spliceR 1.14.0
Johannes Waage , Kristoffer Vitting-Seerup
| Snapshot Date: 2016-10-10 17:20:16 -0700 (Mon, 10 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/spliceR | | Last Changed Rev: 117079 / Revision: 122169 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings spliceR_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/spliceR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spliceR/DESCRIPTION’ ... OK
* this is package ‘spliceR’ version ‘1.14.0’
* 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 ‘spliceR’ can be installed ... OK
* 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 loading without being on the library search path ... 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’
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’
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’
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 ‘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 ‘mcols’
totalNumberOfAS: no visible global function definition for ‘mcols’
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 isoforms mcols mcols<- quantile readCufflinks
reduce runInfo samples seqlevels seqlevels<- seqnames
setTxtProgressBar tableName<- tail translate txtProgressBar
ucscTableQuery write.table
Consider adding
importFrom("stats", "end", "quantile")
importFrom("utils", "flush.console", "setTxtProgressBar", "tail",
"txtProgressBar", "write.table")
to your NAMESPACE file.
* 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 ... 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
generateGTF 6.714 0.093 6.810
spliceRPlot 6.292 0.060 6.347
totalNumberOfAS 6.074 0.052 6.120
spliceR 5.885 0.036 5.926
topIsoShift 5.751 0.052 5.799
* 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
‘/home/biocbuild/bbs-3.3-bioc/meat/spliceR.Rcheck/00check.log’
for details.
* installing *source* package ‘spliceR’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o spliceR.so utils.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/spliceR.Rcheck/spliceR/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (spliceR)