Johannes Waage
| Snapshot Date: 2018-04-29 16:46:14 -0400 (Sun, 29 Apr 2018) |
| URL: https://git.bioconductor.org/packages/spliceR |
| Branch: master |
| Last Commit: 5e21241 |
| Last Changed Date: 2018-03-06 09:27:25 -0400 (Tue, 06 Mar 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2018-04-30 09:36:04 -0400 (Mon, 30 Apr 2018).
| Package 1413/1559 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Johannes Waage
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: spliceR |
| Version: 1.21.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:spliceR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings spliceR_1.21.1.tar.gz |
| StartedAt: 2018-04-30 05:23:55 -0400 (Mon, 30 Apr 2018) |
| EndedAt: 2018-04-30 05:31:10 -0400 (Mon, 30 Apr 2018) |
| EllapsedTime: 434.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: spliceR.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:spliceR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings spliceR_1.21.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/spliceR.Rcheck'
* using R version 3.5.0 RC (2018-04-15 r74605)
* 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 '1.21.1'
* 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 whether package 'spliceR' can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'spliceR' is deprecated and will be removed from Bioconductor
See 'C:/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
* 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
* 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 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/spliceR/libs/i386/spliceR.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/spliceR/libs/x64/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 use Fortran I/O
nor system RNGs. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
generateGTF 6.87 0.86 7.81
conditions 3.58 0.55 8.58
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
generateGTF 9.14 0.25 9.49
topIsoShift 7.58 0.28 7.85
spliceR 6.88 0.14 7.08
spliceRPlot 6.91 0.09 7.00
totalNumberOfAS 5.20 0.19 5.40
* 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
'C:/Users/biocbuild/bbs-3.8-bioc/meat/spliceR.Rcheck/00check.log'
for details.
spliceR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/spliceR_1.21.1.tar.gz && rm -rf spliceR.buildbin-libdir && mkdir spliceR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=spliceR.buildbin-libdir spliceR_1.21.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL spliceR_1.21.1.zip && rm spliceR_1.21.1.tar.gz spliceR_1.21.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 45637 100 45637 0 0 1304k 0 --:--:-- --:--:-- --:--:-- 1437k
install for i386
* installing *source* package 'spliceR' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c utils.c -o utils.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o spliceR.dll tmp.def utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/spliceR.buildbin-libdir/spliceR/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'spliceR'
finding HTML links ... done
CDSSet html
SpliceRList html
annotatePTC.R html
conditions html
dim html
generateGTF html
getCDS html
preSpliceRFilter html
prepareCuff html
prepareCuffExample html
spliceR html
spliceRPlot html
tools html
topIsoShift html
totalNumberOfAS html
** 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
In R CMD INSTALL
install for x64
* installing *source* package 'spliceR' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c utils.c -o utils.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o spliceR.dll tmp.def utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/spliceR.buildbin-libdir/spliceR/libs/x64
** 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
* MD5 sums
packaged installation of 'spliceR' as spliceR_1.21.1.zip
* DONE (spliceR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'spliceR' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
spliceR.Rcheck/examples_i386/spliceR-Ex.timings
|
spliceR.Rcheck/examples_x64/spliceR-Ex.timings
|