Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:12 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for cn.farms on nebbiolo2


To the developers/maintainers of the cn.farms package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cn.farms.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 347/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.farms 1.42.0  (landing page)
Andreas Mitterecker
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/cn.farms
git_branch: RELEASE_3_14
git_last_commit: e1a3008
git_last_commit_date: 2021-10-26 11:58:35 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cn.farms
Version: 1.42.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:cn.farms.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings cn.farms_1.42.0.tar.gz
StartedAt: 2022-04-12 06:52:29 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 06:55:15 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 166.8 seconds
RetCode: 0
Status:   OK  
CheckDir: cn.farms.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:cn.farms.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings cn.farms_1.42.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/cn.farms.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.42.0’
* 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’
plotDensity: no visible global function definition for ‘density’
plotDensity: no visible global function definition for ‘lines’
plotEvalIc: no visible global function definition for ‘rgb’
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 ‘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 ‘makeNWScluster’
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
  makeNWScluster matlines matplot median mtext na.omit nclass.Sturges
  order.dendrogram packageDescription pairs par pchisq pdf 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", "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-3.14-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-3.14-bioc/R/bin/R CMD INSTALL cn.farms
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘cn.farms’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-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++14 -I"/home/biocbuild/bbs-3.14-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]
  442 |  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]
  368 |  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]
  364 |  double I2left=(-leftMy/leftSigma)*I1left+I0left;
      |                ~~~~~~~~~~~~~~~~~~~^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c sparse_farms.c -o sparse_farms.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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.farms000
combineData1.5400.1071.650
createAnnotation000
distributionDistance0.0830.0030.086
dnaCopySf0.0690.0040.073
fragLengCorr1.4080.0961.504
mlSummarization2.4580.1522.611
normalizeAverage0.0010.0000.001
normalizeCels0.0010.0000.000
normalizeNpData000
plotDendrogram0.0830.0110.094
plotDensity0.3530.0000.355
plotEvalIc0.3190.0000.319
plotRegions0.1090.0080.117
plotSmoothScatter0.2670.0040.271
plotViolines0.0870.0000.087
slSummarization2.1500.0562.207
sparseFarmsC0.0010.0000.001
summarizeFarmsExact0.0000.0040.004
summarizeFarmsExact20.0000.0040.003
summarizeFarmsExact30.0030.0000.003
summarizeFarmsGaussian0.0010.0000.001
summarizeFarmsMethods0.0010.0000.001
summarizeFarmsVariational0.0040.0000.004
summarizeWindowBps0.0040.0000.004
summarizeWindowMethods0.0010.0000.001
summarizeWindowStd0.0010.0000.002