BioC 3.2: CHECK report for tRanslatome on oaxaca

Package: tRanslatome

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings tRanslatome_1.8.0.tar.gz

StartedAt: 2015-10-27 08:38:31 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:41:58 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 207.3 seconds

RetCode: 0

Status:  OK

CheckDir: tRanslatome.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 tRanslatome_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/tRanslatome.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tRanslatome/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tRanslatome’ version ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘limma’ ‘sigPathway’ ‘samr’ ‘anota’ ‘DESeq’ ‘edgeR’ ‘RankProd’
  ‘topGO’ ‘org.Hs.eg.db’ ‘GOSemSim’ ‘Heatplus’ ‘gplots’ ‘plotrix’
  ‘Biobase’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘tRanslatome’ can be installed ... [17s/17s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
methodLimma: no visible global function definition for ‘lmFit’
GOEnrichment,DEGs: no visible global function definition for ‘toTable’
* 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 ... [38s/38s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
GOEnrichment 21.79  0.176  22.002
* 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/tRanslatome.Rcheck/00check.log’
for details.

* installing *source* package ‘tRanslatome’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘graph::.__C__dist’ when loading ‘topGO’

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘graph::.__C__dist’ when loading ‘topGO’

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (tRanslatome)

name	user	system	elapsed
CVplot	0.089	0.005	0.094
DEGs	0.001	0.000	0.001
DEGs.table	0.129	0.070	0.199
EnrichedSets	0.001	0.001	0.002
FC.threshold	0.053	0.003	0.056
GOComparison	1.404	0.024	1.487
GOEnrichment	21.790	0.176	22.002
GOsets	0.002	0.001	0.002
GOsims	0.002	0.000	0.002
Heatmap	0.452	0.033	0.485
Histogram	0.063	0.006	0.069
IdentityPlot	0.058	0.007	0.064
MAplot	0.074	0.007	0.080
Radar	0.073	0.007	0.080
RegulatoryEnrichment	3.030	0.038	3.068
SDplot	0.082	0.009	0.091
Scatterplot	0.075	0.007	0.084
SimilarityPlot	0.062	0.006	0.068
TranslatomeDataset	0.002	0.000	0.002
average.similarity.scores	0.063	0.007	0.069
computeDEGs	0.569	0.022	0.591
enriched.table	0.071	0.008	0.078
getConditionA	0.065	0.007	0.072
getConditionB	0.058	0.006	0.064
getConditionC	0.062	0.007	0.069
getConditionD	0.063	0.008	0.070
getConditionLabels	0.065	0.008	0.072
getDEGs	0.064	0.007	0.072
getDEGsMethod	0.062	0.008	0.071
getDataType	0.064	0.008	0.073
getExprMatrix	0.107	0.046	0.153
getLevelLabels	0.062	0.007	0.070
identity.matrix	0.064	0.007	0.071
label.condition	0.059	0.007	0.066
label.level.DEGs	0.059	0.006	0.065
label.level.enriched	0.058	0.006	0.064
newTranslatomeDataset	0.072	0.008	0.079
significance.threshold	0.062	0.004	0.065
similarity.matrix	0.058	0.003	0.060
tRanslatomeSampleData	0.057	0.003	0.061