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CHECK report for plw on malbec2

This page was generated on 2018-10-17 08:22:15 -0400 (Wed, 17 Oct 2018).

Package 1107/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plw 1.40.0
Magnus Astrand
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/plw
Branch: RELEASE_3_7
Last Commit: 7a59826
Last Changed Date: 2018-04-30 10:35:08 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: plw
Version: 1.40.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:plw.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings plw_1.40.0.tar.gz
StartedAt: 2018-10-16 02:45:31 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 02:46:43 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 71.2 seconds
RetCode: 0
Status:  OK 
CheckDir: plw.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:plw.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings plw_1.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/plw.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plw/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘plw’ version ‘1.40.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘plw’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘affy’
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
* 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .C("qnorm_c", ..., PACKAGE = "affy")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/plw.Rcheck/00check.log’
for details.



Installation output

plw.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL plw
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘plw’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c SpecialFunctions.c -o SpecialFunctions.o
SpecialFunctions.c: In function ‘getPosteriorProbsAndSigmaHatStrata0’:
SpecialFunctions.c:154:20: warning: variable ‘s2’ set but not used [-Wunused-but-set-variable]
  double kk,C,s0,s1,s2,temp0,aa;
                    ^
SpecialFunctions.c:154:17: warning: variable ‘s1’ set but not used [-Wunused-but-set-variable]
  double kk,C,s0,s1,s2,temp0,aa;
                 ^
SpecialFunctions.c:154:14: warning: variable ‘s0’ set but not used [-Wunused-but-set-variable]
  double kk,C,s0,s1,s2,temp0,aa;
              ^
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c SpecialOptim.c -o SpecialOptim.o
gcc -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o plw.so SpecialFunctions.o SpecialOptim.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/plw/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (plw)

Tests output


Example timings

plw.Rcheck/plw-Ex.timings

nameusersystemelapsed
HowToPLW0.0000.0000.001
lmw1.3360.0001.342
logitT1.1840.0081.204
plw2.4160.0162.457
scaleParameterPlot1.2240.0041.238
statByIndex0.9760.0000.977
topRankSummary1.2400.0081.253
varHistPlot1.2880.0041.300