Package: geneXtendeR

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings geneXtendeR_1.4.0.tar.gz

StartedAt: 2018-04-12 04:13:55 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 04:23:47 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 591.2 seconds

RetCode: 0

Status:  OK

CheckDir: geneXtendeR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings geneXtendeR_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/geneXtendeR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geneXtendeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geneXtendeR’ version ‘1.4.0’
* 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 ‘geneXtendeR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data      5.8Mb
    extdata   1.2Mb
* 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
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘SnowballC’ ‘networkD3’ ‘org.Ag.eg.db’ ‘org.Bt.eg.db’
  ‘org.Ce.eg.db’ ‘org.Cf.eg.db’ ‘org.Dm.eg.db’ ‘org.Dr.eg.db’
  ‘org.Gg.eg.db’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’ ‘org.Mmu.eg.db’
  ‘org.Pt.eg.db’ ‘org.Sc.sgd.db’ ‘org.Ss.eg.db’ ‘org.Xl.eg.db’
  ‘wordcloud’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘GO.db’ ‘org.Rn.eg.db’
  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
annotate : geneXtender: no visible binding for global variable ‘type’
annotate : geneXtender: no visible binding for global variable ‘seqid’
annotate : geneXtender: no visible binding for global variable
  ‘gene_id’
annotate : geneXtender: no visible binding for global variable
  ‘gene_name’
barChart : geneXtender: no visible binding for global variable ‘type’
barChart : geneXtender: no visible binding for global variable ‘seqid’
barChart : geneXtender: no visible binding for global variable
  ‘gene_id’
barChart : geneXtender: no visible binding for global variable
  ‘gene_name’
cumlinePlot : geneXtender: no visible binding for global variable
  ‘type’
cumlinePlot : geneXtender: no visible binding for global variable
  ‘seqid’
cumlinePlot : geneXtender: no visible binding for global variable
  ‘gene_id’
cumlinePlot : geneXtender: no visible binding for global variable
  ‘gene_name’
diffGO : geneXtender: no visible binding for global variable ‘type’
diffGO : geneXtender: no visible binding for global variable ‘seqid’
diffGO : geneXtender: no visible binding for global variable ‘gene_id’
diffGO : geneXtender: no visible binding for global variable
  ‘gene_name’
diffGO: no visible binding for global variable ‘GO.db’
distinct : geneXtender: no visible binding for global variable ‘type’
distinct : geneXtender: no visible binding for global variable ‘seqid’
distinct : geneXtender: no visible binding for global variable
  ‘gene_id’
distinct : geneXtender: no visible binding for global variable
  ‘gene_name’
hotspotPlot : geneXtender: no visible binding for global variable
  ‘type’
hotspotPlot : geneXtender: no visible binding for global variable
  ‘seqid’
hotspotPlot : geneXtender: no visible binding for global variable
  ‘gene_id’
hotspotPlot : geneXtender: no visible binding for global variable
  ‘gene_name’
linePlot : geneXtender: no visible binding for global variable ‘type’
linePlot : geneXtender: no visible binding for global variable ‘seqid’
linePlot : geneXtender: no visible binding for global variable
  ‘gene_id’
linePlot : geneXtender: no visible binding for global variable
  ‘gene_name’
makeNetwork : geneXtender: no visible binding for global variable
  ‘type’
makeNetwork : geneXtender: no visible binding for global variable
  ‘seqid’
makeNetwork : geneXtender: no visible binding for global variable
  ‘gene_id’
makeNetwork : geneXtender: no visible binding for global variable
  ‘gene_name’
makeNetwork: no visible binding for global variable ‘GO.db’
makeNetwork: no visible global function definition for ‘%>%’
makeNetwork: no visible global function definition for ‘left_join’
makeNetwork: no visible global function definition for ‘rename’
makeNetwork: no visible binding for global variable ‘id’
