BioC 3.5: CHECK report for SLGI on veracruz2

Package: SLGI

Version: 1.36.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SLGI_1.36.0.tar.gz

StartedAt: 2017-10-18 09:11:12 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 09:15:25 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 253.0 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SLGI_1.36.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SLGI.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.36.0’
* 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        21.655  2.105  24.473
siResult-class  12.861  5.621  19.059
plot            12.362  5.724  18.598
compare         11.386  4.738  16.677
modelSLGI       10.036  6.015  16.506
topInteraction   6.447  2.070   8.834
normInteraction  5.269  2.497   8.004
* 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-3.5-bioc/meat/SLGI.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
Atong	0.021	0.007	0.027
AtongFnDomain	3.802	0.120	4.050
AtongPair	0.462	0.036	0.521
SDL	0.005	0.001	0.006
SGA	0.007	0.025	0.031
SGD.SL	0.122	0.028	0.153
TFmat	0.070	0.029	0.100
byComplex	0.231	0.064	0.300
comemberIn	0.554	0.087	0.666
compare	11.386	4.738	16.677
congruence	0.002	0.000	0.003
createSquareMatrix	0.361	0.027	0.399
domainDist	2.980	0.078	3.127
essglist	0.011	0.005	0.017
getInteraction	0.003	0.000	0.004
getSharedDomains	0.011	0.001	0.012
getSharedInteraction	0.023	0.002	0.025
getTestedPairs	0.009	0.001	0.012
getUniquePairs	0.083	0.010	0.098
gi2005	0.047	0.031	0.079
gi2007	0.116	0.035	0.156
gi2Interactome	0.001	0.000	0.002
hyperG	0.006	0.001	0.007
iSummary	21.655	2.105	24.473
modelSLGI	10.036	6.015	16.506
normInteraction	5.269	2.497	8.004
plot	12.362	5.724	18.598
seqMatcherAlign	0.001	0.000	0.001
sharedBy	2.779	0.092	2.975
sharedInt	0.004	0.000	0.004
siResult-class	12.861	5.621	19.059
test2Interact	0.005	0.000	0.004
topInteraction	6.447	2.070	8.834
twoWayTable	4.117	0.118	4.368
withinComplex	0.949	0.108	1.085