BioC 3.3: CHECK report for CODEX on moscato2

Package: CODEX

Version: 1.4.0

Command: rm -rf CODEX.buildbin-libdir CODEX.Rcheck && mkdir CODEX.buildbin-libdir CODEX.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CODEX.buildbin-libdir CODEX_1.4.0.tar.gz >CODEX.Rcheck\00install.out 2>&1 && cp CODEX.Rcheck\00install.out CODEX-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=CODEX.buildbin-libdir --install="check:CODEX-install.out" --force-multiarch --no-vignettes --timings CODEX_1.4.0.tar.gz

StartedAt: 2016-10-13 02:22:56 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 02:31:28 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 511.9 seconds

RetCode: 0

Status:  OK

CheckDir: CODEX.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CODEX.buildbin-libdir CODEX.Rcheck && mkdir CODEX.buildbin-libdir CODEX.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CODEX.buildbin-libdir CODEX_1.4.0.tar.gz >CODEX.Rcheck\00install.out 2>&1 && cp CODEX.Rcheck\00install.out CODEX-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=CODEX.buildbin-libdir --install="check:CODEX-install.out" --force-multiarch --no-vignettes --timings CODEX_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/CODEX.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 'CODEX/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CODEX' version '1.4.0'
* 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 'CODEX' 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
choiceofK: no visible global function definition for 'pdf'
choiceofK: no visible global function definition for 'par'
choiceofK: no visible global function definition for 'plot'
choiceofK: no visible global function definition for 'dev.off'
getbambed: no visible global function definition for 'read.table'
normalize : <anonymous>: no visible global function definition for
  'smooth.spline'
normalize : <anonymous>: no visible global function definition for
  'predict'
normalize: no visible global function definition for 'glm'
normalize: no visible binding for global variable 'poisson'
normalize: no visible global function definition for 'lm'
normalize2 : <anonymous>: no visible global function definition for
  'smooth.spline'
normalize2 : <anonymous>: no visible global function definition for
  'predict'
normalize2: no visible global function definition for 'glm'
normalize2: no visible binding for global variable 'poisson'
normalize2: no visible global function definition for 'lm'
Undefined global functions or variables:
  dev.off glm lm par pdf plot poisson predict read.table smooth.spline
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "glm", "lm", "poisson", "predict", "smooth.spline")
  importFrom("utils", "read.table")
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 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' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
normalize   37.08   0.01   37.09
normalize2  32.65   0.00   32.66
getcoverage 11.82   0.33   59.89
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
normalize   45.27   0.06   45.33
normalize2  37.44   0.00   37.44
getcoverage 12.42   0.30   12.72
* 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
  'E:/biocbld/bbs-3.3-bioc/meat/CODEX.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'CODEX' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'CODEX' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CODEX' as CODEX_1.4.0.zip
* DONE (CODEX)

name	user	system	elapsed
bambedObjDemo	0	0	0
choiceofK	0.13	0.01	1.03
coverageObjDemo	0	0	0
gcDemo	0	0	0
getbambed	0.01	0.01	0.47
getcoverage	11.82	0.33	59.89
getgc	2.14	0.05	2.76
getmapp	0.06	0.00	0.06
mappDemo	0	0	0
mapp_ref	0.02	0.00	0.01
mappability	0.01	0.00	0.02
normObjDemo	0	0	0
normalize	37.08	0.01	37.09
normalize2	32.65	0.00	32.66
qc	0.05	0.00	0.04
qcObjDemo	0	0	0
segment	0.27	0.03	0.30

name	user	system	elapsed
bambedObjDemo	0	0	0
choiceofK	0.11	0.00	0.19
coverageObjDemo	0	0	0
gcDemo	0	0	0
getbambed	0.01	0.01	0.03
getcoverage	12.42	0.30	12.72
getgc	2.48	0.05	2.53
getmapp	0.07	0.00	0.08
mappDemo	0	0	0
mapp_ref	0.04	0.00	0.03
mappability	0	0	0
normObjDemo	0.01	0.00	0.02
normalize	45.27	0.06	45.33
normalize2	37.44	0.00	37.44
qc	0.05	0.00	0.05
qcObjDemo	0	0	0
segment	0.94	0.03	0.96