Package: JunctionSeq

Version: 1.16.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:JunctionSeq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings JunctionSeq_1.16.0.tar.gz

StartedAt: 2020-04-15 03:30:21 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:34:26 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 244.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: JunctionSeq.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:JunctionSeq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings JunctionSeq_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/JunctionSeq.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘JunctionSeq/DESCRIPTION’ ... OK
* this is package ‘JunctionSeq’ version ‘1.16.0’
* 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 ‘JunctionSeq’ can be installed ... 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Rcpp’ ‘RcppArmadillo’
  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 ... OK
* checking Rd files ... NOTE
prepare_Rd: setJunctionSeqCompiledSourcePackage.Rd:23-25: Dropping empty section \examples
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'estimateJunctionSeqSizeFactors':
  ‘...’

Documented arguments not in \usage in documentation object 'fitJunctionSeqDispersionFunction':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* 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
buildAllPlots 13.328  0.164  14.353
* 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: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/JunctionSeq.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL JunctionSeq
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘JunctionSeq’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c DESeq2.cpp -o DESeq2.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o JunctionSeq.so DESeq2.o RcppExports.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-JunctionSeq/00new/JunctionSeq/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘JunctionSeq.Rnw’ 
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (JunctionSeq)

name	user	system	elapsed
JunctionSeqCountSet-class	0.000	0.000	0.003
buildAllPlots	13.328	0.164	14.353
buildAllPlotsForGene	1.636	0.008	1.647
defaultColorList	2.056	0.000	2.060
estimateEffectSizes	3.856	0.004	3.878
estimateJunctionSeqDispersions	0.000	0.000	0.001
estimateJunctionSeqSizeFactors	0.460	0.004	0.463
fitJunctionSeqDispersionFunction	0.616	0.000	0.618
plotDispEsts	0.128	0.000	0.129
plotJunctionSeqResultsForGene	0.132	0.004	0.136
plotMA	0.976	0.000	0.979
readAnnotationData	0.592	0.000	0.613
readJunctionSeqCounts	0.668	0.000	1.390
runJunctionSeqAnalyses	0	0	0
testForDiffUsage	1.872	0.020	1.892
writeBedTrack	0.084	0.004	0.088
writeCompleteResults	0.484	0.004	0.492