spliceR 1.14.0
Johannes Waage , Kristoffer Vitting-Seerup
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/spliceR | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | ERROR | skipped | | |
| 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 | ERROR | skipped | skipped | |
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### Running command:
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### rm -rf spliceR.buildbin-libdir spliceR.Rcheck && mkdir spliceR.buildbin-libdir spliceR.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=spliceR.buildbin-libdir spliceR_1.14.0.tar.gz >spliceR.Rcheck\00install.out 2>&1 && cp spliceR.Rcheck\00install.out spliceR-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=spliceR.buildbin-libdir --install="check:spliceR-install.out" --force-multiarch --no-vignettes --timings spliceR_1.14.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/spliceR.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'E:/biocbld/bbs-3.3-bioc/meat/spliceR.buildbin-libdir/spliceR/libs/i386/spliceR.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
totalNumberOfAS 10.49 0.11 10.62
spliceRPlot 10.20 0.11 11.56
topIsoShift 9.38 0.24 9.61
spliceR 8.91 0.11 9.12
generateGTF 8.80 0.17 9.49
conditions 5.49 0.19 11.78
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
totalNumberOfAS 11.67 0.21 11.89
generateGTF 10.99 0.13 11.16
spliceRPlot 10.64 0.11 11.06
topIsoShift 9.59 0.14 10.55
spliceR 9.34 0.09 9.44
conditions 5.74 0.19 6.43
prepareCuff 5.20 0.15 5.35
tools 5.26 0.09 5.94
preSpliceRFilter 4.48 0.14 5.02
* 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
'E:/biocbld/bbs-3.3-bioc/meat/spliceR.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'spliceR' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c utils.c -o utils.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o spliceR.dll tmp.def utils.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/spliceR.buildbin-libdir/spliceR/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'spliceR' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c utils.c -o utils.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o spliceR.dll tmp.def utils.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/spliceR.buildbin-libdir/spliceR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'spliceR' as spliceR_1.14.0.zip
* DONE (spliceR)