BioC 3.2: CHECK report for ELMER on zin1

Package: ELMER

Version: 1.2.1

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ELMER_1.2.1.tar.gz

StartedAt: 2016-04-23 00:19:28 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:25:12 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 343.6 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_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ELMER.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.2.1’
* 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 ... [23s/23s] 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.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [85s/87s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
get.feature.probe 11.378  0.364  11.765
get.pair           8.266  0.004   8.285
schematic.plot     7.524  0.080   7.612
GetNearGenes       5.641  0.104   5.750
scatter.plot       5.567  0.056   5.634
get.permu          5.612  0.000   5.611
* 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	5.641	0.104	5.750
TCGA.pipe	0	0	0
TF.rank.plot	0.428	0.000	0.428
fetch.mee	1.261	0.000	1.274
fetch.pair	4.427	0.016	4.458
get.TFs	0.445	0.007	0.523
get.diff.meth	0.329	0.000	0.329
get.enriched.motif	2.784	0.060	2.848
get.feature.probe	11.378	0.364	11.765
get.pair	8.266	0.004	8.285
get.permu	5.612	0.000	5.611
getExp	1.086	0.000	1.085
getGeneID	3.191	0.024	3.215
getGeneInfo	4.396	0.068	4.470
getMeth	1.050	0.028	1.082
getPair	0.003	0.000	0.003
getProbeInfo	1.155	0.000	1.183
getSample	1.081	0.000	1.086
getSymbol	3.139	0.067	3.206
getTCGA	0.193	0.091	2.021
motif.enrichment.plot	0.187	0.000	0.190
promoterMeth	0.224	0.004	0.228
scatter.plot	5.567	0.056	5.634
schematic.plot	7.524	0.080	7.612
txs	3.152	0.072	3.227