Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L [M] N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.2: CHECK report for mitoODE on zin1

This page was generated on 2015-08-24 10:49:22 -0700 (Mon, 24 Aug 2015).

Package 635/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mitoODE 1.7.0
Gregoire Pau
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mitoODE
Last Changed Rev: 102594 / Revision: 107696
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  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: 1.7.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings mitoODE_1.7.0.tar.gz
StartedAt: 2015-08-24 01:46:10 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 01:46:44 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 33.4 seconds
RetCode: 0
Status:  OK 
CheckDir: mitoODE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings mitoODE_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/mitoODE.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mitoODE/DESCRIPTION’ ... OK
* this is package ‘mitoODE’ version ‘1.7.0’
* 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 ... [3s/3s] 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 ... [10s/10s] OK
Examples with CPU or elapsed time > 5s
         user system elapsed
plotfit 7.796  0.059   7.914
* 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/mitoODE.Rcheck/00check.log’
for details.


mitoODE.Rcheck/00install.out:

* installing *source* package ‘mitoODE’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c rksolve.c -o rksolve.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o mitoODE.so rksolve.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/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
mitoODE1.2830.0041.311
plotfit7.7960.0597.914