Package: SLGI

Version: 1.43.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SLGI.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SLGI_1.43.0.tar.gz

StartedAt: 2019-04-09 03:49:30 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:54:12 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 281.2 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 --install=check:SLGI.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SLGI_1.43.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SLGI.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.43.0’
* 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 15.8Mb
  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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
iSummary        21.124  3.717  25.098
siResult-class  15.362  7.046  22.632
modelSLGI       14.569  6.954  21.762
plot            14.310  6.997  21.538
compare         12.840  6.958  19.979
topInteraction   7.877  2.918  10.912
normInteraction  6.150  3.293   9.562
* 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-3.9-bioc/meat/SLGI.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SLGI
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘SLGI’ ...
** R
** data
** inst
** byte-compile and prepare 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)

name	user	system	elapsed
Atong	0.024	0.006	0.029
AtongFnDomain	3.309	0.115	3.464
AtongPair	0.061	0.043	0.103
SDL	0.007	0.003	0.010
SGA	0.010	0.034	0.045
SGD.SL	0.262	0.038	0.301
TFmat	0.092	0.038	0.132
byComplex	0.707	0.087	0.799
comemberIn	0.476	0.107	0.588
compare	12.840	6.958	19.979
congruence	0.003	0.001	0.004
createSquareMatrix	0.318	0.035	0.354
domainDist	2.610	0.084	2.714
essglist	0.013	0.006	0.018
getInteraction	0.002	0.000	0.002
getSharedDomains	0.012	0.001	0.013
getSharedInteraction	0.002	0.000	0.003
getTestedPairs	0.015	0.001	0.016
getUniquePairs	0.026	0.002	0.029
gi2005	0.057	0.036	0.093
gi2007	0.161	0.040	0.204
gi2Interactome	0.001	0.000	0.002
hyperG	0.193	0.004	0.198
iSummary	21.124	3.717	25.098
modelSLGI	14.569	6.954	21.762
normInteraction	6.150	3.293	9.562
plot	14.310	6.997	21.538
seqMatcherAlign	0.001	0.000	0.001
sharedBy	2.771	0.089	2.901
sharedInt	0.004	0.000	0.004
siResult-class	15.362	7.046	22.632
test2Interact	0.003	0.000	0.003
topInteraction	7.877	2.918	10.912
twoWayTable	3.928	0.121	4.078
withinComplex	0.803	0.071	0.889