BioC 3.2: CHECK report for MLSeq on windows1.bioconductor.org

Package: MLSeq

Version: 1.8.0

Command: rm -rf MLSeq.buildbin-libdir MLSeq.Rcheck && mkdir MLSeq.buildbin-libdir MLSeq.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MLSeq.buildbin-libdir MLSeq_1.8.0.tar.gz >MLSeq.Rcheck\00install.out 2>&1 && cp MLSeq.Rcheck\00install.out MLSeq-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MLSeq.buildbin-libdir --install="check:MLSeq-install.out" --force-multiarch --no-vignettes --timings MLSeq_1.8.0.tar.gz

StartedAt: 2015-10-27 03:42:48 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:49:06 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 377.5 seconds

RetCode: 0

Status:  OK

CheckDir: MLSeq.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf MLSeq.buildbin-libdir MLSeq.Rcheck && mkdir MLSeq.buildbin-libdir MLSeq.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MLSeq.buildbin-libdir MLSeq_1.8.0.tar.gz >MLSeq.Rcheck\00install.out 2>&1 && cp MLSeq.Rcheck\00install.out MLSeq-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MLSeq.buildbin-libdir --install="check:MLSeq-install.out" --force-multiarch --no-vignettes --timings MLSeq_1.8.0.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/MLSeq.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MLSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MLSeq' version '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'caret' 'DESeq2' 'Biobase' 'limma' 'randomForest' 'edgeR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'MLSeq' 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
classify: no visible global function definition for
  'AnnotatedDataFrame'
classify: no visible global function definition for 'bagControl'
classify: no visible binding for global variable 'svmBag'
predictClassify: no visible global function definition for
  'AnnotatedDataFrame'
* 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' ... [69s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
predictClassify 15.89   0.05   21.45
classify        11.58   0.09   11.69
trained          6.04   0.00    7.26
ref              5.72   0.06    5.78
** running examples for arch 'x64' ... [88s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
classify        17.47   0.12   21.01
predictClassify 13.06   0.01   13.08
confusionMat     6.89   0.02    7.24
deseqTransform   6.24   0.00    6.23
normalization    6.13   0.02    6.14
method           5.94   0.00    5.93
* 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
  'C:/biocbld/bbs-3.2-bioc/meat/MLSeq.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'MLSeq' ...
** R
** data
** inst
** preparing package for lazy loading
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.

install for x64

* installing *source* package 'MLSeq' ...
** testing if installed package can be loaded
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
* MD5 sums
packaged installation of 'MLSeq' as MLSeq_1.8.0.zip
* DONE (MLSeq)

name	user	system	elapsed
MLSeq-class	0	0	0
cervical	0	0	0
classify	11.58	0.09	11.69
confusionMat	3.61	0.02	3.62
deseqTransform	3.76	0.06	3.83
method	4.22	0.00	4.22
normalization	4.58	0.00	4.58
predictClassify	15.89	0.05	21.45
ref	5.72	0.06	5.78
trained	6.04	0.00	7.26

name	user	system	elapsed
MLSeq-class	0	0	0
cervical	0.01	0.00	0.02
classify	17.47	0.12	21.01
confusionMat	6.89	0.02	7.24
deseqTransform	6.24	0.00	6.23
method	5.94	0.00	5.93
normalization	6.13	0.02	6.14
predictClassify	13.06	0.01	13.08
ref	4.49	0.02	4.50
trained	4.28	0.01	4.29