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

Package: MethTargetedNGS

Version: 1.2.0

Command: rm -rf MethTargetedNGS.buildbin-libdir MethTargetedNGS.Rcheck && mkdir MethTargetedNGS.buildbin-libdir MethTargetedNGS.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MethTargetedNGS.buildbin-libdir MethTargetedNGS_1.2.0.tar.gz >MethTargetedNGS.Rcheck\00install.out 2>&1 && cp MethTargetedNGS.Rcheck\00install.out MethTargetedNGS-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MethTargetedNGS.buildbin-libdir --install="check:MethTargetedNGS-install.out" --force-multiarch --no-vignettes --timings MethTargetedNGS_1.2.0.tar.gz

StartedAt: 2015-10-27 03:27:38 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:29:50 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 131.9 seconds

RetCode: 0

Status:  OK

CheckDir: MethTargetedNGS.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf MethTargetedNGS.buildbin-libdir MethTargetedNGS.Rcheck && mkdir MethTargetedNGS.buildbin-libdir MethTargetedNGS.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MethTargetedNGS.buildbin-libdir MethTargetedNGS_1.2.0.tar.gz >MethTargetedNGS.Rcheck\00install.out 2>&1 && cp MethTargetedNGS.Rcheck\00install.out MethTargetedNGS-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MethTargetedNGS.buildbin-libdir --install="check:MethTargetedNGS-install.out" --force-multiarch --no-vignettes --timings MethTargetedNGS_1.2.0.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/MethTargetedNGS.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 'MethTargetedNGS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MethTargetedNGS' version '1.2.0'
* 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 'MethTargetedNGS' 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
methAlign: no visible global function definition for 'subject'
methAlign: no visible global function definition for 'pattern'
* 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' ... [23s] OK
** running examples for arch 'x64' ... [25s] 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: 1 NOTE
See
  'C:/biocbld/bbs-3.2-bioc/meat/MethTargetedNGS.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'MethTargetedNGS' ...
** 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 'MethTargetedNGS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MethTargetedNGS' as MethTargetedNGS_1.2.0.zip
* DONE (MethTargetedNGS)

name	user	system	elapsed
bconv	0	0	0
compare_samples	4.09	0.02	4.11
fishertest_cpg	3.99	0.02	4.00
hmmbuild	0	0	0
methAlign	2.05	0.00	2.05
methAvg	1.90	0.00	1.91
methEntropy	1.99	0.00	1.98
methHeatmap	1.87	0.01	1.89
nhmmer	0	0	0
odd_ratio	3.88	0.00	3.88

name	user	system	elapsed
bconv	0	0	0
compare_samples	4.43	0.02	4.44
fishertest_cpg	4.39	0.00	4.39
hmmbuild	0	0	0
methAlign	2.06	0.00	2.07
methAvg	2.23	0.00	2.23
methEntropy	2.24	0.00	2.23
methHeatmap	2.22	0.00	2.22
nhmmer	0	0	0
odd_ratio	4.20	0.00	4.21