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CHECK report for plw on tokay2

This page was generated on 2019-04-09 11:56:07 -0400 (Tue, 09 Apr 2019).

Package 1201/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plw 1.43.0
Magnus Astrand
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/plw
Branch: master
Last Commit: 3524ffb
Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018)
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 [ OK ] 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: plw
Version: 1.43.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plw.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings plw_1.43.0.tar.gz
StartedAt: 2019-04-09 04:58:37 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 05:00:02 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 85.2 seconds
RetCode: 0
Status:  OK  
CheckDir: plw.Rcheck
Warnings: 0

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:plw.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings plw_1.43.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/plw.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'plw/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'plw' version '1.43.0'
* 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 '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
* 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 ... 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 ... NOTE
.onAttach: no visible global function definition for 'winMenuAddItem'
Undefined global functions or variables:
  winMenuAddItem
Consider adding
  importFrom("utils", "winMenuAddItem")
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 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/plw/libs/i386/plw.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/plw/libs/x64/plw.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/plw.Rcheck/00check.log'
for details.



Installation output

plw.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/plw_1.43.0.tar.gz && rm -rf plw.buildbin-libdir && mkdir plw.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=plw.buildbin-libdir plw_1.43.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL plw_1.43.0.zip && rm plw_1.43.0.tar.gz plw_1.43.0.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  390k  100  390k    0     0  5024k      0 --:--:-- --:--:-- --:--:-- 5503k

install for i386

* installing *source* package 'plw' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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;
              ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c SpecialOptim.c -o SpecialOptim.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o plw.dll tmp.def SpecialFunctions.o SpecialOptim.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/plw.buildbin-libdir/00LOCK-plw/00new/plw/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'plw'
    finding HTML links ... done
    AffySpikeU95Subset                      html  
    HowToPLW                                html  
    estimateMVbeta                          html  
    estimateSigma                           html  
    estimateSigmaMV                         html  
    estimateSigmaMVbeta                     html  
    getKnots                                html  
    lmw                                     html  
    logitT                                  html  
    plw-package                             html  
    plw                                     html  
    scaleParameterPlot                      html  
    statByIndex                             html  
    topRankSummary                          html  
    varHistPlot                             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 'plw' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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;
              ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c SpecialOptim.c -o SpecialOptim.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o plw.dll tmp.def SpecialFunctions.o SpecialOptim.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/plw.buildbin-libdir/plw/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'plw' as plw_1.43.0.zip
* DONE (plw)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'plw' successfully unpacked and MD5 sums checked

Tests output


Example timings

plw.Rcheck/examples_i386/plw-Ex.timings

nameusersystemelapsed
HowToPLW000
lmw1.780.011.80
logitT1.670.041.70
plw4.000.034.04
scaleParameterPlot1.910.001.90
statByIndex1.310.001.31
topRankSummary2.470.012.49
varHistPlot2.120.032.15

plw.Rcheck/examples_x64/plw-Ex.timings

nameusersystemelapsed
HowToPLW000
lmw2.030.022.05
logitT1.840.031.87
plw3.830.033.86
scaleParameterPlot1.860.061.92
statByIndex0.950.001.28
topRankSummary2.140.002.14
varHistPlot1.790.031.82