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BioC 3.6: CHECK report for HMMcopy on tokay1

This page was generated on 2017-08-16 13:30:52 -0400 (Wed, 16 Aug 2017).

Package 641/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HMMcopy 1.19.0
Daniel Lai , Sohrab Shah
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/HMMcopy
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 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
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: HMMcopy
Version: 1.19.0
Command: rm -rf HMMcopy.buildbin-libdir HMMcopy.Rcheck && mkdir HMMcopy.buildbin-libdir HMMcopy.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HMMcopy.buildbin-libdir HMMcopy_1.19.0.tar.gz >HMMcopy.Rcheck\00install.out 2>&1 && cp HMMcopy.Rcheck\00install.out HMMcopy-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=HMMcopy.buildbin-libdir --install="check:HMMcopy-install.out" --force-multiarch --no-vignettes --timings HMMcopy_1.19.0.tar.gz
StartedAt: 2017-08-16 00:11:58 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:14:10 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 132.5 seconds
RetCode: 0
Status:  OK  
CheckDir: HMMcopy.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf HMMcopy.buildbin-libdir HMMcopy.Rcheck && mkdir HMMcopy.buildbin-libdir HMMcopy.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HMMcopy.buildbin-libdir HMMcopy_1.19.0.tar.gz >HMMcopy.Rcheck\00install.out 2>&1 && cp HMMcopy.Rcheck\00install.out HMMcopy-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=HMMcopy.buildbin-libdir --install="check:HMMcopy-install.out" --force-multiarch --no-vignettes --timings HMMcopy_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/HMMcopy.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HMMcopy/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HMMcopy' version '1.19.0'
* 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 'HMMcopy' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
Package in Depends field not imported from: 'geneplotter'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
correctReadcount: no visible global function definition for 'loess'
correctReadcount: no visible global function definition for 'predict'
correctReadcount: no visible global function definition for 'approxfun'
correctReadcount: no visible global function definition for 'lowess'
manualSegment: no visible global function definition for 'dnorm'
plotBias: no visible global function definition for 'par'
plotBias: no visible global function definition for 'plot'
plotBias: no visible global function definition for 'densCols'
plotCorrection: no visible global function definition for 'par'
plotCorrection: no visible global function definition for 'plot'
plotParam: no visible global function definition for 'plot'
plotParam: no visible global function definition for 'lines'
plotSegments: no visible binding for global variable 'segments'
plotSegments: no visible global function definition for 'plot'
plotSegments: no visible global function definition for 'lines'
rangedDataToSeg: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  approxfun densCols dnorm lines loess lowess par plot predict segments
  write.table
Consider adding
  importFrom("grDevices", "densCols")
  importFrom("graphics", "lines", "par", "plot", "segments")
  importFrom("stats", "approxfun", "dnorm", "loess", "lowess", "predict")
  importFrom("utils", "write.table")
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-3.6-bioc/meat/HMMcopy.buildbin-libdir/HMMcopy/libs/i386/HMMcopy.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 the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
HMMcopy-package 5.19   0.14    5.33
** 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/HMMcopy.Rcheck/00check.log'
for details.


HMMcopy.Rcheck/00install.out:


install for i386

* installing *source* package 'HMMcopy' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c forward_backward.c -o forward_backward.o
forward_backward.c: In function 'forward_backward':
forward_backward.c:28:13: warning: unused variable 'tmp' [-Wunused-variable]
   int K, T, tmp;
             ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c register.c -o register.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c viterbi.c -o viterbi.o
viterbi.c: In function 'viterbi':
viterbi.c:21:13: warning: unused variable 'tmp' [-Wunused-variable]
   int K, T, tmp;
             ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o HMMcopy.dll tmp.def forward_backward.o register.o viterbi.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/HMMcopy.buildbin-libdir/HMMcopy/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'HMMcopy' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c forward_backward.c -o forward_backward.o
forward_backward.c: In function 'forward_backward':
forward_backward.c:28:13: warning: unused variable 'tmp' [-Wunused-variable]
   int K, T, tmp;
             ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c register.c -o register.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c viterbi.c -o viterbi.o
viterbi.c: In function 'viterbi':
viterbi.c:21:13: warning: unused variable 'tmp' [-Wunused-variable]
   int K, T, tmp;
             ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o HMMcopy.dll tmp.def forward_backward.o register.o viterbi.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/HMMcopy.buildbin-libdir/HMMcopy/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HMMcopy' as HMMcopy_1.19.0.zip
* DONE (HMMcopy)

HMMcopy.Rcheck/examples_i386/HMMcopy-Ex.timings:

nameusersystemelapsed
HMMcopy-input0.170.010.19
HMMcopy-output0.340.080.42
HMMcopy-package5.190.145.33
HMMcopy-visualize0.910.020.92
HMMsegment0.420.000.42
correctReadcount0.530.000.53
wigsToRangedData0.120.000.13

HMMcopy.Rcheck/examples_x64/HMMcopy-Ex.timings:

nameusersystemelapsed
HMMcopy-input0.340.000.34
HMMcopy-output0.470.040.52
HMMcopy-package4.190.084.27
HMMcopy-visualize0.970.031.00
HMMsegment0.470.030.50
correctReadcount0.760.020.78
wigsToRangedData0.130.000.12