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CHECK report for CFAssay on riesling1

This page was generated on 2020-10-24 11:04:46 -0400 (Sat, 24 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CFAssay PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 265/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CFAssay 1.23.0
Herbert Braselmann
Snapshot Date: 2020-10-23 14:40:36 -0400 (Fri, 23 Oct 2020)
URL: https://git.bioconductor.org/packages/CFAssay
Branch: master
Last Commit: bc395b1
Last Changed Date: 2020-04-27 14:45:10 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ] OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CFAssay
Version: 1.23.0
Command: D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CFAssay.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CFAssay_1.23.0.tar.gz
StartedAt: 2020-10-24 01:55:04 -0400 (Sat, 24 Oct 2020)
EndedAt: 2020-10-24 01:55:30 -0400 (Sat, 24 Oct 2020)
EllapsedTime: 25.3 seconds
RetCode: 0
Status:  OK  
CheckDir: CFAssay.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CFAssay.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CFAssay_1.23.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.12-bioc/meat/CFAssay.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.23.0'
* 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
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plotExp.default
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
  '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 points
  poisson quasipoisson segments text title
Consider adding
  importFrom("graphics", "barplot", "box", "curve", "legend", "par",
             "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: 2 NOTEs
See
  'D:/biocbuild/bbs-3.12-bioc/meat/CFAssay.Rcheck/00check.log'
for details.



Installation output

CFAssay.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/CFAssay_1.23.0.tar.gz && rm -rf CFAssay.buildbin-libdir && mkdir CFAssay.buildbin-libdir && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CFAssay.buildbin-libdir CFAssay_1.23.0.tar.gz && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CFAssay_1.23.0.zip && rm CFAssay_1.23.0.tar.gz CFAssay_1.23.0.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
  6 19057    6  1219    0     0   7087      0  0:00:02 --:--:--  0:00:02  7046
100 19057  100 19057    0     0   107k      0 --:--:-- --:--:-- --:--:--  106k

install for i386

* installing *source* package 'CFAssay' ...
** using staged installation
** R
** inst
** byte-compile and prepare 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
   '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

install for x64

* installing *source* package 'CFAssay' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CFAssay' as CFAssay_1.23.0.zip
* DONE (CFAssay)
* installing to library 'D:/biocbuild/bbs-3.12-bioc/R/library'
package 'CFAssay' successfully unpacked and MD5 sums checked

Tests output


Example timings

CFAssay.Rcheck/examples_i386/CFAssay-Ex.timings

nameusersystemelapsed
cellsurvLQdiff0.140.000.14
cellsurvLQfit0.020.000.01
cfa2way0.030.000.03
pes0.050.000.05
plot.cellsurvLQfit0.20.00.2
plotExp0.100.030.20
plotExp.cellsurvLQfit0.030.000.12
plotExp.cfa2way0.120.000.14
plotExp.default0.020.000.14
print.cellsurvLQdiff0.050.020.06
print.cellsurvLQfit0.030.000.03
print.cfa2way0.010.000.02
sfpmean0.060.000.06

CFAssay.Rcheck/examples_x64/CFAssay-Ex.timings

nameusersystemelapsed
cellsurvLQdiff0.160.000.16
cellsurvLQfit0.030.000.03
cfa2way0.010.010.04
pes0.040.000.05
plot.cellsurvLQfit0.240.000.23
plotExp0.060.000.08
plotExp.cellsurvLQfit0.080.000.10
plotExp.cfa2way0.080.000.09
plotExp.default0.060.000.08
print.cellsurvLQdiff0.030.000.03
print.cellsurvLQfit0.020.000.02
print.cfa2way0.010.000.02
sfpmean0.050.000.04