riboSeqR 1.5.3
Thomas J. Hardcastle
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/riboSeqR | | Last Changed Rev: 109873 / Revision: 109948 | | Last Changed Date: 2015-10-23 10:47:24 -0400 (Fri, 23 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### rm -rf riboSeqR.buildbin-libdir riboSeqR.Rcheck && mkdir riboSeqR.buildbin-libdir riboSeqR.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=riboSeqR.buildbin-libdir riboSeqR_1.5.3.tar.gz >riboSeqR.Rcheck\00install.out 2>&1 && cp riboSeqR.Rcheck\00install.out riboSeqR-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=riboSeqR.buildbin-libdir --install="check:riboSeqR-install.out" --force-multiarch --no-vignettes --timings riboSeqR_1.5.3.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/riboSeqR.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'riboSeqR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'riboSeqR' version '1.5.3'
* 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 'riboSeqR' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.readAlignments : <anonymous>: no visible global function definition
for 'scanBam'
.readAlignments : <anonymous>: no visible global function definition
for 'IRanges'
.tableOverlaps: no visible global function definition for 'seqlevels'
findCDS: no visible global function definition for 'IRanges'
plotCDS : <anonymous> : <anonymous>: no visible global function
definition for 'seqlevels'
Undefined global functions or variables:
IRanges scanBam seqlevels
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [43s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotTranscript 5.51 0.00 5.52
frameCounting 5.33 0.00 5.33
filterHits 5.23 0.02 5.25
rnaCounts 5.15 0.00 5.16
plotCDS 5.05 0.01 5.06
** running examples for arch 'x64' ... [46s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotCDS 6.17 0.01 6.19
sliceCounts 5.79 0.02 5.81
plotTranscript 5.54 0.02 5.56
filterHits 5.39 0.00 5.39
rnaCounts 5.30 0.00 5.30
frameCounting 5.25 0.03 5.28
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [2s]
[3s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [3s]
[3s] OK
* 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: 2 NOTEs
See
'c:/biocbld/bbs-3.3-bioc/meat/riboSeqR.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'riboSeqR' ...
** 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 'riboSeqR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'riboSeqR' as riboSeqR_1.5.3.zip
* DONE (riboSeqR)