makeNetwork: no visible global function definition for ‘forceNetwork’
makeNetwork: no visible global function definition for ‘JS’
makeWordCloud : geneXtender: no visible binding for global variable
  ‘type’
makeWordCloud : geneXtender: no visible binding for global variable
  ‘seqid’
makeWordCloud : geneXtender: no visible binding for global variable
  ‘gene_id’
makeWordCloud : geneXtender: no visible binding for global variable
  ‘gene_name’
makeWordCloud: no visible binding for global variable ‘GO.db’
makeWordCloud: no visible global function definition for ‘VectorSource’
makeWordCloud: no visible binding for global variable ‘removeWords’
makeWordCloud: no visible global function definition for ‘stopwords’
makeWordCloud: no visible global function definition for ‘wordcloud’
makeWordCloud: no visible global function definition for ‘brewer.pal’
meanPeakLength : geneXtender: no visible binding for global variable
  ‘type’
meanPeakLength : geneXtender: no visible binding for global variable
  ‘seqid’
meanPeakLength : geneXtender: no visible binding for global variable
  ‘gene_id’
meanPeakLength : geneXtender: no visible binding for global variable
  ‘gene_name’
peaksInput: no visible binding for global variable ‘chr’
peaksMerge: no visible binding for global variable ‘chr’
peaksMerge: no visible binding for global variable ‘g’
peaksMerge: no visible global function definition for ‘.’
plotWordFreq : geneXtender: no visible binding for global variable
  ‘type’
plotWordFreq : geneXtender: no visible binding for global variable
  ‘seqid’
plotWordFreq : geneXtender: no visible binding for global variable
  ‘gene_id’
plotWordFreq : geneXtender: no visible binding for global variable
  ‘gene_name’
plotWordFreq: no visible binding for global variable ‘GO.db’
plotWordFreq: no visible global function definition for ‘VectorSource’
plotWordFreq: no visible binding for global variable ‘removeWords’
plotWordFreq: no visible global function definition for ‘stopwords’
Undefined global functions or variables:
  %>% . GO.db JS VectorSource brewer.pal chr forceNetwork g gene_id
  gene_name id left_join removeWords rename seqid stopwords type
  wordcloud
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
meanPeakLengthPlot 49.622  5.736  65.101
hotspotPlot        30.882  3.206  38.219
barChart           22.937  1.841  29.026
linePlot           21.354  1.749  26.875
cumlinePlot        18.637  1.630  23.908
makeWordCloud      16.206  0.815  20.704
annotate           16.303  0.454  21.492
makeNetwork        15.584  0.776  19.989
plotWordFreq       14.221  0.743  18.336
meanPeakLength     13.406  0.582  17.643
peakLengthBoxplot  13.263  0.592  17.389
diffGO             13.089  0.709  17.287
distinct           13.112  0.606  17.607
* 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-3.6-bioc/meat/geneXtendeR.Rcheck/00check.log’
for details.

* installing *source* package ‘geneXtendeR’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c annotate.c -o annotate.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c extract_number.c -o extract_number.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c extract_peaks.c -o extract_peaks.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o geneXtendeR.so annotate.o extract_number.o extract_peaks.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/geneXtendeR.Rcheck/geneXtendeR/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (geneXtendeR)

name	user	system	elapsed
allPeakLengths	0.023	0.004	0.027
annotate	16.303	0.454	21.492
barChart	22.937	1.841	29.026
cumlinePlot	18.637	1.630	23.908
diffGO	13.089	0.709	17.287
distinct	13.112	0.606	17.607
hotspotPlot	30.882	3.206	38.219
linePlot	21.354	1.749	26.875
makeNetwork	15.584	0.776	19.989
makeWordCloud	16.206	0.815	20.704
meanPeakLength	13.406	0.582	17.643
meanPeakLengthPlot	49.622	5.736	65.101
peakLengthBoxplot	13.263	0.592	17.389
peaksInput	0.182	0.027	0.218
peaksMerge	0.153	0.004	0.117
plotWordFreq	14.221	0.743	18.336
rat	3.565	0.316	3.939
samplepeaksinput	0.009	0.000	0.010