: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/plotViolines.Rd:10: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/slSummarization.Rd:12: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/slSummarization.Rd:35: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/cn.farms.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
calcDistance: no visible global function definition for 'density'
callSummarizeH01: no visible binding for global variable 'var'
callSummarizeH01: no visible global function definition for 'rnorm'
createAnnotation: no visible global function definition for
'installed.packages'
determineBaselineArray: no visible binding for global variable 'median'
flcSnp6Std: no visible global function definition for 'lowess'
flcSnp6Std: no visible global function definition for 'approx'
flcSnp6StdH01: no visible global function definition for 'lowess'
flcSnp6StdH01: no visible global function definition for 'approx'
flcStd: no visible global function definition for 'lowess'
flcStd: no visible global function definition for 'approx'
flcStdH01: no visible global function definition for 'lowess'
flcStdH01: no visible global function definition for 'approx'
getProbePositionEffectDesignMatrix: no visible global function
definition for 'head'
getVar: no visible global function definition for 'getFromNamespace'
initializeBigMatrix: no visible global function definition for
'isPackageLoaded'
normalizeAverage: no visible binding for global variable 'median'
normalizeAverage: no visible global function definition for 'median'
normalizeSorH01: no visible binding for global variable 'pairs'
normalizeSorH01: no visible global function definition for 'median'
plotDendrogram : colLab: no visible global function definition for
'is.leaf'
plotDendrogram: no visible global function definition for
'as.dendrogram'
plotDendrogram: no visible global function definition for 'hclust'
plotDendrogram: no visible global function definition for
'order.dendrogram'
plotDendrogram: no visible global function definition for 'dendrapply'
plotDendrogram: no visible global function definition for 'plot'
plotDensity: no visible global function definition for 'density'
plotDensity: no visible global function definition for 'plot'
plotDensity: no visible global function definition for 'lines'
plotEvalIc: no visible global function definition for 'rgb'
plotEvalIc: no visible global function definition for 'plot'
plotEvalIc: no visible global function definition for 'rect'
plotEvalIc: no visible global function definition for 'points'
plotEvalIc: no visible global function definition for 'densCols'
plotEvalIc: no visible global function definition for 'mtext'
plotRegions: no visible global function definition for 'pdf'
plotRegions: no visible global function definition for 'plot'
plotRegions: no visible global function definition for 'text'
plotRegions: no visible global function definition for 'par'
plotRegions: no visible global function definition for 'matplot'
plotRegions: no visible global function definition for 'abline'
plotRegions: no visible global function definition for 'matlines'
plotRegions: no visible global function definition for 'legend'
plotRegions: no visible global function definition for 'axis'
plotRegions: no visible global function definition for 'nclass.Sturges'
plotRegions: no visible global function definition for 'dev.off'
plotSmoothScatter: no visible global function definition for 'pdf'
plotSmoothScatter: no visible global function definition for
'smoothScatter'
plotSmoothScatter: no visible global function definition for 'abline'
plotSmoothScatter: no visible global function definition for 'loess'
plotSmoothScatter: no visible global function definition for 'points'
plotSmoothScatter: no visible global function definition for 'dev.off'
setVar: no visible global function definition for 'assignInNamespace'
sfClusterSetupSPRNG: no visible global function definition for 'runif'
sfExport: no visible global function definition for 'getFromNamespace'
sfExportAll: no visible global function definition for 'na.omit'
sfInit: no visible global function definition for 'packageDescription'
sfTest : testCalc1: no visible global function definition for 'runif'
sfTest : testCalc2: no visible global function definition for 'runif'
summarizeFarmsExact: no visible global function definition for 'median'
summarizeFarmsExact: no visible binding for global variable 'median'
summarizeFarmsExact: no visible global function definition for 'pchisq'
summarizeFarmsExact2: no visible global function definition for
'median'
summarizeFarmsExact2: no visible binding for global variable 'median'
summarizeFarmsExact2: no visible global function definition for
'pchisq'
summarizeFarmsExact3: no visible global function definition for
'median'
summarizeFarmsExact3: no visible binding for global variable 'median'
summarizeFarmsExact3: no visible global function definition for
'pchisq'
summarizeFarmsGaussian: no visible global function definition for
'median'
summarizeFarmsGaussian: no visible binding for global variable 'median'
summarizeFarmsGaussian: no visible global function definition for 'var'
summarizeFarmsStatistics: no visible binding for global variable
'median'
summarizeFarmsStatistics: no visible global function definition for
'median'
summarizeFarmsVariational: no visible binding for global variable
'median'
summarizeFarmsVariational: no visible global function definition for
'sd'
summarizeFarmsVariational: no visible global function definition for
'median'
summarizeFarmsVariational: no visible global function definition for
'var'
Undefined global functions or variables:
abline approx as.dendrogram assignInNamespace axis dendrapply
densCols density dev.off getFromNamespace hclust head
installed.packages is.leaf isPackageLoaded legend lines loess lowess
matlines matplot median mtext na.omit nclass.Sturges order.dendrogram
packageDescription pairs par pchisq pdf plot points rect rgb rnorm
runif sd smoothScatter text var
Consider adding
importFrom("grDevices", "densCols", "dev.off", "nclass.Sturges", "pdf",
"rgb")
importFrom("graphics", "abline", "axis", "legend", "lines", "matlines",
"matplot", "mtext", "pairs", "par", "plot", "points",
"rect", "smoothScatter", "text")
importFrom("stats", "approx", "as.dendrogram", "dendrapply", "density",
"hclust", "is.leaf", "loess", "lowess", "median", "na.omit",
"order.dendrogram", "pchisq", "rnorm", "runif", "sd", "var")
importFrom("utils", "assignInNamespace", "getFromNamespace", "head",
"installed.packages", "packageDescription")
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 R/sysdata.rda ... 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/cn.farms/libs/i386/cn.farms.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/cn.farms/libs/x64/cn.farms.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
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: 1 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/cn.farms.Rcheck/00check.log'
for details.
