BioC 3.2: CHECK report for ELMER on linux1.bioconductor.org

Package: ELMER

Version: 1.2.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ELMER_1.2.0.tar.gz

StartedAt: 2015-10-27 03:12:17 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:17:56 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 338.3 seconds

RetCode: 0

Status:  OK

CheckDir: ELMER.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ELMER_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ELMER.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ELMER/DESCRIPTION’ ... OK
* this is package ‘ELMER’ version ‘1.2.0’
* 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 ‘ELMER’ can be installed ... [22s/22s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘ELMER.data’ ‘Homo.sapiens’
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
TF.rank.plot: no visible binding for global variable ‘pvalue’
TF.rank.plot: no visible binding for global variable ‘label’
get.feature.probe: no visible binding for global variable
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
motif.enrichment.plot: no visible binding for global variable ‘upperOR’
motif.enrichment.plot: no visible binding for global variable ‘lowerOR’
motif.enrichment.plot: no visible binding for global variable ‘motif’
motif.enrichment.plot: no visible binding for global variable ‘OR’
scatter: no visible binding for global variable ‘value’
txs: no visible binding for global variable ‘Homo.sapiens’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [88s/88s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
get.feature.probe 12.579  0.464  13.046
get.pair           9.490  0.004   9.503
schematic.plot     7.142  0.088   7.235
get.permu          6.931  0.000   6.951
fetch.pair         5.891  0.024   5.931
GetNearGenes       5.614  0.068   5.685
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/ELMER.Rcheck/00check.log’
for details.

* installing *source* package ‘ELMER’ ...
** R
** inst
** preparing package for lazy loading
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
* DONE (ELMER)

name	user	system	elapsed
GetNearGenes	5.614	0.068	5.685
TCGA.pipe	0.000	0.000	0.001
TF.rank.plot	0.437	0.004	0.441
fetch.mee	1.230	0.000	1.232
fetch.pair	5.891	0.024	5.931
get.TFs	0.377	0.004	0.424
get.diff.meth	0.238	0.004	0.244
get.enriched.motif	3.378	0.116	3.494
get.feature.probe	12.579	0.464	13.046
get.pair	9.490	0.004	9.503
get.permu	6.931	0.000	6.951
getExp	1.068	0.000	1.072
getGeneID	3.156	0.108	3.268
getGeneInfo	4.039	0.088	4.130
getMeth	1.192	0.032	1.232
getPair	0.003	0.000	0.002
getProbeInfo	1.006	0.000	1.007
getSample	0.999	0.000	1.000
getSymbol	2.748	0.100	2.855
getTCGA	0.264	0.087	0.587
motif.enrichment.plot	0.279	0.012	0.290
promoterMeth	0.198	0.008	0.206
scatter.plot	3.996	0.040	4.045
schematic.plot	7.142	0.088	7.235
txs	3.388	0.100	3.494