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CHECK report for CFAssay on tokay1

This page was generated on 2018-04-12 13:25:21 -0400 (Thu, 12 Apr 2018).

Package 201/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CFAssay 1.12.0
Herbert Braselmann
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/CFAssay
Branch: RELEASE_3_6
Last Commit: a00cf6e
Last Changed Date: 2017-10-30 12:40:45 -0400 (Mon, 30 Oct 2017)
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
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CFAssay
Version: 1.12.0
Command: rm -rf CFAssay.buildbin-libdir CFAssay.Rcheck && mkdir CFAssay.buildbin-libdir CFAssay.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CFAssay.buildbin-libdir CFAssay_1.12.0.tar.gz >CFAssay.Rcheck\00install.out 2>&1 && cp CFAssay.Rcheck\00install.out CFAssay-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CFAssay.buildbin-libdir --install="check:CFAssay-install.out" --force-multiarch --no-vignettes --timings CFAssay_1.12.0.tar.gz
StartedAt: 2018-04-11 22:47:45 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:48:30 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 44.7 seconds
RetCode: 0
Status:  OK  
CheckDir: CFAssay.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CFAssay.buildbin-libdir CFAssay.Rcheck && mkdir CFAssay.buildbin-libdir CFAssay.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CFAssay.buildbin-libdir CFAssay_1.12.0.tar.gz >CFAssay.Rcheck\00install.out 2>&1 && cp CFAssay.Rcheck\00install.out CFAssay-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CFAssay.buildbin-libdir --install="check:CFAssay-install.out" --force-multiarch --no-vignettes --timings CFAssay_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CFAssay.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CFAssay/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CFAssay' version '1.12.0'
* 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 'CFAssay' 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
cellsurvLQdiff : fitLQ.MLdiff: no visible global function definition
  for 'glm'
cellsurvLQdiff : fitLQ.MLdiff: no visible global function definition
  for 'quasipoisson'
cellsurvLQdiff : fitLQ.MLdiff: no visible global function definition
  for 'anova'
cellsurvLQdiff : fitLQ.LSdiff: no visible global function definition
  for 'lm'
cellsurvLQdiff : fitLQ.LSdiff: no visible global function definition
  for 'anova'
cellsurvLQdiff : fitLQ1.MLdiff: no visible global function definition
  for 'glm'
cellsurvLQdiff : fitLQ1.MLdiff: no visible global function definition
  for 'quasipoisson'
cellsurvLQdiff : fitLQ1.MLdiff: no visible global function definition
  for 'anova'
cellsurvLQdiff : fitLQ1.LSdiff: no visible global function definition
  for 'lm'
cellsurvLQdiff : fitLQ1.LSdiff: no visible global function definition
  for 'anova'
cellsurvLQdiff : fitLQ1.LSdiffFr: no visible global function definition
  for 'lm'
cellsurvLQdiff : fitLQ1.LSdiffFr: no visible global function definition
  for 'anova'
cellsurvLQfit : fitLQ.ML: no visible global function definition for
  'glm'
cellsurvLQfit : fitLQ.ML: no visible global function definition for
  'quasipoisson'
cellsurvLQfit : fitLQ.LS: no visible global function definition for
  'lm'
cellsurvLQfit : fitLQ1.ML: no visible global function definition for
  'glm'
cellsurvLQfit : fitLQ1.ML: no visible global function definition for
  'quasipoisson'
cellsurvLQfit : fitLQ1.LS: no visible global function definition for
  'lm'
cellsurvLQfit : fitLQ1.LSfr: no visible global function definition for
  'lm'
cfa2way: no visible global function definition for 'formula'
cfa2way: no visible global function definition for 'glm'
cfa2way: no visible global function definition for 'quasipoisson'
cfa2way: no visible global function definition for 'anova'
cfa2way: no visible global function definition for 'lm'
pes : <anonymous>: no visible global function definition for 'glm'
pes : <anonymous>: no visible global function definition for
  'quasipoisson'
pes : <anonymous>: no visible global function definition for 'lm'
pes : <anonymous>: no visible binding for global variable 'logPle'
plot.cellsurvLQfit: no visible global function definition for 'par'
plot.cellsurvLQfit: no visible global function definition for 'curve'
plot.cellsurvLQfit: no visible global function definition for 'points'
plot.cellsurvLQfit: no visible global function definition for
  'segments'
plotExp.cellsurvLQfit: no visible global function definition for 'par'
plotExp.cellsurvLQfit: no visible global function definition for 'glm'
plotExp.cellsurvLQfit: no visible global function definition for
  'quasipoisson'
plotExp.cellsurvLQfit: no visible global function definition for 'plot'
plotExp.cellsurvLQfit: no visible global function definition for
  'segments'
plotExp.cellsurvLQfit: no visible global function definition for
  'curve'
plotExp.cellsurvLQfit: no visible global function definition for
  'legend'
plotExp.cellsurvLQfit: no visible global function definition for 'text'
plotExp.cellsurvLQfit: no visible global function definition for
  'title'
plotExp.cellsurvLQfit: no visible global function definition for 'lm'
plotExp.cfa2way: no visible global function definition for 'par'
plotExp.cfa2way: no visible global function definition for 'barplot'
plotExp.cfa2way: no visible global function definition for 'points'
plotExp.cfa2way: no visible global function definition for 'segments'
plotExp.cfa2way: no visible global function definition for 'text'
plotExp.cfa2way: no visible global function definition for 'title'
plotExp.cfa2way: no visible global function definition for 'box'
sfpmean : sf.mean: no visible global function definition for 'glm'
sfpmean : sf.mean: no visible global function definition for
  'quasipoisson'
sfpmean : sf.mean: no visible global function definition for 'poisson'
Undefined global functions or variables:
  anova barplot box curve formula glm legend lm logPle par plot points
  poisson quasipoisson segments text title
Consider adding
  importFrom("graphics", "barplot", "box", "curve", "legend", "par",
             "plot", "points", "segments", "text", "title")
  importFrom("stats", "anova", "formula", "glm", "lm", "poisson",
             "quasipoisson")
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 installed files from 'inst/doc' ... 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-3.6-bioc/meat/CFAssay.Rcheck/00check.log'
for details.



