Package: spliceR

Version: 1.21.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:spliceR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings spliceR_1.21.1.tar.gz

StartedAt: 2018-04-30 02:25:18 -0400 (Mon, 30 Apr 2018)

EndedAt: 2018-04-30 02:30:51 -0400 (Mon, 30 Apr 2018)

EllapsedTime: 332.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: spliceR.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:spliceR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings spliceR_1.21.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/spliceR.Rcheck’
* using R version 3.5.0 RC (2018-04-15 r74605)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spliceR/DESCRIPTION’ ... OK
* this is package ‘spliceR’ version ‘1.21.1’
* 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 ‘spliceR’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'spliceR' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.8-bioc/meat/spliceR.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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:
  'cummeRbund' 'methods' 'rtracklayer'
  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
.determineAStypeOverlap: no visible global function definition for
  ‘tail’
.determineNonOverlappingAStype: no visible global function definition
  for ‘tail’
.getPreRNA: no visible global function definition for ‘IRanges’
.getPreRNA: no visible global function definition for ‘end<-’
.getPreRNA: no visible global function definition for ‘end’
.getPreRNA: no visible global function definition for ‘reduce’
CDSSet: no visible global function definition for ‘new’
SpliceRList: no visible global function definition for ‘new’
annotatePTC: no visible global function definition for ‘seqnames’
annotatePTC: no visible global function definition for ‘seqlevels<-’
annotatePTC: no visible global function definition for ‘seqlevels’
annotatePTC: no visible global function definition for ‘getSeq’
annotatePTC: no visible global function definition for ‘txtProgressBar’
annotatePTC: no visible global function definition for
  ‘setTxtProgressBar’
annotatePTC: no visible binding for global variable ‘chrom’
annotatePTC: no visible global function definition for ‘DNAString’
annotatePTC: no visible global function definition for ‘translate’
conditions: no visible global function definition for ‘samples’
conditions: no visible global function definition for ‘genes’
exons: no visible global function definition for ‘is’
generateGTF: no visible global function definition for ‘mcols’
generateGTF: no visible global function definition for ‘txtProgressBar’
generateGTF: no visible global function definition for
  ‘setTxtProgressBar’
generateGTF: no visible global function definition for ‘quantile’
generateGTF: no visible global function definition for ‘write.table’
getCDS: no visible global function definition for ‘browserSession’
getCDS: no visible global function definition for ‘genome<-’
getCDS: no visible global function definition for ‘ucscTableQuery’
getCDS: no visible global function definition for ‘tableName<-’
getCDS: no visible global function definition for ‘getTable’
getCDS: no visible global function definition for ‘flush.console’
getCDS: no visible global function definition for ‘new’
preSpliceRFilter: no visible global function definition for ‘mcols’
preSpliceRFilter: no visible global function definition for ‘mcols<-’
prepareCuff: no visible global function definition for ‘genes’
prepareCuff: no visible global function definition for ‘isoforms’
prepareCuff: no visible global function definition for ‘annotation’
prepareCuff: no visible global function definition for ‘diffData’
prepareCuff: no visible global function definition for ‘dbGetQuery’
prepareCuff: no visible global function definition for ‘samples’
prepareCuff: no visible global function definition for ‘GRanges’
prepareCuff: no visible global function definition for ‘IRanges’
prepareCuff: no visible global function definition for ‘new’
prepareCuff: no visible global function definition for ‘runInfo’
prepareCuffExample: no visible global function definition for
  ‘readCufflinks’
spliceR: no visible global function definition for ‘mcols’
spliceR: no visible global function definition for ‘txtProgressBar’
spliceR: no visible global function definition for ‘setTxtProgressBar’
spliceR: no visible global function definition for ‘mcols<-’
spliceRPlot: no visible global function definition for ‘mcols’
spliceRPlot: no visible global function definition for ‘grid.newpage’
spliceRPlot: no visible global function definition for ‘grid.draw’
topIsoShift: no visible global function definition for ‘is’
topIsoShift: no visible global function definition for ‘mcols’
totalNumberOfAS: no visible global function definition for ‘is’
totalNumberOfAS: no visible global function definition for ‘mcols’
transcripts: no visible global function definition for ‘is’
Undefined global functions or variables:
  DNAString GRanges IRanges annotation browserSession chrom dbGetQuery
  diffData end end<- flush.console genes genome<- getSeq getTable
  grid.draw grid.newpage is isoforms mcols mcols<- new quantile
  readCufflinks reduce runInfo samples seqlevels seqlevels<- seqnames
  setTxtProgressBar tableName<- tail translate txtProgressBar
  ucscTableQuery write.table
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "end", "quantile")
  importFrom("utils", "flush.console", "setTxtProgressBar", "tail",
             "txtProgressBar", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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
generateGTF     9.591  0.242   9.937
spliceRPlot     8.601  0.165   8.890
topIsoShift     8.098  0.156   8.355
totalNumberOfAS 7.898  0.152   8.158
spliceR         7.699  0.134   7.926
* 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/spliceR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL spliceR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘spliceR’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils.c -o utils.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 spliceR.so utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/spliceR/libs
** R
** 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
Warning: Package 'spliceR' is deprecated and will be removed from Bioconductor
  version 3.7 . Functionalities moved to IsoformSwitchAnalyzeR
* DONE (spliceR)

name	user	system	elapsed
annotatePTC.R	0.001	0.001	0.001
conditions	4.213	0.213	4.496
generateGTF	9.591	0.242	9.937
getCDS	0.001	0.000	0.001
preSpliceRFilter	4.180	0.156	4.398
prepareCuff	4.282	0.155	4.503
prepareCuffExample	3.076	0.123	3.236
spliceR	7.699	0.134	7.926
spliceRPlot	8.601	0.165	8.890
tools	3.891	0.125	4.064
topIsoShift	8.098	0.156	8.355
totalNumberOfAS	7.898	0.152	8.158