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CHECK report for mitoODE on merida1

This page was generated on 2019-04-16 11:56:57 -0400 (Tue, 16 Apr 2019).

Package 979/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mitoODE 1.20.1
Gregoire Pau
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/mitoODE
Branch: RELEASE_3_8
Last Commit: 60b8815
Last Changed Date: 2019-01-04 13:39:38 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: mitoODE
Version: 1.20.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mitoODE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mitoODE_1.20.1.tar.gz
StartedAt: 2019-04-16 01:21:25 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:22:15 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 50.7 seconds
RetCode: 0
Status:  OK 
CheckDir: mitoODE.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mitoODE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mitoODE_1.20.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/mitoODE.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mitoODE/DESCRIPTION’ ... OK
* this is package ‘mitoODE’ version ‘1.20.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mitoODE’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘KernSmooth’ ‘MASS’ ‘minpack.lm’ ‘mitoODEdata’ ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
buildQC: no visible global function definition for ‘quantile’
buildQC: no visible binding for global variable ‘tab’
buildSuppTab: no visible binding for global variable ‘tab’
buildSuppTab: no visible global function definition for ‘getanno’
buildSuppTab: no visible global function definition for ‘mclapply’
buildSuppTab: no visible global function definition for ‘write.table’
compute.mtvt: no visible binding for global variable ‘tab’
compute.mtvt: no visible global function definition for ‘mclapply’
compute.mtvt : <anonymous>: no visible global function definition for
  ‘sd’
compute.mtvt: no visible global function definition for ‘setNames’
constrain: no visible binding for global variable ‘g.tstop’
figure1: no visible global function definition for ‘pdf’
figure1: no visible global function definition for ‘dev.off’
figure2: no visible global function definition for ‘pdf’
figure2: no visible global function definition for ‘dev.off’
figure3a: no visible global function definition for ‘pdf’
figure3a: no visible global function definition for ‘boxplot’
figure3a: no visible binding for global variable ‘tab’
figure3a: no visible global function definition for ‘dev.off’
figure3a: no visible global function definition for ‘wilcox.test’
figure3a: no visible global function definition for ‘getspot’
figure3b: no visible binding for global variable ‘tab’
figure3b: no visible global function definition for ‘pdf’
figure3b: no visible global function definition for ‘boxplot’
figure3b: no visible global function definition for ‘dev.off’
figure3b: no visible binding for global variable ‘median’
figure3b: no visible global function definition for ‘wilcox.test’
figure3b: no visible global function definition for ‘na.omit’
figure3b: no visible global function definition for ‘getspot’
figure4: no visible binding for global variable ‘tab’
figure4: no visible global function definition for ‘lda’
figure4: no visible global function definition for ‘predict’
figure4: no visible global function definition for ‘mclapply’
figure4 : <anonymous>: no visible binding for global variable ‘median’
figure4: no visible global function definition for ‘pdf’
figure4: no visible global function definition for ‘par’
figure4: no visible global function definition for ‘plot’
figure4 : <anonymous>: no visible global function definition for
  ‘optimize’
figure4: no visible global function definition for ‘contour’
figure4: no visible global function definition for ‘getanno’
figure4: no visible global function definition for ‘points’
figure4: no visible global function definition for ‘text’
figure4: no visible global function definition for ‘legend’
figure4: no visible global function definition for ‘dev.off’
fitmodel: no visible global function definition for ‘nls.lm’
fitmodel: no visible global function definition for ‘nls.lm.control’
fitmodel: no visible global function definition for ‘mclapply’
fitspot: no visible global function definition for ‘mclapply’
fitspot : <anonymous>: no visible global function definition for
  ‘readspot’
getp0: no visible binding for global variable ‘g.tstart’
getp0: no visible binding for global variable ‘g.tstop’
getp0: no visible global function definition for ‘rnorm’
lambda.justification: no visible binding for global variable ‘tab’
lambda.justification: no visible global function definition for ‘lda’
lambda.justification: no visible global function definition for
  ‘predict’
odevaluate: no visible binding for global variable ‘g.tstart’
plotfit: no visible global function definition for ‘readspot’
plotfit: no visible global function definition for ‘matplot’
plotfit: no visible global function definition for ‘matlines’
plotfit: no visible global function definition for ‘abline’
plotk: no visible global function definition for ‘readspot’
plotk: no visible global function definition for ‘plot’
plotk: no visible global function definition for ‘abline’
stats.assay: no visible binding for global variable ‘tab’
stats.assay: no visible global function definition for ‘getanno’
stats.assay: no visible global function definition for ‘na.omit’
stats.assay: no visible global function definition for ‘getsirna’
stats.fitting : <anonymous>: no visible global function definition for
  ‘readspot’
stats.fitting: no visible global function definition for ‘quantile’
suppFig1: no visible global function definition for ‘pdf’
suppFig1: no visible global function definition for ‘plot’
suppFig1: no visible global function definition for ‘text’
suppFig1: no visible global function definition for ‘getanno’
suppFig1: no visible global function definition for ‘abline’
suppFig1: no visible global function definition for ‘dev.off’
suppFig1: no visible global function definition for ‘cor’
Undefined global functions or variables:
  abline boxplot contour cor dev.off g.tstart g.tstop getanno getsirna
  getspot lda legend matlines matplot mclapply median na.omit nls.lm
  nls.lm.control optimize par pdf plot points predict quantile readspot
  rnorm sd setNames tab text wilcox.test write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "boxplot", "contour", "legend",
             "matlines", "matplot", "par", "plot", "points", "text")
  importFrom("stats", "cor", "median", "na.omit", "optimize", "predict",
             "quantile", "rnorm", "sd", "setNames", "wilcox.test")
  importFrom("utils", "write.table")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
plotfit 14.754  0.231  15.228
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/mitoODE.Rcheck/00check.log’
for details.



Installation output

mitoODE.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL mitoODE
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘mitoODE’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c rksolve.c -o rksolve.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o mitoODE.so rksolve.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/mitoODE/libs
** R
** 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
* DONE (mitoODE)

Tests output


Example timings

mitoODE.Rcheck/mitoODE-Ex.timings

nameusersystemelapsed
figures000
mitoODE1.4700.0521.526
plotfit14.754 0.23115.228