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CHECK report for SamSPECTRAL on tokay2

This page was generated on 2019-10-16 12:23:25 -0400 (Wed, 16 Oct 2019).

Package 1451/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SamSPECTRAL 1.38.0
Habil
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/SamSPECTRAL
Branch: RELEASE_3_9
Last Commit: 0e5e2d9
Last Changed Date: 2019-05-02 11:53:13 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: SamSPECTRAL
Version: 1.38.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SamSPECTRAL.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SamSPECTRAL_1.38.0.tar.gz
StartedAt: 2019-10-16 06:52:45 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:53:24 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 38.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: SamSPECTRAL.Rcheck
Warnings: 1

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:SamSPECTRAL.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SamSPECTRAL_1.38.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SamSPECTRAL.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.38.0'
* 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-3.9-bioc/R/library/SamSPECTRAL/libs/i386/SamSPECTRAL.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SamSPECTRAL/libs/x64/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 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: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/SamSPECTRAL.Rcheck/00check.log'
for details.



Installation output

SamSPECTRAL.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/SamSPECTRAL_1.38.0.tar.gz && rm -rf SamSPECTRAL.buildbin-libdir && mkdir SamSPECTRAL.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SamSPECTRAL.buildbin-libdir SamSPECTRAL_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SamSPECTRAL_1.38.0.zip && rm SamSPECTRAL_1.38.0.tar.gz SamSPECTRAL_1.38.0.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
 25  443k   25  112k    0     0   305k      0  0:00:01 --:--:--  0:00:01  310k
100  443k  100  443k    0     0  1198k      0 --:--:-- --:--:-- --:--:-- 1215k

install for i386

* installing *source* package 'SamSPECTRAL' ...
** using staged installation
** 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 Rinit.c -o Rinit.o
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 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-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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:/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/SamSPECTRAL.buildbin-libdir/00LOCK-SamSPECTRAL/00new/SamSPECTRAL/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SamSPECTRAL'
    finding HTML links ... done
    Building_Communities                    html  
    Civilized_Spectral_Clustering           html  
    Conductance_Calculation                 html  
    Connecting                              html  
    SamSPECTRAL-package                     html  
    SamSPECTRAL                             html  
    check.SamSPECTRAL.input                 html  
    eigen.values.10                         html  
    eigen.values.1000                       html  
    kneepointDetection                      html  
    small                                   html  
    stmFSC                                  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 'SamSPECTRAL' ...
** 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 Rinit.c -o Rinit.o
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 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-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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:/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/SamSPECTRAL.buildbin-libdir/SamSPECTRAL/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SamSPECTRAL' as SamSPECTRAL_1.38.0.zip
* DONE (SamSPECTRAL)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'SamSPECTRAL' successfully unpacked and MD5 sums checked

Tests output


Example timings

SamSPECTRAL.Rcheck/examples_i386/SamSPECTRAL-Ex.timings

nameusersystemelapsed
Building_Communities000
Civilized_Spectral_Clustering000
Conductance_Calculation000
Connecting000
SamSPECTRAL-package000
SamSPECTRAL000
check.SamSPECTRAL.input000
eigen.values.100.030.000.03
eigen.values.10000.030.000.03
kneepointDetection0.030.000.03
small0.030.020.05
stmFSC0.250.000.25

SamSPECTRAL.Rcheck/examples_x64/SamSPECTRAL-Ex.timings

nameusersystemelapsed
Building_Communities000
Civilized_Spectral_Clustering000
Conductance_Calculation000
Connecting000
SamSPECTRAL-package000
SamSPECTRAL000
check.SamSPECTRAL.input000
eigen.values.100.020.020.03
eigen.values.10000.030.000.03
kneepointDetection0.050.000.05
small0.030.010.05
stmFSC0.170.000.17