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BioC 3.5: CHECK report for SamSPECTRAL on tokay2

This page was generated on 2017-10-18 14:20:39 -0400 (Wed, 18 Oct 2017).

Package 1176/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SamSPECTRAL 1.30.0
Habil Zare
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/SamSPECTRAL
Branch: RELEASE_3_5
Last Commit: 6c8f510
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS 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
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: SamSPECTRAL
Version: 1.30.0
Command: rm -rf SamSPECTRAL.buildbin-libdir SamSPECTRAL.Rcheck && mkdir SamSPECTRAL.buildbin-libdir SamSPECTRAL.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SamSPECTRAL.buildbin-libdir SamSPECTRAL_1.30.0.tar.gz >SamSPECTRAL.Rcheck\00install.out 2>&1 && cp SamSPECTRAL.Rcheck\00install.out SamSPECTRAL-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=SamSPECTRAL.buildbin-libdir --install="check:SamSPECTRAL-install.out" --force-multiarch --no-vignettes --timings SamSPECTRAL_1.30.0.tar.gz
StartedAt: 2017-10-18 02:50:43 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 02:51:22 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 39.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: SamSPECTRAL.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SamSPECTRAL.buildbin-libdir SamSPECTRAL.Rcheck && mkdir SamSPECTRAL.buildbin-libdir SamSPECTRAL.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SamSPECTRAL.buildbin-libdir SamSPECTRAL_1.30.0.tar.gz >SamSPECTRAL.Rcheck\00install.out 2>&1 && cp SamSPECTRAL.Rcheck\00install.out SamSPECTRAL-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=SamSPECTRAL.buildbin-libdir --install="check:SamSPECTRAL-install.out" --force-multiarch --no-vignettes --timings SamSPECTRAL_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/SamSPECTRAL.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SamSPECTRAL/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SamSPECTRAL' version '1.30.0'
* 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 'SamSPECTRAL' 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.
* 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 ... OK
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

.First.lib: no visible global function definition for 'provide'
Civilized_Spectral_Clustering: no visible global function definition
  for 'lm'
Civilized_Spectral_Clustering: no visible global function definition
  for 'coef'
Civilized_Spectral_Clustering: no visible global function definition
  for 'coefficients'
Civilized_Spectral_Clustering: no visible global function definition
  for 'plot'
Civilized_Spectral_Clustering: no visible global function definition
  for 'abline'
Civilized_Spectral_Clustering: no visible global function definition
  for 'kmeans'
kneepointDetection: no visible global function definition for 'lm'
kneepointDetection: no visible global function definition for 'png'
kneepointDetection: no visible global function definition for 'plot'
kneepointDetection: no visible global function definition for 'par'
kneepointDetection: no visible global function definition for 'axis'
kneepointDetection: no visible global function definition for 'title'
kneepointDetection: no visible global function definition for 'abline'
kneepointDetection: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  abline axis coef coefficients dev.off kmeans lm par plot png provide
  title
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "axis", "par", "plot", "title")
  importFrom("stats", "coef", "coefficients", "kmeans", "lm")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  'eigen'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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-3.5-bioc/meat/SamSPECTRAL.buildbin-libdir/SamSPECTRAL/libs/i386/SamSPECTRAL.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
** 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: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/SamSPECTRAL.Rcheck/00check.log'
for details.

SamSPECTRAL.Rcheck/00install.out:


install for i386

* installing *source* package 'SamSPECTRAL' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Rinit.c -o Rinit.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c conductance_computation.c -o conductance_computation.o
conductance_computation.c: In function 'conductance_computation':
conductance_computation.c:155:17: warning: variable 'repres_ind' set but not used [-Wunused-but-set-variable]
  int *density, *repres_ind;
                 ^
conductance_computation.c:155:7: warning: variable 'density' set but not used [-Wunused-but-set-variable]
  int *density, *repres_ind;
       ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c maximum_of_rows.c -o maximum_of_rows.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o SamSPECTRAL.dll tmp.def Rinit.o conductance_computation.o maximum_of_rows.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/SamSPECTRAL.buildbin-libdir/SamSPECTRAL/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 'SamSPECTRAL' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Rinit.c -o Rinit.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c conductance_computation.c -o conductance_computation.o
conductance_computation.c: In function 'conductance_computation':
conductance_computation.c:155:17: warning: variable 'repres_ind' set but not used [-Wunused-but-set-variable]
  int *density, *repres_ind;
                 ^
conductance_computation.c:155:7: warning: variable 'density' set but not used [-Wunused-but-set-variable]
  int *density, *repres_ind;
       ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c maximum_of_rows.c -o maximum_of_rows.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o SamSPECTRAL.dll tmp.def Rinit.o conductance_computation.o maximum_of_rows.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/SamSPECTRAL.buildbin-libdir/SamSPECTRAL/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SamSPECTRAL' as SamSPECTRAL_1.30.0.zip
* DONE (SamSPECTRAL)

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

nameusersystemelapsed
Building_Communities000
Civilized_Spectral_Clustering000
Conductance_Calculation000
Connecting0.010.000.01
SamSPECTRAL-package000
SamSPECTRAL000
check.SamSPECTRAL.input000
eigen.values.100.050.000.05
eigen.values.10000.050.000.05
kneepointDetection0.080.000.08
small0.060.000.06
stmFSC0.40.00.4

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

nameusersystemelapsed
Building_Communities000
Civilized_Spectral_Clustering000
Conductance_Calculation000
Connecting000
SamSPECTRAL-package000
SamSPECTRAL000
check.SamSPECTRAL.input000
eigen.values.100.050.000.05
eigen.values.10000.030.010.04
kneepointDetection0.130.000.13
small0.040.000.05
stmFSC0.280.060.35