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BioC 3.3: CHECK report for SamSPECTRAL on oaxaca

This page was generated on 2016-10-13 12:57:13 -0700 (Thu, 13 Oct 2016).

Package 1033/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SamSPECTRAL 1.26.0
Habil Zare
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/SamSPECTRAL
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SamSPECTRAL
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SamSPECTRAL_1.26.0.tar.gz
StartedAt: 2016-10-13 06:05:13 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 06:05:34 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 20.9 seconds
RetCode: 0
Status:  OK 
CheckDir: SamSPECTRAL.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SamSPECTRAL_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/SamSPECTRAL.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.26.0’
* 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 ... 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/SamSPECTRAL.Rcheck/00check.log’
for details.


SamSPECTRAL.Rcheck/00install.out:

* installing *source* package ‘SamSPECTRAL’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c Rinit.c -o Rinit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c conductance_computation.c -o conductance_computation.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c maximum_of_rows.c -o maximum_of_rows.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o SamSPECTRAL.so Rinit.o conductance_computation.o maximum_of_rows.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.3-bioc/meat/SamSPECTRAL.Rcheck/SamSPECTRAL/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SamSPECTRAL)

SamSPECTRAL.Rcheck/SamSPECTRAL-Ex.timings:

nameusersystemelapsed
Building_Communities0.0010.0000.001
Civilized_Spectral_Clustering0.0010.0000.002
Conductance_Calculation0.0010.0010.001
Connecting0.0020.0000.002
SamSPECTRAL-package0.0010.0010.001
SamSPECTRAL0.0010.0000.001
check.SamSPECTRAL.input0.0010.0000.001
eigen.values.100.0290.0050.034
eigen.values.10000.0070.0030.010
kneepointDetection0.0870.0010.089
small0.0170.0040.022
stmFSC0.1540.0100.165