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BioC 3.5: CHECK report for CODEX on tokay2

This page was generated on 2017-08-16 13:24:05 -0400 (Wed, 16 Aug 2017).

Package 258/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CODEX 1.8.0
Yuchao Jiang
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/CODEX
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CODEX
Version: 1.8.0
Command: rm -rf CODEX.buildbin-libdir CODEX.Rcheck && mkdir CODEX.buildbin-libdir CODEX.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CODEX.buildbin-libdir CODEX_1.8.0.tar.gz >CODEX.Rcheck\00install.out 2>&1 && cp CODEX.Rcheck\00install.out CODEX-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CODEX.buildbin-libdir --install="check:CODEX-install.out" --force-multiarch --no-vignettes --timings CODEX_1.8.0.tar.gz
StartedAt: 2017-08-15 22:51:52 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:58:40 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 407.4 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-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CODEX.buildbin-libdir CODEX_1.8.0.tar.gz >CODEX.Rcheck\00install.out 2>&1 && cp CODEX.Rcheck\00install.out CODEX-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CODEX.buildbin-libdir --install="check:CODEX-install.out" --force-multiarch --no-vignettes --timings CODEX_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/CODEX.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.8.0'
* 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   22.90   0.19   23.10
normalize2  18.96   0.02   18.96
getcoverage 12.46   0.29   26.61
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
normalize   30.76   0.11   30.87
normalize2  22.31   0.00   22.31
getcoverage  7.88   0.37    8.25
* 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-3.5-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_1.8.0.zip
* DONE (CODEX)

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

nameusersystemelapsed
bambedObjDemo0.000.020.01
choiceofK0.060.000.06
coverageObjDemo000
gcDemo000
getbambed0.000.020.31
getcoverage12.46 0.2926.61
getgc2.150.072.22
getmapp0.050.010.07
mappDemo000
mapp_ref0.030.000.03
mappability000
normObjDemo000
normalize22.90 0.1923.10
normalize218.96 0.0218.96
qc0.030.000.04
qcObjDemo000
segment0.170.040.21

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

nameusersystemelapsed
bambedObjDemo000
choiceofK0.070.000.07
coverageObjDemo000
gcDemo000
getbambed0.030.000.03
getcoverage7.880.378.25
getgc1.720.111.83
getmapp0.080.000.08
mappDemo000
mapp_ref0.030.000.03
mappability000
normObjDemo000
normalize30.76 0.1130.87
normalize222.31 0.0022.31
qc0.040.000.03
qcObjDemo000
segment0.740.050.78