Multiple platform build/check report for BioC 3.6 - CHECK report for SLGI on veracruz1

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SLGI_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/SLGI.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SLGI/DESCRIPTION’ ... OK
* this is package ‘SLGI’ 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 ‘SLGI’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 15.9Mb
  sub-directories of 1Mb or more:
    data      4.2Mb
    extdata  11.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘ScISI’ ‘lattice’ ‘GO.db’
A package should be listed in only one of these fields.
* 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 ... NOTE
'library' or 'require' call to ‘GO.db’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
iSummary        21.379  2.209  24.019
plot            12.034  5.692  18.109
siResult-class  12.162  5.447  17.899
modelSLGI       10.448  6.426  17.158
compare         10.649  4.610  15.485
topInteraction   6.232  2.199   8.630
normInteraction  4.721  2.604   7.455
* 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
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/SLGI.Rcheck/00check.log’
for details.

Installation output

* installing *source* package ‘SLGI’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in package ‘Biobase’ for request: ‘listlen’ when loading ‘RpsiXML’
No methods found in package ‘annotate’ for requests: ‘pubmed’, ‘buildPubMedAbst’ when loading ‘RpsiXML’
No methods found in package ‘BiocGenerics’ for request: ‘plot’ when loading ‘SLGI’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package ‘Biobase’ for request: ‘listlen’ when loading ‘RpsiXML’
No methods found in package ‘annotate’ for requests: ‘pubmed’, ‘buildPubMedAbst’ when loading ‘RpsiXML’
No methods found in package ‘BiocGenerics’ for request: ‘plot’ when loading ‘SLGI’
* DONE (SLGI)

Tests output

Example timings

name	user	system	elapsed
Atong	0.022	0.007	0.028
AtongFnDomain	3.750	0.112	3.937
AtongPair	0.461	0.034	0.512
SDL	0.005	0.001	0.006
SGA	0.008	0.028	0.036
SGD.SL	0.137	0.029	0.169
TFmat	0.067	0.027	0.095
byComplex	0.221	0.061	0.286
comemberIn	0.491	0.085	0.595
compare	10.649	4.610	15.485
congruence	0.002	0.001	0.002
createSquareMatrix	0.158	0.025	0.183
domainDist	2.368	0.073	2.480
essglist	0.014	0.007	0.020
getInteraction	0.003	0.000	0.003
getSharedDomains	0.012	0.001	0.012
getSharedInteraction	0.021	0.002	0.022
getTestedPairs	0.011	0.002	0.013
getUniquePairs	0.083	0.010	0.095
gi2005	0.037	0.024	0.064
gi2007	0.110	0.028	0.140
gi2Interactome	0.001	0.000	0.001
hyperG	0.007	0.001	0.008
iSummary	21.379	2.209	24.019
modelSLGI	10.448	6.426	17.158
normInteraction	4.721	2.604	7.455
plot	12.034	5.692	18.109
seqMatcherAlign	0.002	0.000	0.002
sharedBy	2.377	0.072	2.468
sharedInt	0.004	0.000	0.004
siResult-class	12.162	5.447	17.899
test2Interact	0.003	0.000	0.003
topInteraction	6.232	2.199	8.630
twoWayTable	3.987	0.111	4.137
withinComplex	0.870	0.051	0.940

CHECK report for SLGI on veracruz1

Summary

Command output

Installation output

Tests output

Example timings