BioC 3.4: CHECK report for SLGI on morelia

Package: SLGI

Version: 1.34.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SLGI_1.34.0.tar.gz

StartedAt: 2017-04-15 08:15:50 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 08:19:57 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 247.3 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_1.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/SLGI.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SLGI/DESCRIPTION’ ... OK
* this is package ‘SLGI’ version ‘1.34.0’
* 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        24.232  2.181  26.473
plot            13.195  4.967  18.177
siResult-class  11.550  5.777  17.338
compare         10.788  5.357  16.161
modelSLGI       10.075  5.794  15.882
topInteraction   6.384  3.010   9.401
normInteraction  5.098  2.748   7.853
twoWayTable      5.070  0.122   5.195
* 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-3.4-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	0.024	0.006	0.031
AtongFnDomain	4.426	0.117	4.545
AtongPair	0.071	0.035	0.106
SDL	0.007	0.002	0.010
SGA	0.008	0.024	0.034
SGD.SL	0.198	0.034	0.231
TFmat	0.087	0.030	0.117
byComplex	0.646	0.078	0.747
comemberIn	0.574	0.099	0.675
compare	10.788	5.357	16.161
congruence	0.003	0.000	0.003
createSquareMatrix	0.113	0.036	0.148
domainDist	2.231	0.075	2.308
essglist	0.012	0.006	0.017
getInteraction	0.004	0.000	0.004
getSharedDomains	0.012	0.001	0.012
getSharedInteraction	0.001	0.000	0.001
getTestedPairs	0.010	0.001	0.011
getUniquePairs	0.025	0.003	0.028
gi2005	0.181	0.022	0.203
gi2007	0.664	0.040	0.706
gi2Interactome	0.001	0.000	0.001
hyperG	0.005	0.000	0.005
iSummary	24.232	2.181	26.473
modelSLGI	10.075	5.794	15.882
normInteraction	5.098	2.748	7.853
plot	13.195	4.967	18.177
seqMatcherAlign	0.002	0.000	0.001
sharedBy	3.232	0.082	3.317
sharedInt	0.005	0.001	0.006
siResult-class	11.550	5.777	17.338
test2Interact	0.005	0.000	0.005
topInteraction	6.384	3.010	9.401
twoWayTable	5.070	0.122	5.195
withinComplex	0.890	0.072	0.961