Installation output
cn.farms.Rcheck/00install.out
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### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/cn.farms_1.31.0.tar.gz && rm -rf cn.farms.buildbin-libdir && mkdir cn.farms.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cn.farms.buildbin-libdir cn.farms_1.31.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL cn.farms_1.31.0.zip && rm cn.farms_1.31.0.tar.gz cn.farms_1.31.0.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 2058k 100 2058k 0 0 26.2M 0 --:--:-- --:--:-- --:--:-- 28.7M
install for i386
* installing *source* package 'cn.farms' ...
** 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 R_init_cnfarms.c -o R_init_cnfarms.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c laplace.cpp -o laplace.o
laplace.cpp: In function 'SEXPREC* momentsGauss(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
laplace.cpp:442:6: warning: unused variable 'method' [-Wunused-variable]
int method=0;
^
laplace.cpp: In function 'void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)':
laplace.cpp:368:56: warning: 'I1right' may be used uninitialized in this function [-Wmaybe-uninitialized]
double rightMoment1=1.0*rightMy*I0right+1.0*rightSigma*I1right;
^
laplace.cpp:393:86: warning: 'I1left' may be used uninitialized in this function [-Wmaybe-uninitialized]
moment2 = (-0.5*a+0.25*(b-1/sigmaZ)*(b-1/sigmaZ)+(b*leftWeight)/(sigmaZ)+(leftWeight*I1left*sqrtMa)/(sqrt(2.0)*sigmaZ))/(a*a);
^
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 sparse_farms.c -o sparse_farms.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o cn.farms.dll tmp.def R_init_cnfarms.o laplace.o sparse_farms.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/cn.farms.buildbin-libdir/00LOCK-cn.farms/00new/cn.farms/libs/i386
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'cn.farms'
finding HTML links ... done
callSummarize html
cn.farms html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/cn.farms.Rd:16: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
cnLibrary html
combineData html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/combineData.Rd:10: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/combineData.Rd:13: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/combineData.Rd:29: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
createAnnotation html
createMatrix html
distributionDistance html
dnaCopySf html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/dnaCopySf.Rd:22: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
doCnFarmsSingle html
flcSnp6Std html
flcStd html
fragLengCorr html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/fragLengCorr.Rd:10: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/fragLengCorr.Rd:20: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
getFragmentSet html
getSingleProbeSetSize html
mlSummarization html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/mlSummarization.Rd:10: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/mlSummarization.Rd:36: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
normAdd html
normalizeAverage html
normalizeCels html
normalizeNone html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/normalizeNone.Rd:29: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
normalizeNpData html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/normalizeNpData.Rd:25: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
normalizeQuantiles html
normalizeSequenceEffect html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/normalizeSequenceEffect.Rd:11: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
normalizeSor html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/normalizeSor.Rd:29: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
plotDendrogram html
plotDensity html
plotEvalIc html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/plotEvalIc.Rd:12: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
plotRegions html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/plotRegions.Rd:10: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/plotRegions.Rd:12: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
plotSmoothScatter html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/plotSmoothScatter.Rd:9: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
plotViolines html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/plotViolines.Rd:10: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
slSummarization html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/slSummarization.Rd:12: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqKzIOh/R.INSTALLdbc2f72bc5/cn.farms/man/slSummarization.Rd:35: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
sparseFarmsC html
summarizeFarmsExact html
summarizeFarmsExact2 html
summarizeFarmsExact3 html
summarizeFarmsGaussian html
summarizeFarmsMethods html
summarizeFarmsStatistics html
summarizeFarmsVariational html
summarizeWindowBps html
summarizeWindowMethods html
summarizeWindowStd 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 'cn.farms' ...
** 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 R_init_cnfarms.c -o R_init_cnfarms.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c laplace.cpp -o laplace.o
laplace.cpp: In function 'SEXPREC* momentsGauss(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
laplace.cpp:442:6: warning: unused variable 'method' [-Wunused-variable]
int method=0;
^
laplace.cpp: In function 'void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)':
laplace.cpp:368:56: warning: 'I1right' may be used uninitialized in this function [-Wmaybe-uninitialized]
double rightMoment1=1.0*rightMy*I0right+1.0*rightSigma*I1right;
^
laplace.cpp:367:52: warning: 'I1left' may be used uninitialized in this function [-Wmaybe-uninitialized]
double leftMoment1=1.0*leftMy*I0left+1.0*leftSigma*I1left;
^
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 sparse_farms.c -o sparse_farms.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o cn.farms.dll tmp.def R_init_cnfarms.o laplace.o sparse_farms.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/cn.farms.buildbin-libdir/cn.farms/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cn.farms' as cn.farms_1.31.0.zip
* DONE (cn.farms)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'cn.farms' successfully unpacked and MD5 sums checked
Tests output
Example timings
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cn.farms.Rcheck/examples_i386/cn.farms-Ex.timings
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cn.farms.Rcheck/examples_x64/cn.farms-Ex.timings
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