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 3.0: CHECK report for CMA on moscato1

This page was generated on 2015-04-10 09:45:17 -0700 (Fri, 10 Apr 2015).

Package 170/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CMA 1.24.0
Christoph Bernau
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/CMA
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: CMA
Version: 1.24.0
Command: rm -rf CMA.buildbin-libdir CMA.Rcheck && mkdir CMA.buildbin-libdir CMA.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CMA.buildbin-libdir CMA_1.24.0.tar.gz >CMA.Rcheck\00install.out 2>&1 && cp CMA.Rcheck\00install.out CMA-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=CMA.buildbin-libdir --install="check:CMA-install.out" --force-multiarch --no-vignettes --timings CMA_1.24.0.tar.gz
StartedAt: 2015-04-09 23:51:33 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:53:44 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 130.8 seconds
RetCode: 0
Status:  OK  
CheckDir: CMA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CMA.buildbin-libdir CMA.Rcheck && mkdir CMA.buildbin-libdir CMA.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CMA.buildbin-libdir CMA_1.24.0.tar.gz >CMA.Rcheck\00install.out 2>&1 && cp CMA.Rcheck\00install.out CMA-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=CMA.buildbin-libdir --install="check:CMA-install.out" --force-multiarch --no-vignettes --timings CMA_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/CMA.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CMA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CMA' version '1.24.0'
* 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 whether package 'CMA' 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 ... NOTE
'library' or 'require' calls in package code:
  'MASS' 'class' 'corpcor' 'e1071' 'gbm' 'glmnet' 'limma' 'mgcv'
  'mvtnorm' 'nnet' 'plsgenomics' 'randomForest' 'st'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ROCinternal: no visible binding for global variable 'xlab'
ROCinternal: no visible binding for global variable 'ylab'
ROCinternal: no visible binding for global variable 'main'
ROCinternal: no visible binding for global variable 'lwd'
limmatest: no visible global function definition for 'lmFit'
limmatest: no visible global function definition for 'contrasts.fit'
limmatest: no visible global function definition for 'eBayes'
limmatest: no visible global function definition for 'classifyTestsF'
rfe: no visible binding for global variable 'cost'
rfe: no visible binding for global variable 'svm'
boxplot,evaloutput: no visible binding for global variable 'main'
compare,list: no visible binding for global variable 'main'
flexdaCMA,matrix-numeric-missing: no visible global function definition
  for 'gam'
gbmCMA,matrix-numeric-missing: no visible binding for global variable
  'n.minobsinnode'
gbmCMA,matrix-numeric-missing: no visible binding for global variable
  'bag.fraction'
gbmCMA,matrix-numeric-missing: no visible binding for global variable
  'n.trees'
gbmCMA,matrix-numeric-missing: no visible binding for global variable
  'verbose'
gbmCMA,matrix-numeric-missing: no visible binding for global variable
  'gbm.fit'
knnCMA,matrix-numeric-missing: no visible global function definition
  for 'knn'
ldaCMA,matrix-numeric-missing: no visible global function definition
  for 'lda'
nnetCMA,matrix-numeric-missing: no visible binding for global variable
  'size'
nnetCMA,matrix-numeric-missing: no visible binding for global variable
  'MaxNWts'
nnetCMA,matrix-numeric-missing: no visible global function definition
  for 'class.ind'
pls_ldaCMA,matrix-numeric-missing: no visible global function
  definition for 'pls.regression'
pls_ldaCMA,matrix-numeric-missing: no visible global function
  definition for 'transformy'
pls_ldaCMA,matrix-numeric-missing: no visible global function
  definition for 'lda'
pls_lrCMA,matrix-numeric-missing: no visible global function definition
  for 'pls.regression'
pls_lrCMA,matrix-numeric-missing: no visible global function definition
  for 'transformy'
pls_rfCMA,matrix-numeric-missing: no visible global function definition
  for 'pls.regression'
pls_rfCMA,matrix-numeric-missing: no visible global function definition
  for 'transformy'
pls_rfCMA,matrix-numeric-missing: no visible global function definition
  for 'randomForest'
prediction,data.frame-missing-data.frame-formula: no visible global
  function definition for 'predicition'
qdaCMA,matrix-numeric-missing: no visible global function definition
  for 'qda'
rfCMA,matrix-numeric-missing: no visible global function definition for
  'randomForest'
shrinkldaCMA,matrix-numeric-missing: no visible global function
  definition for 'cov.shrink'
svmCMA,matrix-numeric-missing: no visible binding for global variable
  'cost'
weighted.mcr,character-character-numeric-character-matrix-numeric: no
  visible global function definition for 'make.positive.definite'
weighted.mcr,character-character-numeric-character-matrix-numeric: no
  visible global function definition for 'pmvnorm'
weighted.mcr,character-character-numeric-character-matrix-numeric: no
  visible global function definition for 'rmvnorm'
wmc,matrix-numeric-numeric: no visible global function definition for
  'make.positive.definite'
wmc,matrix-numeric-numeric: no visible global function definition for
  'pmvnorm'
wmc,matrix-numeric-numeric: no visible global function definition for
  'rmvnorm'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [21s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
gbmCMA 4.97   0.02    5.12
** running examples for arch 'x64' ... [19s] 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/CMA.Rcheck/00check.log'
for details.

CMA.Rcheck/00install.out:


install for i386

* installing *source* package 'CMA' ...
** R
** data
** 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 'CMA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CMA' as CMA_1.24.0.zip
* DONE (CMA)

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

nameusersystemelapsed
ElasticNetCMA4.130.094.23
GeneSelection0.340.000.35
GenerateLearningsets0.010.000.01
LassoCMA0.740.000.74
Planarplot0.320.030.36
classification0.020.000.01
compBoostCMA1.190.001.19
compare000
dldaCMA0.20.00.2
evaluation0.140.000.14
fdaCMA0.120.000.12
flexdaCMA0.240.000.24
gbmCMA4.970.025.12
golub0.070.000.06
khan0.070.000.08
knnCMA0.330.000.32
ldaCMA0.220.000.22
nnetCMA0.140.010.15
pknnCMA0.170.000.18
plrCMA0.450.000.45
pls_ldaCMA0.170.000.17
pls_lrCMA0.130.000.14
pls_rfCMA0.080.000.08
pnnCMA0.040.000.04
prediction000
qdaCMA0.160.000.16
rfCMA0.080.000.08
scdaCMA0.140.020.15
shrinkldaCMA0.170.030.21
svmCMA0.670.010.68
tune000
weighted_mcr2.870.102.96

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

nameusersystemelapsed
ElasticNetCMA4.470.064.54
GeneSelection0.280.000.28
GenerateLearningsets000
LassoCMA0.530.020.55
Planarplot0.270.010.28
classification000
compBoostCMA1.260.001.26
compare000
dldaCMA0.230.020.25
evaluation0.140.000.14
fdaCMA0.110.010.13
flexdaCMA0.250.000.25
gbmCMA2.950.003.86
golub0.030.000.03
khan0.050.000.05
knnCMA0.210.010.24
ldaCMA0.140.000.14
nnetCMA0.090.020.11
pknnCMA0.140.000.14
plrCMA0.390.000.39
pls_ldaCMA0.180.000.17
pls_lrCMA0.310.000.32
pls_rfCMA0.080.000.07
pnnCMA0.040.000.05
prediction000
qdaCMA0.120.000.12
rfCMA0.10.00.1
scdaCMA0.110.000.10
shrinkldaCMA0.150.000.16
svmCMA0.560.000.56
tune000
weighted_mcr2.900.123.02