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BioC 3.4: CHECK report for CODEX on tokay1

This page was generated on 2017-04-15 16:19:31 -0400 (Sat, 15 Apr 2017).

Package 242/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CODEX 1.6.0
Yuchao Jiang
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/CODEX
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CODEX
Version: 1.6.0
Command: rm -rf CODEX.buildbin-libdir CODEX.Rcheck && mkdir CODEX.buildbin-libdir CODEX.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CODEX.buildbin-libdir CODEX_1.6.0.tar.gz >CODEX.Rcheck\00install.out 2>&1 && cp CODEX.Rcheck\00install.out CODEX-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=CODEX.buildbin-libdir --install="check:CODEX-install.out" --force-multiarch --no-vignettes --timings CODEX_1.6.0.tar.gz
StartedAt: 2017-04-14 21:38:13 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:44:45 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 391.3 seconds
RetCode: 0
Status:  OK  
CheckDir: CODEX.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CODEX.buildbin-libdir CODEX.Rcheck && mkdir CODEX.buildbin-libdir CODEX.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CODEX.buildbin-libdir CODEX_1.6.0.tar.gz >CODEX.Rcheck\00install.out 2>&1 && cp CODEX.Rcheck\00install.out CODEX-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=CODEX.buildbin-libdir --install="check:CODEX-install.out" --force-multiarch --no-vignettes --timings CODEX_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/CODEX.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.6.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Rsamtools' 'GenomeInfoDb' 'BSgenome.Hsapiens.UCSC.hg19' 'IRanges'
  'Biostrings' 'S4Vectors'
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 '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   23.36   0.09   23.45
normalize2  18.39   0.02   18.41
getcoverage  9.80   0.28   43.97
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
normalize   28.89   0.04   28.92
normalize2  23.55   0.00   23.54
getcoverage  6.58   0.44    7.01
* 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:/Users/biocbuild/bbs-3.4-bioc/meat/CODEX.Rcheck/00check.log'
for details.


CODEX.Rcheck/00install.out:


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_1.6.0.zip
* DONE (CODEX)

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

nameusersystemelapsed
bambedObjDemo000
choiceofK0.050.010.07
coverageObjDemo000
gcDemo000
getbambed0.010.020.16
getcoverage 9.80 0.2843.97
getgc2.160.062.22
getmapp0.030.020.04
mappDemo000
mapp_ref0.010.000.02
mappability0.020.000.02
normObjDemo000
normalize23.36 0.0923.45
normalize218.39 0.0218.41
qc0.010.000.01
qcObjDemo000
segment0.590.070.67

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

nameusersystemelapsed
bambedObjDemo000
choiceofK0.070.000.06
coverageObjDemo000
gcDemo000
getbambed0.030.000.04
getcoverage6.580.447.01
getgc1.430.071.52
getmapp0.050.000.04
mappDemo000
mapp_ref0.020.000.02
mappability000
normObjDemo000
normalize28.89 0.0428.92
normalize223.55 0.0023.54
qc0.030.000.04
qcObjDemo000
segment0.190.000.18