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CHECK report for plw on malbec1

This page was generated on 2020-04-15 12:05:08 -0400 (Wed, 15 Apr 2020).

Package 1279/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plw 1.46.0
Magnus Astrand
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/plw
Branch: RELEASE_3_10
Last Commit: 3b35b57
Last Changed Date: 2019-10-29 13:07:54 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  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: plw
Version: 1.46.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:plw.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings plw_1.46.0.tar.gz
StartedAt: 2020-04-15 00:27:46 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:28:33 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 46.9 seconds
RetCode: 0
Status:  OK 
CheckDir: plw.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:plw.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings plw_1.46.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/plw.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.46.0’
* 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-3.10-bioc/meat/plw.Rcheck/00check.log’
for details.



Installation output

plw.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL plw
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘plw’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c SpecialOptim.c -o SpecialOptim.o
gcc -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o plw.so SpecialFunctions.o SpecialOptim.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-plw/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (plw)

Tests output


Example timings

plw.Rcheck/plw-Ex.timings

nameusersystemelapsed
HowToPLW0.0000.0040.001
lmw1.6640.0121.687
logitT1.5680.0081.593
plw3.0640.0203.118
scaleParameterPlot1.5920.0001.605
statByIndex1.1200.0041.125
topRankSummary1.7080.0001.720
varHistPlot1.6040.0041.619