Back to Multiple platform build/check report for BioC 3.9
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for CFAssay on malbec2

This page was generated on 2019-04-09 11:40:19 -0400 (Tue, 09 Apr 2019).

Package 234/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CFAssay 1.17.1
Herbert Braselmann
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/CFAssay
Branch: master
Last Commit: f1d2fc4
Last Changed Date: 2018-12-18 11:27:29 -0400 (Tue, 18 Dec 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: CFAssay
Version: 1.17.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CFAssay.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CFAssay_1.17.1.tar.gz
StartedAt: 2019-04-08 23:18:09 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:18:29 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 20.4 seconds
RetCode: 0
Status:  OK 
CheckDir: CFAssay.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CFAssay.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CFAssay_1.17.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CFAssay.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CFAssay/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CFAssay’ version ‘1.17.1’
* 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 for sufficient/correct file permissions ... 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
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.cellsurvLQfit plotExp.cellsurvLQfit plotExp.cfa2way
  plotExp.default print.cellsurvLQdiff print.cellsurvLQfit
  print.cfa2way
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 ... 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/CFAssay.Rcheck/00check.log’
for details.



Installation output

CFAssay.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CFAssay
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘CFAssay’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘cfassay.Rnw’ using ‘UTF-8’ 
** 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
* DONE (CFAssay)

Tests output


Example timings

CFAssay.Rcheck/CFAssay-Ex.timings

nameusersystemelapsed
cellsurvLQdiff0.3370.0000.470
cellsurvLQfit0.0820.0000.083
cfa2way0.0320.0000.127
pes0.0510.0040.053
plot.cellsurvLQfit0.2580.0000.258
plotExp0.0620.0000.062
plotExp.cellsurvLQfit0.0710.0000.129
plotExp.cfa2way0.0600.0040.063
plotExp.default0.0950.0030.100
print.cellsurvLQdiff0.0570.0000.057
print.cellsurvLQfit0.0490.0000.049
print.cfa2way0.0150.0000.015
sfpmean0.1170.0000.117