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CHECK report for CODEX on tokay1

This page was generated on 2019-04-13 11:24:46 -0400 (Sat, 13 Apr 2019).

Package 302/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CODEX 1.14.1
Yuchao Jiang
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/CODEX
Branch: RELEASE_3_8
Last Commit: d4c7d54
Last Changed Date: 2019-01-04 13:25:48 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CODEX
Version: 1.14.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CODEX.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings CODEX_1.14.1.tar.gz
StartedAt: 2019-04-13 01:23:21 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:30:05 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 403.8 seconds
RetCode: 0
Status:  OK  
CheckDir: CODEX.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CODEX.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings CODEX_1.14.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/CODEX.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.14.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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
* 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 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
normalize   27.67   0.33   28.01
normalize2  20.83   0.00   20.83
getcoverage  9.58   0.53   10.13
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
normalize2  23.72    0.0   23.72
normalize   22.81    0.0   22.81
getcoverage  9.11    0.5    9.61
* 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-3.8-bioc/meat/CODEX.Rcheck/00check.log'
for details.



Installation output

CODEX.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/CODEX_1.14.1.tar.gz && rm -rf CODEX.buildbin-libdir && mkdir CODEX.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CODEX.buildbin-libdir CODEX_1.14.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL CODEX_1.14.1.zip && rm CODEX_1.14.1.tar.gz CODEX_1.14.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  733k  100  733k    0     0  14.1M      0 --:--:-- --:--:-- --:--:-- 15.2M

install for i386

* installing *source* package 'CODEX' ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CODEX'
    finding HTML links ... done
    CODEX-package                           html  
    bambedObjDemo                           html  
    choiceofK                               html  
    coverageObjDemo                         html  
    gcDemo                                  html  
    getbambed                               html  
    getcoverage                             html  
    getgc                                   html  
    getmapp                                 html  
    mappDemo                                html  
    mapp_ref                                html  
    mappability                             html  
    normObjDemo                             html  
    normalize                               html  
    normalize2                              html  
    qc                                      html  
    qcObjDemo                               html  
    segment                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'CODEX' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CODEX' as CODEX_1.14.1.zip
* DONE (CODEX)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'CODEX' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

CODEX.Rcheck/examples_i386/CODEX-Ex.timings

nameusersystemelapsed
bambedObjDemo000
choiceofK0.060.020.08
coverageObjDemo000
gcDemo000
getbambed0.030.000.03
getcoverage 9.58 0.5310.13
getgc2.780.062.85
getmapp0.050.000.05
mappDemo000
mapp_ref0.020.000.02
mappability000
normObjDemo000
normalize27.67 0.3328.01
normalize220.83 0.0020.83
qc0.010.000.01
qcObjDemo000
segment0.170.050.22

CODEX.Rcheck/examples_x64/CODEX-Ex.timings

nameusersystemelapsed
bambedObjDemo000
choiceofK0.080.000.08
coverageObjDemo000
gcDemo000
getbambed0.020.000.01
getcoverage9.110.509.61
getgc1.750.031.78
getmapp0.010.020.04
mappDemo000
mapp_ref0.020.000.01
mappability000
normObjDemo000
normalize22.81 0.0022.81
normalize223.72 0.0023.72
qc0.010.000.02
qcObjDemo000
segment0.850.000.84