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CHECK report for plrs on tokay1

This page was generated on 2019-04-13 11:22:29 -0400 (Sat, 13 Apr 2019).

Package 1170/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plrs 1.22.0
Gwenael G.R. Leday to
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/plrs
Branch: RELEASE_3_8
Last Commit: 8a760ff
Last Changed Date: 2018-10-30 11:41:50 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] 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: plrs
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plrs.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings plrs_1.22.0.tar.gz
StartedAt: 2019-04-13 04:35:53 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:38:18 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 144.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: plrs.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plrs.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings plrs_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/plrs.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'plrs/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'plrs' version '1.22.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'plrs' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/neveCN17.Rd:15: file link 'cghCall' in package 'CGHbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/neveGE17.Rd:15: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:32: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:33: file link 'cghSeg' in package 'CGHbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:33: file link 'cghCall' in package 'CGHbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:47: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:48: file link 'cghSeg' in package 'CGHbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:48: file link 'cghCall' in package 'CGHbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:50: file link 'cghSeg' in package 'CGHbase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/plrs.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods'
A package should be listed in only one of these fields.
* 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 ... NOTE
'library' or 'require' call to 'mvtnorm' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' call which should be '::': 'CGHbase:::calls'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
Examples with CPU or elapsed time > 5s
            user system elapsed
plrs.series 6.99   0.03    7.01
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
plrs.series  6.8   0.03    6.83
* 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 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/plrs.Rcheck/00check.log'
for details.



Installation output

plrs.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/plrs_1.22.0.tar.gz && rm -rf plrs.buildbin-libdir && mkdir plrs.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=plrs.buildbin-libdir plrs_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL plrs_1.22.0.zip && rm plrs_1.22.0.tar.gz plrs_1.22.0.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  468k  100  468k    0     0  9201k      0 --:--:-- --:--:-- --:--:--  9.9M

install for i386

* installing *source* package 'plrs' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'plrs'
    finding HTML links ... done
    criteria                                html  
    modify.conf                             html  
    neveCN17                                html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/neveCN17.Rd:15: file link 'cghCall' in package 'CGHbase' does not exist and so has been treated as a topic
    neveGE17                                html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/neveGE17.Rd:15: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    plot-methods                            html  
    plrs-class                              html  
    plrs-package                            html  
    plrs                                    html  
    plrs.cb                                 html  
    plrs.select-class                       html  
    plrs.select                             html  
    plrs.series-class                       html  
    plrs.series                             html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:32: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:33: file link 'cghSeg' in package 'CGHbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:33: file link 'cghCall' in package 'CGHbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:47: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:48: file link 'cghSeg' in package 'CGHbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:48: file link 'cghCall' in package 'CGHbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOAgG6h/R.INSTALL1ccc21dc73ad/plrs/man/plrs.series.Rd:50: file link 'cghSeg' in package 'CGHbase' does not exist and so has been treated as a topic
    plrs.sim                                html  
    plrs.test                               html  
    predict.plrs                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'plrs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'plrs' as plrs_1.22.0.zip
* DONE (plrs)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'plrs' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

plrs.Rcheck/examples_i386/plrs-Ex.timings

nameusersystemelapsed
criteria0.230.020.25
modify.conf000
neveCN170.110.020.13
neveGE170.050.000.04
plrs0.010.000.01
plrs.cb1.090.191.32
plrs.series6.990.037.01
plrs.sim0.030.000.03
plrs.test0.020.000.02

plrs.Rcheck/examples_x64/plrs-Ex.timings

nameusersystemelapsed
criteria0.220.010.24
modify.conf000
neveCN170.110.020.12
neveGE170.050.000.05
plrs0.000.010.01
plrs.cb1.230.221.47
plrs.series6.800.036.83
plrs.sim0.030.000.03
plrs.test0.020.000.02