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CHECK report for occugene on tokay1

This page was generated on 2020-04-15 12:17:53 -0400 (Wed, 15 Apr 2020).

Package 1167/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
occugene 1.46.0
Oliver Will
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/occugene
Branch: RELEASE_3_10
Last Commit: b27ed7f
Last Changed Date: 2019-10-29 13:07:45 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 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: occugene
Version: 1.46.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:occugene.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings occugene_1.46.0.tar.gz
StartedAt: 2020-04-15 05:10:05 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 05:10:29 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 24.2 seconds
RetCode: 0
Status:  OK  
CheckDir: occugene.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:occugene.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings occugene_1.46.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/occugene.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'occugene/DESCRIPTION' ... OK
* this is package 'occugene' version '1.46.0'
* 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 'occugene' 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
binInsertHist: no visible global function definition for 'hist'
delta0: no visible global function definition for 'coef'
eMult : unequalApproxEMult: no visible global function definition for
  'runif'
eMult : unequalApproxEMult: no visible binding for global variable
  'hist'
fFit : expModel: no visible global function definition for 'nls'
loadAnnotation: no visible global function definition for 'read.table'
loadInsertions: no visible global function definition for 'read.table'
unbiasB0 : simB0: no visible global function definition for 'coef'
unbiasB0: no visible global function definition for 'coef'
varMult : unequalApproxVarMult: no visible global function definition
  for 'runif'
varMult : unequalApproxVarMult: no visible binding for global variable
  'hist'
varMult : unequalApproxVarMult: no visible global function definition
  for 'var'
Undefined global functions or variables:
  coef hist nls read.table runif var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "coef", "nls", "runif", "var")
  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
** running examples for arch 'x64' ... OK
* 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
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/occugene.Rcheck/00check.log'
for details.



Installation output

occugene.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/occugene_1.46.0.tar.gz && rm -rf occugene.buildbin-libdir && mkdir occugene.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=occugene.buildbin-libdir occugene_1.46.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL occugene_1.46.0.zip && rm occugene_1.46.0.tar.gz occugene_1.46.0.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 12093  100 12093    0     0  50472      0 --:--:-- --:--:-- --:--:-- 51241

install for i386

* installing *source* package 'occugene' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'occugene'
    finding HTML links ... done
    binHist                                 html  
    binInsert                               html  
    binInsertHist                           html  
    checkFormat                             html  
    delta0                                  html  
    eMult                                   html  
    etDelta                                 html  
    fCumul                                  html  
    fFit                                    html  
    loadAnnotation                          html  
    loadInsertions                          html  
    occup2Negenes                           html  
    sampleAnnotation                        html  
    sampleInsertions                        html  
    unbiasB0                                html  
    unbiasDelta0                            html  
    varMult                                 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 'occugene' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'occugene' as occugene_1.46.0.zip
* DONE (occugene)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'occugene' successfully unpacked and MD5 sums checked

Tests output


Example timings

occugene.Rcheck/examples_i386/occugene-Ex.timings

nameusersystemelapsed
binHist000
binInsert000
binInsertHist000
checkFormat0.020.020.03
delta00.040.000.05
eMult0.390.000.39
etDelta0.020.000.02
fCumul000
fFit0.030.000.03
loadAnnotation000
loadInsertions000
occup2Negenes0.020.000.01
unbiasB00.310.000.32
unbiasDelta00.390.000.39
varMult0.40.00.4

occugene.Rcheck/examples_x64/occugene-Ex.timings

nameusersystemelapsed
binHist000
binInsert000
binInsertHist000
checkFormat0.000.030.03
delta00.050.000.04
eMult0.420.000.43
etDelta0.000.010.01
fCumul000
fFit0.030.000.03
loadAnnotation000
loadInsertions000
occup2Negenes0.020.000.02
unbiasB00.360.020.37
unbiasDelta00.450.000.46
varMult0.440.000.43