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This page was generated on 2021-09-20 15:05:09 -0400 (Mon, 20 Sep 2021).

CHECK results for CODEX on tokay2

To the developers/maintainers of the CODEX package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CODEX.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 358/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CODEX 1.24.0  (landing page)
Yuchao Jiang
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/CODEX
git_branch: RELEASE_3_13
git_last_commit: 0051ee2
git_last_commit_date: 2021-05-19 12:10:21 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CODEX
Version: 1.24.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CODEX.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CODEX_1.24.0.tar.gz
StartedAt: 2021-09-19 20:42:57 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 20:49:03 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 365.9 seconds
RetCode: 0
Status:   OK  
CheckDir: CODEX.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CODEX.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CODEX_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CODEX.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.24.0'
* 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
* 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 '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 poisson predict read.table smooth.spline
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  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 LazyData ... 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 (user + system) or elapsed time > 5s
             user system elapsed
normalize   20.17   0.13   20.30
normalize2  16.06   0.06   16.13
getcoverage 11.83   0.62   12.46
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
normalize   22.52   0.01   22.53
normalize2  19.33   0.02   19.35
getcoverage  9.91   0.53   10.43
* 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-3.13-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 http://155.52.207.165/BBS/3.13/bioc/src/contrib/CODEX_1.24.0.tar.gz && rm -rf CODEX.buildbin-libdir && mkdir CODEX.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CODEX.buildbin-libdir CODEX_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CODEX_1.24.0.zip && rm CODEX_1.24.0.tar.gz CODEX_1.24.0.zip
###
##############################################################################
##############################################################################


  % 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  734k  100  734k    0     0  1246k      0 --:--:-- --:--:-- --:--:-- 1246k
100  734k  100  734k    0     0  1246k      0 --:--:-- --:--:-- --:--:-- 1246k

install for i386

* installing *source* package 'CODEX' ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CODEX' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CODEX' as CODEX_1.24.0.zip
* DONE (CODEX)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'CODEX' successfully unpacked and MD5 sums checked

Tests output


Example timings

CODEX.Rcheck/examples_i386/CODEX-Ex.timings

nameusersystemelapsed
bambedObjDemo000
choiceofK0.080.000.08
coverageObjDemo000
gcDemo0.000.010.01
getbambed0.020.020.03
getcoverage11.83 0.6212.46
getgc1.790.021.80
getmapp0.010.010.03
mappDemo000
mapp_ref0.020.000.01
mappability000
normObjDemo000
normalize20.17 0.1320.30
normalize216.06 0.0616.13
qc0.020.000.01
qcObjDemo000
segment0.150.050.21

CODEX.Rcheck/examples_x64/CODEX-Ex.timings

nameusersystemelapsed
bambedObjDemo000
choiceofK0.080.020.09
coverageObjDemo000
gcDemo000
getbambed0.050.000.05
getcoverage 9.91 0.5310.43
getgc1.760.081.85
getmapp0.030.000.03
mappDemo000
mapp_ref0.020.000.02
mappability000
normObjDemo000
normalize22.52 0.0122.53
normalize219.33 0.0219.35
qc0.030.000.03
qcObjDemo000
segment0.190.000.18