Package: SLGI

Version: 1.46.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:SLGI.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings SLGI_1.46.0.tar.gz

StartedAt: 2020-04-15 00:28:33 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 00:32:16 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 222.5 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:SLGI.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings SLGI_1.46.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/SLGI.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SLGI/DESCRIPTION’ ... OK
* this is package ‘SLGI’ version ‘1.46.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
iSummary       17.972  0.284  18.379
compare        12.188  0.080  12.380
siResult-class 12.176  0.008  12.200
modelSLGI      11.420  0.024  11.553
plot           10.276  0.008  10.375
topInteraction  6.264  0.000   6.288
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/SLGI.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL SLGI
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘SLGI’ ...
** using staged installation
** 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 from temporary location
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’
** testing if installed package can be loaded from final location
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’
** testing if installed package keeps a record of temporary installation path
* DONE (SLGI)

name	user	system	elapsed
Atong	0.028	0.000	0.028
AtongFnDomain	2.900	0.028	2.929
AtongPair	0.632	0.008	0.644
SDL	0.004	0.000	0.004
SGA	0.004	0.004	0.005
SGD.SL	0.168	0.004	0.172
TFmat	0.100	0.004	0.103
byComplex	0.216	0.020	0.237
comemberIn	0.564	0.052	0.619
compare	12.188	0.080	12.380
congruence	0.000	0.000	0.002
createSquareMatrix	0.348	0.004	0.351
domainDist	2.580	0.036	2.619
essglist	0.008	0.004	0.012
getInteraction	0.000	0.000	0.003
getSharedDomains	0.016	0.000	0.015
getSharedInteraction	0.000	0.000	0.002
getTestedPairs	0.008	0.004	0.015
getUniquePairs	0.024	0.000	0.021
gi2005	0.300	0.004	0.306
gi2007	0.168	0.004	0.171
gi2Interactome	0.000	0.000	0.001
hyperG	0.008	0.000	0.007
iSummary	17.972	0.284	18.379
modelSLGI	11.420	0.024	11.553
normInteraction	4.532	0.008	4.546
plot	10.276	0.008	10.375
seqMatcherAlign	0	0	0
sharedBy	3.016	0.032	3.074
sharedInt	0.000	0.004	0.003
siResult-class	12.176	0.008	12.200
test2Interact	0.004	0.000	0.004
topInteraction	6.264	0.000	6.288
twoWayTable	4.532	0.036	4.574
withinComplex	0.516	0.024	0.540