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 3.4: CHECK report for OmicsMarkeR on moscato1

This page was generated on 2016-09-21 03:47:00 -0700 (Wed, 21 Sep 2016).

Package 842/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmicsMarkeR 1.5.2
Charles E. Determan Jr.
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OmicsMarkeR
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: OmicsMarkeR
Version: 1.5.2
Command: rm -rf OmicsMarkeR.buildbin-libdir OmicsMarkeR.Rcheck && mkdir OmicsMarkeR.buildbin-libdir OmicsMarkeR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OmicsMarkeR.buildbin-libdir OmicsMarkeR_1.5.2.tar.gz >OmicsMarkeR.Rcheck\00install.out 2>&1 && cp OmicsMarkeR.Rcheck\00install.out OmicsMarkeR-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=OmicsMarkeR.buildbin-libdir --install="check:OmicsMarkeR-install.out" --force-multiarch --no-vignettes --timings OmicsMarkeR_1.5.2.tar.gz
StartedAt: 2016-09-20 13:17:28 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 13:25:26 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 477.4 seconds
RetCode: 0
Status:  OK  
CheckDir: OmicsMarkeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf OmicsMarkeR.buildbin-libdir OmicsMarkeR.Rcheck && mkdir OmicsMarkeR.buildbin-libdir OmicsMarkeR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OmicsMarkeR.buildbin-libdir OmicsMarkeR_1.5.2.tar.gz >OmicsMarkeR.Rcheck\00install.out 2>&1 && cp OmicsMarkeR.Rcheck\00install.out OmicsMarkeR-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=OmicsMarkeR.buildbin-libdir --install="check:OmicsMarkeR-install.out" --force-multiarch --no-vignettes --timings OmicsMarkeR_1.5.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/OmicsMarkeR.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OmicsMarkeR/DESCRIPTION' ... OK
* this is package 'OmicsMarkeR' version '1.5.2'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'OmicsMarkeR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CLA: no visible global function definition for 'head'
EE: no visible global function definition for 'head'
EM: no visible global function definition for 'head'
ES: no visible global function definition for 'head'
MeanSD: no visible binding for global variable 'sd'
create.discr.matrix: no visible global function definition for 'runif'
create.random.matrix: no visible global function definition for 'rnorm'
create.random.matrix: no visible global function definition for 'runif'
extract.features: no visible binding for global variable 'head'
extract.features: no visible global function definition for 'head'
extract.features: no visible global function definition for 'coef'
extract.features : <anonymous>: no visible global function definition
  for 'coef'
fit.only.model: no visible binding for global variable 'sd'
fs.ensembl.stability: no visible binding for global variable 'sd'
fs.ensembl.stability: no visible binding for global variable 'setNames'
fs.stability: no visible binding for global variable 'sd'
fs.stability: no visible binding for global variable 'setNames'
modelTuner: no visible global function definition for 'complete.cases'
modelTuner_loo: no visible global function definition for
  'complete.cases'
noise.matrix: no visible global function definition for 'runif'
optimize.model: no visible global function definition for
  'flush.console'
pamTune: no visible global function definition for 'complete.cases'
perm.class: no visible binding for global variable 'outIndex'
perm.class: no visible global function definition for 'plot'
perm.class: no visible global function definition for 'density'
perm.class: no visible global function definition for 'sd'
perm.class: no visible global function definition for 'abline'
perm.class: no visible global function definition for 'legend'
perm.features: no visible global function definition for 'coef'
plus_minus: no visible global function definition for 'rbinom'
predictNewClasses: no visible global function definition for 'predict'
predicting: no visible global function definition for 'predict'
tune.instructions: no visible global function definition for
  'aggregate'
verify: no visible global function definition for 'complete.cases'
Undefined global functions or variables:
  abline aggregate coef complete.cases density flush.console head
  legend outIndex plot predict rbinom rnorm runif sd setNames
Consider adding
  importFrom("graphics", "abline", "legend", "plot")
  importFrom("stats", "aggregate", "coef", "complete.cases", "density",
             "predict", "rbinom", "rnorm", "runif", "sd", "setNames")
  importFrom("utils", "flush.console", "head")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
perm.class          15.19   0.03   15.23
performance.metrics 13.58   0.03   13.61
predictNewClasses   13.54   0.01   13.57
perm.features       13.41   0.00   15.09
fs.stability        13.29   0.02   13.31
feature.table       12.57   0.02   12.62
fit.only.model       5.53   0.01    5.56
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
perm.class          15.85   0.01   15.87
perm.features       15.43   0.03   16.01
fs.stability        14.71   0.01   14.72
feature.table       14.24   0.02   14.26
predictNewClasses   14.13   0.03   14.17
performance.metrics 13.57   0.02   13.58
fit.only.model       5.47   0.00    5.47
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* 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: 2 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/OmicsMarkeR.Rcheck/00check.log'
for details.


OmicsMarkeR.Rcheck/00install.out:


install for i386

* installing *source* package 'OmicsMarkeR' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'OmicsMarkeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OmicsMarkeR' as OmicsMarkeR_1.5.2.zip
* DONE (OmicsMarkeR)

OmicsMarkeR.Rcheck/examples_i386/OmicsMarkeR-Ex.timings:

nameusersystemelapsed
RPT0.020.000.05
aggregation000
canberra000
canberra_stability000
create.corr.matrix0.000.020.02
create.discr.matrix000
create.random.matrix000
denovo.grid0.020.000.02
feature.table12.57 0.0212.62
fit.only.model5.530.015.56
fs.ensembl.stability000
fs.stability13.29 0.0213.31
jaccard000
kuncheva000
modelList000
ochiai000
pairwise.model.stability0.020.000.02
pairwise.stability000
params0.010.000.01
performance.metrics13.58 0.0313.61
perm.class15.19 0.0315.23
perm.features13.41 0.0015.09
pof000
predictNewClasses13.54 0.0113.57
sorensen000
spearman000
svmrfeFeatureRanking0.080.000.08
svmrfeFeatureRankingForMulticlass0.170.000.17

OmicsMarkeR.Rcheck/examples_x64/OmicsMarkeR-Ex.timings:

nameusersystemelapsed
RPT000
aggregation0.010.000.02
canberra000
canberra_stability000
create.corr.matrix0.020.000.01
create.discr.matrix0.010.000.02
create.random.matrix000
denovo.grid0.020.000.01
feature.table14.24 0.0214.26
fit.only.model5.470.005.47
fs.ensembl.stability000
fs.stability14.71 0.0114.72
jaccard000
kuncheva000
modelList000
ochiai000
pairwise.model.stability0.020.000.01
pairwise.stability000
params0.010.000.02
performance.metrics13.57 0.0213.58
perm.class15.85 0.0115.87
perm.features15.43 0.0316.01
pof000
predictNewClasses14.13 0.0314.17
sorensen000
spearman000
svmrfeFeatureRanking0.100.000.09
svmrfeFeatureRankingForMulticlass0.170.000.17