BioC 3.1: CHECK report for mitoODE on petty

Package: mitoODE

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mitoODE_1.6.0.tar.gz

StartedAt: 2015-10-09 00:24:05 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:25:17 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 71.5 seconds

RetCode: 0

Status:  OK

CheckDir: mitoODE.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mitoODE_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/mitoODE.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mitoODE/DESCRIPTION’ ... OK
* this is package ‘mitoODE’ version ‘1.6.0’
* 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 ‘mitoODE’ can be installed ... [5s/7s] 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 loading without being on the library search path ... 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 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’
compute.mtvt: no visible binding for global variable ‘tab’
compute.mtvt: no visible global function definition for ‘mclapply’
constrain: no visible binding for global variable ‘g.tstop’
figure3a: no visible binding for global variable ‘tab’
figure3a: no visible global function definition for ‘getspot’
figure3b: no visible binding for global variable ‘tab’
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 ‘mclapply’
figure4: no visible global function definition for ‘getanno’
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’
lambda.justification: no visible binding for global variable ‘tab’
lambda.justification: no visible global function definition for ‘lda’
odevaluate: no visible binding for global variable ‘g.tstart’
plotfit: no visible global function definition for ‘readspot’
plotk: no visible global function definition for ‘readspot’
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 ‘getsirna’
stats.fitting : <anonymous>: no visible global function definition for
  ‘readspot’
suppFig1: no visible global function definition for ‘getanno’
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/21s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
plotfit 16.518  0.355  16.964
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/mitoODE.Rcheck/00check.log’
for details.

* installing *source* package ‘mitoODE’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c rksolve.c -o rksolve.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 -L/usr/local/lib -o mitoODE.so rksolve.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/mitoODE.Rcheck/mitoODE/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (mitoODE)

name	user	system	elapsed
figures	0.000	0.001	0.001
mitoODE	1.888	0.037	1.957
plotfit	16.518	0.355	16.964