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BioC 3.2: CHECK report for mitoODE on perceval

This page was generated on 2015-10-27 17:35:40 -0400 (Tue, 27 Oct 2015).

Package 657/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mitoODE 1.8.0
Gregoire Pau
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/mitoODE
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: mitoODE
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mitoODE_1.8.0.tar.gz
StartedAt: 2015-10-27 10:03:33 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 10:04:25 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 51.7 seconds
RetCode: 0
Status:  OK 
CheckDir: mitoODE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mitoODE_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/mitoODE.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.8.0’
* 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 ... [4s/4s] 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 ... [17s/17s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
plotfit 13.423   0.28  13.813
* 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-3.2-bioc/meat/mitoODE.Rcheck/00check.log’
for details.


mitoODE.Rcheck/00install.out:

* 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-3.2-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)

mitoODE.Rcheck/mitoODE-Ex.timings:

nameusersystemelapsed
figures0.0010.0000.001
mitoODE1.4250.0301.495
plotfit13.423 0.28013.813