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CHECK report for cn.farms on malbec2

This page was generated on 2019-10-16 11:59:39 -0400 (Wed, 16 Oct 2019).

Package 299/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.farms 1.32.0
Andreas Mitterecker
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/cn.farms
Branch: RELEASE_3_9
Last Commit: 973011c
Last Changed Date: 2019-05-02 11:53:24 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cn.farms
Version: 1.32.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:cn.farms.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings cn.farms_1.32.0.tar.gz
StartedAt: 2019-10-16 00:37:39 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:41:15 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 216.1 seconds
RetCode: 0
Status:  OK 
CheckDir: cn.farms.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:cn.farms.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings cn.farms_1.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/cn.farms.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cn.farms/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cn.farms’ version ‘1.32.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘cn.farms’ can be installed ... OK
* 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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 2 NOTEs
See
  ‘/home/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:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL cn.farms
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘cn.farms’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c R_init_cnfarms.c -o R_init_cnfarms.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -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:364:35: warning: ‘I1left’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  double I2left=(-leftMy/leftSigma)*I1left+I0left;
                ~~~~~~~~~~~~~~~~~~~^~~~~~~
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c sparse_farms.c -o sparse_farms.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-cn.farms/00new/cn.farms/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cn.farms)

Tests output


Example timings

cn.farms.Rcheck/cn.farms-Ex.timings

nameusersystemelapsed
cn.farms0.0000.0000.001
combineData1.9850.0722.142
createAnnotation000
distributionDistance0.1230.0040.127
dnaCopySf0.1220.0000.125
fragLengCorr2.7080.0202.737
mlSummarization4.7270.1124.839
normalizeAverage0.0020.0000.002
normalizeCels000
normalizeNpData000
plotDendrogram0.1490.0080.159
plotDensity0.5650.0040.569
plotEvalIc0.4170.0000.423
plotRegions0.1630.0080.170
plotSmoothScatter0.3800.0200.401
plotViolines0.1660.0000.166
slSummarization2.5210.0202.541
sparseFarmsC0.0010.0000.001
summarizeFarmsExact0.0040.0000.004
summarizeFarmsExact20.0040.0000.004
summarizeFarmsExact30.0040.0000.004
summarizeFarmsGaussian0.0000.0020.002
summarizeFarmsMethods0.0000.0010.002
summarizeFarmsVariational0.0010.0030.005
summarizeWindowBps0.0040.0000.004
summarizeWindowMethods0.0020.0000.002
summarizeWindowStd0.0030.0000.003