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CHECK report for plrs on tokay2

This page was generated on 2019-10-16 12:27:13 -0400 (Wed, 16 Oct 2019).

Package 1225/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plrs 1.24.0
Gwenael G.R. Leday to
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/plrs
Branch: RELEASE_3_9
Last Commit: 85af8ce
Last Changed Date: 2019-05-02 11:53:39 -0400 (Thu, 02 May 2019)
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 [ WARNINGS ] 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

Summary

Package: plrs
Version: 1.24.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plrs.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings plrs_1.24.0.tar.gz
StartedAt: 2019-10-16 06:02:23 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:04:11 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 107.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: plrs.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plrs.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings plrs_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/plrs.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.24.0'
* 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 'plrs' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8uGrT4/R.INSTALL1e1c390a75b2/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-3.9-bioc/tmpdir/Rtmp8uGrT4/R.INSTALL1e1c390a75b2/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-3.9-bioc/tmpdir/Rtmp8uGrT4/R.INSTALL1e1c390a75b2/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-3.9-bioc/tmpdir/Rtmp8uGrT4/R.INSTALL1e1c390a75b2/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-3.9-bioc/tmpdir/Rtmp8uGrT4/R.INSTALL1e1c390a75b2/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-3.9-bioc/tmpdir/Rtmp8uGrT4/R.INSTALL1e1c390a75b2/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-3.9-bioc/tmpdir/Rtmp8uGrT4/R.INSTALL1e1c390a75b2/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-3.9-bioc/tmpdir/Rtmp8uGrT4/R.INSTALL1e1c390a75b2/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-3.9-bioc/tmpdir/Rtmp8uGrT4/R.INSTALL1e1c390a75b2/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-3.9-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 9.26   0.04    9.31
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
plrs.series 7.07   0.05    7.11
* 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-3.9-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://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/plrs_1.24.0.tar.gz && rm -rf plrs.buildbin-libdir && mkdir plrs.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=plrs.buildbin-libdir plrs_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL plrs_1.24.0.zip && rm plrs_1.24.0.tar.gz plrs_1.24.0.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  467k  100  467k    0     0  7375k      0 --:--:-- --:--:-- --:--:-- 8342k

install for i386

* installing *source* package 'plrs' ...
** using staged installation
** 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-3.9-bioc/tmpdir/Rtmp8uGrT4/R.INSTALL1e1c390a75b2/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-3.9-bioc/tmpdir/Rtmp8uGrT4/R.INSTALL1e1c390a75b2/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-3.9-bioc/tmpdir/Rtmp8uGrT4/R.INSTALL1e1c390a75b2/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-3.9-bioc/tmpdir/Rtmp8uGrT4/R.INSTALL1e1c390a75b2/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-3.9-bioc/tmpdir/Rtmp8uGrT4/R.INSTALL1e1c390a75b2/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-3.9-bioc/tmpdir/Rtmp8uGrT4/R.INSTALL1e1c390a75b2/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-3.9-bioc/tmpdir/Rtmp8uGrT4/R.INSTALL1e1c390a75b2/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-3.9-bioc/tmpdir/Rtmp8uGrT4/R.INSTALL1e1c390a75b2/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-3.9-bioc/tmpdir/Rtmp8uGrT4/R.INSTALL1e1c390a75b2/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 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 'plrs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'plrs' as plrs_1.24.0.zip
* DONE (plrs)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'plrs' successfully unpacked and MD5 sums checked

Tests output


Example timings

plrs.Rcheck/examples_i386/plrs-Ex.timings

nameusersystemelapsed
criteria0.260.000.26
modify.conf000
neveCN170.140.010.16
neveGE170.060.030.09
plrs0.020.020.03
plrs.cb1.780.332.30
plrs.series9.260.049.31
plrs.sim0.040.020.05
plrs.test0.010.000.01

plrs.Rcheck/examples_x64/plrs-Ex.timings

nameusersystemelapsed
criteria0.200.010.22
modify.conf000
neveCN170.110.020.12
neveGE170.050.000.05
plrs0.000.020.02
plrs.cb1.710.182.37
plrs.series7.070.057.11
plrs.sim0.010.020.03
plrs.test0.000.010.02