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CHECK report for SamSPECTRAL on malbec2

This page was generated on 2019-10-16 11:58:09 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SamSPECTRAL.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SamSPECTRAL_1.38.0.tar.gz
StartedAt: 2019-10-16 04:47:10 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:47:45 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 35.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: SamSPECTRAL.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SamSPECTRAL.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SamSPECTRAL_1.38.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/SamSPECTRAL.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 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: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/SamSPECTRAL.Rcheck/00check.log’
for details.



Installation output

SamSPECTRAL.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL SamSPECTRAL
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘SamSPECTRAL’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c Rinit.c -o Rinit.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -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;
       ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c maximum_of_rows.c -o maximum_of_rows.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o SamSPECTRAL.so Rinit.o conductance_computation.o maximum_of_rows.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-SamSPECTRAL/00new/SamSPECTRAL/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 (SamSPECTRAL)

Tests output


Example timings

SamSPECTRAL.Rcheck/SamSPECTRAL-Ex.timings

nameusersystemelapsed
Building_Communities0.0000.0000.001
Civilized_Spectral_Clustering0.0010.0000.000
Conductance_Calculation000
Connecting000
SamSPECTRAL-package000
SamSPECTRAL000
check.SamSPECTRAL.input0.0000.0010.001
eigen.values.100.0260.0010.026
eigen.values.10000.0300.0000.029
kneepointDetection0.0550.0030.062
small0.0320.0000.032
stmFSC0.1930.0120.206