BioC 3.1: CHECK report for ALDEx2 on moscato2

Package: ALDEx2

Version: 1.0.0

Command: rm -rf ALDEx2.buildbin-libdir ALDEx2.Rcheck && mkdir ALDEx2.buildbin-libdir ALDEx2.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ALDEx2.buildbin-libdir ALDEx2_1.0.0.tar.gz >ALDEx2.Rcheck\00install.out 2>&1 && cp ALDEx2.Rcheck\00install.out ALDEx2-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=ALDEx2.buildbin-libdir --install="check:ALDEx2-install.out" --force-multiarch --no-vignettes --timings ALDEx2_1.0.0.tar.gz

StartedAt: 2015-10-08 23:15:19 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:18:02 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 163.0 seconds

RetCode: 0

Status: OK

CheckDir: ALDEx2.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf ALDEx2.buildbin-libdir ALDEx2.Rcheck && mkdir ALDEx2.buildbin-libdir ALDEx2.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ALDEx2.buildbin-libdir ALDEx2_1.0.0.tar.gz >ALDEx2.Rcheck\00install.out 2>&1 && cp ALDEx2.Rcheck\00install.out ALDEx2-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=ALDEx2.buildbin-libdir --install="check:ALDEx2-install.out" --force-multiarch --no-vignettes --timings ALDEx2_1.0.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/ALDEx2.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ALDEx2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ALDEx2' version '1.0.0'
* 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 'ALDEx2' 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:
  'BiocParallel' 'parallel'
  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
aldex.clr.function: no visible global function definition for
  'bplapply'
aldex.clr.function: no visible global function definition for
  'mclapply'
aldex.clr.function: no visible global function definition for
  'detectCores'
aldex.effect: no visible global function definition for 'mclapply'
aldex.effect: no visible global function definition for 'detectCores'
aldex.glm: no visible global function definition for 'mclapply'
aldex.glm: no visible global function definition for 'detectCores'
* 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' ... [20s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
aldex.glm 8.98   0.01       9
** running examples for arch 'x64' ... [26s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
aldex.glm 11.48   0.03   11.52
* 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
  'E:/biocbld/bbs-3.1-bioc/meat/ALDEx2.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'ALDEx2' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'ALDEx2' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'ALDEx2' as ALDEx2_1.0.0.zip
* DONE (ALDEx2)

name	user	system	elapsed
ALDEx2m-package	0	0	0
aldex	2.5	0.2	2.7
aldex.clr-class	0.08	0.04	0.11
aldex.clr.function-methods	0.09	0.00	0.09
aldex.corr	0	0	0
aldex.effect	2.64	0.00	2.64
aldex.glm	8.98	0.01	9.00
aldex.ttest	2.11	0.00	2.11
getFeatureNames-method	0.09	0.00	0.09
getFeatures-method	0.10	0.00	0.09
getMonteCarloInstances-method	0.08	0.00	0.08
getMonteCarloReplicate-method	0.07	0.02	0.10
getReads-method	0.10	0.00	0.09
getSampleIDs-method	0.07	0.01	0.09
numConditions-method	0.08	0.02	0.10
numFeatures-method	0.08	0.00	0.08
numMCInstances-method	0.07	0.01	0.09
plot.aldex	0	0	0

name	user	system	elapsed
ALDEx2m-package	0	0	0
aldex	3.14	0.13	3.26
aldex.clr-class	0.09	0.00	0.10
aldex.clr.function-methods	0.10	0.00	0.09
aldex.corr	0	0	0
aldex.effect	3.43	0.00	3.43
aldex.glm	11.48	0.03	11.52
aldex.ttest	2.35	0.00	2.35
getFeatureNames-method	0.09	0.00	0.42
getFeatures-method	0.26	0.01	0.29
getMonteCarloInstances-method	0.08	0.00	0.08
getMonteCarloReplicate-method	0.10	0.00	0.09
getReads-method	0.09	0.00	0.10
getSampleIDs-method	0.11	0.00	0.11
numConditions-method	0.14	0.00	0.14
numFeatures-method	0.14	0.00	0.14
numMCInstances-method	0.14	0.00	0.14
plot.aldex	0	0	0

BioC 3.1: CHECK report for ALDEx2 on moscato2

Summary

Command output