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CHECK report for mitoODE on tokay2

This page was generated on 2020-10-17 11:57:09 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE mitoODE PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1104/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mitoODE 1.26.1
Gregoire Pau
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/mitoODE
Branch: RELEASE_3_11
Last Commit: e754290
Last Changed Date: 2020-08-10 07:02:33 -0400 (Mon, 10 Aug 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: mitoODE
Version: 1.26.1
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mitoODE.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings mitoODE_1.26.1.tar.gz
StartedAt: 2020-10-17 06:08:41 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:09:50 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 68.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: mitoODE.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mitoODE.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings mitoODE_1.26.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/mitoODE.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mitoODE/DESCRIPTION' ... OK
* this is package 'mitoODE' version '1.26.1'
* 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 whether package 'mitoODE' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'mitoODE' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/mitoODE.Rcheck/00install.out' for details.
* 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
* 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 ... 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 : <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 'is'
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 '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 '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 is lda legend matlines matplot mclapply median na.omit nls.lm
  nls.lm.control optimize par pdf 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", "points", "text")
  importFrom("methods", "is")
  importFrom("stats", "cor", "median", "na.omit", "optimize", "predict",
             "quantile", "rnorm", "sd", "setNames", "wilcox.test")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/mitoODE/libs/i386/mitoODE.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/mitoODE/libs/x64/mitoODE.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
plotfit 6.74    0.2    8.53
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
plotfit 6.31   0.21    6.55
* 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, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/mitoODE.Rcheck/00check.log'
for details.



Installation output

mitoODE.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/mitoODE_1.26.1.tar.gz && rm -rf mitoODE.buildbin-libdir && mkdir mitoODE.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mitoODE.buildbin-libdir mitoODE_1.26.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL mitoODE_1.26.1.zip && rm mitoODE_1.26.1.tar.gz mitoODE_1.26.1.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 72303  100 72303    0     0   879k      0 --:--:-- --:--:-- --:--:--  967k

install for i386

* installing *source* package 'mitoODE' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rksolve.c -o rksolve.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o mitoODE.dll tmp.def rksolve.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/mitoODE.buildbin-libdir/00LOCK-mitoODE/00new/mitoODE/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mitoODE'
    finding HTML links ... done
    figures                                 html  
    mitoODE                                 html  
    plotfit                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'mitoODE' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package can be loaded from final location
Warning: Package 'mitoODE' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'mitoODE' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rksolve.c -o rksolve.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o mitoODE.dll tmp.def rksolve.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/mitoODE.buildbin-libdir/mitoODE/libs/x64
** testing if installed package can be loaded
Warning: Package 'mitoODE' is deprecated and will be removed from Bioconductor
  version 3.12
* MD5 sums
packaged installation of 'mitoODE' as mitoODE_1.26.1.zip
* DONE (mitoODE)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'mitoODE' successfully unpacked and MD5 sums checked

Tests output


Example timings

mitoODE.Rcheck/examples_i386/mitoODE-Ex.timings

nameusersystemelapsed
figures000
mitoODE1.790.031.85
plotfit6.740.208.53

mitoODE.Rcheck/examples_x64/mitoODE-Ex.timings

nameusersystemelapsed
figures000
mitoODE1.340.001.35
plotfit6.310.216.55