Installation output

CFAssay.Rcheck/00install.out


install for i386

* installing *source* package 'CFAssay' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'CFAssay'
    finding HTML links ... done
    cellsurvLQdiff                          html  
    cellsurvLQfit                           html  
    cfa2way                                 html  
    pes                                     html  
    plot.cellsurvLQfit                      html  
    plotExp                                 html  
    plotExp.cellsurvLQfit                   html  
    plotExp.cfa2way                         html  
    plotExp.default                         html  
    print.cellsurvLQdiff                    html  
    print.cellsurvLQfit                     html  
    print.cfa2way                           html  
    sfpmean                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'CFAssay' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CFAssay' as CFAssay_1.12.0.zip
* DONE (CFAssay)
In R CMD INSTALL
In R CMD INSTALL

Tests output


Example timings

CFAssay.Rcheck/examples_i386/CFAssay-Ex.timings

nameusersystemelapsed
cellsurvLQdiff0.610.000.61
cellsurvLQfit0.110.000.11
cfa2way0.090.000.09
pes0.030.000.04
plot.cellsurvLQfit0.190.000.18
plotExp0.080.000.08
plotExp.cellsurvLQfit0.160.000.16
plotExp.cfa2way0.070.000.22
plotExp.default0.050.010.06
print.cellsurvLQdiff0.050.000.05
print.cellsurvLQfit0.050.000.04
print.cfa2way0.010.000.02
sfpmean0.080.000.08

CFAssay.Rcheck/examples_x64/CFAssay-Ex.timings

nameusersystemelapsed
cellsurvLQdiff0.940.010.95
cellsurvLQfit0.170.000.17
cfa2way0.160.020.17
pes0.070.000.08
plot.cellsurvLQfit0.320.000.31
plotExp0.070.000.08
plotExp.cellsurvLQfit0.240.000.23
plotExp.cfa2way0.080.001.06
plotExp.default0.060.010.08
print.cellsurvLQdiff0.060.000.06
print.cellsurvLQfit0.060.000.07
print.cfa2way0.020.000.01
sfpmean0.110.000.11