Package: geneXtendeR

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings geneXtendeR_1.6.0.tar.gz

StartedAt: 2018-10-16 21:37:15 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 22:05:04 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 1668.9 seconds

RetCode: 0

Status:  OK

CheckDir: geneXtendeR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings geneXtendeR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/geneXtendeR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.6.0’
* 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  7.4Mb
  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 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 ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
meanPeakLengthPlot 44.268  4.935 158.135
hotspotPlot        27.904  2.070 100.516
cumlinePlot        22.722  1.387  93.697
linePlot           22.737  1.310 132.475
barChart           22.549  1.299 126.952
annotate           19.483  0.647 134.216
makeWordCloud      18.564  0.995 150.042
diffGO             16.957  0.874 111.169
plotWordFreq       15.879  0.817  78.813
peakLengthBoxplot  15.776  0.649  77.570
makeNetwork        15.565  0.845 111.246
meanPeakLength     15.794  0.551  42.477
distinct           15.453  0.716 100.112
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/geneXtendeR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL geneXtendeR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* 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 /Library/Frameworks/R.framework/Versions/3.5/Resources/library/geneXtendeR/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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	0.025	0.003	0.032
annotate	19.483	0.647	134.216
barChart	22.549	1.299	126.952
cumlinePlot	22.722	1.387	93.697
diffGO	16.957	0.874	111.169
distinct	15.453	0.716	100.112
hotspotPlot	27.904	2.070	100.516
linePlot	22.737	1.310	132.475
makeNetwork	15.565	0.845	111.246
makeWordCloud	18.564	0.995	150.042
meanPeakLength	15.794	0.551	42.477
meanPeakLengthPlot	44.268	4.935	158.135
peakLengthBoxplot	15.776	0.649	77.570
peaksInput	0.290	0.036	0.337
peaksMerge	0.256	0.007	0.204
plotWordFreq	15.879	0.817	78.813
rat	3.498	0.406	3.938
samplepeaksinput	0.008	0.001	0.010