SplicingGraphs 1.4.1
H. Pages
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/SplicingGraphs | | Last Changed Rev: 92575 / Revision: 95116 | | Last Changed Date: 2014-07-16 18:45:03 -0700 (Wed, 16 Jul 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK |
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### Running command:
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### rm -rf SplicingGraphs.buildbin-libdir && mkdir SplicingGraphs.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SplicingGraphs.buildbin-libdir SplicingGraphs_1.4.1.tar.gz >SplicingGraphs-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=SplicingGraphs.buildbin-libdir --install="check:SplicingGraphs-install.out" --force-multiarch --no-vignettes --timings SplicingGraphs_1.4.1.tar.gz
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/SplicingGraphs.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SplicingGraphs/DESCRIPTION' ... OK
* this is package 'SplicingGraphs' version '1.4.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics' 'IRanges' 'GenomicRanges' 'GenomicFeatures'
'GenomicAlignments' 'Rgraphviz'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'SplicingGraphs' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'BiocGenerics' 'IRanges' 'GenomicRanges' 'GenomicFeatures' 'GenomicAlignments' 'Rgraphviz' 'igraph'
A package should be listed in only one of these fields.
* 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
Unexported objects imported by ':::' calls:
'BiocGenerics:::testPackage' 'GenomicAlignments:::fillJunctionGaps'
'IRanges:::decodeRle' 'IRanges:::matchIntegerPairs'
'IRanges:::newCompressedList0' 'IRanges:::orderIntegerPairs'
'IRanges:::selfmatchIntegerPairs' 'IRanges:::setPrototypeFromObject'
See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'txpath-methods.Rd':
'[GenomicRanges]{encodeOverlaps-methods}'
See the information in section 'Cross-references' of the 'Writing R
Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'reportReads'
Undocumented S4 methods:
generic 'reportReads' and siglist 'SplicingGraphs'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'countReads-methods':
'reportReads'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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' ... [167s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotTranscripts-methods 50.54 0.06 50.61
toy_data 29.35 0.01 29.37
countReads-methods 8.99 0.02 9.00
sgedges-methods 6.02 0.00 6.02
** running examples for arch 'x64' ... [196s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotTranscripts-methods 59.08 0.06 59.14
toy_data 34.40 0.01 34.44
countReads-methods 10.39 0.00 10.39
sgedges-methods 6.72 0.03 6.75
rsgedgesByGene-methods 5.52 0.02 5.59
sgedgesByGene-methods 5.06 0.00 5.05
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'run_unitTests.R' [18s]
[19s] OK
** running tests for arch 'x64' ...
Running 'run_unitTests.R' [18s]
[18s] 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
WARNING: There were 3 warnings.
NOTE: There were 3 notes.
See
'E:/biocbld/bbs-2.14-bioc/meat/SplicingGraphs.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'SplicingGraphs' ...
** 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 'SplicingGraphs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SplicingGraphs' as SplicingGraphs_1.4.1.zip
* DONE (SplicingGraphs)